BESA® Wiki - User contributions [en]

Working With Additional Files

2017-04-07T13:14:55Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
== Working with Additional Files ==

=== Binary format (*.foc, *.fsg) ===

Select '''Binary High Resolution''' or '''Binary Compressed Format''' to output segments in binary BESA format. If the file already exists, the segment will be appended. Thus, it is possible to create a file combining several segments of interest in a compact form. BESA Research will only allow you to append segments if the number of channels and the sampling interval in source and target files are the same. In Binary Format all channels (scalp, intracranial, polygraphic, MEG) and file events in the selected time range are exported. '''Note:''' The channels are filtered according to the current filter settings.

Select '''Binary High Resolution''' to retain the resolution of the processed data. This is the preferred binary format for small amplitude signals such as averages. Select '''Binary Compressed Format''' to store raw data using the original resolution or to obtain the space savings of compression (see ''File/Export and Append Data/Convert..'' above). This is the preferred binary format for raw data.

=== ASCII vectorized format (*.avr) ===

Select '''ASCII vectorized Format''' to output segments in BESA ASCII format, one channel (all time points) per line.

'''The Format is as follows:'''

The first of two header lines contains the following data descriptors (6 descriptors, the values shown are only examples):

''Npts= 200'' number of sampled points in each channel

''TSB= -500'' time sweep begin [ms]. Time of first data point relative to zero of epoch

''DI= 5'' digitization or sampling interval [ms]

''SB= 2'' scaling bins/microvolt in file = number corresponding to 1 microvolt

''SC= 50'' scaling calibration, used for setting magnitude of display in BESA

''Nchan= 27'' number of channels

''SegmentName= 60dB''  An optional label describing the data.

The second line of the header contains a label for each channel, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each of the subsequent ''Nchan'' lines of the file contains values for all ''Npts'' time points in floating point or scientific format. For more details about scalp electrodes, see chapter "''Working With Electrodes and Surface Locations/Electrodes/Electrode Conventions".''

A second (older) version of the format (written by BESA versions 1, 2 and 3) omits the '''Nchan=xx''' information in the first line, and there is no second header line. Labels must be defined elsewhere. See "''Electrodes/Electrode file conventions and formats''" and “''Reading MEG files in ASCII format”''. In the older versions, only scalp channels were exported, and the data were average referenced.

=== ASCII Multiplexed format (*.mul) ===

Select '''ASCII Multiplexed Format''' to output segments one time point (all channels) per line.  

The '''ASCII Multiplexed Format '''is as follows:

The first of two header lines contains similar information to that of the ASCII vectorized file:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= -500.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 SegmentName=Condition1''

Note that the item 'SegmentName' is missing if no segment comment is specified when writing a segment to file.

If an epoch of a continuous EEG is exported in ASCII multiplexed format, the first header line contains the additional item 'Time', which indicates the daytime of the first sample in the exported segment:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= 0.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 Time=22:02:53 SegmentName=Segment1''

The second line of the header contains labels for each channel, which may be either the original channel names, or the names of the channels of the current montage, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each subsequent line contains values for all 'Channels' at one time point, in floating point or scientific format. Values are given for the current or the original montage, selected as described above.

Labels for '''source montages''' have the following form: '''TAr-L'''.
* The first two letters indicate the head region:

[[Image:ST addfiles (1).gif]]

* The small letter indicates in part the orientation: r=radial, t=tangential, and in part the relative location of the basal temporal source: l=lateral, m=mesial.
* The final letter after the hyphen indicates L=left, M=middle, R=right.

=== Channel definition file conventions and formats ===

BESA Research can read 3 types of file to define channels. These are identified by different extensions:
* channel definition files containing labels and, optionally, channel types (ASCII, 1 label /line): '''<nowiki>*.ela</nowiki>'''
* channel definition files containing coordinates and, optionally, channel types and labels (ASCII): '''<nowiki>*.elp.</nowiki>''' This is the format of the file written by the ''Channel Configuration Dialog.''
* channel definition files stored by older versions of BESA Research (binary format): '''<nowiki>*.elb.</nowiki>''' This format can still be read, but is no longer written by BESA Research.

BESA Research stores and retrieves the channel configuration after editing in binary files. If you open a data file, BESA Research will search for the related channel information in the following sequence:

# For all data files with the extension '''.eeg''', '''.cnt''' and '''.foc''', check in the additional database file in the data directory with the same basename as the data file and the extension '''.fst''', whether a channel file has been associated previously
# Check in the '''''db''''' subdirectory whether a channel file has been associated previously
# Check if labels are defined in the header of the data file
# Search for a corresponding binary channel definition file with the same basename as the data file in the data folder ('''xxxx.elb''')
# Search for a corresponding channel definition file with the same basename as the data file containing labels in the data folder ('''xxxx.ela)'''
# Search for a corresponding channel definition file with the same basename as the data file containing labels and/or coordinates in the data folder ('''xxxx.elp''')
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' (in this order)) in the data folder
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' one directory above the data folder (e.g. '''..\default.elb''')
# Check if the new data file is of the same type and has the same number of channels as the preceding data file in the list. If this is the case, the electrode configuration of the previous file will be assumed. This will avoid having to load or edit the electrode configuration more than once, if you load several data segments of the same subject from separate files.
# If no channel definition file is found, or digitization points (in files '''<nowiki>*.sfp</nowiki>''', '''<nowiki>*.cot</nowiki>''', '''<nowiki>*.pos</nowiki>''', '''<nowiki>*.pmg</nowiki>''') are found in files with the same basename as the data file, the ''"Channel and digitized surface point'' ''information"'' dialog box is opened, allowing you to specify file names.

'''Channel Label Files (*.ela)'''

Files containing a list of channel labels are an alternative to editing electrode configurations. They can be edited using a standard text editor. Electrode label files ('''.ela''') require a sequence of lines corresponding to the sequence of channels in the data. Each line contains one label and an optional identifier. The format is ' [Identifier] {Label} ', ('Identifier' can be omitted if the electrode label defines the type of signal)

'''Identifiers''' can be one of:

EEG -- scalp electrode

SCP -- scalp electrode

POL -- polygraphic channel

PGR -- polygraphic channel

ICR -- intracranial electrode

MEG -- MEG sensor

REF -- reference electrode (this can only occur once, and must be the last item in the file)

For example:

Fz   ('''scalp''' electrode, coordinates assigned by default.ecd)

Cz   ('''scalp '''electrode, coordinates assigned by default.ecd)

......

VEOG   (vertical EOG,''' Polygraphic''' type is assigned by default)

Exx   (xx=01, 02.. electrode number, '''Polygraphic '''type is assigned by default)

......

EEG xx ('''scalp''' electrode, coordinates must be assigned either by '''default.ecd''' or by a surface point (+'''.sfp''') file. An alternative to the "EEG" prefix is "SCP".

......

POL XX  (identifier sets '''Polygraphic''' type -- an alternative to the "POL" prefix is "PGR")

......

ICR A01  (identifier sets '''Intracranial''' type to electrode A01 - do not use A1!)

ICR A02  (identifier sets''' Intracranial''' type to electrode A02 - do not use A2!)

ICR A03  (identifier sets''' Intracranial''' type to electrode A03)

......

MEG M01  (identifier sets '''MEG '''type to electrode M01 - do not use M1!)

MEG M02  (identifier sets '''MEG''' type to electrode M02 - do not use M2!)

......

REF Cz  (the label is assigned to the electrode reference, no channel is associated with this entry. This must be the last line of the file!)

'''Channel spherical coordinate files (*.elp)'''

These files follow the same rules as the channel label files, with the addition of spherical coordinates (theta, phi) that follow the labels of EEG and MEG channels. Labels can also be omitted. In this case, BESA Research will assign labels according to the nearest coordinate defined in the '''default.ecd''' file. To indicate that the coordinates have been assigned, the label will have a tick, e.g. Fz' instead of Fz.

Channels of other types (polygraphic, intracranial) are defined exactly as in the channel label ('''<nowiki>*.ela</nowiki>''') file.

=== cot (Head center) file ===

'''Function''': to redefine the center of the head for the sphere used in dipole models. If the cot file has the same base name as the data file, it is read automatically by BESA Research. If the coordinates deviate by more than 1 mm from the previously defined head center, a window is opened, asking if the new values should be adopted. This mechanism is turned off if the data have been coregistered to MRI (see online help chapter ''"MRI Coregistration''"), and an MRI Coregistration File ('''<nowiki>*.sfh</nowiki>''') has been associated with the data.

BESA Research uses any head surface points (e.g. electrode locations), excluding those on the lower part of the face, to compute the sphere center automatically. The cot file is used if you want to override the automatic calculation. A mechanism is provided which allows to pass a location from the MRI (viewed by BrainVoyager) to the Source Module and save the resulting location as a ''cot ''file.

'''Format''': one set of coordinates (x y z). These are followed by either "'''DC'''" or "'''HC'''", which specify whether these coordinates are in '''D'''evice or '''H'''ead '''C'''oordinates.

'''Units:''' must be in meters!

(Note: In special cases, a fifth value, the '''head radius''', may follow. This is used when reading simulated MEG data from the DipoleSimulator program. When this value is set, BESA Research uses the specified head radius and head center and does not fit a sphere to the head surface points. and does not create an ellipsoid transformation).

Force BESA Research to use a completely spherical model without creating an ellipsoid: Write "'''DipoleSimulator"''' or "'''Phantom'''" on the second line of the file. Under these circumstances, 100% correspondence between DipoleSimulator and BESA Research is achieved. This is also required for dipole fitting on MEG phantom recordings.

The ''cot ''file has also been extended for reading CTF MEG files. Documentation for these extensions is found in the CTF help file.)

=== pos or pmg (MEG sensor coordinate) file ===

'''Function:''' to define coordinates of MEG sensors. Our convention is to save magnetometer information in '''<nowiki>*.pmg</nowiki>''', and gradiometer information in '''<nowiki>*.pos</nowiki>'''. In practice, BESA Research doesn’t mind which extension is used -- the distinction between gradiometers and magnetometers is based on the number of values on each line in the file.

'''Format:''' one sensor per line.

Magnetometers: label (optional), six coordinates per line (location, orientation)

e.g. for BTi:

" Channel 'A1': -0.0019193 0.0304846 0.1081738 0.1188222 0.2394208 0.9636177"

Gradiometers: label (optional), nine coordinates per line (location of primary sensor, location of secondary sensor, orientation). The program decides whether gradiometers are planar or axial based on the distance between the primary and secondary sensor locations and the center of the head.

e.g. for Neuromag:

" 0.108510 -0.000143 -0.044954 0.108510 0.000463 -0.028766 0.999999 0.001450 0.000000 "

Labels in these files are ignored.

See chapter “''3D Coordinates for Precise Analysis/Data reading rules for MEG''”.

=== sfn (surface point name) file ===

'''Function:''' to match up digitized coordinates with channels that are defined as EEG electrodes and to define labels for additional digitized head surface points (e.g. MEG coils, etc.).

'''Format:''' one label per line.

Contains labels of surface points in the order of digitization. If fiducials are defined, these should be on the first three lines, with the labels 'FidT9', 'FidT10', 'FidNz' or 'FidLPA', 'FidRPA', 'FidNAS'.

If electrodes are defined in the data file, the labels of each electrode as defined in the data file (or in its associated ''ela'', ''elp'', or ''elb ''file) must be present!

The case of labels is not important (e.g. 'Fp1' will match with 'fp1').

The ''sfn'' file need not exist if labels are defined in the ''sfp ''file.

See chapter “''3D Coordinates for Precise Analysis / Data reading rules for EEG”.''

=== sfp (surface point coordinate) file ===

'''Function''': to define coordinates of digitized points on the head surface. The order of points must match with the order in the ''sfn ''file, or if no ''sfn'' file is present, labels must be included in the ''sfp'' file.

Note: If the digitized points include electrodes, the channel labels must correspond to the labels of the digitized points. The sequence of labels in channels and surface point coordinate file need not be the same – the allocation is performed by label matching. Channel labels may be defined in the data file, or they may be assigned using channel definition files ('''<nowiki>*.ela, *.elp, *.elb</nowiki>''').

'''Format:''' one set of coordinates (x, y, z) per line. Coordinate units must be either meter, centimeter or millimeter (BESA Research will perform a plausibility check automatically to determine which units are used). If a label is present this can precede or come after the three coordinate values.

If fiducials are defined, these should be on the first three lines. BESA Research will simulate fiducials if none are defined, but it is preferable to record these locations along with the other head surface points.

If there are MEG sensors, the same coordinate systems must be used in the ''sfp'' file and the ''pos/pmg ''file!

If labels are defined in the ''sfp'' file rather than in an ''sfn'' file, labeling rules apply as for the ''sfn'' file.

Example for the ''sfp'' file format:

[[Image:ST addfiles (2).gif ‎]]

BESA Research will check the coordinates for plausibility. If coordinates are more than 30° away from the expected location on the sphere there will be an error message. Such errors are usually due either to incorrect labeling or to a digitization error.

See chapter “''3D Coordinates for Precise Analysis /'' ''Data reading rules for EEG”.''

=== Generic File Format ===

This reader, incorporated into the '''GenericBesa.dll''' file, allows to read simple multiplexed or vectorized data formats, if you know the structure of the data format.

'''What you have to do'''
* With a text editor, write information about the data file you want to read into BESA Research into a text file, the ''Generic Header''.
* Save the edited text in the same subdirectory as the data file.
* '''Mechanism A:''' The generic header contains the data file name. With BESA Research, navigate to the file you just edited, and open it. The data should then be read into BESA Research.
* '''Mechanism B:''' Alternatively, navigate to the data file. The reader will check if there is a generic header in the same subdirectory, and use that to try to open the file. You have two options:

* <div style="margin-left:1.27cm;margin-right:0cm;">'''Specific:''' if the file has the same basename as the data file, and the extension “'''.generic'''”, this file will be used.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">'''Generalized:''' if a specific file is not found, the reader will look for the file “'''BESA.generic'''” in the same subdirectory.</div>

'''Important note:''' We recommend using mechanism A, using a header with the extension "'''.generic'''". When opening the data file in BESA, select the generic header. Mechanism B sometimes fails when opening the data file in BESA Research, because one of the other readers in BESA may erroneously interpret the file as their "own" data format, sometimes leading to a crash.

'''Format of the Generic Header'''

The first line '''must '''consist of the text: “''BESA Generic Data''” (without the inverted commas).

Subsequent lines '''must''' contain the following parameters, in any order (note that the parameters are case insensitive):

'''''nChannels'''''=''nnn'': The number of channels

'''''sRate'''''=''fff'': The sampling rate (samples/sec)

'''''format'''''=''type'': One of ''short'', ''int, float, double, ASCII''. If the format is ''ASCII'', the parameter''' nSamples''' must be specified as well (see below)

The following parameters are optional (values in square brackets denote optional parameters):

'''''nSamples'''''=''nnn'': The number of time samples in the data. If this value is 0, or the line is omitted, then use the file size to estimate the number of samples.

'''''file''''' = '': The data file name, without path information. If this is omitted, you can only read the data with mechanism B (see above). This line '''must''' be included if you want to read the data with mechanism A.

'''''DataOffset''''' = ''nnn'': Offset of data in bytes for binary data, in lines for ASCII data (default = 0).

'''''Factor'''''=''fff [range]'': Data values are multiplied by this factor to obtain µV values (default = 1). Optional parameters can be appended to define a channel range, e.g. ''1-3''. Thus, this command can be used multiply, to define different scaling factors for different channels. If only one channel is specified, use on number only, e.g. ''5''.

'''''SwapBytes''''' = ''ccc'': One of ''off'' or ''on'' (default = off). If the data block originated from Unix or Mac, this will need to be ''on''. (binary data only)

'''''Prestimulus'''''=''fff'': Prestimulus interval in milliseconds.

'''''Label'''''=''ccc'': Segment label.

'''''Trigger''''' = ''chan….'': Channel number containing triggers. Without further parameters, the values are read directly as digital trigger values. Other parameters are described below, for the case where the trigger channel contains analog signals.

'''''nBlocks'''''=''nnn'': The data are epoched. This specifies the number of equal sized blocks in the data. In BESA Research, each block will be separated by a segment boundary. The number of samples in each epoch is computed from the total number of samples divided by ''nBlocks''.

'''''nEpochs'''''=''nnn'': Same as '''nBlocks'''.

'''''EventFile'''''=''name'': Load events from an event file, using BESA's event file ('''<nowiki>*.evt</nowiki>''') format. See below for a description of how to prepare this file.

'''''Order'''''=''type'': One of ''multiplexed'', ''vectorized''. The default is multiplexed (i.e. channels fastest). Specify ''vectorized'' if your data are ordered so that all time samples for channel 1 are followed by all time samples from channel 2, etc.

'''''Orientation'''''=''type'': Same as '''Order'''.

'''''Arrangement'''''=''type'': Same as '''Order'''.

'''Trigger events'''

This section describes how the reader can be used to encode trigger events when the trigger channel contains analog signals. In this case, a '''Trigger '''command is required for each target code in BESA Research.

Syntax:

'''Trigger''' = ''chan  code  fromLevel  toLevel  timerange''  ''deadtime''

'''''chan''' ''is the channel number on which to find the trigger

'''''code''''' is the trigger number that the reader will assign (must be positive!)

'''''fromLevel'' '''is the value in mV defining the lower range for trigger detection

'''''toLevel'' '''is the value in mV defining the upper range for trigger detection. If this is “-“, then only ''fromLevel ''needs to be exceeded for the trigger to be detected.

'''''timerange '''''is the range in milliseconds to define a trigger. The reader will search for the maximum deviation from baseline within the range to find the level that will define the trigger.

'''''deadtime''' ''defines the time after detecting a trigger during which no further trigger with this code can be detected. This does not affect other codes. Also, if the voltage level stays at a level corresponding to a code, the trigger is only defined at the onset of this voltage level.

Multiple lines are required if different trigger codes and different trigger channels are required, one for each new code.

'''Notes'''

'''Channel labels:''' The data channels are labeled ''E1, E2, E3,…,'' and they are initially classified by BESA Research as polygraphic. As with other BESA Research data files, use a '''<nowiki>*.ela </nowiki>'''file (or '''<nowiki>*.elp</nowiki>''', optionally combined with '''<nowiki>*.sfp</nowiki>''') to redefine labels and channel types.

'''Data formats:'''

* Short 16-bit
* Int 32-bit
* Float 32-bit
* Double 64-bit
* ASCII Decimal numbers separated by spaces or tabs (engineering format also permitted)

'''Prestimulus interval and label:''' If either of these are defined, BESA Research reads the data in to define an averaged data segment. The label is displayed, and a vertical dotted line marks timepoint zero. If no prestimulus interval is defined, a zero prestimulus interval is assumed.

'''Future changes'''

Possible developments:
* Read channel labels

If any of these changes are particularly important to you, please contact [mailto:support@besa.de support@besa.de] and let us know.

'''Event File'''

The event file is a text (ASCII) file containing a header line and subsequent lines, with one event description per line.

Each line contains four parameters:

1. latency (units specified by the header, can be µs, ms, s)

2. code (defines the type of event: trigger, comment, marker, pattern, average segment, data break segment)

3. parameter (depends on the event type, e.g. trigger code)

4. label (label assigned to the event)

'''Header Line:'''

The header line contains four values. The first specifies the time units, e.g. '''Tmu '''specifies microseconds.

''    Tmu    Code    TriNo    Comnt''

'''Tms''' specifies milliseconds. '''Tsec''' specifies seconds.

'''Event Code and Parameter 3 (TriNo):'''

'''Code''' specifies the event type:

1 = trigger -- '''TriNo '''specifies the trigger number

2 = comment

3 = marker

11-15 = patterns 1-5

21 = artifact on

22 = artifact off

31 = epoch on

32 = epoch off

41 = segment onset -- '''TriNo '''is a time string that specifies date and time, in the format ''YYYY-MM-DDTHH:MM:SS'', e.g. ''2010-04-26T15:30:20.31'' (note: seconds are a decimal number).

42 = average segment onset -- '''TriNo '''is a number specifying the prestimulus baseline of the subsequent average in microseconds. '''TriNo '''(parameter) is 0 for markers, comments, artifacts, and epochs.

'''Comment'''

The event label. This is not used for markers, artifacts, and epochs.

'''Example of event file:'''

A simple way to generate example files is to export events from BESA (''ERP/Save Events As...'').

Tmu         Code     TriNo     Comnt

0              42     100000    Ave: 25 avs  

10000000  2       0            Comment at 10s

20000000  41     26-04-2010T15:30:20.000   TestSeg2

21000000  3       0

22000000 1        99          Trigger – 99

This specifies an average segment starting at the beginning of the file, with a prestimulus interval of 100 ms, a comment at 10 s, a new segment specifying date and time at 20 s, a marker at 21 s, and a trigger with code 99 at 22 s.

'''Examples'''

The following reads ASCII multiplexed data that were previously exported from BESA Research:

''BESA Generic Data''

''nchannels = 64''

''srate = 100''

''nsamples = 10000''

''dataoffset = 2''

''format = ASCII''

''file = name.mul''

''factor = 1''

With the sampling rate of 100 Hz and 10000 samples, this represents 100 s of 64-channel data. The first two lines of the data are skipped.

[[Category:Research Manual]]

{{BESAManualNav}}

The Initialization File: BESA.ini

2017-04-07T13:14:38Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
== The Initialization File: BESA.ini ==

=== Introduction ===

'''BESA.ini File'''

BESA Research uses settings provided in the initialization file '''BESA.ini''' whenever BESA Research is started or a new file is opened for the first time. The format of this file conforms with standard initialization files ('''<nowiki>*.ini</nowiki>''') of Windows. You may change the settings in '''BESA.ini''' using NOTEPAD.exe from the ACCESSORIES group, or other plain text editors to adapt BESA Research to '''your own everyday needs'''. The default settings provided in '''BESA.ini''' will be used by BESA Research whenever BESA Research or the launch program is started. It is advised that you make a backup copy of '''BESA.ini''' before you change the default settings.

'''Location of BESA.ini'''

You can place '''BESA.ini''' at three possible locations:

'''a) Private''': each user on a PC should have his/her own private settings. This is normally in ''My'' ''Documents/BESA/Research_6_0''

'''b) Public''':  all users should use one setting, but they can edit '''BESA.ini''' to change the settings. This is normally in ''Shared Documents/BESA/Research_6_0''

'''c) Administrator''': the PC administrator determines the settings. This is normally in ''C:Program'' ''Files/BESA/Research_6_0''

The actual folder names depend on the operating system and the system language.

When BESA starts, it first looks for the''' administrator''' version of '''BESA.ini'''. If this is not found, it looks for the '''private''' version. If this is not found, it looks for the '''public''' version. If this is not found, internal default values are used.

'''There are 13 general sections, and several reader-specific sections:'''

[Defaults]                   -- General settings (filters, scaling, and various other settings)

[Folders]                    -- Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)

[Electrodes]               -- Electrode renaming

[Patterns]                   -- Rename patterns in the '''Tags''' menu

[Artifacts]                   -- Settings for artifact correction

[KEYCONTROLS]     -- Function key definitions

[Search]                     -- Default parameters for search

[FFT]                          -- Frequency band definitions

[Printer]                      -- Printer control

[Calibration]              -- Calibration control

[Video]                      -- Digital video control

[Mapping]                  -- Mapping control

[Matlab]                     -- Settings for the Matlab interface

[Updates]                  -- Options for program updates

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

=== Defaults ===

'''Default settings provided for section [Defaults]:'''

'''DatabaseAllowLocalFiles=Yes''' (If set to "Yes", BESA Research will write filenames "'''datafilename.ftg'''" and "'''datafilename.fst"''' to the data folder, saving current file tag and display settings there. If set to "No", these files are only written to the database. If set to "Yes", you can copy these files along with the data to a new folder, and display settings and tags will be preserved.)

'''DataBuffering=Off''' (If set to "On", an internal buffer of length 180 s of data is kept to speed up paging). This can speed up paging, particularly when the data are in a network folder.

'''DisplayedTime=10''' displayed time window [s] on the screen

'''Montage=Org''' montage used when opening a new file

'''ScpScale=50''' scale of scalp channels in [mV]

'''PgrScale=500''' scale of polygraphic channels in [mV]

'''IcrScale=500''' scale of intracranial channels in [mV]

'''MegScale=500''' scale of MEG/marker channels in [fT]

'''BaselineCorrection=On''' baseline correction, do not switch off in AC systems

'''ClippingPercent= '''set from 100 to 200 if you want to clip artifacts in displayed EEG (not used if empty or 0)

'''LowFilter=''' low filter cutoff frequency [Hz] (variable filter)

'''TimeConstant=0.3''' time constant for low filter cutoff frequency [sec] (fixed forward filter, 0.3 sec is equivalent to 0.53 Hz)

'''HighFilter=70''' high filter cutoff frequency [Hz] (variable filter)

'''NotchFilter=50''' notch filter center frequency [Hz]

'''NotchFilterStatus=Off''' notch filter is off, set=On if you want to use as default

'''BandFilter=12''' band pass filter center frequency [Hz]

'''BandFilterStatus=Off''' band pass is off, set=On if you want to use as default

'''AdditionalChannelFile=''' defines the full path and name of an additional channels montage file, e.g. '''C:\Program Files\BESA\Research_x\Montages\AdditionalChannels\EKG.sel'''

'''ColoredWaveforms=On''' scalp waveforms are (not) colored according to region

'''WriteSegmentPath=''' defines default path for saving segments/averages. If blank, the path of the current data file is used.

'''ShowSubjectInfo=Off''' subject info will (not) be displayed.

The following optional parameters are not defined as default and can be set manually in''' BESA.ini''':

'''TextEditor="Notepad.exe"''' defines the path to your preferred text editor. This will be used when you press the '''Edit''' button the ''Load Coordinate Files dialog box''.

'''NeuroScanDataNumberOfBits=32''' defines the format of NeuroScan data files ('16' for 16-bit, '32' for 32-bit). If this variable is not specified, BESA uses a heuristic to (try to) decide which of the two data formats is used. This variable overrides the heuristic. If you want to specify the NeuroScan data format for specific files, create a file, named "16bit" or "32bit", and place it in the data folder.

'''ScaleAmplitudesForNNChannels=25''' Scale waveforms as if a fixed number of channels were displayed in the window (here: 25). A minimum of 10 channels can be used for the scaling. This parameter is superseded if the parameter "''ScaleAmplitudesFixedPixelHeight"'' is specified.

'''ScaleAmplitudesFixedPixelHeight=70''' Set the scale bar for amplitudes to a fixed pixel height (here: 70). If this parameter is set in the '''.ini''' file, it supersedes the parameter "''ScaleAmplitudesForNNChannels''".

'''Notes'''

Check the Menu descriptions for the various definitions of filters, montages etc. For montage preselection, use the labels as visible on the montage push-buttons.

The additional channels file should contain all polygraphic channels (e.g. EKG, EOG, respiratory) that you want to view regularly along with the scalp channels. The entry AdditionalChannelFile must specify the full path pointing to the location of additional channel files (recommended: ''Montages\AdditionalChannels''). If no drive is specified, the installation drive of BESA is used.

If BaselineCorrection is set to 'On', before displaying a screen of data, BESA subtracts for each channel the mean over its displayed time points. This optimizes viewing, because it ensures that the vertical position of each channel is not shifted upward or downward from the channel label at the left of the screen. There are some cases in which you will not want baseline correction, i.e. when the DC level in the data is already correctly defined. This is usually the case, for instance, when reading in files that have been processed by BESA. In this case, BaselineCorrection should be set to 'Off', because otherwise maps and source montage displays may be distorted.

=== Folders ===

'''The [Folders] section defines where BESA Research places its files. In versions 5.1 and earlier, files were located in various subfolders of the program folder. This led to problems if the user did not have administrator rights, e.g. to create or write to a file. For Vista compatibility, many folders are now located by default in locations where normal users can create and write files. If you wish, you can also specify paths in the [Folders] section to use the previous locations. The previous location is given for each variable.'''

These settings allow some flexibility that can be useful if you want to tune BESA Research for use by several users, or on a network. For instance, the Examples and Montages folders might be located on a network disk. For the current defaults, the database, Examples, Montages, and Scripts are set up for use by all users on the PC on which BESA Research is installed. The settings files ('''Besa.set''', '''Besa.cfg''', etc.) are located in private folders so that each user retains his or her own settings.

The '''default''' settings (i.e. settings that BESA Research uses if the entries are omitted in the '''.ini''' file) are shown for each variable definition.

The folder definitions can use '''placeholders''', labels enclosed by a % sign (e.g. %localapp%), to define paths that vary depending on the language version and on the system (XP or Vista). These are defined below.

'''The Variables'''

'''Database=%localapp%''' The path of the BESA Research database folder (used to be ''%progdir%System\DB'' in BESA versions up to 5.1.x). Unless the provided path ends with ''\DB'' or ''\Database'', BESA Research will automatically create a folder named ''Database'' in the provided path.

'''Settings=%privatprog%Settings''' The path of the BESA Research settings folder (used to be ''%progdir%System'' in BESA versions up to 5.1.x)

'''Montages=%publicprog%Montages''' The path of the BESA Research montages folder (used to be ''%progdir%Montages'' in BESA versions up to 5.1.x)

'''Scripts=%publicprog%Scripts''' The path of the BESA Research Scripts folder (used to be ''%progdir%Scripts'' in BESA versions up to 5.1.x)

'''Examples=%publicprog%Examples''' The path of the BESA Research Examples folder (used to be ''%progdir%Examples'' in BESA versions up to 5.1.x)

'''User=%privatprog%Settings''' The path for user defined settings (used to be ''%progdir%System\Userdirs'' in BESA versions up to 5.1.x)

'''Placeholders'''

The strings enclosed by percent signs (%) are placeholders for the following folders in English-language versions of Windows. Folder names are different for Vista and XP/2000 and for other language settings. BESA Research will substitute the placeholders by the appropriate folder name for the system (W2K, XP, Vista, or Win7) and the system language:

* '''Windows 7(English):'''

'''%localapp%''' = "''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Libraries\Documents\Public'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Libraries\Documents\My'' ''Documents\Research_6_0''" or "''Desktop\[User]\My Documents\BESA\Research_6_0''.

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

* '''Windows Vista (English'''):

'''%localapp% '''<nowiki>= "</nowiki>''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Desktop\Public\Public Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''  

* '''Windows XP (English):'''

'''%localapp% '''<nowiki>= "</nowiki>''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0". ''This folder is directly accessible from the Windows Explorer under "''My Computer\Shared'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''My Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%  '''

* '''Windows 2000 (English):'''

'''%localapp%''' = "''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer '''as "'''''My Documents\BESA\Research_6_0'''''". '''

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

=== Electrodes ===

'''This section allows for automatic relabeling of electrodes. For instance, the 10-20 label "T3" can be replaced by the 10-10 convention "T7".'''

'''Default settings provided for section [Electrodes]:'''

T7=T3 replace 10-10 label with old 10-20 convention

T8=T4 replace 10-10 label with old 10-20 convention

P7=T5 replace 10-10 label with old 10-20 convention

P8=T6 replace 10-10 label with old 10-20 convention

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

Other examples, depending on your electrode input box definition, could be:

PG1=LO1 define X3 as lateral orbital eye electrode left

PG2=LO2 bipolar LO1-LO2 defines horizontal EOG (additional channel)

X3=IO1 infraorbital, e.g. use with FP1 as additional channel for VEOG

X9=Rsp define X9 channel to be a respiratory channel

Relabeling of channel names (as stored in the EEG file header) is helpful to predefine your standard sequence of channels and to avoid the need for reading and/or editing a Channel Configuration file for every EEG file.

'''Note 1''': For polygraphic channels, or if your EKG has been recorded differentially, you should edit and define an ''Additional Channels Montage'' according to your recording channel configuration (e.g. Fp1-IO1=vertical EOG). The Additional Channels group permits to display these channels regularly below the scalp montages with individual scales.

'''Note 2''': EOG channels record both eye and scalp activity. In digital EEG systems, EOG electrodes should be labeled according to their position in the 10-10 system (see "''Electrode Conventions''"). This permits use of these electrodes for mapping and suppression of eye artifacts. The standard definitions above give an example of how to relabel extra channels (X1...X10, PG1, PG2) for the use of EOG, EKG and respiratory (Rsp) channels. Use an ''Additional Channels'' file to define horizontal and vertical EOG channels by using the appropriate electrodes in a bipolar montage (an example is provided in '''eog-ecg.mtg''' in ''Montages\AdditionalChannels''). Differentially recorded EKG and respiratory channel can be defined in the same file.

=== Patterns ===

'''Default settings provided for section [Patterns]:'''

These settings define labels for each of the five patterns. The labels are shown* in the''' Tags''' menu,
* in the '''TAG push-button''' popup menu, and
* when displaying tag info clicking with the right mouse on a tag at the bottom of the EEG or on the event bar.

By default, no labels are defined. Define a label, e.g. for Pattern1 and Pattern2, as in the following example:

Pattern1=Spike

Pattern2=Sharp Wave

=== Artifacts ===

'''Artifact default settings:'''

See the chapter "''Artifact Correction / Reference / Artifact settings in the BESA.ini file''" in the online help.

=== Search ===

Default settings for pattern search.

'''Default Settings for the ''Search/Options ''Dialog box:'''

'''CorrelationThreshold''' = '''75%'''

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

'''Default Settings for the ''Search/Average/View'' (SAV) Dialog box:'''

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

'''HighPassSlope = 12 dB/Octave'''

'''HighPassType = 0 (0 = zero phase, 1 = forward, 2 = backward'''

'''LowPassFreq = 35 Hz'''

'''LowPassSlope = 24 dB/Octave'''

'''LowPassType = 0 (0 = zero phase, 1 = forward, 2 = backward)'''

'''CorrelationThresholdNoMarked = 60%'''

Default correlation threshold if no channel labels are marked when the SAV Dialog is opened.

'''CorrelationThresholdOneMarked = 85%'''

Default correlation threshold if one channel label is marked when the SAV Dialog is opened.

'''CorrelationThresholdFourMarked = 65%'''

Default correlation threshold if between two channel labels are marked when the SAV Dialog is opened.

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

If set to "Yes", a File Save dialog will open, to allow to save the search average to a file (as with the SAW function).

'''WriteAfterSearchCheckBox = No'''

If set to "Yes", an additional checkbox "Write after search" is displayed at the bottom of the SAV Dialog, allowing to choose whether or not to write the search average after a search:

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

If set to "No", the SAV Dialog will open with the same boxes checked as the last time the dialog was opened during the current session.

If set to "Yes", the default frequency, buffer width, selected view after search, and default threshold are always checked when the dialog is opened.

=== KeyControls ===

In the [KeyControls] section you can specify functions that can be allocated to '''function keys''' or to the ''Del'' key. Specify using the form:

'''Fn=function''' or

'''Del=function'''

where "''n''" is a number between 2 and 12 (F1 is reserved for Help). For example:

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

'''Pattern''n''''', where ''n''<nowiki>=1-5: Sets the tag number </nowiki>''n'' at the cursor latency.

'''Epochfast:''' sets one boundary of an epoch at the cursor latency, but does not open the epoch text box to define a label.

'''Marker:'''  sets a marker at the cursor latency.

'''Comment:''' sets a comment at the cursor latency and opens the comment box to enter text.

'''Epoch:''' sets one boundary of an epoch at the cursor latency and opens the epoch text box to enter a label.

'''Artifact:''' sets one boundary of an artifact segment at the cursor latency.

'''Delete:'''  deletes a tag at the cursor latency

'''Batches and Montages:'''

'''Batch''n''''', where n=1-12: Runs a predefined batch file corresponding to the number ''n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a batch, pressing it will open a ''File Open Dialog'' to select a batch. The setting you have chosen will be retained across BESA Research sessions. Holding the '''<shift>''' key while pressing the '''function key''' will always open the dialog. Hold the''' <ctrl> '''key with the function key to open the associated batch in the batch edit dialog.</div>

'''Montage''n''''', where n=1-12: Sets a montage corresponding to the number'' n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a montage, pressing it will generate a message asking you to associate a montage as follows: Holding the '''<shift> '''key while pressing the '''function key''' will remove the current association, and substitute it with the current montage.</div>

The default settings after program installation are listed in the online help chapter ''Review / Reference / Controls / Mouse and Keyboard / Keyboard Controls''.

=== FFT ===

'''Default settings provided for section [FFT]:'''

These settings define the setup in the Spectral Analysis section of the BESA Research program (FFT window, see the chapter "''Spectral Analysis / FFT''"). Up to 7 frequency bands may be defined. Five are defined by default.

'''FFTBand1=On''' FFT Bands 1-5 are defined

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

'''FFTBand6=Off''' FFT Bands 6-7 are not defined

'''FFTBand7=Off'''

'''FFTNameBand1=Delta''' Names of the defined bands

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

'''FFTColorBand1=RGB(0,0,0)'''  Default color of each band

'''FFTColorBand2=RGB(0,128,64)'''

'''FFTColorBand3=RGB(128,0,0)'''

'''FFTColorBand4=RGB(255,0,0)'''

'''FFTColorBand5=RGB(255,128,0)'''

'''FFTColorBand6=RGB(255,192,0)'''

'''FFTColorBand7=RGB(255,255,0)'''

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

'''FFTLowBand3=8''' Alpha from 8-14 Hz

'''FFTHighBand3=14'''

'''FFTLowBand4=14''' Beta from 14-30 Hz

'''FFTHighBand4=30'''

'''FFTLowBand5=30''' Gamma from 30-50 Hz

'''FFTHighBand5=50'''

These values are best set from within BESA Research, using the '''Options''' menu in the FFT window (see the chapter "''Spectral Analysis / FFT / FFT Options Menu''"). Current settings are stored after each session and retrieved in the next session.

=== Printer ===

'''Default settings provided for section [Printer]:'''

'''PrinterMarginPercent=100''' controls size of printout

'''PrinterColors=256''' set to 1/2 for black&white, 0/256 for color printers

'''PrinterLineMode=1''' set to 2 for thicker lines and to save printer memory

'''PrinterMapResolution=1''' set to 2, 3, 4 to save printer memory and increase speed

=== Calibration ===

'''Default settings provided for section [Calibration]:'''

'''AutoCalibration=Off''' On: automatic calibration of signals >= 4 cycles

'''MicrovoltCalibration=50''' peak voltage of calibration signal

If calibration is set to'' On'', the menu item ''Calibration ''will appear in the''' Process '''menu. Position your current screen at an epoch containing at least 4 regular cycles of the calibration signal (in all channels!) and select Calibration.

=== Video ===

'''Default settings provided for section [Video]:'''

'''DVCFilePath=C:\DVC\DVPlay.exe''' holds the path to the digital video player

'''DVCCommandLineArguments=/S:3 /M:P /T:M'''  arguments to be passed to the digital video player

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

'''MappingRepetitionRateWithVideoInMS=100'''  gives the number of milliseconds between two maps if the mapping window is open while the video is running. If the graphics board encounters problems during the display, this value should be increased.

=== Mapping ===

'''Default settings provided for section [Mapping]:'''

'''UseBitmapDrawing=Off'''

Set this to "On" if 3D maps show a strange pattern of black triangular shapes (this is frequently observed with modern Intel On-Board graphics controllers, and is a result of inadequate drivers for Open-GL).

'''Use3DVBlending=Auto'''

Set this to "Off" if the 3D view in the Montage Editor or the Source Analysis window does not show up properly (this may happen with some older graphics cards).

Set this to "On" if the 3D view in the Montage Editor or the Source Analysis window shows a ragged surface boundary.

'''MapSmoothing=0 '''

Set a non-zero value to specify a default map smoothing parameter (normally specified in ''Options/Mapping/Spline Interpolation Smoothing Constant'').

=== Matlab ===

'''Default settings for the [Matlab] section:'''

'''Platform=32'''

'''Set Platform=64''' if you want to use the 64-bit version of Matlab

=== Updates ===

This section is not normally required, but the variables here can be altered or defined to determine how BESA Research checks for dongle and program updates.

'''DaysBetweenUpdateChecks=7'''

Sets the number of days between automatic checks for updates. Set the value to 0 to check every time BESA Research is started. Set to -1 to turn off automatic update checks.

'''CheckNetworkDongle=Off'''

For the network administrator: If set to "On", BESA Research will check the dongle on the network for updates. Otherwise the state of the network dongle will be ignored.

'''LocalPath'''

For the network administrator. This can be set to a path on the local network to the BESA update files, so that users can obtain their updates locally. The path is given to the text file "'''UpdateVersions.txt'''" (e.g. ''LocalPath=\\transtec-sak\zarascratch\BESA\Updates\UpdateVersions.txt''), which contains further details for the program to obtain its updates. If you want to use this feature, please contact us at [mailto:support@besa.de support@besa.de].

The following variables are not required, because BESA Research has the paths hardwired:

'''FTP1 (also FTP2, FTP3)'''

ftp download server

'''Path1 (also Path2, Path3)'''

Path on the server to UpdateVersions.txt.

'''HaspPath1 (also HaspPath2, HaspPath3)'''

Path on the server to HASP (dongle) update files.

'''History'''

Path on the server to general history file

=== Reader-Specific Settings ===

'''BrainLab'''

'''Default settings provided for section [BrainLab]:'''

'''BrainLabFormat=New''' this entry ensures that the newer BrainLab file format can be read by BESA Research.

'''Bio-Logic'''

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:
* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>
* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

'''EDF+/BDF/Trackit'''

'''TriggerScan=On'''

Set '''TriggerScan=Off '''to prevent BESA Research from scanning the file for triggers. This is done separately for EDF+, BDF, and Trackit files in sections '''[EDF+], [BDF],''' and '''[Trackit]''' in the '''BESA.ini''' file.

'''EGI'''

The treatment of DIN events can be modified in the''' [EGI] '''section:

'''CombineDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you want to treat DIN events separately, and not generate combined values.

'''SeparateDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you don’t want to treat DIN events separately.

Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

'''CombineDINeventsPrefix'''<nowiki>=dinComb</nowiki>

<div style="margin-left:0.953cm;margin-right:0cm;">This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

'''Harmonie'''

'''Default settings provided for section [Harmonie] (Stellate Harmonie systems):'''

'''SeizurePreEpoch=60''' length of the epoch preceding a seizure detection in s

'''SeizurePostEpoch=60''' length of the epoch following a seizure detection in s

'''PushButtonPreEpoch=60''' length of the epoch preceding a push button detection

'''PushButtonPostEpoch=60''' length of the epoch following a push button detection

When BESA Research encounters a seizure detection event or a push button detection event in a Stellate Harmonie file, it automatically sets an epoch around the event, which makes it convenient to view just those epochs for analysis. The length of the epochs preceding and following the events can be adjusted in the '''.ini''' file.

'''Neuroscan Keys'''

'''Note that there is a setting "NeuroScanDataNumberOfBits" in the [Defaults] section of BESA.ini that is used for distinguishing the data format of Neuroscan files (16 or 32-bit).'''

'''Default settings provided for section [NeuroScan Keys] (NeuroScan systems):'''

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

'''NKT2100'''

'''Default settings provided for section [NKT2100] (Nihon Kohden EEG 21xx systems):'''

'''TriggerScan=On'''   Set to "Off" to prevent a scan for trigger events.

'''Country=NotKanji''' set to NotKanji for non-Kanji characters else to Kanji

'''KanjiCharSize=16''' Kanji character size

'''KanjiPrinterCharSize=32''' Kanji printer character size

'''EEG_Sensitivity=50''' default sensitivity of Nihon Kohden EEG-2100 system

'''DC_Sensitivity=50''' default sensitivity of Nihon Kohden DAE-2100 system

'''QJ_Sensitivity=100''' default sensitivity of Nihon Kohden QJ-403 system

'''Mark_Sensitivity=100''' default sensitivity of EEG-2100 marker channels

These settings need to be changed only if the manufacturer has specified different gains for your system. Otherwise do not alter these settings.

'''Vangard'''

'''AlwaysOpenFileSelect=Yes'''

If "Yes" is selected, each time a Vangard file is opened, a dialog box will open, asking for a selection of the segment type to display.

If "No" is selected, the selection dialog is opened whenever a Vangard file is opened for the first time, or if the ''Channel and digitized head surface point information dialog box'' is opened (e.g. with '''ctrl-L''' or ''File/Head Surface Points and Sensors/Load Coordinate Files...'' ).

'''XLTEK'''

'''TriggerScan=Off '''Set to "On" to scan the data file for trigger events

'''MontageNo=2''' Set to 1 or 2. If two montages for the data file are defined, this variable determines whether the first or the second alternative should be used.

[[Category:Research Manual]]

{{BESAManualNav}}

Electrodes and Surface Locations

2017-04-07T13:14:18Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
= Working with Electrodes and Surface Locations =

== Introduction - Electrodes and Surface Locations ==

Here you will find out how BESA Research works with electrode and MEG sensor coordinates and labels, and how head surface points can be used to improve source modeling and coregistration of source models with the MRI. In most cases, electrode positions are sufficiently defined by their labels. The section "''Electrode Conventions''" lists the standard position which BESA Research assigns to EEG channels. In some cases, especially for larger electrode arrays or for MEG measurements, additional information is required to add sufficient information for mapping and for source analysis. The additional information is supplied in additional, auxiliary files which are read by BESA Research and associated with the data files. The auxiliary files, and how they are supplied to BESA Research, are described in this chapter.

Examples for using auxiliary files to define the 3D locations of electrodes are found in the chapter "''Special Topics / Working with Electrodes... / Examples''" in the online help.

Descriptions of file formats that BESA Research uses are given in the online help chapter "''Special Topics'' ''/ Working with additional files''".

== Working with auxiliary files ==

Data files come with varying amounts of prior information about electrode/sensor locations, depending on the recording system. BESA Research allows you to read auxiliary files that define additional information, such as channel labels, and coordinates of the electrodes, sensors, and other head surface points. The information is required for mapping and for source montages.
* '''Mapping.''' BESA Research uses spherical spline mapping. For this, electrode/sensor locations are projected onto a sphere. The minimum requirement is 10-10 or 10-20 labels: if only channel labels are available without additional information, BESA Research uses default spherical coordinates.
* '''Source modeling'''. Spherical coordinates of electrode locations are sufficient, but digitized locations are better. Digitized locations can be defined in the data file or in auxiliary files. BESA Research will use digitized head surface points (electrodes + additional points) to fit a sphere for the spherical model. Points anterior to the left and right preauricular points and below the plane formed by these points and the nasion are excluded when fitting the sphere.

Files can also be written, for instance for
* '''Source modelling with MRI coregistration'''. BESA Research allows for the export of surface points in a special format ('''sfh''' file) which can be read by the BESA MRI (or BrainVoyager) program. These are fitted to the head surface defined by BESA MRI (or BrainVoyager) in order to define rotation, translation, and deformation parameters required to coregister the coordinate systems (see "''Integration with MRI and fMRi''").
* '''Export of coordinates.''' Electrode, other surface point locations, and MEG sensor coordinates and other surface point locations can be written to ASCII files so that they can be reread when reading other files into BESA Research (e.g. ASCII files), or used by other programs.

Feedback and control over how these files are read is provided by
* '''the Channel and digitized head surface point information dialog box.''' This dialog is usually opened when you open a file for the first time. It allows you to specify the names of auxiliary files, and it makes initial checks on the files to see whether they are consistent with each other and with the data file. If the check is OK, you will see a green tick at the top right hand corner of the dialog box. If there are inconsistencies, the tick is replaced by a red exclamation mark. In this case, you will usually need to edit the auxiliary files or specify other files. The dialog box is not opened if the file is recognized to contain all the necessary information (files with the '''foc''', '''fsg''' extensions), or if the program only finds a channel definition file (with extensions '''ela, elp,''' or '''elb'''). The dialog box is not opened if the data file has been opened before. You can always open the dialog box manually by specifying ''" File / Head Surface Points and Sensors/Load Coordinate'' ''Files.''
* '''The log file''' ('''<nowiki>*_LoadFile.log</nowiki>''')'''.''' Coordinating the information between the data file and its auxiliary files can be a complex procedure. To help you check whether the coordination is being done properly, if you select the menu entry ''" Options / File / Generate Log "'' during File Open, BESA Research writes a log file with the same base name as the data file, appending "'''_LoadFile.log'''" to the base name, recording which files have been read, and some of the parameters that have been found. This file is created every time auxiliary files are read (e.g. on file open, when reading in channel configuration files, head surface point files, MEG sensor locations), or changed ("''Edit /'' ''Channel Configuration''").
* '''The log window. '''If there are inconsistencies during the processing of auxiliary files and 3D coordinates, a logging window is opened showing the information that would be written to the log file. You can read what has been done to help diagnose the problems. Select '''OK''' to continue in spite of the problems, or''' Reset''' to reject. Typing '''Reset''' also deletes the database files associated with the current data file, thus allowing you to start reading this file from scratch.

'''BESA Research remembers which auxiliary files are associated with the current file'''. When a data file is first opened, and BESA Research finds auxiliary files with the same base name as the data file, you will be asked if you want this file to be read. The decision you make will be recorded in the database for this data file. Next time the file is opened, the files will or will not be read, according to your previous decision. Similarly, when an auxiliary file is read using the menu, this is recorded in the database, and the file will be opened automatically next time the data file is opened. To override previous decisions, you must delete the database files (see the''' log window '''above) or change the entries in the Channel and digitized head surface point information dialog box (see the chapter ''"Electrode Conventions / Channel and digitized head surface point information dialog box''").

== Coordinate systems ==

We need to deal with four different coordinate systems. These differ in how the x, y, and z axes are defined, and in the units of measurement (e.g. mm, cm, m). The first three are illustrated in the following figure:

[[Image:ST Electrodes (1).gif ]]

'''Device coordinates.''' These are the coordinates used by the recording system. The axes may be anywhere in relation to the head. For instance, in the Polhemus digitizer, the axes go through the magnetic field transmitter which is located somewhere outside the head. The units of measurement may be millimeters, centimeters, or meters.

'''Head coordinates'''. This coordinate system is defined by reference points on the head known as ''fiducials''. The reference points are normally the nasion (Nz, NAS), the left preauricular point (T9, LPA), and the right preauricular point (T10, RPA). The x axis is defined by the line joining T9 and T10, positive towards T10. The y axis is defined by the line through Nz that is perpendicular to the x axis (positive towards Nz). The z axis is perpendicular to the x and y axes, and goes up out of the head in the vicinity of Cz. The units of measurement may be millimeters, centimeters, or meters. In BESA Research these are labelled with the prefix 'Fid', e.g. 'FidT9', 'FidNz'.

'''BESA Research coordinates.''' For dipole analyses the head model consists of a sphere. In the default situation where no digitized sensor information is available, the center of the sphere is defined by the crossing point between the lines joining T7 (=T3) and T8 (=T4) and Fpz and Oz.. The x axis is the T8-T7 line, positive at T8. The y axis is the Oz-Fpz line, positive at Fpz. The z-axis goes up out of the head through Cz. If digitized information is available, the axes are defined by the best fit between the idealized electrode locations and the real locations. The diameter of the sphere is also defined by the best fit. Units given in the display are in millimeters.

The '''center of the spherical model''' is on average about 4 cm above the origin of the Head Coordinates. If digitized surface points are available, the sphere is fitted to these points. Using a cot file, it is possible to override the fit and define your own head center. In conjunction with BrainVoyager, you can use the MRI to seed the location of the head center (e.g. a fixed distance anterior to the posterior commissure) and save it as a cot file. Using MRI coregistration (see "''Integration with MRI and'' ''fMRi''"), the center is placed between the anterior (AC) and posterior (PC) commissures, at the half-way point between the anterior and posterior points (AP and PP). Without coregistration, the center corresponds to a point 17.5 mm behind AC in the standard MRI head.

'''MRI coordinates.''' These are the coordinates used by BrainVoyager. These are defined by the MRI slices. Measurement units are millimeters.

== The Channel and Digitized Head Surface Point Information Dialog Box ==

Many data formats read by BESA Research require additional information about data channel, which are specified by additional, auxiliary files. This dialog box allows you to specify which auxiliary files are read in to supplement the information in the data file.

The dialog box is opened automatically the first time a data file is opened, if
* auxiliary files other than a channel definition file ('''<nowiki>*.ela</nowiki>''', '''<nowiki>*.elp</nowiki>''', '''<nowiki>*.elb</nowiki>''') are found
* no auxiliary files are found, and the data file was not written in compressed binary format ('''<nowiki>*.foc</nowiki>''', '''<nowiki>*.fsg</nowiki>''') by BESA Research

When a data file is closed, the information about which auxiliary files have been read is stored in the database. When the file is opened for a second time the dialog box is not opened automatically, because the information is assumed to be correct – the files are read automatically.

The dialog box can be opened manually by selecting "''File / Head Surface Points and Sensors/Load'' ''Coordinate Files''", or using the shortcut '''ctrl-L'''

[[Image:ST Electrodes (2).gif ]]

The dialog box is divided into several sections:

* '''Internal data file information.''' Here you can see the file name, the originating system (file format), the name of the database file, if any, and the channel information as specified by the data file alone.

[[Image:ST Electrodes (4).gif ]]

* '''Suggestions.''' This box makes suggestions about what needs to be filled in, e.g. "Please enter electrode thickness"

[[Image:ST Electrodes (5).gif ]]

* '''Main feedback (top right hand corner).''' A green tick indicates that the currently selected data files are consistent among themselves and with the data file. A red exclamation mark indicates an inconsistency. Check the feedback texts in the subsequent sections for more information:

[[Image:ST Electrodes (8).gif ]][[Image:ST Electrodes (7).gif ]]

* '''Channel configuration file specification.''' If the channel labels and types defined in the data file ("Internal data file information") need to be changed, enter a file name here ('''<nowiki>*.ela</nowiki>''', '''<nowiki>*.elp</nowiki>''', '''<nowiki>*.elb</nowiki>'''). If a channel definition file exists with the same basename as the data file, or if a channel definition file has been specified previously (database entry exists), it will be selected automatically. To the right of the file name, feedback is provided about the number of channels and channel types found. If the labels are consistent with the data file, to the right the text "Good" is shown. If they are inconsistent, e.g. the file contains the wrong number of channel definitions, the text "Bad" is shown.

[[Image:ST Electrodes (9).gif ]]

* '''Digitized head surface point specification.''' Here you may specify a file containing digitized electrode and other head surface points. Optionally, the information can be split into two files, containing the coordinates ('''<nowiki>*.sfp, .eps</nowiki>''') and the coordinate names ('''.sfn'''). Alternatively, both labels and names can be contained in the coordinate file. If the files specify electrode coordinates, there '''must''' be a coordinate name for each electrode. The sequence may be different. BESA Research will use the names to assign each coordinate to the electrodes. Additional head surface points can have any other names. It is recommended that the first three digitized coordinates are the fiducials (fiduciary points), labelled "FidT9", "FidT10", "FidNz". If your electrode labels not follow the 10-10- or 10-20 standard (e.g. in high-density electrode recordings), it is recommended to tick the box "Electrode labels non -conforming to 10-10 standard". This will prevent BESA Research from using electrodes for an optimal rotation of the coordinate system which should not be used (e.g. A1, A2 which have known locations in 10-10, but are sometimes used in a nomenclature outside of 10-10). The example below shows the sphere adaption for an example data set with and without taking this into account. The right picture shows that when discarding the non-conforming electrodes, the fiducials are correctly placed along the x any y axes.

[[Image:ST Electrodes (10).gif ]] [[Image:ST Electrodes (11).gif ]]

(In the special case of Neuromag files with electrode channels, the data file contains head surface points with the wrong labels. Here you may provide a label file ('''<nowiki>*.sfn</nowiki>''') without a corresponding digitized coordinate file.)

[[Image:ST Electrodes (12).gif ]]

* '''Coregistration file.''' Here you may specify a file containing the coordinates of the head center ('''<nowiki>*.cot</nowiki>''') or an ''MRI Coregistration File ''('''<nowiki>*.sfh</nowiki>'''). Head center redefinition is only necessary if you want to provide an external definition, e.g. from the MRI. The ''MRI Coregistration File ''is used if the data are to be coregistered with individual MRI. (see "''Integration with MRI and fMRi'' "). '''Note''' that if a head center file (cot file) with the same base name as the data file exists, it will be read automatically if the head center coordinates deviate by more than 1 mm from the internally calculated values. Changes are ignored if the radio button is set to "No". This automated function allows you to change the head center during a session, using BrainVoyager's view of the MRI and the Source Module.

[[Image:ST Electrodes (14).gif ]]

* '''MEG sensor specification'''. If the file contains MEG channels, you may enter the name of a sensor coordinate file ('''<nowiki>*.pmg</nowiki>''', '''<nowiki>*.pos</nowiki>'''). This field is grayed if there are no MEG channels.

[[Image:ST Electrodes (15).gif ]]

* '''Artifact coefficients file.''' If the data are to be artifact corrected, your pre-prepared coefficient file may be defined here. See the chapter "''Artifact Correction''". Selecting the file here is equivalent to loading the file using the menu entry "''Artifact / Load''".

[[Image:ST Electrodes (17).gif ]]

For each of the selected files, make sure the radio button "'''Yes"''' is selected on the left-hand side of the dialog box. If files have been selected automatically, and you do not wish them to be read, select the "'''No'''" radio button.

If some of the settings are incorrect or the text "Bad" is shown, you may edit the auxiliary files (the file is opened with the NotePad program) or browse for another file by pressing the '''Edit''' or '''Browse''' buttons.

After you have entered the required information, and the green tick at the top right indicates consistency, press '''OK''' to continue. Press '''Cancel''' to ignore the current settings. Press '''Clear DB''' to delete the database files. Press '''Clear Events''' to delete the tag files (the part of the database that records events). Both '''Clear''' buttons close the currently-opened data file.

== General Reading Rules for Data Files and Auxiliary Files ==

Auxiliary files can complement the information in the data file. Here we specify what happens when a data file is opened:

'''1.''' If the data file has been read previously, the database entry specifies which auxiliary files should be read. The file and the specified auxiliary files are opened and the data are displayed.

'''2'''. If a) there is a channel definition file '''(*.el'''''?'') with the same basename as the data file, and

b) this file includes spherical coordinates for the EEG channels (including labels with entries in the '''default.ecd''' file), and

c) there are no other auxiliary files with the same base name, the file will be opened and the data displayed. If files with the same basename are not found, BESA Research will look for files with the basename “default” (e.g. '''default.ela''') in the data folder. If such files are not found, BESA Research will look for files with the basename “default” one folder above (e.g.''' ..\default.ela''').

'''3'''. If the data file has been written in binary format ('''<nowiki>*.foc</nowiki>''', '''<nowiki>*.fsg</nowiki>''') by BESA Research (after Jan.2000), the file will be read, and all information is assumed to be complete. The file is opened and the data are displayed.

'''4.''' In all other cases, the ''Channel and digitized head surface point information dialog box'' will be opened for you to specify and check auxiliary files. Auxiliary files with the same base name as the data file will be specified in the text boxes for file names. If files with the same basename are not found, BESA Research will look for files with the basename “default” (e.g. '''default.ela''') in the data directory. If such files are not found, BESA Research will look for files with the basename “default” one directory above (e.g. '''..\default.ela'''). Otherwise the text boxes will be left blank.

'''5.''' Auxiliary files can be specified at a later time by selecting ''File/Head Surface Points'' and ''Sensors/Load'' ''Coordinate Files''. The ''Channel and digitized head surface point information dialog box'' will be opened.

== Electrodes ==

=== Electrode Conventions ===

BESA Research adheres to the 10/20 and to the new 10/10 standard of the IEF (international EEG Federation). BESA Research will recognize the labels defined by these standards. The labels are stored in most EEG file headers. Otherwise, or in the case of erroneous labeling or sequencing of the recording channels, you may edit the channel labels and/or coordinates, or you may read an electrode file stored previously on disk. In addition to the 10/20 and 10/10 standard labels BESA Research recognizes the following labels: M1, M2 (left, right mastoids), SP1, SP2 (sphenoidal), CB1, CB2 (cerebellar), Chin, Neck, LO1, LO2 (lateral ocular), SO1, SO2 (supra-ocular), IO1, IO2 (infra-ocular). BESA Research will translate all the labels into spherical coordinates for spherical spline interpolation, mapping and source imaging. The following assignments are stored in the file '''default.ecd''' in the BESA folder:

[[Image:ST Electrodes (19).gif ]]

''Electrode labels in the file '''default.ecd '''and their spherical coordinates. 10-20 electrodes are shown in red and italic.''

The spherical coordinates are defined in degrees by the azimuth (from Cz, positive = right, negative = left hemisphere) and the latitude (counterclockwise from T7/T3 for left and from T8/T4 for right hemisphere) of each electrode. Please do not modify the existing labels or coordinates in this file, because this would adversely affect the interpolated (virtual) montages, the maps and the source montages and source images in BESA Research. However, you may add additional labels for scalp electrodes at the end of this file if needed (up to a total of 196). When you edit the electrode configuration or read in electrode files, BESA Research may replace the 10/20 standard labels T3, T4, T5, T6 by their new 10/10 equivalents T7,

T8, P7, P8. However, in the initialization file '''BESA.ini '''you can reset to the old 10/20 standard by relabeling T7=T3, P7=T5, T8=T4, P8=T6 under the heading [Electrodes]. You may use the same feature to assign appropriate labels to the X1..X8 channels which exist in many systems, e.g. X1=EKG1 etc.

=== Recommendations for electrode placement ===

For source montages and source analysis two principles are important:

# Covering of the lower head with inferior electrodes to record activity from the inferior surfaces of the brain, especially from the basal temporal lobe, from the temporal pole, from orbito-frontal cortex, and from basal occipital and cerebellar areas.
# Equal spacing of the electrodes over the whole head to cover all brain areas.

In the following montage EEGxx the number xx indicates the number of electrodes.

'''EEG25 - Minimum 10-20 configuration including inferior electrodes'''

This covers the 19 standard 10-20 electrodes:

Fp1, Fp2, F7, F3, Fz, F4, F8 ....

plus 6 inferior electrodes on both sides:

F11, A1, P11, F12, A2, P12

with a recommended continuation of the 20% distances, i.e. use F11 instead of F9, P11 instead of P9, A1 instead of T9 to have a wider coverage of the inferior head. A1 / A2 may be replaced by T9 / T10 (or FT9 / FT10) for convenience and comfort.

[[Image:ST Electrodes (21).gif ]]

''Left: recommended configuration for 25 electrodes. Right: left temporal basal activity mapped with 25 electrodes.''

'''EEG33 - Additional 10-10 electrodes within the major squares'''

To the above electrodes add the following 8 intermediate electrodes:

FC5, FC1, FC2, FC6,   CP5, CP1, CP2, CP6

[[Image:ST Electrodes (23).gif]]

''Left: recommended configuration for 33 electrodes. Right: left temporal basal activity mapped with 33 electrodes.''

'''EEG35 - Additional supraorbital electrodes for better EOG separation'''

SO1, SO2

'''EEG37 - Wider inferior coverage at interlaced 20% distances'''

Continue 20% down from F7, FC5, CP5, P7 etc. and use the following 8 inferior electrodes instead of 6:

F11, FT9, TP9, P11,    F12, FT10, TP10, P12

'''EEG41 – Improved frontal and occipital coverage'''

Additional electrodes halfway between Fz and Fp1 / FP2 and Pz and O1 / O2:

AF1, AF2,   PO1, PO2

'''EEG43 – Inferior chain with 5 electrodes including A1 / A2'''

F11, FT9, A1, TP9, P11,    F12, FT10, A2, TP10, P12

EEG43 represents the widest coverage with relatively even spacing.

[[Image:ST Electrodes (25).gif]]

''Left: recommended configuration for 43 electrodes. Right: left temporal polar activity mapped with 43 electrodes.''

'''EEG64-256'''

With 64 or more channel caps, it is similarly recommended to use a sufficient number of inferior electrodes all around the head. At least 4 inferior temporal electrodes on each side and additional electrodes above or below the eyes (outside of the cap) are suggested.

=== Editing the channel configuration ===

Only use the channel configuration editing facility if the electrodes or the common reference have not been correctly defined by your digital EEG system, or if you want to define specific spherical coordinates for your scalp electrodes. It is your responsibility to check and provide the correct sequence of electrode labels in correspondence with the sequence of channels in the EEG data file. If these sequences do not match exactly, errors will occur in the computation of maps, source images and interpolated montages.

We will use the example EEG file '''eeg2.eeg''' in the subdirectory ''Examples/EEG-Focus'' of the BESA Research directory to explain the editing of electrode labels and coordinates:

1. Select ''File'', then click on ''Open'', or click on '''eeg2.eeg '''if this file is contained in the list of currently selected EEG files.

2. Select ''Edit'', then click ''Channel Configuration''. The dialog box shown below will appear.

[[Image:ST Electrodes (27).gif]]

At the upper left of the figure you see the dropdown menu after selecting the '''File '''menu in the dialog box. This menu allows to edit a new ('''''New''''') or an existing ('''''Open''''') electrode file and to save the changes to the same ('''''Save''''') or a different ('''''Save As''''') file. Normally, it will not be necessary to use this menu. The control fields on the right will be sufficient. If you type ''''''Ok'''''', you will be given the option of saving the changes to a file.

3. Click on '''Reload org. Labels''' to reread the original labels as stored in the file header of '''eeg2.eeg'''. BESA Research quits editing and redisplays the EEG. Repeat step 2 and select "''Edit / Channel'' ''Configuration''" again. Note: The button '''Reload org. Labels''' is not available if there are no labels in the file header.

4. Click on the empty space of the scroll bar below the '''scroll '''button and on the '''down arrow''' of the '''scroll bar''' to display the remaining electrodes in the file.

5. Click on electrode '''R''' (line 32), then on the button '''Delete Electrode''' to remove the associated channel, which does not contain any signal. Note that you may not omit intermediate channels, even if they do not exhibit signals, because the correct correspondence between the series of electrodes and the EEG channels will not be maintained. Use the '''"Edit / Bad Channels"''' menu to disable artifactual or empty channels.

6. Click on''' EOG''' (line 30) and change the entry to '''EOG1'''. Do not type '''<Enter>,''' but click on the next or a different electrode box to accept the changes.

7. '''Double click''' on '''EOG '''(line 31). This will highlight the entry. Simply type the new name '''EOG2''', and note that the old label is replaced when highlighted. Electrodes '''30 '''and '''31 '''are now defined as distinct electrodes. Next, we want to replace the label '''T10 '''by '''A2'''.

8. Click on the label '''T10''' (line 24). Then click on the '''drop down''' arrow right of the highlighted label to obtain the list of default scalp electrodes (read from '''default.ecd''' and sorted alphabetically). Type '''A''' to jump to the electrodes beginning with letter A (see below). Type '''2''' or '''click''' on '''A2''' in the list. Click on the '''type '''box (Scalp channel) to close the list and display the new entry in line 24. Note that this is the most convenient way to edit an electrode label.

[[Image:ST Electrodes (28).gif]]

9. Exercise: repeat step 8 to replace '''T9''' by '''A1'''. Restore labels '''T10''' and '''T9''' in lines 24 and 21.

10. Replace SO1 and SO2 (supra-orbital) by '''PSO1 '''and '''PSO2 '''and note that these electrodes are changed to the''' 'Polygraphy'''' type, because no coordinates are associated with these labels.

11. After you click ''''OK'''', the box '''Write Channel Configuration File''' will appear and display a name for the current electrode file. By default, the BESA electrode file path and current file name will be used and supplemented by the extension ''''.elb''''. The electrode file path may be set in the '''BESA.ini''' file [Defaults] section under ElectrodeFilePath. If no electrode file path is specified in the '''BESA.ini''' file, the default electrode file path ''Montages\Channels ''is used. Simply click ''''OK'''' or type '''<Enter> '''to save the changes to this file, or select a new file name and/or path, if you do not want to store the electrode file in the BESA Research electrode file directory.

Note that by using the default 10/10 labels (see chapter "''Electrode conventions''") you specify that the associated electrode is a scalp electrode. Hence, different labels must be used for polygraphic, intracranial or MEG channels. After you have entered a new non-scalp label, you may select the type of the electrode/channel amongst the different groups ('''Polygraphy, Intracranial, MEG Channel''') from the drop down list in the ''''''Type'''''' box. This will allow for using separate selection and scaling facilities of the channel group control push-buttons at the right of the screen ('''All, Scp, Pgr, Icr, MEG'''). If you have entered a new non-scalp label and select the type '''Scalp Channel''', or if you click on the ''''Advanced>>'''' field, boxes will appear to enter the spherical coordinates (azimuth and latitude) of this electrode (cf. Fig. 6.5). These features may be used to specify non-standard scalp electrodes. Please check the earlier sections of this chapter for electrode conventions. You may view the locations of the scalp electrodes on the head schemes in the mapping window. Select '''Show Electrodes in Maps''' in the "'''View / Options'''" menu.

[[Image:ST Electrodes (29).gif]]

'''Hint:''' If you want to specify the spherical coordinates of an electrode which is close to a standard electrode, click on the ''''Advanced >>'''' field, enter the label of the standard electrode and append a single quotation mark. This will specify that the electrode is close to the labeled location but has different coordinates. The ''Scalp Channel'' type will not be replaced by '''Polygraphy.''' Then edit '''Azimuth''' and '''Latitude'''. This convention is used by BESA Research when reading electrode coordinate files '''(*.elp'''), e.g. from the BESA program. The coordinates are read and compared with the default coordinates to assign the closest label. Then a single quotation mark is appended to the label, and the coordinates are assigned as specified in the '''.elp''' file. For example, open '''segm1.eeg''' in the ''Examples\EEG-Focus'' subdirectory.

Note that the file '''segm1.elp '''is searched for automatically in the directory of the data file when opening the data file.

'''Edit Common Scalp Reference'''

There is a separate line at the bottom in the ''Channel Configuration dialog box'' to enter the label and coordinates of the '''Common Scalp Reference electrode'''. If this is specified and enabled (click on field '''Enabled'''), the information provided by the fact that all scalp electrodes were recorded against a common recording reference will be used for mapping, source imaging and virtual montages. This information will be lost if the common reference has not been specified or if a combination of electrodes has been used as reference during recording. Specify the '''Common Scalp Reference electrode''' only if all electrodes have been referenced to the same single electrode and if a standard 10/10 location has been used for the common recording reference.

'''Note that BESA Research cannot process digital EEG data correctly if there is no common recording reference''', and if different recording references were used for the various scalp electrodes. For intracranial and polygraphic channels different references may be used. It is preferable to use the common reference also for electrode channels near the eyes, because these electrodes provide valuable information for mapping, source imaging and interpolated montages. The traditional bipolar channels (e.g. horizontal and vertical '''EOG''') may be '''reconstructed digitally''' using the ''Selected Channels'' group or user-defined montages.

== 3D Coordinates for Precise Analysis ==

=== Introduction - Working with Digitized 3D Coordinates ===

Working with digitized electrode coordinates usually requires reading in additional (auxiliary) files. The procedure is described in the chapter "''Working with auxiliary files''".

=== Data reading rules for EEG ===

This section explains which additional files are read, or which files have to be read in order to provide the necessary information for mapping and source montages.

Assume file name is '''datafile.xxx'''. datafile is the base name, '''.xxx''' is the extension. Replace the text ''datafile'' by the base name of your own file, and the extension'' xxx'' by the extension of your own file.

'''Channel definitions for EEG:'''

Labels have 10-10 names: default locations will be used.

Labels do not have 10-10 names: Channels are interpreted as '''polygraphic'''. Mapping is not possible without one or more of the following additional files.

'''Define channel names and types.''' File '''datafile.ela''', '''datafile.elp''', or '''datafile.elb''' exist, or files '''default.ela''', '''default.elp''', or '''default.elb''' exist, or files '''..\default.ela''', '''..\default.elp''', or '''..\default.elb''' exist (i.e. files with basename d''efault ''one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The ''ela'' file contains just labels and, optionally, types. The ''elp'' file contains spherical coordinates and can contain labels and types. The ''elb'' file contains the same information in binary format. See chapter "''Working with additional files / Channel Definition File Conventions''".

'''Define order in which electrodes were digitized.''' File '''datafile.sfn '''exists, or file '''default.sfn''' exists, or file '''..\default.sfn''' exists (i.e. file '''default.sfn''' one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file. These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. If fiducials exist, they should be defined on the first three lines. If they do not exist, BESA Research will simulate them (so that it can define the head coordinate system). See chapter ''"Working with additional files / sfn (surface point name) file''".

'''Define electrode coordinates.''' File '''datafile.sfp''' exists, or file '''default.sfp''' exists, or file '''..\default.sfp''' exists (i.e. file default.sfp one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If '''datafile.sfn''' does not exist, labels can also be defined in this file. If fiducials exist, they should be defined on the first three lines. If they do not exist, BESA Research will simulate them. See chapter "''Working with additional files / sfp (surface point coordinate) file''".

'''Define coregistration information.''' File '''datafile.sfh''' exists, or file '''default.sfh''' exists, or file '''..\default.sfh''' exists (i.e. file''' default.sfh '''one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration between EEG and MRI. See online help chapter "''Integration with MRI and fMRI".''

'''Define head center.''' No coregistration file exists ('''<nowiki>*.sfh</nowiki>''', see above). File '''datafile.cot''' exists, or file '''default.cot''' exists, or file '''..\default.cot''' exists (i.e. file''' default.cot '''one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''

=== Data reading rules for MEG ===

Assume file name is ''''datafile.xxx''''. '''datafile''' is the base name. '''xxx''' is the extension. Replace the text '''datafile''' by the base name of your own file, and the extension '''xxx''' by the extension of your own file.

Here we consider cases a) MEG alone, b) MEG+EEG.

'''Automatic procedure:'''

Labels have names defined in the files '''bti.ecd''' or '''nmag.ecd'''. Channels are interpreted as MEG. However, sensor locations and head surface point locations must be defined in additional files as described below. Mapping and source analysis are not possible without one or more of the following additional files.

'''Define channel names and types.''' File '''datafile.ela''', '''datafile.elp''', or '''datafile.elb''' exist, or files '''default.ela''', '''default.elp''', or '''default.elb''' exist, or files '''..\default.ela''', '''..\default.elp''', or '''..\default.elb''' exist (i.e. files with basename'' default'' one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The'' ela'' file contains just labels and (optionally) channel types. The ''elp'' file contains spherical coordinates and can contain labels and types. The'' elb'' file contains the equivalent information in binary format. See chapter “''Electrode file conventions'' ''and formats.”''

'''MEG+EEG.''' Define order in which electrodes were digitized. File '''datafile.sfn''' exists, or file '''default.sfn '''exists, or file '''..\default.sfn''' exists (i.e. file '''default.sfn''' one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file (or in the location descriptor in the data file: e.g. Neuromag). These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. See chapter “''Working with additional files/ sfn (surface point name) file”.''

'''MEG+EEG.''' Define head surface point/electrode coordinates. File '''datafile.sfp''''' ''exists, or file '''default.sfp''' exists, or file '''..\default.sfp''' exists (i.e. file '''default.sfp''' one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If '''datafile.sfn''' does not exist, labels can also be defined in this file. See chapter “''Working with additional files/ sfp (surface point'' ''coordinate) file''”. The labels of electrode coordinates '''must '''match to those defined for the data channels. BESA Research will use the labels to associate coordinates with the correct channel.

'''Define sensor coordinates'''. File '''datafile.pos''' or '''datafile.pmg''' exists, or file '''default.pos(.pmg)''' exists, or file '''..\default.pos(.pmg)''' exists (i.e. file '''default.pos(.pmg)''' one folder above the data file): coordinates are defined in this file. The convention is that'' pos'' files contain gradiometer coordinates and'' pmg'' files contain magnetometer coordinates. This is not necessary for the program to read in values properly: the program makes its decision about the sensor type on the basis of the number of coordinate values on one line in the file (6 = magnetometers, 9 = gradiometers). See chapter “''Working with additional files/ pos or pmg (MEG sensor coordinate) file”.''

'''Define coregistration information.''' File '''datafile.sfh''' exists, or file''' default.sfh '''exists, or file '''..\default.sfh''' exists (i.e. file '''default.sfh''' one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration of the head coordinates with MRI. See (online) help chapter ''"Integration with MRI and fMRI".''

'''Define head center.''' No coregistration file exists ('''<nowiki>*.sfh</nowiki>''', see above). File '''datafile.cot''' exists, or file '''default.cot''' exists, or file '''..\default.cot''' exists (i.e. file '''default.cot '''one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''

=== Reading MEG files in ASCII format ===

'''BESA Research uses labeling or channel type definitions to decide whether channels are EEG or MEG. '''Based on the labels defined for the channels, or the type specified by the channel definition file, the program will try to find auxiliary files that define electrode coordinates or MEG sensors.

BESA Research uses four files to make its decision:
* '''.ela/.elp''' The channel type defined here overrides definitions in '''<nowiki>*.ecd</nowiki>''' (below).
* '''default.ecd''' defines electrode labels and default spherical coordinates based on the 10-20 and 10-10 naming system
* '''bti.ecd''' defines labels and default spherical coordinates for the BTi whole-head system
* '''nmag.ecd''' defines labels and default spherical coordinates for the Neuromag whole-head system

If the program finds a label in '''default.ecd''', the channel will automatically be defined as EEG. If not, if it finds a label in one of the other files, the channel will be defined as MEG. If it doesn't find the label anywhere, the channel will be defined as Polygraphic.

The spherical coordinates defined in these files are sufficient for mapping the data. Auxiliary files defining the real sensor coordinates are required for source analysis.

'''Defining default label and coordinate file for a new MEG system'''

When preparing an MEG from a system other than BTi-WHS or Neuromag for import to BESA Research, you should edit either '''bti.ecd''' or '''nmag.ecd '''to conform with your system. If sensor files ('''<nowiki>*.pos/*.pmg</nowiki>''') are always available for your files, the coordinates in the ''ecd ''files are irrelevant: all you need do is define the labels for your own MEG system or use the labels as already defined.

'''Files to prepare for reading in each data file'''

Each auxiliary file should have the same base name as your data file.

'''Define channel labels.''' There are several possibilities:
* Generate your data file according to the BESA'' avr'' ''format or the ASCII multiplexed format.'' Labels are listed in the second line of the file.
* Generate a ''label file'' (extension '''.ela''') with one MEG channel label per line (matching with your ''ecd ''file as defined above) or with the type "MEG" and a label for each line.

Label definitions are also possible using ''elp'' or ''elb'' files, but the above two solutions are recommended because they are the simplest.

'''Define sensor coordinates.''' Generate a ''pos'' or ''pmg'' file. Make sure that the number of sensors matches with the number of MEG channel definitions in your data file.

'''Define fiducials and other head surface points.''' Generate an ''sfp'' file. The first three lines define the fiducials. Subsequent lines define additional surface points.

'''Define coordinates of the center of the head.''' Generate a ''cot'' file. If this file is absent, BESA Research generates the coordinates by fitting a sphere to the head surface points.

Note that all coordinates should be within the same frame of reference, i.e. the same coordinate system. Units must be in meters, centimeters, or millimeters.

== Example: Defining Channel Labels ==

The files described in these examples can be found in the ''.\Examples\Xtras\EEG+Channel Labels'' subdirectory.

The simplest way to define electrode coordinates is to use BESA Research’s default settings (defined in the file, '''default.ecd'''). In this case, you only need to provide a list of channel labels. If a channel label is defined in '''default.ecd''' (i.e. if the labels belong to the 10-20 or 10-10 system), BESA Research will recognize the channel as EEG, and will allocate 3D coordinates.

Labels are not always supplied correctly in the data file. You can override the internal labels in several ways:
* Read the data file, and then use "''Edit / Channel Configuration''" to redefine the channels. The configuration is stored in a file with the name '''basename.elb''' (for binary data) or '''basename.elp''' (for ASCII data), where basename is the base name (name without the extension) of your data file.
* Prepare a label file (with the extension ''ela'') containing a list of labels. This can also specify channel types (e.g. EEG, Polygraphic, Intracranial, MEG).
* Prepare a file (with the extension ''elp'') containing spherical coordinates of the channels. This is the method used with the previous version of BESA Research. If the file doesn’t contain labels, labels are allocated based on their proximity to the 10-20 or 10-10 definitions in '''default.ecd'''.

The following examples illustrate the above three methods. The input files are all in ''BESA avr format, ''although these examples apply to all EEG data formats in which only EEG channels exist.

If the data file contains polygraphic or other types of non-EEG channel, the types need to be defined. See the ''EEG+Polygraphic channels example.'' MEG is a special case, because the sensor coordinates need to be defined. See the ''MEG ASCII and the MEG+EEG'' ''examples''.

'''Example 1. EEG file containing wrong labels – use ''Edit/Channel Configuration ''to redefine labels'''
* The'' avr'' file, '''EEGwithLabels.avr''', contains the EEG labels. Channels 4 and 14 have been mislabeled – the labels need to be swapped.
* Open the file with '''''File/Open''''' (Select file type ''BESA avr''. Find the correct directory ''Xtras\EEG+Channel Labels'').
* The file should open correctly, displaying 32 channels of EEG.
* The channel coordinates can be viewed by typing the '''‘V’ '''key (make sure the cursor is off). There will be a 3D display of the electrodes. Clicking on an electrode will display the label and the coordinates.
* In this file, channels 4 and 14 have been mislabeled as P3 and F3. In fact, the labels should be the other way around. We will now correct this:
* Select '''''Edit / Channel Configuration'''''.
* Type ‘F3’ into the label for channel 4, and ‘P3’ into the label for channel 14. Then type ‘'''OK'''’. The new channel configuration will be saved in '''EEGwithLabels.elp'''.
* In the data display, the labels of channels 4 and 14 will now be displayed correctly.
* Close the file ('''''File/Close''''') and open it again. Note that the labels are still correct. This is because the new channel configuration file, '''EEGwithLabels.elp''', is read automatically.

'''Example 2. EEG file with no labels – channel labels in auxiliary file'''
* The ''avr'' file, '''EEGwithoutLabels.avr''', has no labels.
* EEG labels are defined in '''EEGwithoutLabels.ela'''. This is read automatically when the file is opened.
* In this example, labels are correct. Each label in the ''ela'' file is on one line:

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F7''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F3''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fz''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''...''</div>

'''Example 3. EEG file with no labels – channel labels derived from spherical coordinates'''
* The ''avr'' file, '''EEGwithSphericalCoords.avr''', has no labels.
* Spherical coordinates are defined in the ''elp'' file, '''EEGwithSphericalCoords.elp'''. This contains spherical coordinates (theta and phi) and no labels:

<div style="margin-left:1.3cm;margin-right:0cm;">''-93 -72''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''92 74''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''-97 -40''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''-61 -49''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''-46 -88''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''62 51''</div>

* When the data file is opened, the ''elp'' file is read automatically, and BESA Research uses the tables in '''default.ecd''' to assign channel labels. To indicate that it has assigned user defined coordinates and matched with the closest standard electrode, BESA appends an apostrophe (‘) to each label:

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp1’''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp2’''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F7’''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F3’''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fz’''</div>

* We advise to assign specific labels as well as spherical coordinates if you want to use your own spherical coordinate system, e.g.:

<div style="margin-left:1.3cm;margin-right:0cm;">''FP1u -90 -72''</div>

'''Example 4. EEG file with no labels – channel labels not in basename.el?'''
* The ''avr ''file, '''EEGnoLabelsNoElaFile.avr''', has no corresponding ''ela, elp'', or ''elb'' file, i.e. no file with the same base name and the ''el?'' extension.
* When you open the file, BESA Research will ask for a channel configuration file. The ''File Open'' ''dialog ''will select the ''directory .\Montages\Channels''. The idea is that standard (= frequently used) electrode configurations should be kept in this directory.
* Select the file '''XtrasExample.ela'''.
* Close the data file and reopen it. The file will open with the correct labels. In the BESA window title you will see that the file '''EEGnoLabelsNoElaFile.elp''' has been read automatically. This file was created when '''XtrasExample.ela''' was read.

== Example: Mixed EEG and Polygraphic Data ==

The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Polygraphic'' subdirectory.

The data are in '''EEG+Polygraphic.avr'''.

The third channel is defined as polygraphic in the '''EEG+Polygraphic.ela '''file:

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''POLY Test''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F3''</div>

The prefix "''POLY''" specifies that the channel is polygraphic. Most other channels are interpreted as EEG because the labels are known in the 10-20 system.

Similarly, channel 31 is defined as intercranial, using the prefix "''ICR''".

Note that you can also define channels as EEG by specifying the ''"EEG" ''prefix (e.g. ''"EEG E1". ''This is useful if there are many more channels than are defined in the 10-10 or 10-20 systems, and if the channel coordinates are defined.

== Example: EEG with Digitized Coordinates ==

The files described in this example can be found in the .''\Examples\Xtras\ EEG+Digitization Points ''subdirectory.

In the previous examples, we have illustrated how to assign labels to channels using channel definition files. In those examples, only spherical coordinates were defined. Here we will show how to read digitized surface points into BESA Research, using the surface point (''sfp'') coordinate file and the surface point name (''sfn'') file.

The principles of defining digitization coordinate files are:
* The labels in the ''sfp/sfn'' file combination are used to assign coordinates to electrodes. Thus, if a coordinate has the name ‘''Fz''’ it will be assigned to the channel with the label ‘''Fz''’.
* In consequence, digitization of surface points can be in a different order to the sequence of channels in the data file. Matching to channels is done by comparing the labels.
* We recommend that the fiducial points, '''nasion, left preauricular point, right preauricular point''' be digitized. If you do not digitize them, BESA Research will simulate these locations (see ''“Example: Digitization points with and without Fiducials”''). Fiducial points, labeled '''FidNz, FidT9, FidT10''' should be the first three coordinates in the ''sfp'' file.
* As with the channel definition files, it is easiest for BESA Research if you name the ''sfp/sfn'' files using the base name of the data file, e.g. if the data file is named '''doodah.avr''', name the'' sfp'' file '''doodah.sfp''' and the ''sfn'' file '''doodah.sfn'''.
* You specify the files to be read in the ''Channel and digitized head surface point information dialog box.''

See ''“Example: Polhemus Digitizer Data” ''for a discussion of how to format the files originating from Polhemus and other digitizers.

'''Example 1. EEG file containing labels, ''sfp'' file containing coordinates, ''sfn ''file containing coordinate names'''
* The ''avr'' file, '''EEGdigitized1.avr''', contains the channel labels. Therefore, we don’t need a channel definition file.
* The ''sfp'' file, '''EEGdigitized1.avr''', contains digitized coordinates of electrodes and of additional surface points. The labels in the file do not correspond to the electrode labels in the ''avr ''file.
* The ''sfn'' file contains the corrected labels (1 line for each corresponding line in the'' sfp'' file). Now it is possible to match up electrode labels with the labels in the ''avr ''file.
* Open the data file, '''EEGdigitized1.avr'''. The ''Channel and digitized head surface point information dialog box'' will open automatically.
* Note the green tick mark at the top right of the dialog box. This is feedback to say that coordinates of all 32 electrodes have been found.
* Look at the entry ‘''Digitized head surface points’''. Here you will see that the ''sfp'' and the ''sfn ''files have been read automatically (because of the common base name). There are 51 locations. Note that the digitizer file can contain many more locations than the electrodes. BESA Research uses the locations for fitting the sphere of the spherical head model in source analysis. BESA Research can export these locations for coregistration with the MRI.
* Define the electrode thickness as 6 mm (at the right of the ‘''Digitized head surface points’'' box. This is the distance of the digitized point on the electrode to the surface of the head.
* Press '''‘OK’''' in the dialog box and view the coordinates by pressing the '''‘V’''' key.

'''Example 2. EEG file without labels, channel labels in ''ela'' file, surface point coordinates and names in ''sfp'' file'''
* The ''avr'' file, '''EEGdigitized2.avr''', has no channel label. Therefore, a label file is required. Here, the label file is '''EEGdigitized2.ela'''.
* The ''sfp'' file, '''EEGdigitized2.sfp''', contains digitized coordinates of electrodes and of additional surface points. The labels are defined correctly in the ''sfp ''file, i.e. for every EEG channel label there is a corresponding coordinate. Therefore, no ''sfn'' file is required.
* When you open the file, don’t forget to define the electrode thickness as 6 mm in the ''Channel and digitized head surface point information dialog box.''

== Example: Polhemus Digitizer Data ==

The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Digitization Points'' subdirectory.

Data from the Polhemus (other digitizers too) may often not fit the format BESA Research requires for the surface point file. Note that Polhemus data can be exported directly into BESA-compatible ''sfp''-files using the LOCATOR software.

BESA Research requires either
* just the cartesian coordinates (x, y, z) values -- one set of coordinates per line. In this case, labels must be defined in a parallel surface point name file, e.g.

<div style="margin-left:1.27cm;margin-right:0cm;">''0.5  3.75  12.68''</div>

<div style="margin-left:0cm;margin-right:0cm;">or</div>

* the cartesian coordinates plus a label. The label can be in front of or behind the coordinates on the line, e.g.

<div style="margin-left:1.27cm;margin-right:0cm;">''0.5    3.75  12.68  Fz''</div>

<div style="margin-left:2.54cm;margin-right:0cm;">or</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''Fz  0.5  3.75  12.68'' </div>

Here is an example of a few lines of a (''sfp'') file that are not read correctly by BESA Research:

<div style="margin-left:1.27cm;margin-right:0cm;">''Nz  0  87.721  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''T9  -79.131  0  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''T10  67.253  0  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''1  -34.192  103.374  31.868''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''2  23.642  103.048  30.351''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''3  -81.179  62.913  27.596''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''4  -60.701  79.631  78.273''</div>

What is wrong?

* First, some of the points are just numbered. These numbers don't tell BESA Research which electrode channel to which the coordinates should be assigned – assignments should be via channel labels and not numbers.
* Second, Nz, T9, T10 define the fiducials. Instead, the labels FidNz, FidT9, FidT10 are required (prefix "Fid").

What should be done? Probably the best way is

 a) keep only the coordinates in the '''<nowiki>*.sfp </nowiki>'''file:

<div style="margin-left:1.27cm;margin-right:0cm;">''0  87.721  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''-79.131  0  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''67.253  0  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''-34.192  103.374  31.868''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''23.642  103.048  30.351''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''-81.179  62.913  27.596''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''-60.701  79.631  78.273''</div>

b) prepare a surface point name file ('''<nowiki>*.sfn</nowiki>''') containing the corresponding labels:

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidNz''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidT9''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidT10''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''Fp1''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''Fp2''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''F7''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''F3''</div>

Keeping labels and coordinates separate means that the label file needs generating only once. The coordinate file is different for each subject.

Alternatively, if your digitizer program attaches the labels correctly to the coordinates, then you can prepare the ''sfp'' file like this:

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidNz    0       87.721   0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''FidT9  -79.131    0       0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidT10  67.253    0       0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''Fp1    -34.192  103.374  31.868''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''Fp2     23.642  103.048  30.351''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''F7     -81.179   62.913  27.596''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''F3     -60.701   79.631  78.273''</div>

== Example: Digitization points with and without Fiducials ==

We recommend that if electrodes are digitized, you should also digitize the three fiduciary points:''' Nasion''', '''and left and right preauricular points'''. We refer to these points as "fiducials". We name them '''"FidNz",''' '''"FidT9",''' and '''"FidT10".'''

If you do not digitize these points, BESA Research will simulate them, i.e. it will generate the points where it expects them to be, based on the fit of a sphere to the existing points, and on the names of surface points of known locations. "Known locations" means: the surface point name must be a 10-20 or 10-10 electrode name (e.g. "Cz" -- arbitrary labels, such as "E10" is not a known location). Therefore, BESA Research requires that at least 3 surface points with known labels are defined.

In a file containing digitization points ('''<nowiki>*.sfp</nowiki>'''), the fiducials should be the first three sets of coordinates, i.e. the first three lines of the file. The remaining coordinates in the file can be electrode (or other surface point) coordinates, in any order. The assignment of electrode coordinates to data channels is achieved by matching the coordinate labels to data channel labels.

'''Consequences of omitting fiducials'''

When these files have been read into BESA Research, look at the head surface points in 3D using ''File/Head Surface Points'' ''and Sensors/View'' (or use the shortcut '''‘V’'''). You will see small differences in fiducial locations between the real and the simulated locations. You can expect very slight influences on the results of source modeling (the spherical head may be rotated slightly, although the head center and radius will be identical), and output of source locations in head coordinates will be different, because these coordinates are based on fiducial locations (see chapter ''“Working with Electrodes and Surface'' ''Locations/ Coordinate systems''”).

== Example: ASCII Import ==

The files described in this example can be found in the ''.\Examples\Xtras\ASCII Import'' subdirectory.

When should the Import ASCII function be used? If you have data in BESA Research average referenced or multiplexed format, use the Open File function to read in a file directly. If you have data in a different ASCII format, BESA Research offers a flexible import function to import data from an array of numbers in an ASCII file.

The array can be '''vectorized '''(one channel, all time points, per line) or '''multiplexed''' (one time point, all channels, per line). These alternatives are illustrated in the two example files '''vectorized.asc''' and '''multiplexed.asc''', and in the tables below:

'''Vectorized array:'''

{| style="border-spacing:0;width:12.993cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 1 ''
|| ''channel 1, time 2''
|| ''channel 1, time 3''
|| ''channel 1, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 2, time 1''
|| ''channel 2, time 2''
|| ''channel 2, time 3''
|| ''channel 2, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 3, time 1''
|| ''channel 3, time 2''
|| ''channel 3, time 3''
|| ''channel 3, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 4, time 1''
|| ''channel 4, time 2''
|| ''channel 4, time 3''
|| ''channel 4, time 4''
|-
|}

'''Multiplexed array:'''

{| style="border-spacing:0;width:12.993cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 1 ''
|| ''channel 2, time 1''
|| ''channel 3, time 1''
|| ''channel 4, time 1''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 2''
|| ''channel 2, time 2''
|| ''channel 3, time 2''
|| ''channel 4, time 2''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 3''
|| ''channel 2, time 3''
|| ''channel 3, time 3''
|| ''channel 4, time 3''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 4''
|| ''channel 2, time 4''
|| ''channel 3, time 4''
|| ''channel 4, time 4''
|-
|}

BESA Research needs channel labels. If the labels are in the 10-20 or 10-10 system, BESA Research will assign the channels default coordinates. This is the minimum requirement to be able to map EEG.

If you have 3D digitized coordinates, these can also be specified in ASCII files. This is described under the chapter “''Example: EEG with Digitized Coordinates''”.

'''Example 1. Vectorized data'''
* The file '''vectorized.asc''' contains the data. The file should be imported via ''File/Import ASCII File''.
* First you will be asked for a name for the binary target file. The name '''vectorized.fsg''' is suggested. You may accept this name by pressing '''‘OK’''' or choose an alternative name. Note that if the file already exists, the imported data will be appended to the file.
* Next, the ''ASCII File Properties dialog box'' will open. First select ''‘Vectorized’'', and make sure the subsequent entries are correct:

<div style="margin-left:1.27cm;margin-right:0cm;">Header Lines = 0 (i.e. in this example the numbers start on the first line)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Bins/Microvolt = 1.0 (i.e. a value 1 in the data represents 1 µV)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Sampling Rate = 320 Hz (When the dialog box is opened, BESA Research always chooses the setting it used previously)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Number of channels = 32 (the number of rows in the matrix)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Number of Samples = 640 (the number of columns in the matrix)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Prestimulus Time = 1000 ms (defines the zero time point 1 s after the beginning)</div>

* Press '''‘OK’''' to accept the settings.
* Next, the ''Channel and digitized head surface point information dialog box'' will open. In the ''‘Channel configuration’'' box, the label file, '''vectorized.ela''', will be detected automatically. Automatic detection occurs when the label file has the same base name as the data file (in this case, vectorized). To the right of the file name is a summary of channel types: 32 channels found, 30 are EEG, 1 is intercranial, 1 is polygraphic.

Note the green tick at the top left of the dialog box. This indicates that BESA Research thinks that it has sufficient information to read the file, and map and do source analysis on the data.

* To see how channel types are specified in '''vectorized.ela''', click on the '''Edit '''button to view the file with the Notepad program. Here you will see that most channels have 10-20 electrode names. Channel 3 has the prefix ‘''POLY''’, specifying that this channel is polygraphic. Channel 31 has the prefix ‘''ICR''’, specifying that this channel is intercranial. Close Notepad, and click ‘'''OK'''’ in the dialog box.
* A final dialog box asks for a Segment Comment. This is a label that will be displayed in the resulting file. The label is particularly useful if you import several ASCII files into one target file. Each segment is then easily identified by its own label.

'''Example 2. Multiplexed data'''
* This example is similar to Example 1. In this case, import the file '''multiplexed.asc''', and select ‘Multiplexed’ in the ''ASCII File Properties dialog box''. Other settings in the dialog box stay as they were.

'''Notes'''
# The numbers in the source files can be split into several lines per channel or per time point. Then you will have to enter the correct number of time points and channels in the dialog box. In the present examples, the lines are not split (the vectorized file has all 640 time points in each line, and the multiplexed file has all 32 channels in each line). In this case, BESA Research selects the correct numbers of time points and channels automatically.
# If you have digitized coordinates, these can be specified in the Channel and digitized head surface point information dialog box. Since the procedure is the same as when reading data, this is described elsewhere under “''Example: EEG with Digitized Coordinates''”.

== Example: MEG ASCII ==

The files described in this example can be found in the'' \Examples\Xtras\ MEG ASCII'' subdirectory of the BESA Research installation folder.

'''Multiplexed MEG ASCII file with labels in the header (''med.mul'')'''

For reading MEG data, BESA Research expects
* Correct channel definitions, i.e. channels should be defined as MEG.
* Head surface points.
* Sensor coordinates, in '''the same coordinate system''' as the head surface points.
* Optionally, you can define the coordinates of the center of the head. This will be important if too few head surface points are available to specify where to place the spherical head used by BESA Research for source modeling, or if you want to use some external definition, e.g. from the MRI.

As with digitized EEG coordinates, we use the ''Channel and digitized head surface point information'' ''dialog box'' to specify the files which need to be read.

'''Example 1. File Open'''
* The file, '''MEGASCII.mul''', contains MEG data in the ASCII multiplexed format. This format contains channel labels. The labels used are recognized by BESA Research as originating from the Neuromag system. They are therefore identified as MEG and do not need further identification.
* The ''sfp'' file, '''MEGASCII.sfp''', defines fiducials and head surface points. Coordinate labels are included in the file, so no'' sfn'' file is required.
* The cot file, '''MEGASCII.cot''', defines the coordinates of the head center. If this were missing, BESA Research would compute the head center based on the sphere that best fits the head surface points.
* The ''pos'' file, '''MEGASCII.pos''', defines the coordinates of the 122 sensors. For the Neuromag system there are 9 values per line, defining primary coil location, secondary coil location, and orientation cosines. The sequence of coordinates in the ''pos'' file '''must''' match the sequence of MEG channels! The file format and locations of the primary and secondary coils allow BESA Research to identify the sensor type as planar gradiometers. If the file had only six values per line, BESA Research would classify the sensors as magnetometers (one primary coil and the orientation cosines).
* Open the file, selecting current file type as ''‘*,m''??’. The ''Channel and digitized head surface point'' ''information dialog box'' will open, displaying the different auxiliary file names. The green tick indicates that BESA Research finds everything to be OK.
* Press the '''‘OK’''' button and then the''' ‘V’ '''key to view the coordinates.

'''Example 2. File Import'''
* The file, '''MEGASCIIimport.asc''', contains MEG data in a multiplexed array, without a header. This needs to be imported using ''File/Import ASCII'' (see ''“Example: ASCII Import”).''
* On import you have to specify the file as ‘Multiplexed’, the number of time points (285), the number of channels (132), the bins/µV (or bins/fT) (=1), the time at which the stimulus occurred (50 ms), and the sampling rate (949.667 Hz).
* This format contains no channel labels. The labels in '''MEGASCIIimport.ela''' are recognized by BESA Research as originating from the Neuromag system. They are therefore identified as MEG and do not need further identification.
* Since it recognizes the channels as MEG, the ''Channel and digitized head surface point information dialog box'' will open, displaying the different auxiliary file names as before. Since all necessary files with the same base name as the data file are supplied, they are read automatically.
* Press the ‘'''OK’''' button, enter a segment name, and then the '''‘V’''' key to view the coordinates.

'''Example 3. File Open -- MEG information recorded elsewhere'''

This example illustrates the case where the auxiliary files have a different base name from the data file: you must select the file name in the ''Channel and digitized head surface point information dialog box''.

* Open the file, '''MEGASCIIelsewhere.mul'''. It is read as an MEG magnetometer file.
* In the ''Channel and digitized head surface point information dialog box'', specify
<div style="margin-left:1.27cm;margin-right:0cm;">'''MEGASCII.sfp''' for the head surface points, and</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''MEGASCII.pos''' for the MEG sensors</div>
* MEG coordinates will be correct. The sensor definition file specifies the sensors as planar gradiometers.
* Where the auxiliary files came from will be recorded in the database. If you open the file again, the auxiliary files will be found automatically, without asking any questions.

== Example: Reading combined EEG and MEG from an ASCII file ==

The files described in this example can be found in the ''Examples\Xtras\MEG+EEG'' subdirectory of the BESA Research installation folder.

Here are two examples containing mixed MEG, EEG, and polygraphic channels:
* Open a file using the ''File/Open'' command
* Import a file using ''File/Import ASCII'' command

In both cases

* The '''<nowiki>*.ela</nowiki>''' file defines the channel labels. Based on the labels, BESA Research knows which channels are EEG and MEG. The remainder are classified as polygraphic channels.
* The '''<nowiki>*.pos</nowiki>''' file defines the MEG sensor coordinates. The number of values on a line of this file (=9) defines the MEG as gradiometers. The relative locations of primary and secondary coils identify the gradiometers as planar.

'''1. Example with ''File/Open'''''
* Open the file '''MEG+EEG.mul'''. The ''Channel and digitized head surface point information dialog box'' will open automatically (unless the file has already been read once and the information is in the database).
* You will see under ''‘internal data file information’'' that BESA Research finds 122 MEG sensors, and 162 channels in all.
* Under ‘''Channel configuration’'', you will see that as a result of reading the file '''MEG+EEG.ela''', 32 channels are defined as EEG, and 8 channels as polygraphic.
* Under ‘''Digitized head surface points’'' is the feedback that out of the 51 locations in the file '''MEG+EEG.sfp''', all electrode locations have been defined.
* Under ‘''MEG sensors’'', the sensors have been identified as gradiometers.
* The green tick at the top right of the window indicates that BESA Research classifies everything as OK.

'''2. Example with ''File/Import ASCII'''''
* Import the file '''MEG+EEGimport.asc'''. Select '''MEG+EEGimport.fsg '''as the target file (see ''“Example: ASCII Import”'').
* Select 320 Hz sampling rate, and 500 ms pre-stimulus time. Other selections in the dialog box should be ‘Multiplexed’, 1 bin/microvolt (this is interpreted as 1 bin/fT for MEG), 162 channels and 320 samples.
* The ''Channel and digitized head surface point information dialog box'' will open as above.

[[Category:Research Manual]]

{{BESAManualNav}}

MATLAB Interface

2017-04-07T13:14:01Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}

= MATLAB Interface =

== Introduction ==

BESA Research has menu items ''"Send to MATLAB..."'' at various locations that allow to send data as structures to Matlab. After sending the data, BESA Research starts a Matlab script that can be used to start further data analysis on the data structure. These scripts, located in the ''Scripts\Matlab'' folder in the BESA Research installation, can be edited by the user to perform further data analysis in Matlab. For example, if "''Send to MATLAB''" is selected in the ''File Export Dialog'', a data structure "''besa_channels''" will be created. After filling the structure, the script "''besa_action_channels.m''" will be started.

All the Matlab export functions are batchable. Thus, a complete data analysis can be performed, in which BESA Research does the preprocessing, and passes the data on to Matlab for a statistical analysis of the results.

An example for the application of the MATLAB interface is demonstrated in the BESA Research Tutorial on Batch Scripts, Multiple Subjects & Conditions, MATLAB-Interface. You can download this tutorial from our website at http://www.besa.de/tutorials/hands_on.

Some MATLAB scripts that can be used in conjunction with the BESA Research MATLAB interface are also available on our website at http://www.besa.de/updates/matlab. You are invited to send your own scripts for data analysis or to submit any questions or feedback here: http://besa.de/contact/support/form.php.

'''Important! Please follow the instructions in the “''Installation” ''chapter! Then read the “''How the interface'' ''works” ''section to get started.'''

== Configuration ==

In order for the BESA-Matlab interface to work, please follow the instructions below. If you start BESA Research, and the file menu does not display the "''Send to MATLAB''" item, the interface is not installed correctly!

'''1'''. '''Matlab must be installed.'''

For step 2 (required for MATLAB versions 2009b and over), we need to know whether the 32-bit or 64-bit version of Matlab is installed. We also need to know the path to the Matlab installation (e.g. ''c:\Program'' ''Files\MATLAB\2009b\)''.

'''2'''. '''PATH environment variable:'''

For versions 2009b and over, make sure that the path to the Win32 or Win64 folder in the Matlab installation to the PATH environment variable is defined:

* The path for the 64-bit version for Matlab 2009b is typically ''c:\Program'' ''Files\MATLAB\2009b\bin\win64''. For the 32-bit version, the path is typically ''c:\Program Files\MATLAB\2009b\bin\win32''.
* Open the "System Properties" Dialog by holding down the '''Windows''' key and pressing the '''Pause '''button. In XP, the dialog is opened directly. In Vista and Window 7, the key combination opens the System Display. Click on the link "Change Settings".

[[Image:Matlab (1) .gif]]

* Select the "Advanced" tab.

[[Image:Matlab (2) .gif]]

* Press the "'''Environment Variables'''" button.

[[Image:Matlab (3) .gif]]

* Under "System variables" click on the "Path" variable and press "'''Edit'''". In the resulting dialog, enter a semicolon (;) at the end of the path string, and add the path after the semicolon.

[[Image:Matlab (4) .gif]]

* Press "'''OK'''" to close and save the path variable. Press "'''OK'''" to close the "System Properties" Dialog.

'''3. Additional configuration''' (only required after a change of your MATLAB configuration after installation of BESA Research):

During the installation process of BESA Research, the program "''SetupBesaMatlabInterface.exe''" in the BESA Research root folder was executed. Run this program again when your MATLAB configuration has changed, e.g. after updating your MATLAB version.

In the dropdown list, select the Matlab version that you are using.

This program does two operations:

1. it copies the appropriate interface Dll to the BESA Research root folder and renames it to "'''BesaMatlab.dll'''" (32-bit version) or "'''BesaMatlab64.dll'''" (64-bit version), and

2. if you are using a 64-bit version it creates an entry in '''BESA.ini''' as follows:

[Matlab]

Platform=64

'''4. Testing:'''

Start BESA Research and check if ''Send to MATLAB ''is displayed in the''' File '''menu. If it is, the interface is set up correctly. (Note that the item will be grayed if no file is open in BESA Research.)

Test the interface: open a data file, mark a short (e.g. 1 s) time range, and select ''File / Send to Matlab'' to open the ''Export Dialog'':

[[Image:Matlab (5) .gif]]

The Matlab window should open, and BESA Research will display a progress bar:

[[Image:Matlab (6) .gif]]

After the window closes, open the Matlab window, and type "''Workspace''" to open the workspace window, or "''Desktop''" to open the standard Matlab desktop.

Examine the "besa_channels" variable, which contains the data for the marked data segment.

[[Image:Matlab (7) .gif]]

'''Troubleshooting if the interface is not working after the above steps'''

If the ''File / Send to MATLAB''... menu item is not shown, this means that either the path (step 2 above) is not defined properly, or that the interface Dll '''BesaMatlab.dll''' or '''BesaMatlab64.dll''' is not compatible with the currently installed version of Matlab.

If the path is correct, then please contact our support team here: [http://besa.de/contact/support/form.php http://besa.de/contact/support/form.php], including the following information:
* Which Matlab version are you using?
* Specify also if you are using the 32-bit or 64-bit version.

== How the interface works ==

'''The interface'''

The interface uses libraries supplied by Matlab. Their descriptions can be found in Matlab Help under the keywords "Engine Library". The Matlab libraries are incorporated into the interface Dll ('''BesaMatlab.dll''' or '''BesaMatlab64.dll''') that provides the interface between BESA Research and Matlab. As newer versions of Matlab are released, it may be necessary to generate new versions of the dll to match the new library versions.

'''Matlab automation window'''

On the first call to one of the Matlab routines, the Matlab Automation Window is opened. This is not the same as the window that is normally opened when Matlab is started directly in Windows (the window can also be opened by typing "Matlab /automation" from the command line). From the Automation Window one can run normal Matlab scripts. It is also possible to type "desktop" in the Automation Window to open the standard Matlab desktop. All variables that have been sent from BESA Research are then visible there.

'''BESA Research "Send to MATLAB" commands and scripts'''

Send to MATLAB commands generate data structures that differ depending on the type of data that are sent. After each export the corresponding script is executed. They are available at the following locations in BESA Research:
* From the Main program window ('''File''' Menu), as part of the ''Export Dialog''. Structure name ''besa_channels''. Script name ''besa_action_channels.m''.
* From the FFT analysis ('''File''' Menu). Structure name ''besa_fft''. Script name ''besa_action_fft.m''.
* From Combine Conditions (''Run Scripts Tab''), in the export of peaks and mean amplitudes. Structure name ''besa_peak''. Script name ''besa_action_peak.m''.
* From Source Analysis ('''File''' Menu), for exporting source waveforms (''besa_sourcewaveforms''), source models (''besa_sourcemodel''), data, residual and model waveforms (''besa_sa_channels''), and 3D images (''besa_image''). Script names ''besa_action_sourcewaveforms.m'', ''besa_action_sourcemodel.m'', ''besa_action_sa_channels.m'', and ''besa_action_image.m''.
* From Time-Frequency/Coherence Analysis ('''File''' Menu). Structure names ''besa_tfc'', and ''besa_tfc_trials'' (for single-trial time-frequency data). Script names ''besa_action_tfc.m'' and ''besa_action_tfc_trials.m''.

Some additional scripts are used for specific data types. For example, when exporting raw data, two scripts, ''besa_helper_channels_event.m'' and ''besa_helper_channels_continuousdata.m'' are used to collect events from each data block and to combine the exported data blocks into a single matrix.

'''Command script path'''

When the commands are executed, BESA Research automatically executes an "addpath" command in Matlab to add the ''Scripts\MATLAB'' folder (in Windows 7 typically ''C:\Users\Public\Public'' ''Documents\BESA\Research_6_0\Scripts\MATLAB'') and its first-level subfolders to the Matlab search path.

'''Units'''

Unless otherwise stated, distances are in meters, times are in seconds, and the head-frame (fiducial-based) coordinate system is used.

[[Category:Research Manual]]

{{BESAManualNav}}

Export

2017-04-07T13:13:03Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
= Export =

== Exporting files from BESA ==

Data can be exported from BESA Research in the following formats:
* BESA's own binary format (compressed or uncompressed)
* ASCII multiplexed
* ASCII vectorized (short files only)
* EDF+
* simple floating point matrix (e.g. for exporting data to MatLab)
* Send the data directly to Matlab

You can export
* The entire data set or between markers
* The currently marked segment
* Epochs around triggers
* Standard deviations from binary average files ('''<nowiki>*.fsg)</nowiki>'''

Export is allowed to various montages:
* filtered or unfiltered data
* original data
* current montage (including artifact correction if applied)
* standard 81-electrode montage.

On export, you can choose to change the sampling rate.

If exporting to BESA's binary format, you can optionally append the data to a preexisting data set, if sampling rates and the number of channels match. Therefore, please use the Combine Conditions module.

Export is started either
* select File / Export...
* press the '''WrS '''button.
* In both cases, you are taken to the ''Export Dialog''.
* for Send to Matlab only: select File / Send To MATLAB... This also opens the Export Dialog, but only the '''Send To Matlab radio''' button is enabled as target format in the dialog.

== Export Dialog ==

[[Image:Export (1).gif ]]

The dialog is started when you select'' File / Export...'' or press the '''WrS''' button or select '''Write Segment''' in the right click context menu when a segment has been highlighted.

The dialog is divided into four sections. Please read the following chapters for more details:
* ''Data to export''. Describes which data are to be exported.
* ''Montage and Filters.'' Which montage is to be exported, and whether or not filters are used.
* ''Target data formats''. Specify the format of the exported data.
* ''Resampling.'' Specify a new sampling rate in the exported data.

== Type of data to export ==

[[Image:Export (2).gif ]]

The types of data to export are:
* '''Continuous data'''. The whole data set or the data between markers are exported.
* '''Marked segment.''' If a segment of data is highlighted, this radio button is enabled. Select Marked segment to export just this segment.
* '''Epochs around triggers.''' Export data segments around triggers. If this item is selected, the two buttons '''Interval'''... and '''Triggers'''... are enabled. They allow to select the interval (cf ''Edit / Default'' ''Block Epoch''...), and choose among the available triggers (see ''Edit / Trigger Values''...). Note that the default block epoch values are persistent across BESA Research sessions. The trigger selection is not persistent!
* '''Standard Deviations (from fsg file only).''' If the average file was generated using the BESA Research ERP module, standard deviations are saved in the file. Check this item to export these values to an ASCII file.

'''Between markers.''' If there are markers in the file, and '''Marked segment''' is not selected, selecting '''Between markers''' will result in the export of data between markers relative to the current position in the file (as defined by the middle of the current display), either:
* if there is no previous marker, from the beginning of the file to the next marker, or
* from the previous to the next marker, or
* if there is no next marker, from the previous marker to the end of the file.

== Montages and Filters ==

[[Image:Export (3).gif ]]

The data can be exported either
* '''Original data.''' The data are exported using the original montage
* '''Current montage.''' The currently selected montage is exported. If extra channels, e.g. selected channels or artifact waveforms are displayed, these are exported as well. Notes:

* <div style="margin-left:0.635cm;margin-right:0cm;">When 'Current Montage' is selected, no auxiliary files are exported. When re-importing the data into BESA Research, all channels will be defined as polygraphic.</div>
* <div style="margin-left:0.635cm;margin-right:0cm;">If the current data is artifact-corrected, the artifact-corrected data will be exported when 'Current Montage' is selected.</div>

* '''Standard 81 electrode locations.''' EEG data are interpolated to a set of 81 electrodes on a standard head (average over 24 mainly Caucasian heads).

Export can be performed either with or without the currently selected filters. Press the '''Filters'''... button to change the current filter settings (see also ''Filters / Edit Filter Settings''...).

== Target Data Formats ==

[[Image:Export (4).gif ]]

The following target formats are available:
* '''BESA binary'''. Data are saved with the extension "'''.foc'''" or "'''.fsg'''". You can select whether to export with no compression (recommended for averages), or compressed (recommended for raw data). Note that compression can result in loss of resolution in averaged data. See ''Data Compression.''
* '''ASCII multiplexed.''' Data are normally saved as text with the extension "'''.mul'''". See ''ASCII multiplexed format'' for a description of the data format. If the type of data to export is '''Epochs''' '''around triggers''', one file is exported for each trigger, and the file extension is a number, starting with ".000", and continuing ".001", ".002", etc.
* '''ASCII vectorized'''. Data are normally saved as text with the extension "'''.avr'''". See ''ASCII Multiplexed format ''for a description of the data format. If the type of data to export is '''Epochs around triggers''', one file is exported for each trigger, and the file extension is a number, starting with ".000", and continuing ".001", ".002", etc. The data are not average referenced before saving. They will only be average referenced if the data are exported using an average referenced '''Current montage'''. You are only allowed to export small segments in vectorized format. If you have selected '''Continuous data''', this item will be disabled if the data are longer than 20 s in duration.
* '''European Data Format (EDF+).''' Data are saved with the extension "'''.edf'''". Export of '''Epochs around triggers''' to EDF+ is currently not possible.
* '''Simple binary matrix.''' Data are written to a floating point binary matrix with the extension "'''.da'''t". The matrix has the dimension no of samples x no of channels. In addition, a header file with the extension "'''.generic'''" is also written. The header file is a text file contains information about the number of channels, sampling rate, and number of samples. These follow the specifications of the Generic File Format that can also be read by BESA Research if the Generic Reader is installed. This data format can be useful as a means of transferring data to other programs (e.g. '''MATLAB''') in a relatively compact form. If the type of data to export is '''Epochs around triggers''', the epochs are concatenated in the same target file. In this case, the header file contains a line specifying the number of epochs (cf. ''Generic File Format''). The number of samples in each epoch is the total number of samples, divided by the number of epochs.
* '''Send To MATLAB'''. The data are exported directly to MATLAB into the struct variable besa_channels. For more information on the data transfer from BESA Research to MATLAB, please refer to Help chapter ''The MATLAB interface''.

== Resampling ==

[[Image:Export (5).gif ]]

Check '''Resample data''' to change the sampling rate of the target data. The edit box is enabled, and you specify a sampling rate.

Data are resampled using splines. Thus, the new sampling rate is not limited to fractions or multiples of the original rate.

Note that if '''Resample data''' is not checked, the sampling rate of the source data is displayed.

'''Resampling and aliasing'''. If you want to reduce the sampling rate it is important to avoid aliasing! It is recommended that a low-pass filter with a boundary frequency of not more than 1/3 of the original sampling rate is used. When you set a new sampling rate, BESA Research checks the current filter settings. If export without filters is selected, or if the current low-pass filter is set to a value that is higher than 1/3 of the sampling rate, BESA Research sets the filter, and opens a message box with a warning:

[[Image:Export (6).gif ]]

You may adjust the filters by pressing the''' Filter''' button, e.g. if the original data were already recorded with a sufficiently low low-pass filter setting, so that additional filtering is unnecessary.

== Data Compression ==

When exporting to BESA binary format, you can compress the data to save space. Here we describe properties and pitfalls of the compression algorithm.

'''How compression works'''

The compression algorithm works on two principals:
* '''Data resolution can often be reduced without losing data quality.''' For instance, a data resolution of 0.1µV or higher is unnecessary for viewing normal EEG -- 0.5µV or 1 µV steps are sufficient. Similarly for event-related potentials: the raw data only require a resolution of 0.5µV or 1 µV to achieve a much higher resolution after averaging.
* '''Differences between successive data samples '''on a signal are generally much smaller than''' '''the absolute values of the data'''.''' Thus, one start value, and then a series of subsequent differences can be stored in a much smaller space than an equivalent series of absolute values. A consequence of this principle is that smoothed signals (with high frequencies removed) can be compressed into a smaller space than signals with a lot of high frequency noise.

'''Compression parameter'''

The parameter you need to choose is the data resolution, or step size. Steps smaller than this size will no longer be represented in the compressed data. The BESA Research Export Module allows the following steps for the compression of EEG signals:

0.1µV, 0.2µV, 0.5µV, 1µV

For raw EEG data, we recommend using a step size of 0.5µV.

'''Different compression parameters for different data types (pitfalls!)'''

As described above, the step sizes make sense for EEG signals. For other types of data, other step sizes make more sense. In addition, a polygraphic signal can have the same order of signal magnitude as the EEG (e.g. an EOG or EKG signal), but it might have a completely different scale, e.g. a voice signal, recorded in mV or V. To help accommodate different orders of signal magnitude, BESA Research applies the following rules:
* '''MEG data:''' Step sizes (in units of fT) are 20 x the step size in µV. Thus, a step size of 0.5 µV will lead to a step size of 10fT for MEG data.
* '''Polygraphic and ICR data''': The step size depends on the current amplitude scaling factor in BESA Research. A multiplication factor is used that is the current scaling factor, divided by 100. Thus, if the scale is set to 1V, the factor is 10 mV. If you have chosen an EEG step size of 0.5µV, the resulting step size will be 10 x 0.5 = 5 mV.

A pitfall in compression is that if the current amplitude scaling for polygraphic or ICR data does not display the signal sensibly, compression may lead to complete loss of the signal. Note that this only applies to polygraphic and ICR channel types.

* '''Averages:''' We recommend that averaged ERPs are not compressed. Since the signals are generally much smaller than the raw data, compression will lead to unacceptable loss of data resolution.

[[Category:Research Manual]]

{{BESAManualNav}}

Integration with MRI and fMRI

2017-04-07T13:11:22Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher and BESA MRI
|version = 6.1 or higher
}}
= BESA Research Integration with MRI and fMRI =

Both for developing and evaluating dipole source models of EEG or MEG activity, it is useful to have access to structural MRI or fMRI data.

The BESA MRI software allows to preprocess structural MRI data so that the individual anatomical information contained in the MRI can be utilized in BESA Research. BESA MRI makes it possible ...
* ... to align the EEG and MEG sensors with the structural MRI data.
* ... to read and display the aligned, individual Talairach structural MRIs directly in the BESA Research Source Analysis module. In this way, source analysis results can be presented on top of the aligned MRIs, which allows us to evaluate the anatomical regions to which the reconstructed sources may correspond.
* ... to use an individual, realistically shaped FEM head model for source analysis in BESA Research. FEM head models take into account the individual volume conduction properties of the subject's head derived from the structural MRI data. This allows for more accurate source analysis (Yvert 1997, Lanfer 2012).

To offer an easy integration with fMRI data we have, in collaboration with Rainer Goebel, optimized the interface between BESA Research and BrainVoyagerQX.

With these tools, we can ...
* ... use fMRI BOLD regions or MRI structures to initialize dipole models.
* ... visualize dipoles from BESA Research models together with the structural MRI in BrainVoyager in order to evaluate the regions to which the dipoles may correspond.
* ... combine the localization advantages of (f)MRI with the high temporal resolution of EEG and MEG, for instance by using (f)MRI to place the sources, and the source waveforms of BESA Research to provide feedback about the time course of the source activity.
* ... overlay source analysis results obtained in BESA Research with fMRI data.

'''Note:''' For simpler coregistration, we recommend to use BrainVoyagerQX rather than the older BrainVoyager, but BESA Research will work with both program versions.

The chapters below describe the steps necessary to integrate the MRI and fMRI data with BESA Research. Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website (http://brainvoyager.com/Downloads.html).

'''Aligning Coordinate Systems'''

* For a given BESA data set, the electrode and other head surface points need to be aligned to the MRI coordinates.
* The basic steps necessary to align the EEG electrode locations, the MEG sensors and the MRI are described in Section “''How Coregistration is done”''.
* Detailed instructions on how to align EEG / MEG and MRI data using BESA MRI can be found in the coregistration quick guide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).
* Detailed instructions on how to align EEG / MEG and MRI data using BrainVoyager are described in Section “''How To set up Coregistration between BESA and BrainVoyager”.''
* In BESA Research all necessary settings with regard to the alignment are made in the ''Coregistration Dialog.''
* Requirements with respect to the MRI data for a good coregistration can be found in Section “''MRI Requirements for Good Coregistration”.''
* Requirements with respect to EEG and MEG data for a good coregistration can be found in Section “''EEG/MEG Data Requirements for Good Coregistration”.''

'''Generating an individual, realistically shaped FEM head model'''

* The generation of a FEM head model that can be used in BESA Research is done in BESA MRI as an additional step following the EEG / MEG to MRI coregistration.
* Detailed instructions on how to generate the FEM head model can be found in the coregistration quick guide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).

'''Co-locating dipoles and MRI locations'''

* After aligning the EEG / MEG and the MRI data it is possible to co-locate dipoles and MRI locations. This means, it is possible to visualize the dipoles and to specify the dipole parameters in the MRI coordinate system.
* ''“How to Co-locate sources'' ''and MRI”'' in the BESA Research Source Module describes how in the BESA Research Source Analysis module dipoles can directly be visualized in the space of the individual MRI.
* ''“How to Send a Dipole from BESA Research to BrainVoyager”'' describes how to send a source model from BESA Research to BrainVoyager for further inspection.
* ''“How to Define a Dipole in BESA Research at a Location Defined in the MRI”'' describes how to insert a dipole at a location defined in the MRI in BrainVoyager.

'''References'''

Lanfer, B., I. Paul-Jordanov, M. Scherg, and C. H. Wolters. “Influence of Interior Cerebrospinal Fluid Compartments on EEG Source Analysis.” In Proceedings BMT 2012, Vol. 57. Jena: De Gruyter, 2012. doi:10.1515/bmt-2012-4020.

Yvert, B., O. Bertrand, M. Thévenet, J. F. Echallier, and J. Pernier. “A Systematic Evaluation of the Spherical Model Accuracy in EEG Dipole Localization.” Electroencephalography and Clinical Neurophysiology 102, no. 5 (May 1997): 452–59. doi:16/S0921-884X(97)96611-X.

== How Coregistration is done ==

This section outlines the basic steps to coregister the EEG / MEG data to an individual MRI. These steps are necessary to load an individual MRI into BESA Research.

'''What happens:'''

* EEG / MEG sensor locations and the MRI data are defined in different coordinate systems. Setting up coregistration is the process of aligning the two coordinate systems.
* BESA Research uses the ''Coregistration Dialog'' to coordinate the alignment procedure.
* Alignment is done with the ''AC-PC-transformed MRI''.
* BESA Research displays the ''Talairach-transformed MRI'' in the source analysis module.
* A coregistration file (with the extension "'''.sfh'''") is used to mediate between BESA Research and BESA MRI (or BrainVoyagerQX):
* BESA Research writes the coregistration file which contains the coordinates of head surface points (fiducials, electrodes, other digitized surface points).
* The coordinates are read into BESA MRI (or BrainVoyager), and aligned with the AC-PC-transformed MRI. The alignment information is then appended to the ''coregistration file''. The names of the AC-PC MRI ('''<nowiki>*.vmr</nowiki>''') and the surface mesh ('''<nowiki>*.srf</nowiki>'''), and, if available, the Talairach transformation, are also appended.
* BESA Research reads the coregistration file and appends the name of the Talairach-transformed MRI and head surface. If a brain surface has been created, this is also appended.
* Subsequently, BESA Research reads the coregistration file automatically when loading the data file.
* In the BESA Research source module, the individual MRI is displayed instead of the standard MRI. Talairach coordinates of dipoles are the "real" Talairach coordinates as defined, e.g., in BrainVoyager.

'''The steps you have to take (once for each data set):'''

* From the BESA Research ''Coregistration Dialog'', write a coregistration file. Switch to BESA MRI (or BrainVoyagerQX).
* If BESA MRI is used follow the steps in the coregistration quickguide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).
* If BrainVoyager is used follow the steps in Section “''How to set up coregistration between BESA and BrainVoyager”.''
* Back in BESA Research, reload the altered '''coregistration file'''. When using BESA MRI the file names of the generated surface and volume data files will be automatically filled in. When using BrainVoyager file names are only filled in automatically when the files are named according to the file naming conventions. Otherwise, file names have to be set manually.
* The coregistration file is now associated with the data file in the BESA Research database and will be used automatically the next time the file is opened in BESA Research. If the database entry is cleared, and the data are reloaded, you must make sure the coregistration file is also loaded (either using the ''Coregistration Dialog'' or the ''Channel and digitized head surface point information Dialog'').

== Alignment of BESA and MRICoordinate Systems ==

=== The Coregistration Dialog ===

The dialog is opened either from the ''Channel and digitized head surface point information'' ('''Ctrl-L''') ''dialog ''by pressing the '''Edit/Coreg''' button, or from the main menu ("'''File/MRI Coregistration...'''").

'''Note:''' If the coregistration dialog is invoked from an EEG data set in which no digitized electrode coordinates are available (i.e. standard electrode positions located on a sphere are assumed), BESA Research presents a warning message, saying that for MRI coregistration realistic electrode coordinates produce better results. BESA Research has a list of such realistic standard coordinates (i.e. located on a pre-defined standard head surface) for various electrodes available in file '''Default.sfp''', which is located in the Standard Electrode folder. If all electrodes in the dataset are listed in this file, a dialog window suggests to apply this file to the current data set, i.e. to switch from standard sphere coordinates to the standard realistic electrode coordinates in file '''Default.sfp'''. If the suggestion is accepted, '''default.sfp''' is assigned to the dataset (see Channel and digitized head surface point information ('''Ctrl-L''') dialog).

'''The Dialog:'''

[[Image:MRI Integration (1).gif ‎]]

* Press the '''Select MRI prog''' button to select your preferred MRI program. The current choice is between ''BESA MRI.exe'' and ''BrainVoyagerQX.exe''. The path to the MRI program is saved (in ''System\BESA.set'') and will be remembered by BESA Research. The top right hand button (now showing '''BESA MRI''') shows the current selection.
* Press the '''BESA MRI''' button to start the process of aligning the BESA Research and MRI coordinate systems. If no coregistration ('''<nowiki>*.sfh</nowiki>''') file is defined in the dialog (empty ''Surface coregistration file edit box''), BESA Research will first prompt for a file name. We recommend saving this file to the folder where the MRIs are kept. The MRI program will then be started. When you return to the ''Coregistration Dialog'', BESA Research checks if the ''Coregistration File'' has changed. If so, the dialog is updated with the new information.
* Press the top '''Browse... '''button to select a preexisting ''Coregistration File''.
* The entries in the edit boxes below show the files that will be used in the BESA Research Source Analysis module when the individual MRI is loaded. When using BESA MRI the file names will be automatically filled in. If you are using BrainVoagerQX and you are following our (and the BrainVoyagerQX) recommended naming conventions for files, and the files exist, then the names will be filled in automatically after you have completed the alignment procedure in BrainVoyagerQX. Otherwise you may have to browse for the files.
* Below the edit boxes the FEM field states whether all necessary information for the individual FEM head model were found in the coregistration file. If the field says ''Individual FEM for EEG'' ''defined!'' then all necessary data was found and the individual FEM EEG head model can be used in the BESA Research Source Analysis module. A similar message indicates whether the FEM MEG head model is available.
* Note that the MRI and the surfaces are Talairach-transformed! Alignment between BESA Research and the individual MRI is done with the MRI transformed to the AC-PC coordinate system, but the BESA Research Source Analysis module uses the Talairach-transformed image data and surfaces.

<div style="color:#ff0000;"></div>

=== Setting Up Coregistration Using BrainVoyager ===

It is assumed that you know how to load an MRI as a 3D data set into BrainVoyagerQX, and how to clean the image so that regions outside the head are black. We also assume knowledge of how to create AC-PC-aligned and Talairach-transformed MRIs.

Perform the following steps:

* BESA Research. Start the ''Coregistration Dialog''. Export the Coregistration File (head surface points) from your data by pressing the''' BrainVoyagerQX''' button in the dialog. Save the file to the directory where your MRI is located. BrainVoyagerQX is started.
* BrainVoyagerQX. Load the MRI corresponding to the EEG/MEG data. For optimal performance, the MRI should be cleaned so that regions outside the head are black. Prepare an AC-PC-transformed MRI and a Talairach MRI. For each, generate a surface mesh. Save these files following our recommended naming conventions (see chapter “''MRI File Name Conventions''”). Save the Talairach coordinate file ('''<nowiki>*.tal</nowiki>'''). If these steps have already been performed, load the ACPC MRI and load the ACPC mesh. If you want to generate a brain surface mesh, see chapter “''How to Generate a Brain Surface Mesh''”.
* BrainVoyagerQX. Load the Coregistration File (''EEG-MEG BESA/Load Surface Points''). The points will be displayed, but they are not aligned to the head:

<div style="color:#ff0000;"></div>

[[Image:MRI Integration (2).gif ‎]]

* BrainVoyagerQX. Define fiducial points on the head surface. Right click on the 3D head display and select the ''Fiducials Dialog'' in the drop-down menu:

[[Image:MRI Integration (3).gif ‎]]

 [[Image:MRI Integration (4).gif ‎]]

* BrainVoyagerQX. Rotate the head (by holding the '''Shift '''button down and clicking and dragging with the mouse) so that the Nasion is clearly visible. Move the mouse to the Nasion, and press '''Ctrl+Left Click'''. The coordinates of the Nasion are inserted into the dialog. Repeat for the left preauricular point, and then for the right preauricular point.

[[Image:MRI Integration (5).gif ‎]]

Note: if you have defined your fiducials differently in your BESA Research data (e.g. ear holes), click on the corresponding points in the MRI. If you have additional head surface points (step 8), accuracy in pinpointing the fiducials is not critical.

* BrainVoyagerQX. In the Fiducials Dialog, press the '''Fit fiducials''' button. The head surface points are now more or less aligned to the head.

[[Image:MRI Integration (6).gif ‎]]

* BrainVoyagerQX. Now select '''''EEG-MEG BESA/Fit Surface Points...'''''

[[Image:MRI Integration (7).gif ‎]]

If you do not see the right half of the dialog, press the '''Advanced >>''' button.

* Specify the distances of the digitization points from the skin. In the illustration above, the digitization points for electrodes are estimated to be 8 mm from the surface of the head. For the purpose of accurate alignment, the distance of digitization points from skin section of the dialog needs to be filled in correctly. We recommend that "Restrain solution around fiducials" is checked, and a reasonable limit (here 3 mm) of the restraint is defined. Then press '''OK'''.

[[Image:MRI Integration (8).gif ‎]]

BrainVoyager fits the points to the head, stretching x, y, and z coordinates to obtain a better fit than before.

Note: The fit performed during this step accounts for scaling inequalities between the x, y, and z axes in the MRI. Coregistration gains in accuracy over the use of fiducials alone a) because more head surface points are used, and b) because the scaling inequalities are accounted for.

* Alignment is now completed. If you only want to display the structural MRI in the BESA Source Module, you can return to the BESA Coregistration Dialog.
* BESA Research. When you switch back to the Coregistration Dialog, BESA Research will try to fill in the names of the Talairach MRI and surface meshes. If the names are not filled in, use the '''Browse...''' buttons to select the MRI and surface meshes. Press '''OK''' to save the Coregistration File. Alignment is completed!

The alignment steps need only be performed once for a given MRI and EEG/MEG data set. Otherwise, after starting BrainVoyager, just load the MRI, the surface mesh, and the surface points (see “''How to Set Up Coregistration with BrainVoyager after Alignment'' ''has been Done”''). Now the following actions are possible: see chapters “''How to Co-Locate Sources and MRI in the BESA Research Source Module”, '' ''“How to Send a Dipole from BESA Research to BrainVoyager”, “How to Define a Dipole in BESA Research at a Location Defined in the MRI”). ''

=== MRI file Name Conventions ===

If you follow the naming conventions for file names as described here, BESA Research detects the file names it requires, and the ''Coregistration Dialog'' is filled in automatically.

Please note that BESA MRI automatically uses these naming conventions for the generated files.

* '''The AC-PC MRI file name''' should end with "'''_ACPC.vmr'''", and the corresponding surface mesh name should end with "'''_ACPC.srf'''". After alignment, BrainVoyagerQX writes these names to the Coregistration File.
* '''The Talairach MRI file name '''should end with "'''_TAL.vmr'''", and the corresponding surface mesh name should end with "'''_TAL.srf'''". If defined, the brain surface mesh should end with "'''_TAL_WM.srf'''" ('''WM''' = '''w'''hite '''m'''atter).
* '''How BESA Research finds the Talairach files.''' When BESA Research rereads the Coregistration File after alignment of the coordinate systems, it finds the ACPC file names and defines the corresponding TAL file names. If these files exist, the names are entered into the Coregistration Dialog. For instance, if the Coregistration File contains the name "'''MRI''' '''PB_ACPC.vmr'''", BESA Research will look for the files "'''MRI_PB_TAL.vmr'''", "'''MRI_PB_TAL.srf'''", and "'''MRI_PB_TAL_WM.srf'''". If these files exist, they are entered into the dialog.
* '''Older BrainVoyager version.''' If you use BrainVoyager.exe to align coordinate systems, the file names are not saved with the Coregistration File. In this case, browse for the Talairach or the ACPC MRI from the Coregistration Dialog. BESA Research will use the rules as described above to insert the correct file names into the dialog.
* '''Missing Talairach coordinates.''' If, after aligning coordinate systems, the Talairach coordinates are missing from the Coregistration File (you forgot to load the Talairach coordinates in BrainVoyagerQX, or you used BrainVoyager.exe), BESA Research will look for a file ending with "'''_ACPC.tal'''", and read the coordinates from this file. You can also browse for a '''<nowiki>*.tal</nowiki>''' file in the Coregistration Dialog. For instance, if the MRI file is named "'''MRI_PB_ACPC.vmr'''" or "'''MR_''' '''PB_TAL.vmr'''", BESA Research will look for "'''MRI_PB_ACPC.tal'''" to find the Talairach coordinates.
* '''File names in the Coregistration File are saved relative to the Coregistration File location, if they are in the same folder.''' If the MRIs are in the same folder as the Coregistration File they will be recorded as ".\filename" (e.g. "'''.\MRI PB_tal.vmr'''"). This means that you can copy the Coregistration File together with the MRIs and meshes to a different folder, and BESA Research will be able to locate the files when the Coregistration File is opened. If the MRIs are saved in a different folder from the Coregistration File, the absolute paths are saved in the file. If the files are moved to new locations, you will have to restart the Coregistration Dialog and redefine the file locations.

=== How to Generate a Brain Surface Mesh ===

BESA Research is able to compute surface images, such as (Cortical LORETA, Cortical CLARA, Minimum Norm) using an individual cortex surface as the source space. A suitable cortex surface for this purpose can be effortlessly created using BESA MRI. Alternatively, BrainVoyager can be used for the creation of the brain surface mesh.

'''BESA MRI'''
* The brain surface generation is performed as one work step of the BESA MRI segmentation workflow.
* The cortex surface reconstruction is done using a robust and accurate automatic segmentation procedure.
* Details on how to generate the brain surface mesh in BESA MRI can be found in the coregistration quickguide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).

'''BrainVoyager'''
* BrainVoyagerQX provides a semiautomatic procedure to generate meshes for the brain surface of the Talairach MRI. Please refer to the BrainVoyager Help to find out how to do this.
* The result of the BrainVoyager procedure is two meshes, one for the left and one for the right hemisphere.
* BESA Research requires a single mesh. Therefore, load first one mesh (''Meshes/Load Mesh..''.), and append the other mesh (''Meshes/Add Mesh...''). Merge these two meshes (''Meshes/Merge'' ''meshes in surface window'') and then save the result (''Meshes/Save Mesh...''). If possible, use the recommended name conventions for the resulting file (file name ends in "'''_TAL_WM.srf"). '''For instance, if the Talairach MRI is named "'''MRI PB_TAL.vmr'''", name the brain surface mesh "'''MRI PB_TAL_WM.srf'''".
* See also the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website (http://brainvoyager.com/Downloads.html).

== Co-locating Dipoles and MRI Locations ==

=== Co-locating Sources and MRI in the BESA Research Source Module ===

If the alignment procedure using BESA MRI (or BrainVoyager) has been completed then you can load the individual structural MRI in the Source Module by pressing ''''A'''' or using a mouse right click and selecting '''''Display MRI'''''.

Sources in the current model are then overlayed onto the individual MRI.

A double-click at any location in the MRI will define a new source at the corresponding location in the BESA Research head model.

[[Image:MRI Integration (9).gif ‎]]

=== Coregistration with BrainVoyager after Alignment has been Done ===

Alignment between BESA Research and BrainVoyager is only required once for a given BESA Research data set and the corresponding MRI. At a later time, if you want to Co-locate sources between BESA Research and BrainVoyager, perform the following steps in BrainVoyager:
* Load the MRI.
* Load the head surface mesh (''Meshes/Load Mesh..''.).
* Load the Coregistration File (''EEG-MEG BESA/Load Surface Points..''.).

BrainVoyager is now ready for Co-location.

=== Send a Dipole from BESA Research to BrainVoyager ===

First, start BrainVoyager(QX). This can be done from the BESA Research Source Module by pressing the '''BrainVoyager '''button. Note that in the Source Module, the ''Options / Preferences / BrainVoyager'' tab allows to define the path to BrainVoyager.

In BrainVoyager, set up coregistration.

In the BESA Research Source Module, highlight the dipole of interest.

In the BESA Research Source Module, click on the '''BrainVoyager''' button.

Program control will automatically switch to BrainVoyager. The head will be cut at the section corresponding to the dipole of interest.

[[Image:MRI Integration (10).gif ‎]]

Note that all dipoles in the current model are sent to BrainVoyager. The highlighted dipole (here, the red dipole) determines the plane at which the head will be cut.

Note that the dipoles are visible in both the surface module and in the 2D view:

[[Image:MRI Integration (11).gif ‎]]

=== Define a Dipole in BESA Research at a Location Defined in the MRI ===

First set up coregistration (see chapter ''“Coregistration with BrainVoyager after Alignment has been'' ''Done”'').

In the BrainVoyager 2D MRI view, place the mouse over the point at which you would like to define a dipole. Right click at this point. If this point lies within an fRMI cluster, BrainVoyager will automatically determine its center and use it as a seeding point instead. Press '''Send Seed Point To BESA....'''

[[Image:MRI Integration (12).gif ‎]]

The following Dialog is opened:

[[Image:MRI Integration (13).gif ‎]]

Press '''Send to BESA'''.

The BESA Source Analysis window appears. The new dipole or regional source (depending on the setting in the ‘Options’ dialog in the Source Analysis window is now displayed at the corresponding location. If a dipole is seeded, BESA automatically fits its orientation. For further adjustment of the model, you may need to refit the orientation, e.g. at a certain time range, or in the presence of other sources.

Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website ([http://brainvoyager.com/Downloads.html http://brainvoyager.com/Downloads.html]).

[[Category:Research Manual]]

{{BESAManualNav}}

Source Coherence How to...

2017-04-07T13:10:26Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Complete
|version = 6.1 or higher
}}

= Source Coherence: How to... =

== How to Start the Beamformer from the Time-Frequency Window ==

This chapter shows how to start the BESA Multiple Source Beamformer from the time-frequency window. The displayed screenshots are taken using the file '''BESA5/Examples/Learn-by-Simulations/AC''-''Coherence/AC-Osc20.foc''' (see BESA Tutorial 6: "''Tutorial on source coherence''" on our website http://www.besa.de).

The time-frequency beamformer is especially useful to image induced oscillatory activity in- or decrease. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot.

In the time-frequency diagram of any channel, left-drag to mark a time-frequency region of interest, e.g. a region of power increase. When the left mouse button is released, select '''Image' ''from the popup menu.

[[Image:Image001.gif]]

'''Note:''' The current montage and the type of time-frequency plot currently displayed (TSE, amplitude/power, Coherence) does not affect the output of the beamformer image, because the image is always based on the complex single-trial spectral density of the original recording montage. The status of the 'subtract average signal' button is considered, however. This allows to image either evoked and induced activity or induced activity only.

The 'Image' edit window is displayed. It allows for adjusting the time-frequency range of the target interval and for a re-definition of the baseline interval. If a control condition has been specified, you can choose to reference the power in the target time-frequency interval to the corresponding interval in the control condition instead of the baseline interval by checking 'Compare Conditions'.

[[Image:Image002.gif]]

Note: The text within the window emphasizes that it is recommended to use the same duration for the Baseline Interval and the Target Interval to obtain a reliable beamformer image. The reason is the dependence on the noise estimate on the number of trials that enter the covariance matrix computation. The same recommendation holds if two conditions are compared: It is recommended to define conditions such that they contain approximately the same number of trials. If the baseline interval defined in the Time-Frequency window (the red bar on the x-axis) is larger than the target time interval specified by the dragged rectangle, the baseline interval in the'' 'Image' ''dialog window is automatically shortened to match the duration of the Target Interval. If for some reason these requirements cannot be met, it is recommended to compute a beamformer image with regularization. This is achieved by adjusting the SVD cutoff in the Source Analysis window using the menu entry '''Image/Settings'.''

Press the ''''Go' '''button to start the beamformer computation.

BESA Research now computes mean time-frequency covariance matrices for the target and the reference interval. The source analysis window opens with an enlarged 3D imaging display that compares the power in the target and the reference interval as computed with a bilateral beamformer. The result is superimposed onto the individual or standard MRI.

For more information on the multiple-source beamformer (MSBF), please refer to chapter ''"Source'' ''Analysis".''

[[Image:Image003.gif]]

== How to Start DICS computation from the Time-Frequency Window ==

How to create DICS images you will find in the chapter “''Source Analysis / 3D Imaging / Dynamic Imaging of Coherent Sources (DICS)”.''

== How to Compute Time Lags between oscillations using Phase Diagrams ==

The phase diagram option is used to analyze phase differences between coherent channels. This can give an insight into a possible coupling of brain regions which may be necessary e.g. to integrate input from various specialized neurons to a common perception. However, the measured coupling is also influenced by volume conduction effects (scalp coherence) or the modeling parameters (source coherence).

If brain regions show oscillatory coupling in the same frequency range, the phase relationship should be constant over some time:

[[Image:Image005.gif]]

Since we cannot obtain an ideal frequency resolution using a time-frequency transform, any oscillation frequency is smeared out over several sampling frequencies in the transformed signal. If the delay between the two oscillations is constant, the phase shift between the signals rises linearly with the frequency. We can get a precise estimate of the delay if we use several neighboring frequencies for the calculation. Practically, you can achieve this by the following steps:

1. Enter '''coherence''' mode, either by '''double-clicking''' on the channel of interest, or by right-clicking on it and selecting coherence from the popup menu.

2. In a coherence plot, '''drag''' over an area of interest which comprises the time interval where the oscillation occurs and the relevant frequency range. The left-mouse popup menu appears (see the leftmost channel termed ACsL in the example below):

[[Image:Image006.gif]]

3. Select the menu entry ''''''View Phase Diagram''''''. In all channels where coherence was shown previously, the plot changes to display the phase diagram. Inside the marked time-frequency region, the mean phase difference ϕi within the time window is calculated for each frequency νi, and the values are plotted. The phase is calculated from the cross-spectral matrices of the single trials. The error bars shown in the display are the standard deviations of the phase over the time.

The time lag is calculated from a regression fit to the values. The fitting procedure takes phase shifts of π into account, which can occur due to volume currents, or due to dipole orientations. First, a straight line is fitted to the data. Then, one of two different approaches are used to compute the time lag, depending on the characteristics of the values.
* If extrapolation of the line to ν= 0 Hz yields a phase difference of approximately 0 or approximately π, or if a zero crossing at the origin is within the error margins of the fit, the delay can be calculated directly from the data values. For each data value, the relationship ∆ti <nowiki>= ϕ</nowiki>i/ (2π νi) holds. The time lag is calculated as the weighted mean, where the weights are given by the individual errors of fi (the errors are given by the standard deviation over the time samples).
* If the regression line does not cross the origin, the gradient of the fit is used to calculate the time lag as ∆t=grad(f(ν)) / 2π

'''Note:''' In both cases, any frequency only enters the calculation if the coherence value reaches or exceeds 70% of the current color map maximum for at least one time sample inside the selected time-frequency window. At least 3 valid values are required for the estimation. Channels with less than 3 valid values are not evaluated.

Phase values and fitted lines are only displayed for the channels where the above condition is satisfied. In the example below, the condition was only fulfilled for one channel (ACsL) due to the good separation of activities by the source montage. The calculated delay is displayed beside the channel label (in this case: 5 milliseconds).

[[Image:Image009.gif]]

To get back to coherence, '''right-click '''into the reference channel and select ''''Coherence'''' from the popup menu that appears.

== How to Compute a Probability Map ==

'''Statistical testing with one condition'''

This example uses the simulated data set in the file ''''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''' (see also BESA Research Tutorial on source coherence on www.besa.de).

After the data file is loaded, start coherence analysis by
# selecting the montage "RC0" from the user montages (toolbar button "'''Usr'''")
# loading the paradigm (menu "''ERP/Open Paradigm''", select paradigm file "'''Auditory/AC_Osc.pdg'''")
# performing an artifact scan (paradigm tab "'''Artifact'''", press the "'''Scan'''..." button and adjust the amplitude threshold to about 135µV)
# starting analysis (paradigm tab "Coherence", press the "'''Go'''" button)

The progress bar runs through, and the temporal-spectral evolution (TSE) display is shown.

'''Statistics on TSE'''

In the TSE display, press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu that appears. Alternatively, select "''Statistics/Current Condition"'' from the menu. This starts the bootstrap test. The result looks somewhat like this:

[[Image:Image012.gif]]

''Example for p map of TSE, correction on p=0.05 level. Both significant synchronization and desynchronization is shown (red and blue colors; negative p values indicate desynchronization). The correction yields significant results only at the modelled time-frequency spots, with the exception of the frequency edges in channel PrM, FrR, and the occipital channels. The baseline interval is not tested.''

By default, the results are corrected for multiple testing, and only values with a significance of p < 0.05 after correction are kept. Correction can be switched off using statistics options (''Statistics/Options ''from the menu, or use the toolbar button [[Image:Image010.gif]] and select "''Options''" from the dropdown menu). This '''Options '''menu also enables correcting on the significance level p < 0.01. The text at the bottom left of the window indicates that a correction took place to find the significant sampling points, but the remaining p values were not corrected.

'''Statistics on Coherence and phase coherence'''

Double-click on a channel (e.g. ACsL) to display its coherence with the other channels. Then press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu (or select "''Statistics/Current'' ''Condition''" from the menu). This starts the permutation test, which is quite time-consuming. The result looks somewhat like this:

[[Image:Image013.gif]]

''Example for the p map of source coherence; correction on p=0.05 level. In all channels, alpha band coherence is significant. Furthermore, significant noise coherence can be observed in the proximate source channels, which only recedes where signal is present which is modelled by the reference channel. The oscillatory coupling between ACsL and ACsR is also significant.''

The same procedure applies for a phase coherence analysis. To switch to the p map for phase coherence, simply press the toolbar button [[Image:Image015.gif]] . If statistics mode is already active, the new p map will be computed automatically.

'''Statistical testing comparing conditions'''

This example uses the error-related negativity data set in the file ''''Examples/TFC-Error-Related''' '''Negativity/Correct+Error.foc'''' (see also BESA Research Tutorial on source coherence on [http://www.besa.de www.besa.de]).

After the data file is loaded, start coherence analysis by
# selecting the user montage "ERN9" from the user montages (toolbar button "'''Usr'''")
# Loading the paradigm (menu "'''ERP/Open Paradigm'''", select paradigm file "'''Cognitive/ERN.pdg'''")
# performing an artifact scan (paradigm tab "''Artifact''", press the "'''Scan'''..." button and adjust the amplitude and gradient thresholds to about 180 µV and 75 µV)
# select the conditions with error and correct response for analysis, triggered on the stimulus (tab "''Coherence''", select "''StErr''" as target condition, check the tick mark "''Use Control Condition''", and select "''StCor''" as control condition (see figure below). Press the "'''Go'''" button. The progress bar is displayed, followed by the temporal-spectral evolution (TSE) display for the target condition.

[[Image:Image017.gif]]

''Settings for comparing conditions in the time-frequency analysis.''

'''Statistics on TSE'''

Press the [[Image:Image018.gif]] toolbar button to see the difference between target and control condition.

Then press the toolbar button "" and select "''Compare Conditions''" from the dropdown menu that appears. Alternatively, select "''Statistics/Compare Conditions''" from the menu. This starts the permutation test. The result looks somewhat like this:

[[Image:Image019.gif]]

''Example of TSE p map when comparing conditions; correction on p=0.05 level. Both significant increase and decrease of TSE in target condition with respect to control condition is shown (red and blue colors; negative p values indicate decrease). The baseline interval is not tested.''

As in the case of one condition, the statistics options can be used to switch correction on or off, and to correct on two different significance levels.

'''Statistics on Coherence and phase coherence'''

Double-click on a channel (e.g. CgA) to display its coherence with the other channels. Then press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu (or select "''Statistics/Current Condition''" from the menu). This starts the permutation test, which is quite time-consuming. The result looks somewhat like this:

[[Image:Image021.gif]]

''Example for p-map of coherence comparing conditions; correction on p=0.05 level. The regions where coherence differs significantly between conditions are depicted in red. The main coherent regions are seen in channels CgP and TbR at low frequencies.''

Please note that the problems with noise coherence, which arise when testing within one condition, do not arise when comparing conditions. Computation is also much faster, since a different approach is used.

The same procedure applies for a phase coherence analysis. To switch to the p map for phase coherence, simply press the toolbar button [[Image:Image015.gif]] . If statistics mode is already active, the new p map will be computed automatically.

[[Category:Research Manual]]

{{BESAManualNav}}

Source Coherence Introduction and Concepts

2017-04-07T13:10:02Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Complete
|version = 6.1 or higher
}}
= Source Coherence =

== Source Coherence Module - Introduction ==

The Source Coherence Module provides new insights into interaction between brain regions using brain source montages. These are derived from multiple source models of the data. Transforming the scalp surface into the brain signals using source montages greatly enhances the spatial resolution and largely removes one of the major drawbacks of traditional coherence analysis, the widespread overlap at the scalp due to volume conduction.

The Source Coherence Module provides a variety of tools for time-frequency based event-related data analysis.
* Time-frequency diagrams based on brain source or surface channels
* Display of temporal-spectral evolution (TSE) in percent
* Separation of evoked and induced activity  
* Joint display of time-frequency or coherence plots with the evoked potential of individual channels
* Coherence estimate between any combination of surface or source channels (coherence or phase coherence)
* Computation and display of phase delay and latency difference between channels in a graphically defined time and frequency window
* Display of the inter-trial phase locking (ITPL)
* Comparison of two conditions
* Probability plots transforming all time-frequency parameters into statistical p-values
* Export of analysis results into ASCII text files
* Time-frequency transforms are obtained in a very fast implementation based on complex demodulation. Apart from source channels, intracranial channels, and scalp channels, also other polygraphic channels, e.g. rectified EMG, can be included into the analysis.
* A highly optimized graphical user interaction enables a fast testing of hypotheses, and quick focusing onto the features of interest.

For an introduction and an outline of the underlying concepts of source coherence, please continue with the next topic, "''Concepts of Source Coherence''"

For more details check the following topics:
* Layout of the Source Coherence Window
* Reference (in the online help)

Please also refer to our website at http://www.besa.de for the latest tutorial on source coherence and related topics.

== Concepts of Source Coherence ==

Recently, an increasing number of papers on oscillatory coupling between brain regions in animal studies and on time-frequency analysis of human EEG and MEG data has been published. BESA Research introduces several tools for fast and user-friendly time-frequency analysis including source and scalp coherence.

First, let us introduce some terminology in order to clarify the concepts:
* Surface waveform: a time signal recorded from EEG-electrodes or MEG sensors
* Source waveform: a time signal calculated for a specified brain region or cortical surface
* Source montage: transformation of the on-going EEG into the estimated contributions or source waveforms of a set of brain regions

[[Image:SourceCoh Concepts (1).gif ]]

* Time-frequency analysis: analysis or display of the event-related time-locked or induced activity in the time-frequency domain
* Time-locked activity: event-related signal with similar wave shape over trials
* Induced activity: oscillatory activity occurring in a certain event-related time window with varying time lag and phase
* Oscillatory activity: activity occurring with several oscillations in a narrow frequency band; can be time-locked and/or induced

[[Image:SourceCoh Concepts (2).gif ]]

* TSE: temporal spectral evolution, change in amplitude or power over time relative to the baseline interval
* ERD/ERS: event-related (de)-synchronization, used as a synonym for TSE
* ERSP: event-related spectral perturbations, change in power or amplitude over time. This is the more general term and comprises ERD/ERS/TSE that are related to baseline.
* Correlation: correlation between two time signals, i.e. scalar product of normalized signals in time domain

[[Image:SourceCoh Concepts (3).gif ]]

* Spectral-temporal density function S(f,t) = A(f,t)*ei*ϕ(f,t): quantifies amplitude A and phase ϕ of a signal at a certain frequency f and latency t relative to an event
* Coherence: squared correlation of two spectral density functions S1(f,t) and S2(f,t) over trials, i.e. squared scalar product of S1(f,t) and S2(f,t) over trials, normalized across all trials
* Phase coherence: correlation of two normalized spectral density functions S1(f,t) and S2(f,t) over trials, quantified by the phase locking value (PLV)
* Phase locking value (PLV): scalar product of S1(f,t) and S2(f,t) over trials, where S1(f,t) and S2(f,t) are normalized, i.e. they become unit vectors in the complex plane

[[Image:SourceCoh Concepts (4).gif ]]

Phase coherence uses only the phase relationships between channels for the coherence estimate, not the amplitudes. The method implemented here was described by Lachaux et al. (1999). Phase coherence is described by the so-called "phase locking value" (PLV).

Comparison of the formulae for coherence and PLV illustrates that for constant amplitudes, PLV is equivalent to the square root of coherence.

'''Scalp Coherence'''

When coherence is calculated at the surface between 2 EEG channels or 2 MEG sensors, activity from various brain regions is picked up in each of the surface channels. Oscillatory activity in one brain region can already lead to a strong coherence between 2 surface channels because of the wide distribution of focal brain activity at the surface. This is due to the nature of the dipole fields when recording remotely and due to the smearing effect of the volume conduction in EEG. As a consequence, a coherence measure between surface channels cannot distinguish between coherence due to propagation and real coherence between the oscillatory activities in two coupled brain regions.

[[Image:SourceCoh Concepts (5).gif ]]

Whether true coherence can be detected at the scalp, depends mainly on the relative orientation of the source currents in the underlying brain regions and, to a lesser extent, on their distance in location. In the case of the auditory cortex, for example, both the left and right temporal planes produce vertical activity with strong bilateral contributions centrally (e.g. at C3/C4 and F3/F4). The spatial correlation of the radial activities at the lateral surfaces of the superior temporal gyrus is also very large between right and left scalp electrodes, e.g. at T3/T4. A current-source density montage (CSD or Laplacian) can reduce the effects of propagation on scalp coherence to a certain extent, because it enhances the radial current from the underlying cortex relative to more remote sources to some extent.

[[Image:SourceCoh Concepts (6).gif ]]

'''Source Coherence'''

An optimal separation is obtained by a source montage derived from a multiple source model. The model is used to create an inverse spatial filter, i.e. a source montage that separates the different brain activities. Activities that are not accounted for by the model, e.g. from background noise or EEG, are distributed amongst the sources and may therefore lead to 'noise coherence' between source channels. This 'noise coherence' can be large for sources which have very similar spatial topographies. It can be reduced by increasing the regularization constant of the inverse at the expense of a larger cross-talk between the sources or by including specific sources accounting for the 'noise'.

The principal steps to calculate a time-frequency diagram and source coherence are illustrated in the figure below for the real data example of error-related negativity (ERN). A multiple source model is created from averaged ERP data and/or sources in brain regions known to contribute from fMRI/PET studies using a similar task. The source model is then used to calculate a source montage and the source waveforms of the single trials. Next, each single trial is transformed into the time-frequency domain by selecting a certain temporal resolution using complex demodulation (a principle similar to FM radio). From the single trials, time-frequency displays are generated by averaging spectral density amplitude or power over trials. Source coherence is calculated by averaging the cross-spectral density of one reference channel with all other channels over trials and normalizing by the averaged auto-spectral densities (cf. figure above).

[[Image:SourceCoh Concepts (7).gif ]]

In this figure, you can see the separation of the occipital alpha rhythm (top 3 source waveforms) from the frontal midline ERN components (lowest 2 traces) which become prominent in most single trials after transforming from the 128 scalp electrodes onto 9 source areas in the brain. The time-frequency display shows a strong evoked ERN activity in the anterior and posterior cingulate gyrus (CG) sources and an induced suppression and rebound of ~20 Hz activity in the sensori-motor cortex bilaterally. Alpha suppression is most prominent in the midline occipital source. A double click onto the TF display of a selected channel leads to the rapid calculation of the coherence between this channel and all other channels.

For more information, see the following sections ''(Layout of the Source Coherence Window'' and ''Tutorial)''.

== Layout of the Source Coherence Window ==

The source coherence window consists of
* title bar with information on the current display mode and the data file name
* menu bar where the display mode and analysis options are selected
* toolbar for quick access to the menu functions
* display area where time-frequency diagrams of all channels are shown
* information text about the current display mode and units (e.g. Power, Amplitude,
* color map with minimum and maximum normalization values at the center bottom. Any value higher or lower than the normalization value is assigned the color of the normalization value
* information text about the condition which is analyzed at the bottom right
* status bar with information about the channel, frequency, latency, and signal amplitude

[[Image:Coherence (1).gif]]

[[Category:Research Manual]]

{{BESAManualNav}}

Source Analysis 3D Imaging

2017-04-07T13:09:18Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = 6.1 or higher
}}
== 3D Imaging ==

BESA Research features a set of new functions that provide 3D images that are displayed superimposed to the individual subject's anatomy. This chapter introduces these different images and describe their properties and applications.

The 3D images can be divided into three categories:

'''Volume images:'''
* '''The Multiple Source Beamformer (MSBF)''' is a tool for imaging brain activity. It is applied in the time-frequency domain and based on single-trial data. Therefore, it can image not only evoked, but also induced activity, which is not visible in time-domain averages of the data.
* '''Dynamic Imaging of Coherent Sources (DICS)''' can find coherence between any two pairs of voxels in the brain or between an external source and brain voxels. DICS requires time-frequency-transformed data and can find coherence for evoked and induced activity.

The following imaging methods provide an image of brain activity based on a distributed multiple source model:
* '''CLARA''' is an iterative application of LORETA images, focusing the obtained 3D image in each iteration step.
* '''LAURA '''uses a spatial weighting function that has the form of a local autoregressive function.
* '''LORETA''' has the 3D Laplacian operator implemented as spatial weighting prior.
* '''sLORETA''' is an unweighted minimum norm that is standardized by the resolution matrix.
* '''swLORETA '''is equivalent to sLORETA, except for an additional depth weighting.
* '''SSLOFO '''is an iterative application of standardized minimum norm images with consecutive shrinkage of the source space.
* '''A User-defined volume image''' allows to experiment with the different imaging techniques. It is possible to specify user-defined parameters for the family of distributed source images to create a new imaging technique.

'''Surface image:'''
* The '''Surface Minimum Norm Image'''. If no individual MRI is available, the minimum norm image is displayed on a standard brain surface and computed for standard source locations. If available, an individual brain surface is used to construct the distributed source model and to image the brain activity.
* '''Cortical LORETA'''. Unlike classical LORETA, cortical LORETA is not computed in a 3D volume, but on the cortical surface.
* '''Cortical CLARA'''. Unlike classical CLARA, cortical CLARA is not computed in a 3D volume, but on the cortical surface.

'''Discrete model probing:'''

These images do not visualize source activity. Rather, they visualize properties of the currently applied discrete source model:
* The '''Multiple Source Probe Scan (MSPS)''' is a tool for the validation of a discrete multiple source model.
* The''' Source Sensitivity image''' displays the sensitivity of a selected source in the current discrete source model and is therefore data independent.

=== Multiple Source Beamformer (MSBF) ===

'''Short mathematical introduction'''

The BESA beamformer is a modified version of the linearly constrained minimum variance vector beamformer in the time-frequency domain as described in Gross et al., "Dynamic imaging of coherent sources: Studying neural interactions in the human brain", PNAS 98, 696-699, 2001. It allows to image evoked and induced oscillatory activity in a user-defined time-frequency range, where time is taken relative to a triggered event.

The computation is based on a transformation of each channel's single trial data from the time domain into the time-frequency domain. This transformation is performed by the BESA Research Source Coherence module and leads to the complex spectral density Si (f,t), where i is the channel index and f and t denote frequency and time, respectively. Complex cross spectral density matrices C are computed for each trial:

[[Image:SA 3Dimaging (1).gif]]

The output power P of the beamformer for a specific brain region at location r is then computed by the following equation:

[[Image:SA 3Dimaging (2).gif]]

Here, Cr-1 is the inverse of the SVD-regularized average of Cij(f,t) over trials and the time-frequency range of interest; L is the leadfield matrix of the model containing a regional source at target location r and, optionally, additional sources whose interference with the target source is to be minimized; tr'[] is the trace of the [3x3] (MEG:[2x2]) submatrix of the bracketed expression that corresponds to the source at target location r.

In BESA Research, the output power P(r) is normalized with the output power in a reference time-frequency interval Pref(r). A value q ist defined as follows:  

[[Image:SA 3Dimaging (3).gif]]

Pref can be computed either from the corresponding frequency range in the baseline of the same condition (i.e. the beamformer images event-related power increase or decrease) or from the corresponding time-frequency range in a control condition (i.e. the beamformer images differences between two conditions). The beamformer image is constructed from values q(r) computed for all locations on a grid specified in the '''General Settings tab'''. For MEG data, the innermost grid points within a sphere of approx. 12% of the head diameter are assigned interpolated rather than calculated values).

q-values are shown in %, where q[%] = q*100. Alternatively to the definition above, q can also be displayed in units of dB:

[[Image:SA 3Dimaging (4).gif]]

A beamformer operator is designed to pass signals from the brain region of interest r without attenuation, while minimizing interference from activity in all other brain regions. Traditional single-source beamformers are known to mislocalize sources if several brain regions have highly correlated activity. Therefore, the BESA beamformer extends the traditional single-source beamformer in order to implicitly suppress activity from possibly correlated brain regions. This is achieved by using a multiple source beamformer calculation that contains not only the leadfields of the source at the location of interest r, but also those of possibly interfering sources. As a default, BESA Research uses a bilateral beamformer, where specifically contributions from the homologue source in the opposite hemisphere are taken into account (the matrix L thus being of dimension Nx6 for EEG and Nx4 for MEG, respectively, where N is the number of sensors). This allows for imaging of highly correlated bilateral activity in the two hemispheres that commonly occurs during processing of external stimuli.

In addition, the beamformer computation can take into account possibly correlated sources at arbitrary locations that are specified in the current solution. This is achieved by adding their leadfield vectors to the matrix L in the equation above.

'''Applying the Beamformer'''

This chapter illustrates the usage of the BESA beamformer. The displayed figures are generated using the file ''''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''' (see BESA Tutorial 6: "''Tutorial on source coherence''").

'''Starting the beamformer from the time-frequency window'''

The BESA beamformer is applied in the time-frequency domain and therefore requires the Source Coherence module to be enabled. The time-frequency beamformer is especially useful to image in- or decrease of induced oscillatory activity. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot. For instructions on how to initiate a beamformer computation in the time-frequency window, please refer to Chapter "''How''

''to Create Beamformer Images".''

After the beamformer computation has been initiated in the time-frequency window, the source analysis window opens with an enlarged 3D image of the q-value computed with a '''bilateral beamformer'''. The result is superimposed onto the MR image assigned to the data set (individual or standard).

[[Image:SA 3Dimaging (5).gif]]

''Beamformer image after starting the computation in the Time-Frequency window. A bilateral pair of sources in the auditory cortex accounts for the highly correlated oscillatory induced activity. Only the bilateral beamformer manages to separate these activities; a traditional single-source beamformer would merge the two sources into one image maximum in the head center instead.''

'''Multiple source beamformer in the Source Analysis window'''

The 3D imaging display is part of the source analysis window. If you press the '''Restore''' button at the right end of the title bar of the 3D window, the window appears at the bottom right of the source analysis window. In the channel box, the averaged (evoked) data of the selected condition is shown. When a control condition was selected, its average is appended to the average of the target condition.

[[Image:SA 3Dimaging (6).gif]]

''Source Analysis window with beamformer image. The two sources have been added using the '''''Switch to''''' '''''Maximum''''' and '''''Add Source '''''toolbar buttons (see below). Source waveforms are computed from the displayed averaged data. Therefore, they do not represent the activity displayed in the beamformer image, which in this simulation example is induced (i.e. not phase-locked to the trigger)!''

When starting the beamformer from the time-frequency window, a bilateral beamformer scan is performed. In the source analysis window, the beamformer computation can be repeated taking into account possibly correlated sources that are specified in the current solution. Interfering activities generated by all sources in the current solution that are in the 'On' state are specifically suppressed (they enter the matrix L in the beamformer calculation, see Chapter ''Short mathematical description'' above). The computation can be started from the '''Image''' menu or from the '''Image selector button dropdown''' menu. The '''Image''' menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window.

[[Image:SA 3Dimaging (7).gif]]

''Multiple source beamformer image calculated in the presence of a source in the left hemisphere. A single source scan has been performed. The source set in the current solution accounts for the left-hemispheric q-maximum in the data. Accordingly, the beamformer scan reveals only the as yet unmodeled additional activity in the right hemisphere (note the radiological convention in the 3D image display).''

The beamformer scan can be performed with a single or a bilateral source scan. The default scan type depends on the current solution:
* When the beamformer is started from the Time-Frequency window, the Source Analysis window opens with a new solution and a bilateral beamformer scan is performed.
* When the beamformer is started within the Source Analysis window, the default is

* a scan with a single source in addition to the sources in the current solution, if at least one source is active.
* a bilateral scan if no source in the current solution is active.

The default scan type is the multiple source beamformer. The non-default scan type can be enforced using the corresponding ''Volume Image / Beamformer'' entry in the '''Image '''menu.

'''Inserting Sources out of the Beamformer Image'''

The beamformer image can be used to add sources to the current solution. A simple double-click anywhere in the 2D- or 3D view will generate a non-oriented regional source at the corresponding location. However, a better and easier way to create sources at image maxima and minima is to use the toolbar buttons '''Switch to Maximum''' [[Image:SA 3Dimaging (8).gif]] and '''Add Source''' [[Image:SA 3Dimaging (9).gif]].

Use the '''Switch to Maximum''' button to place the red crosshair of the 3D window onto a local image maximum or minimum. Hitting the '''Add Source''' button creates a regional source at the location of the crosshair and therefore ensures the exact placement of the source at the image extremum. Moreover, the '''Add Source''' button generates an oriented regional source. BESA Research automatically estimates the source orientation that contributes most to the power in the target time-frequency interval (or the reference time-frequency interval, if its power is larger than that in the target interval). The accuracy of this orientation estimate depends largely on the noise content of the data. The smaller the signal-to-noise ratio of the data, the lower is the accuracy of the orientation estimate. This feature allows to use the beamformer as a tool to create a source montage for source coherence analysis, where it is of advantage to work with oriented sources.

'''Notes:'''

* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image '''menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the''' Image''' menu.
* For scaling options, use the [[Image:SA 3Dimaging (10).gif]] and [[Image:SA 3Dimaging (11).gif]] '''Image Scale toolbar''' buttons.
* Parameters used for the beamformer calculations can be set in the '''General Settings tab''' of the ''Image Settings dialog box.''

=== Dynamic Imaging of Coherent Sources (DICS) ===

'''Short mathematical introduction'''

Dynamic Imaging of Coherent Sources (DICS) is a sophisticated method for imaging cortico-cortical coherence in the brain, or coherence between an external reference (e.g. EMG channel) and cortical structures. DICS can be applied to localize evoked as well as induced coherent cortical activity in a user-defined time-frequency range.

DICS was implemented in BESA closely following Gross et al., "Dynamic imaging of coherent sources: Studying neural interactions in the human brain", PNAS 98, 696-699, 2001.

The computation is based on a transformation of each channel's single trial data from the time domain into the frequency domain. This transformation is performed by the BESA Research Coherence module and results in the complex spectral density matrix that is used for constructing the spatial filter similar to beamforming.

DICS computation yields a 3-D image, each voxel being assigned a coherence value. Coherence values can be described as a neural activity index and do not have a unit. The neural activity index contrasts coherence in a target time-frequency bin with coherence of the same time-frequency bin in a baseline.

'''DICS for cortico-cortical coherence is computed as follows:'''

Let L(r) be the leadfield in voxel r in the brain and C the complex cross-spectral density matrix. The spatial filter W(r) for the voxel r in the head is defined as follows:

[[Image:SA 3Dimaging (12).gif]]

The cross-spectrum between two locations (voxels) r1 and r2 in the head are calculated with the following equation:

[[Image:SA 3Dimaging (13).gif]]

where <nowiki>*T</nowiki> means the transposed complex conjugate of a matrix. The cross-spectral density can then be calculated from the cross spectrum as follows:

[[Image:SA 3Dimaging (14).gif]]

where λ1{} indicates the largest singular value of the cross spectrum. Once the cross spectral density is estimated, the connectivity¹(CON) between the two brain regions r1 and r2 are calculated as follows:

[[Image:SA 3Dimaging (15).gif]]

where cssig is the cross-spectral density for the signal of interest between the two brain regions r1 and r2, and csbl is the corresponding cross spectral density for the baseline or the control condition, respectively. In the case DICS is computed with a cortical reference, r1 is the reference region (voxel) and remains constant while r2 scans all the grid points within the brain sequentially. In that way, the connectivity between the reference brain region and all other brain regions is estimated. The value of CON(r1, r2) falls in the interval [-1 1]. If the cross-spectral density for the baseline is 0 the connectivity value will be 1. If the cross-spectral density for the signal is 0 the connectivity value will be -1.

'''DICS for cortico-muscular coherence is computed as follows:'''

When using an external reference, the equation for coherence calculation is slightly different compared to the equation for cortico-cortical coherence. First of all, the cross-spectral density matrix is not only computed for the MEG/EEG channels, but the external reference channel is added. This resulting matrix is Call. In this case, the cross-spectral density between the reference signal and all other MEG/EEG

channels is called cref. It is only one column of Call. Hence, the cross-spectrum in voxel r is calculated with the following equation:

[[Image:SA 3Dimaging (16).gif]]

and the corresponding cross-spectral density is calculated as the sum of squares of Cs:

[[Image:SA 3Dimaging (17).gif]]

where n is 2 for MEG and 3 for EEG. This equation can also be described as the squared Euclidean norm of the cross-spectrum:

[[Image:SA 3Dimaging (18).gif]]

The power in voxel r is calculated as in the cortico-cortical case:

[[Image:SA 3Dimaging (19).gif]]

At last, coherence between the external reference and cortical activity is calculated with the equation:

[[Image:SA 3Dimaging (20).gif]]

where Call(k, k) is the (k,k)-th diagonal element of the matrix Call.

DICS is particularly useful, if coherence is to be calculated without an a-priory source model (in contrast to source coherence based on pre-defined source montages). However, the recommended analysis strategy for DICS is to use a brain source as a starting point for coherence calculation that is known to contribute to the EEG/MEG signal of interest. For example, one might first run a beamformer on the time-frequency range of interest and use the voxel with the strongest oscillatory activity as a starting point for DICS. The resulting coherence image will again lead to several maxima (ordered by magnitude), which in turn can serve as starting points for DICS calculation. This way, it is possible to detect even weak sources that show coherent activity in the given time-frequency range.

The other significant application for DICS is estimating coherence between an external source and voxels in the brain. For example, an external source can be muscle activity recoded by an electrode placed over the according peripheral region. This way, the direct relationship between muscle activity and brain activation can be measured.

'''Starting DICS computation from the Time-Frequency Window'''

DICS is particularly useful, if coherence in a user-defined time-frequency bin (evoked or induced) is to be calculated between any two brain regions or between an external reference and the brain. DICS runs only on time-frequency decomposed data, so time-frequency analysis needs to be run before starting DICS computation.

To start the DICS computation, left-drag a window over a selected time-frequency bin in the Time-Frequency Window. Right-click and select “Image”. A dialogue will open (see fig. 1) prompting you to specify time and frequency settings as well as the baseline period. It is recommended to use a baseline period of equal length as the data period of interest. Make sure to select “DICS” in the top row and press

“'''Go”.'''

[[Image:SA 3Dimaging (21).gif]]

''Fig. 1: Time and frequency settings for DICS and MSBF''

Next, a window will appear allowing you to specify the reference source for coherence calculation (see fig. 2). It is possible to select a channel (e.g. EMG) or a brain source. If a brain source is chosen and no source analysis was computed beforehand, the option “Use current cross-hair position” must be chosen. In case discrete source analysis was computed previously, the selected source can be chosen as the reference for DICS. Please note that DICS can be re-computed with any cross-hair or source position at a later stage.

[[Image:SA 3Dimaging (1).jpg]]

''Fig. 2: Possible options for choosing the reference''

Confirming with “'''OK'''” will start computation of coherence between the selected channel/voxel and all other brain voxels. In case DICS is computed for a reference source in the brain, it can be advantageous to run a beamforming analysis in the selected time-frequency window first and use one of the beamforming maxima as reference for DICS. Fig. 3 shows an example for DICS calculation.

[[Image:SA 3Dimaging (22).gif]]

''Fig. 3: Coherence between left-hemispheric auditory areas and the selected voxel in the right auditory cortex.''

Coherence values range between -1 and 1. If coherence in the signal is much larger than coherence in the baseline (control condition) then the DICS value is going to approach 1. Contrary, if coherence in the baseline is much larger than coherence in the signal, then the DICS value is going to approach -1. At last, if coherence in the signal is equal to coherence in the baseline, then the DICS value is 0.

In case DICS is to be re-computed with a different reference, simply mark the desired reference position by placing the cross-hair in the anatomical view and select “DICS” in the middle panel of the source analysis window (see Fig. 4). In case an external reference is to be selected, click on “DICS” in the middle panel to bring up the DICS dialogue (see. Fig. 2) and select the desired channel. Please note that DICS computation will only be available after running time-frequency analysis.

[[Image:SA 3Dimaging (23).gif]]

''Fig. 4: Integration of DICS in the Source Analysis window''

<nowiki>--------------------------------------------------------------------------------</nowiki>

¹Here, the term connectivity is used rather than coherence, as strictly speaking the coherence equation is defined slightly differently. For simplicity reasons the rest of the tutorial uses the term coherence.

=== CLARA ===

CLARA ('Classical LORETA Analysis Recursively Applied') is an iterative application of weighted LORETA images with a reduced source space in each iteration.

In an initialization step, a LORETA image is calculated. Then in each iteration the following steps are performed:

# The obtained image is spatially smoothed (this step is left out in the first iteration).
# All grid points with amplitudes below a threshold of 1% of the maximum activity are set to zero, thus being effectively eliminated from the source space in the following step.
# The resulting image defines a spatial weighting term (for each voxel the corresponding image amplitude).
# A LORETA image is computed with an additional spatial weighting term for each voxel as computed in step 3.  By the default settings in BESA Research, the regularization values used in the iteration steps are slightly higher than that of the initialization LORETA image.

The procedure stops after 2 iterations, and the image computed in the last iteration is displayed. Please note that you can change all parameters by creating a user-defined volume image.

The advantage of CLARA over non-focusing distributed imaging methods is visualized by the figure below. Both images are computed from the N100 response in an auditory oddball experiment (file '''Oddball.fsg''' in subfolder ''fMRI+EEG-RT-Experiment'' of the ''Examples'' folder). The CLARA image (right) is much more focal than the sLORETA image, making it easier to determine the location of the image maxima.

'' sLORETA image''

[[Image:SA 3Dimaging (24).gif]]

''CLARA image''

[[Image:SA 3Dimaging (25).gif]]

'''Notes:'''

* Starting CLARA: CLARA can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to ''Chapter Regularization of distributed volume images'' for important information on regularization of distributed inverses.

=== LAURA ===

LAURA ("Local Auto Regressive Average") belongs to the distributed inverse method of the family of weighted minimum norm methods (R. Grave de Peralta Menendez 2001, BrainTopography 14(2), 131-137). LAURA uses a spatial weighting function that includes depth weighting and that term has the form of a local autoregressive function.

The source activity is estimated by applying the general formula for a weighted minimum norm:

[[Image:SA 3Dimaging (26).gif]]

Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings.''

In LAURA, V contains both a depth weighting term W and a representation of a local autoregressive function A. V is computed as:

[[Image:SA 3Dimaging (27).gif]]

Where

[[Image:SA 3Dimaging (28).gif]]

Here, "x" denotes the Kronecker product. I3 is the [3x3] identity matrix. W is an [sxs] diagonal matrix (with s the number of source locations on the grid), where each diagonal element is the inverse of the maximum singular value of the corresponding regional source's leadfields. The formula for the diagonal components Aii and the off-diagonal components Aik are as follows:

[[Image:SA 3Dimaging (29).gif]]

[[Image:SA 3Dimaging (30).gif]]

Here, Vi is the vicinity around grid point i that includes the 26 direct neighbors.

The LAURA image in BESA Research displays the norm of the 3 components of S at each location r. Using the menu function ''Image / Export Image As... ''you have the option to save this norm of S or alternatively all components separately to disk.

'''Notes:'''

* '''Grid spacing:''' Due to memory limitations, LAURA images require a grid spacing of 7 mm or more.
* '''Computation time:''' Computation speed during the first LAURA image calculation depends on the grid spacing (computation is faster with larger grid spacing). After the first computation of a LAURA image, a '''<nowiki>*.laura</nowiki>''' file is stored in the data folder, containing intermediate results of the LAURA inverse. This file is used during all subsequent LAURA image computations. Thereby, the time needed to obtain the image is substantially reduced.
* '''MEG:''' In the case of MEG data, an additional constraint is implemented in the LAURA algorithm that prevents solutions from containing radial source currents (compare Pascual-Marqui, ISBET Newsletter 1995, 22-29). In MEG, an additional source space regularization is necessary in the inverse matrix operation required compute V
* '''Starting LAURA:''' LAURA can be started from the''' Image''' menu or from the '''Image Selection''' button.
* '''Regularization:''' Please refer to Chapter'' “Regularization of distributed volume images” ''for important information on regularization of distributed inverses.

=== LORETA ===

LORETA ("Low Resolution Electromagnetic Tomography") is a distributed inverse method of the family of ''weighted minimum norm'' methods. LORETA was suggested by R.D. Pascual-Marqui (International Journal of Psychophysiology. 1994, 18:49-65). LORETA is characterized by a smoothness constraint, represented by a discrete 3D Laplacian.

The source activity is estimated by applying the general formula for a weighted minimum norm:

[[Image:SA 3Dimaging (26).gif]]

Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings.''

In LORETA, V contains both a depth weighting term and a representation of the 3D Laplacian matrix. V is computed as:

[[Image:SA 3Dimaging (27).gif]]

Where

[[Image:SA 3Dimaging (28).gif]]

Here, "x" denotes the Kronecker product. I3 is the [3x3] identity matrix. W is an [sxs] diagonal matrix (with s the number of source locations on the grid), where each diagonal element is the inverse of the maximum singular value of the corresponding regional source's leadfields. A contains the 3D Laplacian and is computed as

[[Image:SA 3Dimaging (31).gif]]

with Is the [sxs] identity matrix, where s is the number of sources (= three times the number of grid points) and

[[Image:SA 3Dimaging (32).gif]]

Where

[[Image:SA 3Dimaging (33).gif]]

The LORETA image in BESA Research displays the norm of the 3 components of S at each location r. Using the menu function ''Image / Export Image As... ''you have the option to save this norm of S or alternatively all components separately to disk.

'''Notes:'''
* '''Grid spacing:''' Due to memory limitations, LORETA images require a grid spacing of 5 mm or more.
* '''Computation time:''' Computation speed during the first LORETA image calculation depends on the grid spacing (computation is faster with larger grid spacing). After the first computation of a LORETA image, a '''<nowiki>*.loreta</nowiki>''' file is stored in the data folder, containing intermediate results of the LORETA inverse. This file is used during all subsequent LORETA image computations. Thereby, the time needed to obtain the image is substantially reduced.
* '''MEG''': In the case of MEG data, an additional constraint is implemented in the LORETA algorithm that prevents solutions from containing radial source currents (Pascual-Marqui, ISBET Newsletter 1995, 22-29). In MEG, an additional source space regularization is necessary in the inverse matrix operation required compute V.
* '''Starting LORETA:''' LORETA can be started from the''' Image''' menu or from the '''Image Selection '''button.
* '''Regularization:''' Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed source models.

=== sLORETA ===

This distributed inverse method consists of a ''standardized, unweighted minimum norm''. The method was originally suggested by R.D. Pascual-Marqui (Methods & Findings in Experimental & Clinical Pharmacology 2002, 24D:5-12) Starting point is an unweighted minimum norm computation:

[[Image:SA 3Dimaging (34).gif]]

Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings''.

This minimum norm estimate is now standardized to produce the sLORETA activity at a certain brain location r:

[[Image:SA 3Dimaging (35).gif]]

SsMN,r is the [3x1] (MEG: [2x1]) minimum norm estimate of the 3 (MEG: 2) dipoles at location r. Rrr is the [3x3] (MEG: [2x2]) diagonal block of the resolution matrix R that corresponds to the source components at the target location r. The resolution matrix is defined as:

[[Image:SA 3Dimaging (36).gif]]

The sLORETA image in BESA Research displays the norm of SsLORETA, r at each location r. Using the menu function ''Image / Export Image As...'' you have the option to save this norm of SsLORETA, r or alternatively all components separately to disk.

'''Notes:'''

* sLORETA can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed inverses.

=== swLORETA ===

This distributed inverse method is a ''standardized, depth-weighted minimum norm'' (E. Palmero-Soler et al 2007 Phys. Med. Biol. 52 1783-1800). It differs from sLORETA only by an additional depth weighting.

Starting point is a depth-weighted minimum norm computation:

[[Image:SA 3Dimaging (37).gif]]

Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings''.

V is the diagonal depth weighting matrix. For s grid locations, V is of dimension [3s x 3s] (MEG: [2s x 2s]). Each diagonal element of V is the inverse of the first singular value of the leadfield of the corresponding regional source. Hence, the first 3 (MEG: 2) diagonal elements equal the inverse of the largest eigenvalue of the leadfield matrix of regional source 1, and so on.

This minimum norm estimate is now standardized to produce the swLORETA activity at a certain brain location r:

[[Image:SA 3Dimaging (38).gif]]

SsMN,r is the [3x1] (MEG: [2x1]) depth-weighted minimum norm estimate of the regional source at location r. Rrr is the [3x3] (MEG: [2x2]) diagonal block of the resolution matrix R that corresponds to the source components at the target location r. The resolution matrix is defined as:

[[Image:SA 3Dimaging (39).gif]]

The swLORETA image in BESA Research displays the norm of SswLORETA, r at each location r. Using the menu function ''Image / Export Image As...'' you have the option to save this norm of SswLORETA, r or alternatively all components separately to disk.

'''Notes:'''

* sLORETA can be started from the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed inverses.

=== sSLOFO ===

SSLOFO ('standardized shrinking LORETA-FOCUSS') is an iterative application of weighted distributed source images with a reduced source space in each iteration (H. Liu et al. 2005, IEEE Transactions on Biomedical Engineering 52(10), 1681-1691).

In an initialization step, an sLORETA image is calculated. Then in each iteration the following steps are performed:

# A weighted minimum norm solution is computed according to the formula [[Image:SA 3Dimaging (40).gif]]. Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D is the data at the time point under consideration. V is a diagonal spatial weighting matrix that is computed in the previous iteration step. In the first iteration, the elements of V contain the magnitudes of the initially computed LORETA image.  
# Standardization of this weighted minimum norm image is performed with the resolution matrix as in sLORETA.
# The obtained standardized weighted minimum norm image is being smoothed to get Ssmooth.
# All voxels with amplitudes below a threshold of 1% of the maximum activity get a weight of zero in the next iteration step, thus being effectively eliminated from the source space in the next iteration step.
# For all other voxels, compute the elements of the spatial weighting matrix V to be used in the next iteration as follows:

[[Image:SA 3Dimaging (41).gif]]

The procedure stops after 3 iterations. Please note that you can change all parameters by creating a user-defined volume image.

'''Notes:'''
* '''Starting sSLOFO''': sSLOFO can be started from the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed inverses.

=== User-Defined Volume Image ===

In addition to the predefined 3D imaging methods in BESA Research, it is possible to create user-defined imaging methods based on the general formula for distributed inverses:

[[Image:SA 3Dimaging (26).gif ‎ ]]

Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. Custom-defined parameters are:* The spatial weighting matrix V: This may include depth weighting, image weighting, or cross-voxel weighting with a 3D Laplacian (as in LORETA) or an autoregressive function (as in LAURA).
* Regularization: The term in parentheses is generally regularized. Note that regularization has a strong effect on the obtained results. Please refer to chapter “''Regularization of Distributed Volume Images” ''for more information.
* Standardization: Optionally, the result of the distributed inverse can be standardized with the resolution matrix (as in sLORETA).
* Iterations: Inverse computations can be applied iteratively. Each iteration is weighted with the image obtained in the previous iteration.

All parameters for the user-defined volume image are specified in the User-Defined Volume Tab of the Image Settings dialog box. Please refer to chapter “''User-Defined Volume Tab”'' for details.

'''Notes:'''
* Starting the user-defined volume image: the image calculation can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed inverses.

=== Regularization of distributed volume images ===

Distributed source images require the inversion of a term of the form L V LT. This term is generally regularized before its inversion. In BESA Research, selection can be made between two different regularization approaches (parameters are defined in the ''Image Settings dialog box''):

* '''Tikhonov regularization''': In Tikhonov regularization, the term L V LT is inverted as (L V LT +λ I)-1. Here, l is the regularization constant, and I is the identity matrix.
* One way of determining the optimum regularization constant is by minimizing the ''generalized cross'' ''validation error'' (CVE).
* Alternatively, the regularization constant can be specified manually as a percentage of the trace of the matrix L V LT.
* '''TSVD''': In the truncated singular value decomposition (TSVD) approach, an SVD decomposition of L V LT is computed as  L V LT = U S UT, where the diagonal matrix S contains the singular values. All singular values smaller than the specified percentage of the maximum singular values are set to zero. The inverse is computed as U S-1 UT, where the diagonal elements of S-1 are the inverse of the corresponding non-zero diagonal elements of S.

Regularization has a critical effect on the obtained distributed source images. The results may differ completely with different choices of the regularization parameter (see examples below). Therefore, it is important to evaluate the generated image critically with respect to the regularization constant, and to keep in mind the uncertainties resulting from this fact when interpreting the results. The default setting in BESA Research is a TSVD regularization with a 0.03% threshold. However, this value might need to be adjusted to the specific data set at hand.

The following example illustrates the influence of the regularization parameter on the obtained images. The data used here is condition '''St-Cor of dataset Examples \ TFC-Error-Related-Negativity''' '''\ Correct+Error.fsg''' at 176ms following the visual stimulus. Discrete dipole analysis reveals the main activity in the left and right lateral visual cortex at this latency.

[[Image:SA 3Dimaging (42).gif ‎ ]]

''Discrete source model at 176ms: Main activity in the left and right lateral visual cortex, no visual midline activity.''

LORETA images computed at this latency depend critically on the choice of the regularization constant. The following 3D images are created with TSVD regularization with SVD cutoffs of 0.1%, 0.005%, and 0.0001%, respectively. The volume grid size was 9mm. The example demonstrates the dramatic effect of regularization and demonstrates the typical tradeoff between too strong regularization (leading to too smeared 3D images that tend to show blurred maxima) and too small regularization (resulting in too superficial 3D images with multiple maxima).

[[Image:SA 3Dimaging (43).gif ‎ ]] ''SVD cutoff 0.1%: Regularization too strong. No separation between sources, mislocalization towards the middle of the brain.''

[[Image:SA 3Dimaging (44).gif ‎ ]] ''SVD cutoff 0.005%: Appropriate regularization. Separation of the bilateral activities. Location in agreement with the discrete multiple source model.''

[[Image:SA 3Dimaging (45).gif ‎ ]]. ''SVD cutoff 0.0001%: Too small regularization. Mislocalization, too superficial 3D image''

The automatic determination of the regularization constant using the CVE approach does not necessarily result in the optimum regularization parameter either. In this example, the unscaled CVE approach rather resembles the TSVD image with a cutoff of 0.0001%, i.e. regularization is too small. Therefore, it is advisable to compare different settings of the regularization parameter and make the final choice based on the above-mentioned considerations.

=== Cortical LORETA ===

Cortical LORETA is principally the same technique as LORETA, however, Cortical LORETA is not computed in a 3D volume, but on the cortical surface.

The cortical reconstruction in BESA Research fed from BESA MRI is a closed 2D surface with no boundaries and a very close approximation of the actual cortical form. It consists of an irregular triangulated grid.

The Laplace operator that is used for identifying a smooth solution in a three-dimensional space is exchanged with a Laplace operator that runs on the two-dimensional cortical surface.

There is a wide variety of 2D Laplace operators with different characteristics.

The general form of the discrete Laplace operator is

[[Image:SA 3Dimaging (2).jpg ‎ ]]

where '''pi''' is the '''i-th''' node of the triangular mesh, '''f(pi) '''is the value of a function f defined on the cortical mesh at the node '''pi''', '''wij''' is the weight for the connection between the nodes '''pi''' and '''pj''' and '''di''' is a normalization factor for the '''i-th''' row of the operator. Furthermore, '''N(i)''' is the set of indices corresponding to the direct (also called "1-ring") neighbors of '''pi'''.

BESA offers the choice of three Laplace operators with slightly different characteristics.

* '''Unweighted Graph Laplacian''': This is the simplest operator. It takes into account only the adjacency of the nodes and not the geometry of the mesh:

[[Image:SA 3Dimaging (3).jpg ‎ ]]

[[Image:SA 3Dimaging (4).jpg ‎]]

* '''Weighted Graph Laplacian:''' This operator is similar to the unweighted graph Laplacian but with different weights for the different connections. The connections between nearby nodes get larger weights than the connections between farther nodes:

[[Image:SA 3Dimaging (5).jpg ‎]]

<div style="margin-left:0cm;margin-right:0cm;">Where '''dist''' ('''pi''' , '''pj''') is the distance between the nodes '''pi '''and '''pj'''.</div>

[[Image:SA 3Dimaging (6).jpg ‎]]

* '''Geometric Laplacian with mixed area weights''': This operator takes into account the angles in the corresponding triangles into account as well as the area around the nodes in order to determine the connection weights:

[[Image:SA 3Dimaging (7).jpg ‎]]

<div style="margin-left:1.27cm;margin-right:0cm;">where '''αij''' and '''βij''' denote the two angles opposite to the edge ('''i , j''') and '''Amixed '''is either the Voronoi area, or 1/2 of the triangle area or 1/4 of the triangle area depending on the type of the triangle.</div>

[[Image:SA 3Dimaging (8).jpg ‎]]

'''Regularization and other parameters.'''

[[Image:SA 3Dimaging (46).gif ‎]]

'''SVD cutoff:''' The regularization for the inverse operator as a percent of the largest singular value.

'''Depth weighting:''' Turn depth weighting on or off.

'''Laplacian type:''' Selection of Laplacian operators (see above).

'''Notes:'''
* '''Starting Cortical LORETA''': Cortical LORETA can be started from the sub-menu '''Surface Image''' of the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images” ''for important information on regularization of distributed inverses.

=== Cortical CLARA ===

Cortical CLARA is principally the same technique as CLARA, but Cortical CLARA is not computed in a 3D volume, but on the cortical surface. Instead of using a LORETA image as the basis for the iterative application, cortical CLARA uses cortical LORETA.

'''Regularization and other parameters.'''

[[Image:SA 3Dimaging (47).gif]]

'''SVD cutoff:''' The regularization for the inverse operator as a percent of the largest singular value.

'''Depth weighting:''' Turn depth weighting on or off.

'''Laplacian type:''' Selection of Laplacian operators (see Cortical LORETA).

'''No of iterations''': Number of iterations for CLARA. The more iterations are used, the sparser becomes the solution.

'''Automatic''': The algorithm tries to determine the number of iterations automatically. The goodness of fit (GOF) is calculated after every iteration and if there is a big jump in the GOF then the algorithm will stop. If no jumps appear during the calculations then CLARA iterates until the specified number of iterations is reached.

'''Regularize iterations:''' If one wants to use different regularization for the CLARA iterations than the value specified as "SVD cutoff", this option should be selected.

'''Amount to clip from img (%):''' Cortical CLARA uses the solution from the previous iteration as an additional weighting matrix for the current iteration. That weighting matrix is constructed by cutting the "low" activity from the solution. This number specifies how much of the activity should be cut from the previous solution in order to construct the weighting matrix. This value is given as a percentage of the maximal activity. Default value is 10%.

'''Notes:'''
* '''Starting Cortical CLARA:''' Cortical CLARA can be started from the sub-menu '''Surface Image''' of the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed inverses.

=== Cortex Inflation ===

The inflated cortex (fig. 1) is a smoothened version of the individual cortical surface with minimal metric distortions (Fischl, B. et al. (1999). Cortical Surface-Based Analysis: II: Inflation, Flattening, and a Surface-Based Coordinate System. ''NeuroImage, ''9(2), 195–207).

Gyri and sulci are smoothened out. The original distances between each point on the cortex and its neighbors are, however, mostly preserved.

[[Image:SA 3Dimaging (48).gif]]

''Figure 1 Cortical LORETA map overlaid on top of the inflated cortical surface.''

A lighter gray color overlaid on top of the surface image indicates the location of a gyrus of the individual cortex surface, while a darker gray color indicates the location of a sulcus. The inflated cortical surface can be computed in BESA MRI 2.0. For more details please refer to the BESA MRI 2.0 help.

=== Surface Minimum Norm Image ===

'''Introduction'''

The minimum norm approach is a common method to estimate a distributed electrical current image in the brain at each time sample (Hämäläinen & Ilmoniemi 1984). The source activities of a large number of regional sources are computed. The sources are evenly distributed using 1500 standard locations 10% and 30% below the smoothed standard brain surface (when using the standard MRI) or using between 3000-4000 locations on the individual brain surface defined by the gray-white-matter boundary.

Since the number of sources is much larger than the number of sensors in a minimum norm solution, the inverse problem is highly underdetermined and must be stabilized by a mathematical constraint, the minimum norm. Out of the many current distributions that can account for the recorded sensor data, the solution with the minimum L2 norm, i.e. the minimum total power of the current distribution is displayed in BESA Research.

First, the forward solution (leadfield matrix L) of all sources is calculated in the current head model. Then, the source activities S(t) of all source components are computed from the data matrix D(t) using an inverse regularized by the estimated noise covariance matrix:

[[Image:SA 3Dimaging (49).gif]]

Here, L is the leadfield matrix of the distributed regional source model, CN denotes the noise correlation matrix in sensor space, and R is a weighting matrix in source space. R and CN can be designed in different ways in order to optimize the minimum norm result. The total activity of each regional source is computed as the root mean square of the source activities S(t) of its 3 (MEG:2) components. This total source activity is transformed to a color-coded image of the brain surface. (When the standard brain is used, two sources are assigned to each surface location, located 10% and 30% below the surface, respectively. The color that is displayed on the standard brain surface is the larger of the two corresponding source activities.)

'''Weighting options'''

The minimum norm current imaging techniques of BESA Research provide different weighting strategies. Two weighting approaches are available: Depth weighting and spatio-temporal approaches.
* '''Depth weighting:''' Without depth weighting, deep sources appear very smeared in a minimum-norm reconstruction. With depth weighting, both deep and superficial sources produce a similar, more focal result. If this weighting method is selected, the leadfield of each regional source is scaled with the largest singular value of the SVD (singular value decomposition) of the source's leadfield.
* '''Spatio-temporal weighting''': Spatio-temporal weighting tries to assign large weight to sources that are assumed to be more likely to contribute to the recorded data.

* <div style="margin-left:1.9cm;margin-right:0cm;">'''Subspace correlation after single source scan''': This method divides the signal into a signal and a noise subspace. The correlation of the leadfield of a regional source i with the signal subspace (pi) is computed to find out if the source location contributes to the measured data. The weighting matrix R becomes a diagonal matrix. Each of the three (MEG: 2) components of a regional source get the same weighting value pi2. This approach is based on the signal subspace correlation measure introduced by J.C. Mosher, R. M. Leahy (Recursive MUSIC: A Framework for EEG and MEG Source Localization, IEEE Trans. On Biomed. Eng. Vol. 45, No. 11, November 1998)</div>
* <div style="margin-left:1.9cm;margin-right:0cm;">'''Dale & Sereno 1993:''' In the approach of Dale and Sereno (J Cogn Neurosci, 1993, 5: 162-176) a signal subspace needs not be defined. The correlation pi of the leadfield of regional source i with the inverse of the data covariance matrix is computed along with the largest singular value λmax of the data covariance matrix. The weighting matrix R is a diagonal matrix with weights:</div>

<div style="margin-left:1.905cm;margin-right:0cm;">[[Image:SA 3Dimaging (50).gif]]Each of the three (MEG: 2) components of a regional source receives the same weighting value.</div>

'''Noise regularization'''

Two methods to estimate the channel noise correlation matrix CN are provided by the program:
* '''Use baseline:''' Select this option to estimate the noise from the user-definable baseline. The signal is computed from the data at non-baseline latencies.
* '''Use 15% lowest values:''' The baseline activity is computed from the data at those 15% of all displayed latencies that have the lowest global field power. The signal is computed from all displayed latencies.

In each case, the activity (noise or signal, respectively) is defined as root-mean-square across all respective latencies for each channel.

The noise covariance matrix CN is constructed as a diagonal matrix. The entries in the main diagonal are proportional to the noise activity of the individual channels (if selected) or are all equally proportional to the average noise activity over all channels. The noise covariance matrix CN is then scaled such that the ratio of the Frobenius norms of the weighted leadfield projector matrix (LRLT) and the noise covariance matrix CN equals the Signal-to-Noise ratio. This scaling can be multiplied by an additional factor (default=1) to sharpen (<1) or smoothen (>1) the minimum norm image.

'''Applying the Minimum Norm Image'''

The minimum-norm algorithm is started via the ''Surface minimum norm image dialog box'', which is opened from the''' Image''' menu, or by typing the shortcut '''Ctrl-M''': Please refer to Chapter ''“Surface'' ''Minimum Norm Tab”'' for more details.

As opposed to the other 3D images available from the '''Image '''menu, the surface minimum norm image is not computed on a volumetric grid, but rather for locations on the brain surface. Accordingly, the results of the minimum norm image are displayed superimposed to the brain surface mesh rather than to the volumetric MR image.

The figure below shows a minimum norm image computed from the file '''Examples\Epilepsy\Spikes\Spikes-Child4_EEG+MEG_averaged.fsg'''. The EEG spike peak was imaged using the individual brain surface of the subject. A baseline from -300 to -70 ms was used. Minimum norm was computed with depth weighting, Spatio-temporal weighting according to Dale & Sereno 1993 and individual noise weighting with a noise scale factor of 0.01. The minimum norm image reveals the location of the spike generator in the close vicinity of the frontal left-hemispheric lesion in this subject.

[[Image:SA 3Dimaging (51).gif]]

=== Multiple Source Probe Scan (MSPS) ===

'''Introduction'''

The MSPS function provides a tool for the validation of a given solution. It is based on the following theoretical consideration: If the recorded EEG/MEG data has been modeled adequately, i.e. all active brain regions are represented by a source in the current solution, then any additional probe source added to the solution will not show any activity apart from noise. The only exception occurs if this probe source is placed in close vicinity to one of the sources in the current solution. In that case, the solution's source and the probe source will share the activity of the corresponding brain area. The MSPS applies these considerations by scanning the brain on a pre-defined grid with a regional probe added to the current solution. Grid extent and density can be specified in the Image settings. The power P of the probe source at location r in the signal interval is compared with the power of the probe source in a reference interval, defining a value q:

[[Image:SA 3Dimaging (52).gif]]

MSPS can be computed on time domain or time-frequency domain data:
* In the time domain, q(r) is computed from the source waveform of the probe source. Here, P(r) is the mean power of the probe source at location r in the marked latency range, and Pref(r) is the mean probe source power in the user-definable baseline interval.
* In the time-frequency domain, an MSPS image can be computed from the complex cross spectral density matrices. By applying the inverse operator for a source configuration consisting of the current solution and the probe source, the power of the probe source can be computed for the target interval [P(r)] and the reference time-frequency interval [Pref(r)]. In the resulting MSPS image, q-values are shown in %, where q[%] = q*100.

The inverse operator used to determine the probe source power uses different regularization constants for the probe source and the sources in the current solution. The regularization constant of the sources in the current solution can be specified in the Image settings (default 4%). The regularization constant of the probe source is internally set to 0%.

Alternatively to the definition above, q can also be displayed in units of dB:

[[Image:SA 3Dimaging (4).gif]]

Values of q smaller than zero are not shown in the MSPS image.

According to the considerations above, an MSPS of a correct source model should optimally yield image maxima around the sources in the current solution only. If the MSPS image is blurred or shows maxima at locations different from the modeled sources, this indicates a non-sufficient or incorrect solution.

'''Applying the MSPS'''

This chapter illustrates the application of the Multiple Source Probe Scan. The figures are generated with data from file '''Examples/Epilepsy/Spikes/Rolandic-Spike-Child.fsg''' (-300 : +200 ms, filtered from 3 Hz [forward] to 40 Hz [zero-phase]).

'''Time domain versus time-frequency domain MSPS'''

The multiple source probe scan can be computed in the time domain or the time-frequency domain. The latter is possible only when time-frequency domain data is available for the current condition, i.e. if the condition has been created by starting a multiple source beamformer (MSBF) computation from the source coherence window. In this case, evoking the MSPS calculation from the '''Imaging '''button or from the '''Image''' menu will bring up the following dialog window that allows to choose between time- or time-frequency MSPS. If only time domain data is available, this dialog window will not appear and MSPS will be computed in the time domain.

[[Image:SA 3Dimaging (53).gif]]

For a time-frequency domain MSPS, the target and the reference time-frequency interval have been specified already in the Time-Frequency window (see Chapter "''How To Create Beamformer Images''"). For a time-domain MSPS, the target and the reference epoch have to be specified in the Source Analysis window as described below.

'''Time domain MSPS'''

The time-domain MSPS image displays the ratio of the power of a regional probe source in the signal and the baseline interval. The currently set baseline is indicated by a horizontal line in the upper left corner of the channel box.

[[Image:SA 3Dimaging (54).gif]]

''The black horizontal bar in the upper part of the channel box (here circled in red) indicates the baseline interval.''

By default, BESA Research defines the pre-stimulus interval of the current data segment as baseline. The baseline should represent a latency range in which no event-related activity is present in the data. There are several possibilities to modify the baseline interval: by clicking on the horizontal line with the left mouse button or by using the corresponding entry in the '''Condition '''menu or '''Fit Interval''' popup menu.

Mark an interval to define the target epoch, i.e. the time-interval for which the current solution is to be tested. Start the MSPS by selecting it from the '''Image selection '''button or from the '''Image''' menu to start the probe source scan. The''' Image '''menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window. The 3D window opens and displays the scan result.

[[Image:SA 3Dimaging (55).gif]]

''This figure shows the MSPS image applied on the three left-hemispheric sources in the solution ''''Rolandic-Spike-Child-RS2.bsa''''. The baseline is set from -300ms to -50 ms. The right-hemispheric sources have been switched off. The fit interval is set to the latency range of large overall activity in the data (-43 ms : 117 ms). A realistic FEM model appropriate for the subject's age (12 years, cr 50) is applied. The MSPS image does not show maxima at the modeled source locations and rather shows a spread q-value distribution.''

[[Image:SA 3Dimaging (56).gif]]

''The MSPS image for the same latency range when the right-hemispheric sources have been included. The MSPS image appears more focal and shows maxima around the modeled brain regions. This indicates the substantial improvement of the solution by adding the right-hemispheric sources that model the propagation of the epileptic spike from the left to the right hemisphere (note the radiological side convention in the 3D window).''

'''Time-Resolved MSPS'''

If the MSPS has been computed on time domain data, the image can be shown separately for each latency in the selected interval. After the MSPS has been computed for the marked epoch, double-click anywhere within this epoch to display the ratio of the probe source magnitude at the selected latency and the mean probe source magnitude in the baseline. Scanning the latency range by moving the cursor (e.g. with the left and right arrow cursor keys) provides a time-resolved MSPS image.

Time-resolved MSPS images are not available if the MSPS has been computed on data in the time-frequency domain.

[[Image:SA 3Dimaging (57).gif]]

''MSPS image of the spike peak activity at 0ms. The activity mainly occurs in the left hemisphere. This fact is illustrated by the source waveforms and confirmed in the MSPS image, which shows a focal maximum around the location of the red sources.''

[[Image:SA 3Dimaging (58).gif]]

''Around +27 ms, the spike has propagated to the right hemisphere. This becomes evident from the waveforms of the blue sources, which show a significant latency lag with respect to the first three sources, and from the MSPS image, which shows the maximum around blue sources at this latency.''

'''Notes:'''
* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image''' menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the''' Image''' menu.
* For scaling options, please refer to the '''scaling buttons''' popup menu [Link!].
* Parameters used for the MSPS calculations can be set in the ''General Settings tab'' of the ''Image Settings dialog box.''

=== Source Sensitivity ===

'''Introduction'''

The 'Source sensitivity' function displays the sensitivity of the selected source in the current source model to activity in other brain regions. Sensitivity is defined as the fraction of power at the scanned brain location that is mapped onto the selected source.

To compute the source sensitivity, unit brain activity is modeled at different locations (probe source) throughout the brain. To this data, the current source model is applied to compute the source waveforms SCM of all modeled sources:

SCM = LCM-1 * LPS   

Here LCM-1 is the regularized inverse operator for the current model and LPS is the leadfield of the regional probe source (dimension [Nx3] for EEG and [Nx2] for MEG, respectively, where N is the number of sensors). The source amplitude SSS of the selected source in the model is a 3x3 (MEG: 2x2) sub-matrix of SCM (if the selected source is a regional source) or a 1x3-matrix (MEG: 1x2) (if the selected source is a dipole). The root mean square of the singular values of SCM is defined as the source sensitivity.

The 3D source sensitivity image displays this value for all locations on a grid specified under '''Image/Settings'''. Grid density can be specified in the Image Settings.

'''Applying the Source Sensitivity Image'''

The Source Sensitivity image is evoked from the '''Image''' menu or by pressing the corresponding hot key (default: '''V''').

This function is enabled only when a solution with an active selected source is present in the Source Analysis window. The source sensitivity image then displays the sensitivity of the selected source to activity in other brain regions.

[[Image:SA 3Dimaging (59).gif]]

''Source Sensitivity image for the selected frontal source (green) in model ''''''High_Intensity_3RS.bsa'''''' in folder 'Examples/ERP_Auditory_Intensity'. The data displayed is the '100dB' condition in file ''''''All_Subjects_cc.fsg''''''. The selected source is sensitive to activity in the frontal brain region (yellow/white), while it is not influenced by activity in the vicinity of the left and right auditory cortex areas, which are modeled by the red and blue source in the model (transparent/gray).''

'''Notes:'''
* The sensitivity image is independent of the recorded sensor signals. It only depends on the current source model, the sensor configuration, the head model, and the regularization constant.
* If the regularization constant is set to zero, each source has a sensitivity of 100% to activity around its own location. With increasing regularization, the spatial filter becomes less focused, and the sensitivity of a source to activity at its location decreases.
* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image''' menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the '''Image''' menu.

{{BESAManualNav}}

Source Analysis Head Models

2017-04-07T13:08:47Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = 6.1 or higher
}}
== Head Models ==

BESA Research provides head models that are based either on multi-shell spherical head models, standardized realistic head models using finite elements (FEM), or individual realistic FEM models that were created in BESA MRI. Standard FEM models are currently only available for EEG.

It is highly recommended that you carefully read the specifications of the different head models below to understand what assumptions you are making in your data analysis when selecting a particular head model.

The ''Head Model'' chapter is subdivided into four sections:* '''Individual FEM model''': Realistic head model for EEG and MEG
* '''Standardized FEM model''': Realistic approximation for EEG
* '''Age-appropriate template models:''' Realistic head models from infancy to adulthood
* '''Spherical and Ellipsoidal Head Models for EEG'''
* '''Spherical Head Model for MEG'''

To select a different head model, use the ''Head Model Selection'' list in the ''parameter box''. If you right click onto the ''Head Model dropdown list in'' the ''parameter box'' or on the EEG/MEG button in the ''channel box'', a special '''Head Model Selection''' popup menu will appear.

=== Individual FEM Model ===

The head model is the link between the dipole sources and the EEG / MEG signals. It describes the electrical conductivity distribution inside of the head. By segmenting the different tissues having different conductivities based on the subject's MRI an individual head model can be constructed which takes into account anatomical differences between subjects. Using the finite element method (FEM) it is then possible to accurately simulate the EEG / MEG signal generated by a given source distribution.

By using an individual FEM model the inverse solution can become more precise (Vanrumste et al. 2002, Roth et al. 1993, Cuffin 1996, Haueisen 1997). This is especially true (a) for sources in brain regions that are not described well by a spherical head model (e.g. basal temporal lobe); (b) when individual heads show deviations from the norm (e.g. lesions). Thus, if the research target is to achieve maximal localization precision, an individual realistic head model is strongly recommended.

BESA MRI creates four-layer FEM models which differentiate between the tissues scalp, skull, cerebrospinal fluid (CSF), and brain, and which allow arbitrarily complex geometries. Default conductivity values of 0.33 S/m for scalp and brain tissue, 0.0042 S/m for skull tissue, and 1.79 S/m for CSF tissue are used. Different conductivity values can be chosen by the user when creating the models in BESA MRI.

In contrast to three-layer realistic head models, four-layer FEM models gain additional precision as the CSF layer is associated with yet another conductivity value than the other head tissues (Baumann et al. 1997). Neglecting CSF for EEG forward modeling can lead to larger localization errors (Ramon et al. 2003, Wendel et al. 2008, Lanfer et al. 2012).

The FEM modeling in BESA MRI was developed in cooperation with the research group around Dr. Carsten Wolters (Münster).

'''Using Individual FEM Models in BESA Research'''

Individual FEM models can be used in BESA Research after coregistration has been performed in BESA MRI. Detailed instructions on how to perform the coregistration can be found in the ''BESA help'' or in the quick guide which is available on the BESA homepage (www.besa.de/tutorials/quickguides).

In the coregistration process BESA MRI will generate a leadfield table, and a description of the source space. The leadfield table contains the simulated EEG potentials or MEG signals for sources in x-, y-, and z-direction distributed on a regular grid covering the entire source space. The source space specifies the locations where BESA Research is allowed to place dipole sources.

After successfully running the coregistration the coregistration dialog in BESA Research indicates that an individual FEM model is defined. The model can now be used in the Source Analysis module. To do so select the entry Individual FEM from the head model selection dropdown list. BESA Research will now load the leadfield table and the source space definitions. During dipole fitting BESA Research computes the EEG potentials or MEG signals for any given dipole source employing cubic Bezier-spline interpolation. This way, the individual FEM model can be used for the source analysis like any of the other head models.

'''References:'''

Baumann, S.B., D.R. Wozny, S.K. Kelly, and F.M. Meno. “The Electrical Conductivity of Human Cerebrospinal Fluid at Body Temperature.” IEEE Transactions on Biomedical Engineering 44, no. 3 (March 1997): 220–223. doi:10.1109/10.554770.

Cuffin, B. N. “EEG Localization Accuracy Improvements Using Realistically Shaped Head Models.” IEEE Transactions on Biomedical Engineering 43, no. 3 (March 1996): 299–303. doi:10.1109/10.486287.

Haueisen, J., C. Ramon, M. Eiselt, H. Brauer, and H. Nowak. “Influence of Tissue Resistivities on Neuromagnetic Fields and Electric Potentials Studied with a Finite Element Model of the Head.” Biomedical Engineering, IEEE Transactions on 44, no. 8 (1997): 727–35. doi:10.1109/10.605429.

Lanfer, B., I. Paul-Jordanov, M. Scherg, and C. H. Wolters. “Influence of Interior Cerebrospinal Fluid Compartments on EEG Source Analysis.” In Proceedings BMT 2012. Vol. 57. Jena: De Gruyter, 2012. doi:10.1515/bmt-2012-4020.

Ramon, Ceon, P. Schimpf, J. Haueisen, M. Holmes, and A. Ishimaru. “Role of Soft Bone, CSF and Gray Matter in EEG Simulations.” Brain Topography 16 (2003): 245–248. doi:10.1023/B:BRAT.0000032859.68959.76.

Roth, Bradley J., Marshall Balish, Alexander Gorbach, and Susumu Sato. “How Well Does a Three-sphere Model Predict Positions of Dipoles in a Realistically Shaped

Head?” Electroencephalography and Clinical Neurophysiology 87, no. 4 (October 1993): 175–184. doi:10.1016/0013-4694(93)90017-P.

Vanrumste, Bart, Gert Van Hoey, Rik Van de Walle, Michel R. P. D’Havé, Ignace A. Lemahieu, and Paul A. J. M. Boon. “Comparison of Performance of Spherical and Realistic Head Models in Dipole Localization from Noisy EEG.” Medical Engineering & Physics 24, no. 6 (July 2002): 403–418. doi:16/S1350-4533(02)00036-X.

Wendel, K, N G Narra, M Hannula, P Kauppinen, and J Malmivuo. “The Influence of CSF on EEG Sensitivity Distributions of Multilayered Head Models.” IEEE Transactions on Bio-Medical Engineering 55, no. 4 (April 2008): 1454–1456. doi:10.1109/TBME.2007.912427.

=== Standardized FEM Model: Realistic Approximation for EEG ===

The standardized FEM model has been created from an averaged head using 50 individual MRIs in Talairach space. The averaged head is used for the standard MRI displays and shows a smoothed brain. Major sulci can be identified. In the 3D mapping window, the averaged skin surface is used for the voltage and CSD maps and the smoothed averaged cortical surface is used for the surface image maps.

The standardized FEM model provides a realistic approximation to the averaged head in Talairach space and uses three compartments: brain/CSF, skull, scalp. The interfaces between the compartments brain, skull and scalp were segmented from the average MRI employing threshold segmentation, manual segmentation and smoothing steps. The skull thickness was modeled to be approximately half of the distance between the brain and the scalp surface, at maximum 6 mm.

It is a common feature to all realistic head models that little is known about the different brain tissues, their conductivities and anisotropies. Especially at the lower parts of the brain, it is extremely difficult to segment bone, CSF and cavities from structural MRI scans. Therefore, all so-called realistic head models

make simplifying assumptions on these tissues and round off and smooth their geometries. For numerical reasons, the BESA Research standardized FEM model does not explicitly model the CSF layer. However, the smoothing effect of the CSF layer is partly compensated for by assuming an anisotropic skull conductivity: The tangential conductivity within the skull is modeled to be 3 times larger than the radial conductivity across the skull.

Bone conductivities are age dependent, with children having higher bone conductivities as compared to adults. For that reason, BESA Research provides several standardized head models with different conductivity ratios (cr) of radial skull conductivity and brain conductivity. The adult FEM model with a cr of 80 produces comparable locations in depth to the 4-shell ellipsoidal model with default parameters. Precise conductivity values are generally not known. Rough estimates have been obtained by comparing the depth of sources in subjects of different age groups. For that purpose, in combined EEG/MEG recordings of SEP/SEFs and epileptic spikes, the dipole fit results to the EEG and the MEG data were compared and matched. This resulted in the approximate age recommendations given in the ''Head Model'' ''Selection list'' for the different FEM models:

{| style="border-spacing:0;width:4.992cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| '''Age'''
|| '''Recommended cr'''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
||
||
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| 3-4
|| 10
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| 4-6
|| 15
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| 6-8
|| 20
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| 8-10
|| 30
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| 10-12
|| 40
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| 12-14
|| 50
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| 14-16
|| 60
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| 16-20
|| 70
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| adult
|| 80 (default)
|-
|}

'''Practical implementation of the FEM model'''

When selecting a realistic approximation model from the ''Head Model Selection list'' or from the '''Head''' '''Model Selection''' popup menu, a precalculated leadfield table is loaded. Each table contains the forward solution for a standard set of electrode locations and orthogonal dipoles at fixed grid points in the brain. Different tables have been precalculated for the various conductivity ratios using the same standard MRI average of 50 subjects.  Individual realistic models will simply need separate tables and MRI volume and surface files.

The standardized FEM model currently uses 81 standard electrodes of the 10-10 electrode system. The locations of these electrodes have been obtained by projecting the default spherical coordinates of these electrodes (cf. Default.ecd) onto the averaged skin surface. These locations are very similar to the averaged locations obtained using the individual landmarks to construct the 10-10 electrode system on each individual MRI surface according to the distance rules. The center of the equivalent sphere is at Talairach location (0, -17.6, -1.0). It is located approximately 5 mm anterior to the posterior commissure.

The leadfield of a given dipole inside the head is computed by first interpolating the pre-calculated leadfields of the neighboring grid points using a second order Bezier interpolation. This leadfield, obtained for the 81 standard electrodes, is then interpolated to the actual electrode positions of the data set under analysis.

=== Age-appropriate template models: Realistic head models from infancy to adulthood ===

It is often not possible to record MRI images from all subjects, especially so if the subjects are children or infants. Therefore, BESA Research provides the possibility to use age-appropriate realistic templates for source analysis. The templates were derived by non-linear averaging across real brains in according age-ranges from infancy to adulthood.

Template brains used for age-appropriate models were kindly provided by John E. Richards, University of South Carolina, USA.

If you would like to publish results obtained with the use of the age-specific models, please reference the publications below:

* <div style="margin-left:2.529cm;margin-right:0cm;">Richards, J.E., & Xie, W. (2015). Brains for all the ages: Structural neurodevelopment in infants and children from a life-span perspective. In J. Bensen (Ed.), Advances in Child Development and Behavior (Vol 48, Chapter 1, pps 1-52)</div>
* <div style="margin-left:2.54cm;margin-right:0cm;">Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015). A database of age-appropriate average MRI templates. Neuroimage,doi:10.1016/j.neuroimage.2015.04.055. </div>

In detail, the template brains used are described in the following publications:

*0-4 years:

* NIH Pediatric MRI Database (NIHPD; Almli, C. R., Rivkin, M. J., & McKinstry, R. C. (2007). The NIH MRI study of normal brain development (objective-2): Newborns, infants, toddlers, and preschoolers. ''Neuroimage'', 35(1), 308-325)
* Sanchez, C.E., Richards, J.E., & Almli, C.R. (2011). Neurodevelopmental MRI brain templates for children from 2 weeks to 4 years of age, ''Developmental Psychobiology''
* Richards, J.E. (2009). Attention in the brain and early infancy. In S.P. Johnson (Ed.), ''Neoconstructism: The new science of cognitive development''
* Richards, J.E. (2010). What's inside a baby's head? Structural and functional brain development in infants. International Conference on Infant Studies, Baltimore, MD, March, 2010.
* Richards, J.E., & Xie, W. (2015). Brains for all the ages: Structural neurodevelopment in infants and children from a life-span perspective. In J. Bensen (Ed.), ''Advances in Child Development and Behavior'' (Vol 48, Chapter 1, pps 1-52).;
* Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015). A database of age-appropriate average MRI templates, ''Neuroimage'', doi:10.1016/j.neuroimage.2015.04.055
* Fillmore, P.T., Richards, J.E., Phillips-Meek, M.C., Cryer, A., & Stevens, M. (2015). Stereotaxic MRI brain atlases for infants from 3 to 12 months of age. ''Developmental Neuroscience'', doi:10.1156/000438749

* 6-18 years:

* NIHPD (Evans, A. C. (2006). The NIH MRI study of normal brain development. ''Neuroimage'', 30(1), 184-202.)
* Sanchez, C.E., Richards, J.E., & Almli, C.R. (2010). Age-specific MRI brain templates for healthy brain development from 4 to 24 years, Unpublished ms.
* Sanchez, C.E., Richards, J.E., & Almli, C.R. (2012). Age-specific MRI templates for pediatric neuroimaging. ''Developmental Neuropsychology'', 37, 379-399.
* Richards, J.E., & Xie, W. (2015). Brains for all the ages: Structural neurodevelopment in infants and children from a life-span perspective. In J. Bensen (Ed.), ''Advances in Child Development and Behavior'' (Vol 48, Chapter 1, pps 1-52)
* Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015). A database of age-appropriate average MRI templates. ''Neuroimage'', doi:10.1016/j.neuroimage.2015.04.055.

* 20-24 years:

* Sanchez, C.E., Richards, J.E., & Almli, C.R. (2012). Age-specific MRI templates for pediatric neuroimaging. ''Developmental Neuropsychology'', 37, 379-399. Fillmore, P.T., Phillips-Meek, M.C., and Richards, J.E. (2013), Age-specific MRI brain and head templates for healthy adults from 20 through 89 years of age. ''Frontiers in Aging Neuroscience.''6, doi: 10.3389/fnagi.2015.00044
* Richards, J.E., & Xie, W. (2015). Brains for all the ages: Structural neurodevelopment in infants and children from a life-span perspective. In J. Bensen (Ed.), ''Advances in Child Development and Behavior'' (Vol 48, Chapter 1, pps 1-52),
* Richards, J.E., Sanchez, C., Phillips-Meek, M., & Xie, W. (2015). A database of age-appropriate average MRI templates. ''Neuroimage'', doi:10.1016/j.neuroimage.2015.04.055.
* Work from the IXF and OASIS MRI projects

=== Spherical and Ellipsoidal Head Models for EEG ===

'''4 shell ellipsoidal'''

The basis of this model is the multi-shell spherical head model with the fast algorithm by P. Berg and M. Scherg (A fast method for forward computation of multiple-shell spherical head models. Electroenceph. clin. Neurophysiol., 1994: 90, 58-64). The 4 homogeneous shells are the brain, the CSF, the bone and the skin. You can modify the thicknesses of the shells and their conductivities in the parameter box. The center of the sphere is determined from the 3D electrode locations. If you use standard electrodes without 3D coordinates (see chapter [Special-Topics.chm::/Electrode_conventions.htm Electrodes].), the multi-shell model is spherical. If 3D electrode coordinates have been defined, the spherical shells are distorted into an ellipsoid that best fits the 3D electrode cloud. The transformation from spherical to ellipsoidal is achieved via a 3*3 distortion-rotation matrix calculated by a least squares fit of the true 3D electrodes with their projection onto the best fitting sphere. Bone thickness and conductivity is age dependent, with children having higher bone conductivities as compared to adults. Precise conductivity values are generally not known. Rough estimates have been obtained by comparing the depth of sources in subjects of different age groups. For that purpose, in combined EEG/MEG recordings of SEP/SEFs and epileptic spikes, the dipole fit results to the EEG and the MEG data were compared and matched. This resulted in the following recommendations for bone thickness and conductivity depending on the subject's age:

 

{| style="border-spacing:0;width:8.363cm;"
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| '''Age'''
|| '''Bone thickness'''
|| '''Bone Conductivity'''
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
||  
||  
||  
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 3
|| 4.7 mm
|| 0.040
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 4
|| 4.8 mm
|| 0.030
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 5
|| 4.9 mm
|| 0.022
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 6
|| 5.0 mm
|| 0.018
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 7
|| 5.2 mm
|| 0.016
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 8
|| 5.4 mm
|| 0.014
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 9-10
|| 5.7 mm
|| 0.012
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 11-12
|| 6.0 mm
|| 0.010
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 13-14
|| 6.3 mm
|| 0.008
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| 15-16
|| 6.7 mm
|| 0.006
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
|| adult
|| 7.0 mm (default)
|| 0.0042 (default)
|- style="border:none;padding-top:0.026cm;padding-bottom:0.026cm;padding-left:0.265cm;padding-right:0.265cm;"
||
||
||
|-
|}
'''3 shell Ary approximation'''

The forward solution is calculated using a homogeneous head model after transforming the eccentricity of the dipole according to a non-linear equation (Scherg 1990; Ary 1981). Essentially, this model uses the similarity of the voltage topography of a dipole within a homogeneous sphere at a deeper location (e.g.

60% eccentricity) with the topography of a dipole in a 3-shell spherical model at a shallower location (e.g. 84% eccentricity).

 

'''Homogenous sphere'''

This model uses a dipole in a sphere with homogeneous conductivity. The homogeneous model is most suitable for the calculation of epicortical potentials.

 

'''Polynomial 4 shells'''

This model employs the widely-used polynomial expansion to calculate an iterative forward model using multiple spherical shells. This model is much slower than the fast 4-shell ellipsoidal head model, but has been provided for the purpose of comparison.

=== Spherical Head Model for MEG ===

BESA Research currently uses the spherical head model by Sarvas (1987). If no coregistration with the individual MRI has been performed in BESA Research (i.e. no individual MRI has been specified, see chapter ''Integration with MRI and fMRI''), you can define the center for the sphere using the individual MRI by seeding a dipole at the assumed center using BrainVoyager. Then perform the '''Write Sphere Center''' '''File (*.cot)''' entry of the '''Head Box''' popup menu.  

For additional information please see the BrainVoyager help system at [http://www.brainvoyager.com www.brainvoyager.com].

[[Category:Research Manual]]

{{BESAManualNav}}

Source Analysis Functions of the Window

2017-04-07T13:07:53Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = 6.1 or higher
}}

== Functions of the Source Analysis Window ==

The Source Analysis module window is subdivided into six main parts (boxes) which will be explained briefly in the following sections:* The Channel Box (left)
* The Variance Box (top center)
* The Source Box (bottom center)
* The Parameter Box (top right)
* The Head Box (mid right)
* The 3D Window (bottom right)

Note that the 3D window will not normally appear automatically (unless specified in the '''Options/Preferences''' menu), and the head box will take up more space if the 3D window is not displayed.

[[Image:Functions SAwindow (1).gif ]]

''(Click on the region of interest to jump to the associated section. Use the Back button of the Windows® help to jump back to this page.)''

The '''title bar''' contains information about the data file, the filename, the condition name, the filter settings, and the selected time interval.

Most of the functions and commands can be chosen from the main '''menu bar''' below the title bar. However, all important commands are also available via a right mouse click. Whenever you right-click, a context-sensitive popup menu will appear containing the available commands.

A detailed description of the commands of the '''menu bar''' and the different popup menus is given in the online help ''Reference ''chapter.

At the bottom, you will notice the '''status bar''', which gives information about the current mouse position (latency or 3D position) and the current cursor location or the fit interval(s). (See the section on the '''status bar''' in the online help ''Reference ''chapter).

The individual size of the boxes can be modified: Try placing the mouse over the vertical double line that separates the source box and the head box. The horizontal arrow that appears indicates that you can move this separator by dragging with the left mouse button.

The same is possible for the horizontal double line bounding the variance box.

=== Channel Box ===

The channel box normally shows the signals at each channel. The display depends on the state of the push buttons at the top of the channel box.

The figure below shows an example with the display of the measured data waveforms (violet) and the residual waveforms (red) at each channel. The channel labels are displayed to the left of each waveform.

An overplot of all waveforms is displayed above the single waveforms (labeled ''All'').

[[Image:Functions SAwindow (2).gif]]

''(Click on the region of interest to view a description.)''

Below the first row of buttons, there is a '''description of the current condition''' containing the condition name, the filter settings and the condition epoch. Below the condition epoch, the baseline of the current condition is displayed as horizontal black line.

At the bottom, you see the''' figure legend '''describing the used colors and the number of displayed channels (or PCA components).

The '''Channel buttons''' at the top of the channels box specify which waveforms are displayed.

* The''' Data''' button toggles the display of the data (measured signals) of the visible channels (violet waveforms). If you double click on this button the''' Model '''and''' Residual''' buttons are released and the channels are re-sorted by the amplitude of the measured data.
* Press the '''Model''' button to toggle the display of the modeled data (blue waveforms). The modeled data are calculated from the waveforms of the active sources in the current solution using the currently chosen head model. (The source waveforms are displayed in the source box, the head model is set and displayed in the parameter box.) Pressing the '''Model '''button toggles between the display of all active sources (button is labeled '''M-A''') and the display of the model waveforms which result from the contributions of all sources whose Fit/No fit button is pressed (button is labeled M-F). Note that the '''Residual''' button is released if the '''Model''' button is pressed without holding the '''Control-key'''.
* Press the''' Residual''' button to toggle the residual (unexplained) signal (red waveforms), i.e. the difference between measured and modeled data. If you double click on this button the '''Data''' and '''Model''' buttons are released and the channels are re-sorted by the amplitude of the residual. Note that the''' Model''' button is released if the''' Residual''' button is pressed without holding the '''Control-key.'''
* The '''Sort''' button (fourth button from the left) changes the ordering of the channels. Pushing this button switches between original order (button is labeled '''Order''' or '''Ord'''.), sorting by the amplitude of the measured data (||Data|| or ||D||), and sorting by the amplitude of the residual (||Res.|| or ||R||). In practice, by using one of the sorting modes ||Data|| or ||Residual||, you will only have to display the first few channels during the fitting procedure, since the channels with the largest signals are shown at the top.
* Use the '''P.C.A.''' button to start a Principal Components Analysis (PCA) over the marked fit interval(s) (if no fit interval is set the PCA is computed over the whole epoch). The percentage variance accounted for by each component is shown at the left of each waveform. When the PCA is displayed, data, model, and residual waveforms are not visible. Note that if the '''Residual '''button is down and the '''Data''' button is up, the PCA is computed for the residual data and not the measured data.
* The button at the far right is the '''EEG/MEG''' button. Pushing this button toggles between the data sets (EEG and MEG) of the current condition, if combined EEG and MEG have been recorded. The label of the button shows which data set is currently displayed.

At the top left below the''' Data''' button, the '''Switch Condition''' buttons (labeled with two arrows) enable fast switching between different conditions. They are enabled only if at least two conditions have been loaded.

Below the '''Switch Condition''' buttons, the '''Toggle Electrode Configuration''' button toggles between using the original channels (button is labeled '''Org''') or using an interpolated montage of 81 electrodes at standard locations (button is labeled '''Std'''). This montage allows comparison of different subjects at standard electrode locations. Note: If MEG channels are displayed this button is not available.

The channel box is bounded at the right by three scroll bars. Use the topmost one to change the number of displayed channels. The scroll bar below ('''select displayed channels''') can be used to scroll through the channels. The bottom one, consisting only of two arrows, changes the amplitude scaling of the displayed signals ('''scale waveforms''').

The '''MAG '''and '''GRD''' buttons at the bottom of the channel box appear only if an MEG data set containing both magnetometer and gradiometer sensors is displayed. The buttons are used to toggle the display of the magnetometer and gradiometer channels.

In the figure above you see one '''fit interval''', shown in a darker color. The fit interval is used for fitting, computing the PCA, and more.

'''Using the Mouse'''

In the channel box, it is possible to set the cursor or a fit interval with the left mouse button. If you click on the text in the top left corner, you may change the condition name. By clicking on the baseline, a new baseline interval can be specified.

If you click the right mouse button somewhere in the channel box, the '''Channel Box''' popup menu appears with commands specific to this box.

=== Variance Box ===

The variance box shows the global field power (blue) and the residual variance (red) in logarithmic scaling, relative to the maximum global field power. The global field power is the sum of squares of the activity over all channels of the current data set, the residual variance is the sum of squares of the unexplained signal. Note that the global field power is scaled from bottom to top, whereas the residual variance is scaled from top to bottom. The corresponding waveform scales at the left of the variance box are given in percent.

[[Image:Functions SAwindow (3).gif]]

''(Click on the region of interest to view a description or jump to the associated chapter.)''

At the top left the '''residual variance''' (RV) over all samples inside the fit interval(s) is displayed (labeled ''R.V''.). Below, the minimum residual variance inside the fit intervals (labeled ''Best'') is shown. If no fit interval is selected, values for the whole epoch are given. If a cursor is set, the RV over the whole epoch and the value of the RV at the cursor sample are displayed (labeled ''Curs''.).

At the top right, second row, you see the current value of the '''regularization constant''', a parameter used to reduce the interaction between sources. (You can set the regularization constant with the '''Regularization''' '''Constant: X%''' menu entry in the '''Options''' menu or by clicking on the current value.)

The '''Fit Criterion''' buttons at the top of the variance box toggle the corresponding fit criteria on and off. Starting from the left the buttons represent the residual variance criterion, the energy criterion, the minimum distance criterion, and the residual variance - q value (S/N) criterion. You will find additional information in the section '''Fit Criterion''' Buttons in the online help ''Reference'' chapter.

'''Using the Mouse'''

In the variance box, it is possible to set the cursor or a fit interval with the left mouse button. If you click on the regularization constant (''RC''), you may set a new value.

If you click the right mouse button somewhere in the variance box, the '''Variance Box''' popup menu appears with commands specific to this box.

=== Source Box ===

The source box shows the source waveforms of the current solution. The source waveforms are computed over the whole epoch of the current data set using the currently chosen head model. (The head model is set and displayed in the parameter box.) If no solution is available the source box is empty.

A single dipole or a spatial component has one source waveform, a regional source has three waveforms for EEG and two for MEG (one waveform for each component). A spatial component is labeled SC just below its waveform.

[[Image:Functions SAwindow (4).gif]]

''(Click on the region of interest to view a description.)''

At the top of the source box you will find the following buttons:

* The '''All on''' button activates or deactivates all sources (switches all sources on or off). Spatial components whose principal vector does not match with the current data set cannot be activated.
* The '''All fit''' button enables all active sources (not spatial components) for fitting.
* The''' Start fit '''button fits the enabled sources within the specified fit interval(s). If no fit interval is set the sources the whole epoch is used for fitting, if a cursor is set they are fitted only at the cursor sample. Another way to start fitting is given by the ''Fit Enabled Sources''... entry in the standard popup menu.
* The '''Image selection''' button allows for a quick computation of a 3D image. The type of the image to be computed is shown in the button label. By default, this is the previously computed 3D image. For details on the available image types in BESA Research, please refer to chapter 3D imaging.
* The '''BrainVoyager '''button will start the BrainVoyager program. If the BrainVoyager path has not been set correctly the BrainVoyager tab of the ''Preferences ''dialog box is displayed to allow you to set the valid path. If the BrainVoyager program is already running the current solution is sent to BrainVoyager for display in the structural MRT image (c.f. ''Integration with MRI/fMRI'').

Each source waveform has two push buttons assigned to it:

* The '''On/Off''' buttons to the left of the source waveforms activate or deactivate the associated sources. Spatial components whose principal vector does not match with the current data set cannot be activated. If a source is inactive, it does not contribute to the model.
* The '''Fit/No fit '''buttons below the '''On/Off''' buttons enable or disable the associated source for fitting. If a source is selected, it is enabled for fitting automatically. On the other hand, a source is automatically selected if you push the corresponding '''Fit/No fit''' button. Note that spatial components have no '''Fit/No fit''' button since they cannot be enabled for fitting. You can enable several sources for fitting by keeping the '''Control-key''' on your keyboard pressed and pushing the '''Fit/No fit''' buttons of the sources you would like to fit simultaneously. If the model waveforms of fit enabled sources are displayed in the channel box (the '''Model''' button in the channel box shows ''M-F''), or if the model data of fit enabled sources are mapped in the 3D window, only sources whose '''Fit/No fit''' button is down are taken into account for the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map.
* The '''Map/No map''' buttons are visible only if the model waveforms of fit enabled sources are displayed in the channel box (the''' Model''' button in the channel box shows ''M-F'') or if the model data of fit enabled sources are mapped in the 3D window. They are available for spatial components only, since other sources use the '''Fit/No fit''' buttons to enable/disable the source for mapping or to display the model waveforms. Only spatial components whose '''Map/No map''' button is down are taken into account in the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map. You can enable several sources for mapping by keeping the '''Control-key''' on your keyboard pressed and pushing the '''Map/No map '''buttons (for spatial components) or '''Fit/No fit''' buttons (for other source types) of the sources you would like to contribute to the model waveforms or model map.

Use the '''Waveform Scale''' buttons (labeled with two arrows) at the bottom right of the source box to adjust the waveform amplitude scale. If you hold the '''Control-key''' in combination, the scale is reset to default.

'''Using the Mouse'''

Click on a source waveform if you want to select the associated source. The selected source is marked by a colored rectangle around its '''On/Off''' and '''Fit/No fit''' buttons.

If the current solution contains more than one sources you can change the source order by dragging the baseline of the source waveform up and down.

As in the Channel Box, you can set the cursor or a fit interval with the left mouse button.

You may double click on the '''source label''' to specify a new label.

If you click the right mouse button somewhere in the source box, the '''Source Box''' popup menu appears with commands specific to this box.

If you click the right mouse button on a source label or source number at the right-hand side of the source waveforms, the '''Source Label''' popup menu is displayed.

=== Parameter Box ===

The parameter box shows either the parameters of the current head model or of the selected source.

If no source is selected the parameter box looks like the figure below:

[[Image:Functions SAwindow (5).gif]]

''(Click on the region of interest to view a description.)''

The top row shows the currently selected head model. The default model for EEG is the 4-shell ellipsoidal model. Different EEG models can be selected using the ''Head Model Selection'' list.

For EEG, you can select a standardized Realistic Head Model Approximation based on finite elements (FEM) with different conductivity ratios of brain to skull and anisotropies. For a detailed description of the different head models see chapter ''Head Models''.

If the current channel type is MEG (as indicated by the '''EEG/MEG''' button in the '''channel box'''), the spherical MEG head model (Sarvas, 1987) and the individual FEM head model are available. Please note, that the individual FEM head model first has to be created in BESA MRI.

The '''head radius''' in millimeters which is used in the head models is given in the first text field labeled head. If the head radius is computed from the individual head it cannot be modified.

The '''head model parameters '''of the different head compartments are given in the text fields: The thicknesses of the scalp, of the bone, and of the cerebral spinal fluid (csf) are displayed in the second, third and fourth text fields of the upper row. The relative conductivities of brain, scalp, bone, and csf are displayed in the bottom row. Click onto the text fields to edit the current value.

If you click the right mouse button on a text filed while at least one head model parameter differs from its default value, the '''Head Model Text Field''' popup menu appears which allows to reset values to the default.

'''Note:''' The head model parameters are used in the ''4 shell ellipsoidal'' and ''Polynomial'' ''4 shells'' head models only.

If a source is selected, the parameter box looks like this:

[[Image:Functions SAwindow (6).gif]]

''(Click on the region of interest to view a description.)''

The coordinate system which is used to display or modify the source coordinates can be switched with the '''Coordinate System''' button at the top left. The following coordinate systems are available:
* ''(Cartesian) head coordinates'': Defined by three reference points on the head known as ''fiducials''. The unit is millimeter. The button is labeled '''Cart./HC'''.
* ''Talairach coordinates'':

<div style="margin-left:1.27cm;margin-right:0cm;">1) Talairach coordinates calculated using the individual MRI information of the current condition. The button is labeled '''Talairach'''. </div>

<div style="margin-left:1.27cm;margin-right:0cm;">2) Approximate ''Talairach coordinates'' estimated by a default transformation to the BESA Research standard brain that is used for the 3D anatomical view if an individual MRI is not available for the current condition. The button is labeled '''Tal.''' (''appr''.). For additional information, please see the chapter ''Integration with MRI and fMRI''),</div>

* (''Cartesian) unit sphere coordinates'' (BESA coordinates): Defined by the best fit sphere. The button is labeled '''Cart./US'''.
* ''Polar unit sphere coordinates'' (polar BESA coordinates): Same coordinate system as above, but the coordinates are given in'' polar coordinates''. The button is labeled '''Polar/US'''.

Note: A detailed description of the coordinate systems is given in the chapter ''Working with Electrodes'' ''and Surface Locations''.

To the left of the '''Coordinate System''' button the location and orientation coordinates of the selected source are given in the text fields labeled as follows:* '''x-loc''', '''y-loc''', and '''z-loc''': Location of the selected source in cartesian coordinates.
* '''x-ori''', '''y-ori''', and '''z-ori''': Orientation of the selected source in cartesian coordinates (the length of the vector specified by the three orientation coordinates is 1)
* '''ecc''', '''theta''', and '''phi''': Location of the selected source in polar coordinates (eccentricity, azimuth, and polar angle), visible only if polar coordinates are displayed.
* '''o-the''' and '''o-phi''': Orientation of the selected source in polar coordinates (azimuth and polar angle). These text fields are visible only if polar coordinates are displayed.

The second and third row shows the '''current location and orientation constraints''' for the selected source. Four states are possible:* '''Free:''' No constraint is set. The source location/orientation can be fitted.
* '''Fixed''': The source location/orientation is fixed during the next fit and will not be modified.
* '''Symmetric to''' (available for the source location only): The source location is set symmetric (mirrored into the other hemisphere) to the referenced source which is specified in the middle text field. The offsets to the symmetric location of the referenced source are given in the text field to the right.
* '''Bound to''' (available for the source location only): The source location is bound to the referenced source which is specified in the middle text field. The offsets to the location of the specified source are given in the text field to the right.

If you click onto the middle text field of the referenced source or the text field containing the location offset, the ''Set source constraint ''dialog box will open which allows to modify the referenced source and the location offset.

'''Using the Mouse'''

A left mouse click in the ''parameter ''box will toggle the display of the selected source parameters and the display of the head model parameters.

If you click the right mouse button somewhere in the parameter box, the '''Parameter Box''' popup menu appears with specific commands to this box.

Click on the '''source label''' to specify a new label.

=== Head Box ===

The Head Box shows six head schemes with the sources of the current solution. Each of the three standard views is displayed twice from opposite directions: First row sagittal view from left (left scheme) and from right (right scheme), second row transversal top view (left) and transversal view from bottom (right), and third row coronal view from behind (left) and frontal coronal view (right).

Note: If the ''3D window'' is open the appearance of the head box is different. Only two head schemes are displayed. You will find more information at the end of this page.

[[Image:Functions SAwindow (7).gif]]

''(Click on the region of interest to view a description.)''

A source is plotted in one view only if it is located in the forward hemisphere or slightly in the back hemisphere, so that, e.g. for the sagittal view (first row), a source is plotted only in the left head scheme if it is located in the left hemisphere, and not in the right top head scheme (in the figure below all sources except for the green one).

Note: You can specify the depth up to which sources are plotted in the back hemisphere (the so-called ''source transparency'') in the'' Boxes'' Tab of the ''Preferences ''dialog box.

If the cursor is set, the size of the source plot depends on the strength of the source (the amplitude of the source waveform) at the cursor.

The '''description and filename''' of the current solution is given at the top of the head box. If the solution has not been stored yet the text ''New solution...'' is displayed. If any modifications of the solution have not yet been saved, this is indicated by appending the text ''"modified"'' to the filename. Set a new description by clicking on the text with the left mouse button.

The '''Switch Solution''' buttons at the top left corner, marked with small arrows, allow to switch between solutions. They are enabled only if there are at least two solutions. If you right click on these buttons while they are enabled the '''Switch Solution '''popup menu opens which allows for changing to a specified solution.

The '''Hold''' button below the '''Switch Solution''' buttons becomes important if more than one condition has been uploaded or the condition has more than one data set. It toggles between two settings:
* '''Up:''' When the user switches between data sets or conditions, it will also be switched to the solution which was last modified when the new data set was active.
* '''Down:''' When the user switches between conditions, the current solution will not be changed.

Clicking on the ''''+' '''button at the top right creates a new solution and copies the current solution to the new one. If the solution which was copied already has a file path (i.e. has been loaded or saved before), the file path of the new solution is modified such that it does not specify an existing file.

The button is disabled if no solution is available.

Note: The entry ''New Copy of Displayed Solution'' in the '''Solution''' menu provides the same functionality.

The '''Source Plot Scale''' buttons at the bottom right of the head box are used to adjust the size of the source plots. Note that two different settings are stored: One for the source display if the cursor has been set, one for the display without cursor. If you hold the '''Control-key''' in combination, the scale is reset to default.

'''Using the Mouse'''

A double-click on one of the head schemes creates a new source at that location. The type of the new source can be specified using the menu entry '''Options/Default Source Type'''. A double click on an existing source deletes it.

If a source is under the mouse the mouse changes to [[Image:|top]]. A single click with the left button turns the source under the mouse into the selected source. A double click deletes the source.

If the source under the mouse can be moved the mouse changes to [[Image:|top]]. You can move the source by dragging with the left mouse button (spatial components may not be moved). The source location is bound to the limits which have been set in the ''Limit of source location section'' in the'' Preferences'' dialog box.

If the orientation of a source can be modified the mouse changes to [[Image:|top]]( single dipoles only). Drag the vertex of the orientation to rotate the dipole. Use the '''Shift-key''' in combination if you want to rotate the orientation in the specified view only.

Note: If you want to drag the orientation even if it is hidden use the '''Control-key''' in combination.

If you double click on the filename of the solution, which is given at the top of the head box, a text box is displayed in which you may enter a description. If a solution description has been set, it is displayed instead of the filename. This description will be stored when the solution is saved.

If you click the right mouse button somewhere in the head box, the '''Head Box''' popup menu appears with commands specific to this box.

'''Head box display if the 3D window is open'''

If the ''3D window'' is open the appearance of the head box is different. Only two head schemes are displayed.

[[Image:Functions SAwindow (11).gif]]

''(Click on the region of interest to view a description.)''

The '''Flip Head Scheme''' buttons (labeled '''Flp''') at the bottom right and left of the window flip the associated head scheme. E.g. clicking onto the left '''Flp''' button in this image would switch the sagittal view from the left to the sagittal view from the right.

Use the '''Shift Head Scheme''' buttons (second and third button to the left, marked with small arrows) to scroll the head schemes until you see your desired view.

The '''Transparency scroll bar '''in the mid bottom changes the source transparency. A source is plotted in one view only if it is located in the forward hemisphere or as far in the back hemisphere as set by the transparency value - the depth up to which sources are plotted in the back hemisphere. Please see additional information in the section ''Source Transparency'', (''Preferences'' dialog box), use the '''Back''' button

of the Windows® help to jump back to this page.

=== 3D Window ===

The 3D window is opened if a 3D map (fig. 1) or the anatomical view of an individual MRI or the BESA Research standard Brain (fig. 2) is displayed. It also opens if any of the 3D volume imaging or 3D surface imaging methods are used. (Use the popup menu entries '''Display MRI''' or '''Display 3D Maps'''.)

[[Image:Functions SAwindow (12).gif]]

[[Image:Functions SAwindow (13).gif]]

''(Click on the region of interest to view a description.)''

The sources of the current solution are displayed in the anatomical view (fig. 2), or in the cortical imaging view if this is activated via the popup menu using the right mouse button. The selected source is displayed with a golden halo around the source body.

The '''3D window toolbar''' is explained in details in the ''3D Window Toolbar'' section in the online help ''Reference'' chapter.

'''Using the Keyboard'''

A number of key combinations are useful for navigation/display in the 3D window if the 3D window is active (the title bar is blue). The most important commands with their default keys are listed here. Note that you can change the default keys in the ''Define hot keys'' dialog box, which also allows to specify additional key commands.

Command default key(s) and effects

* '''Decrement/Increment scale''' '''Num-, Num+:''' Decrements/Increments the map scale in the 3D map or the source plot size in the anatomical view.
* '''Move down/left/right/up''' '''Numpad-2, Numpad-4, Numpad-6, Numpad-8''': If a source is selected, the source is moved within the current slice in steps of one millimeter in the corresponding direction. If no source is selected, the slicing center is moved instead. This only applies to the anatomical view.
* '''Slice backwards/forward''' '''Down, Up''': If a source is selected the source is moved into the next slice, one millimeter out of or into the current anatomical view. If no source is selected the slicing center is sliced down or up instead. This only applies to the anatomical view.
* '''Switch to specific slice''' '''Shift-C, Shift-S, Shift-T''': Switches to the coronal, sagittal, or transversal slice (anatomical view only).
* '''Display 3D maps''' '''M''': Switches from the anatomical view to the 3D map. Works only if the cursor has been set.
* '''Display standard MRI''' '''A''': Switches from the 3D map to the anatomical view.

'''Using the Mouse'''

Whenever an action with the left mouse button is possible the mouse cursor will change from the standard arrow to a special icon. The following mouse actions are possible:

'''New source'''

A double click on a surface (skin or brain) or inside an anatomical view will insert a new source at the associated 3D location. The type of the new source can be specified using the menu entry '''Options/Default Source Type'''.

'''Delete source'''

A double click on an existing source will delete the source after a confirmation box is closed with ''Yes''.

[[Image:Functions SAwindow (14).gif]]'''Rotate'''

Dragging with the left mouse button will rotate the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Rotation Mode''' button of the '''3D window toolbar '''or the '''Shift-key''' have to be pressed.

[[Image:Functions SAwindow (15).gif]]'''Zoom'''

Dragging with the left mouse button will zoom the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Zoom Mode '''button of the '''3D window toolbar''' or the '''Shift-''' and '''Control-key''' have to be pressed.

[[Image:Functions SAwindow (16).gif]]'''Move'''

Dragging with the left mouse button will rotate the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Move Mode''' button of the''' 3D window toolbar '''or the '''Control-key''' have to be pressed.

[[Image:Functions SAwindow (17).gif]]'''Slice Vertically'''

Dragging with the left mouse button will slice the current slicing center up and down. This action is available on the anatomical view only. The '''Slice Mode '''button of the '''3D window toolbar''' or the '''Alternate-key''' have to be pressed in combination.

[[Image:Functions SAwindow (18).gif]]'''Slice Horizontally'''

Dragging with the left mouse button will slice the current slicing center horizontally. This action is available on the 2D anatomical views only. The '''Slice Mode '''button of the '''3D window toolbar''' or the '''Alternate-key''' must not be pressed.

[[Image:Functions SAwindow (19).gif]]'''Set Slicing Center to Source Location'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

This action is available on the anatomical view only if a source is under the mouse and this source must not be moved (e.g. a spatial component).

[[Image:Functions SAwindow (9).gif]]'''Move Source'''

A single click with the left mouse button will select the source under the mouse (if not already selected). A double click will delete the source.

Dragging with the left mouse button will move the source horizontally to the displayed slice.

This action is available only if a source is under the mouse, this source may be moved (no spatial component), and the '''Move Mode''' button of the '''3D window toolbar''' or the '''Control-key''' are pressed.

[[Image:Functions SAwindow (20).gif]]'''Move Source and Slice Horizontally'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

Dragging with the left mouse button will move the source horizontally to the displayed slice and set the current slicing center to the new source location.

This action is available only if a source is under the mouse, this source may be moved (no spatial component) and the '''Move Mode''' button, the '''Slice Mode '''button (of the '''3D window toolbar'''), the '''Control-''' and '''Alternate-key''' are not pressed.

[[Image:Functions SAwindow (21).gif]]'''Move Source and Slice Vertically'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

Dragging with the left mouse button will move the source vertically to the displayed slice and set the current slicing center to the new source location.

This action is available only if a source is under the mouse, this source may be moved (no spatial component) and the '''Slice Mode''' button of the '''3D window toolbar''' or the '''Alternate-key''' are pressed.

If you click the right mouse button somewhere in the 3D window, the '''3D Window''' popup menu appears with commands specific to this window.

{{BESAManualNav}}

Source Analysis Introduction

2017-04-07T13:07:22Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = 6.1 or higher
}}
= Source Analysis =

== Introduction ==

The Source Analysis module provides a highly interactive environment for analyzing the sources of electric or magnetic brain activity.

The following chapters will guide you through the most important features of the Source Analysis module in chronological order of data processing. For a thorough introduction to source analysis, we also recommend that you work through the tutorials that are available for download on our website.

The ''Reference'' chapter in our online help offers a detailed description of the available features. It is subdivided into the following sections: ''Menu Bar, Popup Menus, Special Controls, Dialog Boxes.''

== Starting the Source Analysis Module ==

Once you have opened a file for source analysis, you can decide which part of the averaged data will be analyzed. The BESA format for file segments (fsg-format) separates different averaged conditions by segment boundaries, as in the example file shown below.

[[Image:SA-Introduction (1).gif|top]]

To mark the entire condition on the left, simply click the right mouse button somewhere in the condition and select the popup menu entry '''Whole Segment'''.

To mark a part of the condition, create a block somewhere within the left condition by dragging with the left mouse button. Then press the right mouse button to obtain a popup menu containing the following entries:

[[Image:SA-Introduction (2).gif |top]]

Choosing ''Source Analysis'' opens the following dialog box:

[[Image:SA-Introduction (3).gif |top]]

* The left-hand '''Block Size and Position''' section controls the time interval which is sent to the Source Analysis module. The predefined setting is to make a custom definition of the block size. You can change the settings to mark the whole segment. If you choose ''Custom Definition'', the bottom part of the section becomes active, and you can enter the exact time range you wish to analyze. If you choose ''All Conditions'', all conditions in the current data set are sent to the Source Analysis module. [[Image:SA-Introduction (4).gif|top]]
* In the '''Filter Settings''' section, high frequency cutoff filters or low frequency cutoff filters can be quickly switched on and off using the'' Enabled'' tick mark. [[Image:SA-Introduction (4).gif|top]]
* The '''Source Analysis''' button applies the settings and immediately starts the Source Analysis module. [[Image:SA-Introduction (4).gif|top]]
* You can apply the settings to the data block using the '''Set Block''' button. [[Image:SA-Introduction (4).gif |top]]
* The''' Cancel''' button closes the dialog box without modifications. [[Image:SA-Introduction (4).gif|top]]
* If the option ''All Conditions'' is selected while the '''Source Analysis''' button is pressed, all conditions of the current data file (instead of only the selected c condition) are sent into the Source Analysis window simultaneously using the specified parameters.

'''Tip:'''

If you want to analyze a second data block with the same settings as before, mark an arbitrary block within the other data segment and click the right mouse button. The settings that you chose previously are displayed in the popup menu:

[[Image:SA-Introduction (5).gif |top]]

Selecting the entry at the bottom automatically reproduces the settings and starts the Source Analysis module with the specified data block.

{{BESAManualNav}}

BESA Research Batch Processing

2017-04-07T13:06:38Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
== Batch Processing and Combining Conditions ==

=== Combine Conditions and Batch Module: Introduction ===

Functions of this module are started by selecting the menu operations "'''ERP / Combine Conditions..."''' and '''"Process / Batch Scripts...".'''

* '''Combine Condition Scripts''' provides various operations on BESA averages.
* '''Batch Scripts''' provides batch operations on all data files.
* Note that a batch script can also be performed on the current file by selecting '''Process / Run''' '''Batch...''' or by typing the shortcut key '''"R'''".

=== File List Tab ===

Define a list of files on which the operations will be performed. The tab is the same for Combine Conditions Scripts and for Batch Scripts. Combine Conditions Scripts only allows you to open BESA average files (e.g. '''<nowiki>*.fsg</nowiki>''' and '''<nowiki>*.avr</nowiki>''', but also '''.mul''', '''.raw''', '''.swf''', and '''.foc''' if the files have a defined pre-stimulus interval), whereas Batch Scripts allows you to open any data file whose format is known to BESA Research.

When the Combine-Conditions or the Batch module is started, all currently opened (Combine-Conditions: averages only) files are displayed in the list.

To the right of each file name, the number of electrodes, total number of channels, and the sampling rate used in the file are displayed. In the Combine-Conditions module, the number of Epochs (segments) and the number of differently-named conditions are also shown.

'''Add files to the list'''

* Press the '''Add File '''button.
* Drag one or more files from Windows Explorer onto the window.

<div style="color:#00000a;"></div>

'''Remove files from the list'''

* Right click on the file name and confirm the delete operation in the resulting dialog.
* Mark one or more file names in the list (e.g. hold down the''' Ctrl''' key to mark multiple files). Right click to obtain the context menu and select "'''Delete'''", or just press the '''Del '''key.

<div style="color:#00000a;"></div>

'''Reorder files within the current file list'''

* Right click on the file name and select "'''''Move Up'''''" or "'''''Move Down'''''".
* Mark one or more file names in the list (e.g. hold down the '''Ctr'''l key to mark multiple files). Right click to obtain the context menu and select "'''''Move Up'''''" or "'''''Move Down'''''", or hold down the''' Ctrl''' key '''and '''press the '''Up''' and '''Down arrows'''.

<div style="color:#00000a;"></div>

'''Sort the current file list alphabetically'''

* Click on the File bar above the list

<div style="color:#00000a;"></div>

'''Save the current file list'''

* Press the '''Save File List''' button.

<div style="color:#00000a;"></div>

'''Load a file list'''

* Press the '''Load File List''' button, or the '''Load Previous''' button to load the most recently used file list.

<div style="color:#00000a;"></div>

'''Which conditions are read from a source file? (Combine-Conditions module only)'''

* Normally, all conditions are read from a source file. To exclude one or more segments from operations in the Combine Conditions module, mark the segments as artifacts in the main program display. It is sufficient for the beginning or the end of an artifact interval to be within the segment for the segment to be excluded.

<div style="color:#00000a;"></div>

'''File list from Combine Conditions:'''

[[Image:Batch processing (1).png]]

'''Don't try to open here... (Batch only)'''

By default, this checkbox is unchecked.

In the checked state, BESA Research doesn't check if it can open the file. Use this function '''only''' if the file is ASCII and you want to use the '''ImportASCII '''batch command.

'''File List from Batch Scripts''':

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Batch processing (2).png]]

=== Batch Processing ===

==== Batch Processing Scripts ====

With Batch Scripts, you can define a set of operations (e.g. Artifact Scan, Average) and apply these to several data files.

These operations include

* Load Paradigm
* Artifact Scan
* Average
* Export (and Merge)
* File Open (switch to another data file)
* Set filters
* Specify a montage (used, for example, for export to current montage)
* Run automatic eye and EKG artifact correction
* Turn artifact correction and view on and off
* Read and write events
* Edit default block epoch (for export around triggers)
* Edit triggers (for export around triggers)
* Mark a block for export, or send the block to Source Analysis or Top View
* Convert patterns to triggers
* Attach auxiliary files (e.g. elp, sfp) to the data file
* Send to MATLAB
* Specify display configurations for the BESA Research Main, SA, and Top View windows

<div style="color:#00000a;"></div>

An additional set of commands are available for operations in the '''Source Analysis Module''', allowing to load, create and fit dipole models, and save the results.

A further set of commands apply to '''Time-Frequency Analysis''', allowing to start TFC, change the display, save results, and run the beamformer or DICS analyses on a selected time-frequency range.

[[Image:Batch processing (3).png]]

These operations will be extended in future program releases.

The module includes two tabbed windows:

* '''File List''': Define a list of files on which the operations will be performed.
* '''Batch''': Define or load '''batch commands'''. Run the batch.

==== Batch Tab ====

Load or define batch commands, and then apply them to the files in the File List.

<div style="color:#00000a;"></div>

[[Image:Batch processing (4).png]]

'''Add Command'''

* Press '''Add Command''' to add a new command to the batch. The following dialog is opened, showing the available commands:

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

[[Image:Batch processing (3).png]]

* Select the desired command and press''' OK '''or double-click on the command. A dialog box is opened, allowing to specify individual command parameters.
* If you click on "Apply at beginning of batch" or "Apply at end of batch", the command will only be run at the beginning or the end of a batch. You can use this, for example, at the end of a batch to start a Matlab script to perform statistics on the results of the batch.

'''Load and Save Batch'''

* Press '''Load Batch''' to load a previously defined batch or '''Save Batch''' to save the current batch to a file ('''<nowiki>*.bbat</nowiki>''').

'''Load Previous'''

* Press '''Load Previous''' to load the most recently used batch file. Whenever a batch is run, the current set of commands is written to the file '''Previous.bbat in''' the '''Scripts/Batch''' subdirectory. This file is loaded when you press '''Load Previous'''.

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

'''Clear All'''

* Clears all commands from the window.

'''View Log File'''

* Each time a batch is run, BESA Research adds information about the batch to a log file, with headings showing the date and time the batch was started. The file is opened automatically in Internet Explorer if errors occurred during processing. Otherwise you may open the file by pressing the '''View Log File''' button here or in the dialog that is displayed at the end of batch processing. 
* The log file is saved in xml format, and a JavaScript is used to format the display in Internet Explorer or Netscape family browsers. JavaScript should be enabled in the browser to obtain an optimal display of the results. If JavaScript is enabled, the log file is displayed as a list of headings for each batch. Click on a heading to display the results of the corresponding batch.
* To open the log file in NotePad, hold the''' Shift '''key down when pressing the '''View Log File''' button.

<div style="color:#00000a;"></div>

'''Batch Command List'''
* Double-click on a command to edit it. See chapter “''Batch Commands”'' for descriptions of the dialogs that are opened to edit each command.
* Right click on a command to open a context menu allowing more options.

[[Image:Batch processing (5).png]]

* '''Delete''', '''Move Up''', '''and Move Down''' can also be applied to multiple selections.
* If you have made a multiple selection, the '''Del '''button will delete all the marked commands. '''Ctrl '''plus '''Up''' or '''Down''' '''cursor keys''' will move the marked commands up or down.
* '''Toggle Comment''' will add or remove a semicolon (;) in front of the command, to deactivate or reactivate the command.
* '''Toggle Command Only at Start/End''' will add or remove the text "Start_" or "End_" in front of the command. With these prefixes, the command will only be performed when the first file ("Start_") or the last file ("End_") in the file list is being processed.

<div style="color:#00000a;"></div>

'''Single Step Mode'''

* Check this item to step through the batch, one command at a time. A dialog is opened after each command, allowing to run the next command, continue the batch without single steps, or stop running the batch. See the'' “Pause''” command for further details.
* During a batch, press and hold down the '''Pause''' or '''Delete''' key to interrupt the batch and enter Single Step Mode. Press and hold down the '''Esc''' key to cancel the batch.

<div style="color:#00000a;"></div>

'''Changes in batch written to database'''

* Checked by default. If this item is unchecked, file display settings, such as Montage setting and Artifact correction display, are not written to the database. When the file is next opened in BESA Research, the settings made in the batch are not retained.

<div style="color:#00000a;"></div>

'''Leave files in the file list open after running the batch'''

* If this item is checked, files in the file list will remain open after the batch. This is useful, for instance, if you want to open a set of files, specifying the same montage and/or filter settings for each file.

<div style="color:#00000a;"></div>

Press '''OK''' to start running the batch. Each command is then applied in succession to each file in the 

File List.

Note that, while a batch is running press and hold down the''' Pause''' or '''Delete''' key to interrupt the batch and enter Single Step Mode. Press and hold down the '''Esc''' key to cancel the batch.

==== The log file ====

A protocol of each batch is written to the log file '''Scripts/Log/Batch.xml.'''

When you press the '''View Log File '''button, the file is opened in your default browser for xml files. The file will be opened automatically if there was an error during batch processing, unless you have used the ''BatchError'' batch command to suppress this behavior.

'''DHTML formatting of the log file'''

The xml file is formatted using JavaScript (Dynamic HTML). If JavaScript is enabled in your browser, you will first see a list of batch protocol titles, labeled by the date and time at which the batch was started. The most recent batch is at the top of the list.:

[[Image:Batch processing (6).png]]

Click on the title to view the protocol for the corresponding batch:

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Batch processing (7).png]]

'''JavaScript and XP Service Pack 2'''

By default, if the log file is opened in Internet Explorer after XP Service Pack 2 has been installed, IE will warn you with the message: "''To help protect your security, Internet Explorer has restricted this file from'' ''showing active content that could access your computer".'' All the protocols in the log file are displayed. You may safely click on the options to allow active content in the log file, if you want to display the file as described above.

'''Backup of the log file'''

When the log file is written, a backup of the previous version is written to '''batch.xml.bak'''.

If the size of the log file exceeds 200 KB, it is renamed to '''batch.xml_date_time''' (e.g. '''Batch.xml_2004-10-08_10-53-32'''), and a new version of '''batch.xml''' is created.

==== Placeholders ====

A powerful feature of the batch commands is the ability to define file names and specify standard paths using placeholders. These are text strings enclosed by percentage (%) signs. They can be used in all batch commands where file names are specified.

<div style="color:#00000a;"></div>

'''Basename'''

'''%basename%''' -- replaced by the basename of the data file in the File List. For example, if the data file is named "'''f-spike.fsg'''", "'''%basename%-export.fsg'''" will be interpreted as "'''f-spike-export.fsg'''".

'''%basename-n%''' -- replaced by the basename of the data file in the File List, but removing the last "n" characters from the name. For example, if the data file is named "'''dongle-BB.fsg'''", "%basename-3%" will be replaced by "dongle", because the last 3 characters of the basename have been removed.

'''%-nbasename%''' -- replaced by the basename of the data file in the File List, but removing the first "n" characters from the name. For example, if the data file is named "'''BB-dongle.fsg'''", "%-3basename%" will be replaced by "dongle", because the first 3 characters of the basename have been removed.

'''%scripts%''' -- replaced by the path to the Scripts folder (e,g, "%scripts%Batch" is where batches are saved by default; "%scripts%MATLAB" is the location of the standard Matlab scripts used by BESA Research).

'''%montages%''' --replaced by the path to the Montages folder.

'''%examples%''' -- replaced by the path to the Examples folder.

<div style="color:#00000a;"></div>

'''Placeholders for folders'''

The following placeholders are the same as those used in the [Folders] section of '''Besa.ini''':

The strings enclosed by percent signs (%) are placeholders for the following folders in English-language versions of Windows. Folder names are different for Vista and XP/2000 and for other language settings. BESA Research will substitute the placeholders by the appropriate folder name for the system (W2K, XP, Vista, or Win7) and the system language:

* '''Windows 7 (English)'''

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%localapp%''' = "C:\Users\[user]\AppData\Local\BESA\Research_5_3", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as "Desktop\[user]\AppData\Local\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%publicprog%''' = "C:\Users\Public\Public Documents\BESA\Research_5_3". This folder is directly accessible from the Windows Explorer under "Libraries\Documents\Public Documents\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%privateprog%''' = "C:\Users\[user]\Documents\BESA\Research_5_3", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "Libraries\Documents\My Documents\Research_5_3" or "Desktop\[User]\My Documents\BESA\Research_5_3.</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%progdir%''' = the BESA Research root folder. In a default installation, this is "C:\Program Files\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%besaroot%''' is the same as''' %progdir%'''</div>

* '''Windows Vista (English):'''

<div style="color:#00000a;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%localapp%''' = "C:\Users\[user]\AppData\Local\BESA\Research_5_3", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "Desktop\[user]\AppData\Local\BESA\Research_5_3".</div>

<div style="color:#00000a;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%publicprog%''' = "C:\Users\Public\Public Documents\BESA\Research_5_3". This folder is directly accessible from the Windows Explorer under "Desktop\Public\Public Documents\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%privateprog%''' = "C:\Users\[user]\Documents\BESA\Research_5_3", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "Desktop\[user]\Documents\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%progdir%''' = the BESA Research root folder. In a default installation, this is "C:\Program Files\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%besaroot%''' is the same as''' %progdir%  '''</div>

* '''Windows XP (English):'''

<div style="color:#00000a;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%localapp%''' = "C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_5_3", where [user] is the logon name of the current user.</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%publicprog%''' = "C:\Documents and Settings\All Users\Documents\BESA\Research_5_3". This folder is directly accessible from the Windows Explorer under "Desktop\Shared Documents\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%privateprog%''' = "C:\Documents and Settings\[user]\My Documents\BESA\Research_5_3", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "Desktop\My Documents\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%progdir%''' = the BESA Research root folder. In a default installation, this is "C:\Program Files\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%besaroot%''' is the same as '''%progdir%'''  </div>

* '''Windows 2000 (English):'''

<div style="color:#00000a;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%localapp%''' = "C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_5_3", where [user] is the logon name of the current user.</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%publicprog%''' = "C:\Documents and Settings\All Users\Documents\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%privateprog%''' = "C:\Documents and Settings\[user]\My Documents\BESA\Research_5_3", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "Desktop\My Documents\BESA\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%progdir%''' = the BESA Research root folder. In a default installation, this is "C:\Program Files\BESA\\Research_5_3".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%besaroot%''' is the same as '''%progdir%'''</div>

==== Batch Commands ====

Batch commands are selected when the "'''Add Command'''" button is pressed in the Batch Tab. The commands are subdivided into five categories: General commands, commands for the Main module, for the Source Analysis module, imaging commands in the Source Analysis module, and commands for Time-Frequency Analysis. The commands have prefixes,''' GEN''', '''MAIN''',''' SA''', '''SAIMAGE''', and''' TFC'''), which identify the category. For compatibility with older program versions, old batches without the prefixes are accepted.

Detailed descriptions of each batch command are available in the electronic help chapter “''Batch Processing and Combining Conditions / Batch Processing / Batch Commands”.''

'''General commands''' -- prefixed with "'''GEN'''" (can be used anywhere):* GENBatchError -- used to change program behavior when errors occur.
* GENComment -- comment in the batch script: no batch functionality
* GENMATLABcommand -- send a command string to Matlab.
* GENMATLABwaitForVariable -- tells BESA to wait until Matlab has created a variable with the specified name.
* GENPause -- pause batch operations, allowing step-by-step operations
* GENFor/GENEndFor -- a programming language-like FOR loop
* GENRunProcess -- runs a command line process, e.g. an external program to perform part of the data analysis in the batch
* GENWindowPosition -- set window size and positions to a selection of standard settings, e.g. for bitmap export

'''Commands for the Main Module''' -- prefixed with "'''MAIN'''":
* MAINArtifactCorrect -- run automatic artifact correction
* MAINArtifactMethod -- specify the method for artifact correction
* MAINArtifactOn -- turn artifact correction an artifact view on or off
* MAINArtifact Scan -- run an artifact scan as from the Paradigm Dialog
* MAINAuxiliaryFiles -- associate auxiliary files (e.g. *.''ela'', *.''sfp'') with the data file
* MAINAverage -- average the data
* MAINBaseline -- specify the parameters for baseline correction
* MAINEditDefaultEpoch -- edit the default block epoch
* MAINEventRead -- read events from an ASCII event file
* MAINEventWrite -- write events to an ASCII event file
* MAINExport -- export or append data in the selected target format
* MAINFFT -- calculates the FFT spectrum of the marked data interval
* MAINFFTmean -- starts an averaging procedure which calculates the mean spectral properties in pre-defined regions
* MAINFFTsave -- saves FFT data (generated using the ''FFT Average option'' in the ''Average ''command) to disk (*.''fma)''
* MAINFileOpen -- close the current file and open a new file to which the remaining batch commands will be applied
* MAINFilter -- set filters
* MAINGoTo -- jumps with the cursor to the specified time point
* MAINICA -- starts ICA decomposition of data on the current screen
* MAINICAsave -- saves selected ICA components as topographies in a file
* MAINICAselect -- opens component selection dialog for managing ICA components
* MAINImportASCII -- import an ASCII file into a ''<nowiki>*.fsg</nowiki>'' file.
* MAINMarkBlock -- mark a data block (optionally send to Source Analysis)
* MAINMontage -- change the montage (used by the Export command when saving to current montage)
* MAINParadigm -- load a paradigm file
* MAINPatternToTrigger -- convert a tag into a trigger
* MAINSendToMATLAB -- send data to Matlab
* MAINTriggerSelect -- edit the trigger list (cf. ''Edit / Trigger Values''...)

'''General commands for Source Analysis''' -- prefixed with "'''SA'''" (but see also ''MarkBlock'', which is used to send a block of data to SA and open the SA window):
* SAAddSource -- add a dipole or regional source to a model
* SAChannelTypeForFit -- switch between EEG, magnetometers or axial gradiometers, and planar gradiometers
* SAConvertSource -- convert a source from dipole to regional source, or from regional source to dipole
* SAcorticalClara -- run Cortical CLARA
* SAcorticalLoreta -- run Cortical LORETA
* SADelete -- delete current solution or all solutions, or remove current fit interval or cursor
* SADICS -- start DICS computation (if DICS has been precomputed in the time-frequency image command)
* SADisplayMRI -- switch MRI display on/off and select small or large window
* SAExit -- close Source Module
* SAFit -- start fit
* SAFitConstraint -- set fit constraints, e.g. Residual Variance, Energy, Maximum Distance, Image Weighting, and their weights.
* SAFitInterval -- set fit or baseline interval
* SAMinimumNorm -- run a minimum norm analysis
* SANewSolution -- open a new solution
* SAOpenSolution -- open a solution from a file
* SAPCA -- toggle PCA display of data or residual, and transfer a selected number of components to the source model
* SARegularization -- set the regularization values both for discrete and distributed source images
* SASaveBitmap -- save a screenshot of the Source Analysis or the 3D window
* SASaveLeadfields -- save the leadfields of the current source model
* SASaveModelWaveforms -- save model waveforms
* SASaveResidualWaveforms -- save residual waveforms
* SASaveRVandGFPWaveforms -- save residual variance and global field power waveforms
* SASaveSolution -- save the current solution
* SASaveSourceMontage -- save a source montage
* SASaveSourceWaveforms -- save source waveforms
* SASendToMATLAB -- send data, model, source waveforms, images, etc. to Matlab
* SASetCursor -- set the cursor
* SASetDefaultSourceType -- set the default source type (dipole or regional source)
* SASetOrActivateSource -- Turn specified source on or off, or enable/disable source for fitting
* SASetOrientation -- set orientation (of regional source)
* SASwitchCondition -- switch to a specified condition

'''Commands for Distributed 3D Volume Images'''
* SAIMAGEBeamformer -- switch between Single Source and Bilateral Beamformer image
* SAIMAGECLARA -- generate CLARA image
* SAIMAGEExport -- save the results of minimum norm or 3D imaging method
* SAIMAGEGotoMax -- set the crosshair cursor at the nth maximum in the image
* SAIMAGEImport -- load a 3D volume image from file
* SAIMAGELAURA -- create LAURA image
* SAIMAGELORETA -- create LORETA image
* SAIMAGESLoreta -- create sLORETA image
* SAIMAGESSLOFO -- create SSLOFO image
* SAIMAGEUser-Defined -- create user-defined image
* SAIMAGESaveLeadfields -- save the leadfields of all the voxel sources in a 3D image
* SAIMAGEClip -- clip current 3D image
* SAIMAGESmooth -- smooth current 3D image
* SAIMAGESetCrosshair -- set the position of the crosshair in the 3D image

'''Commands for Time-Frequency Analysis''' ('''TFC''')
* TFCStartTFAnalysis --(previously TFCgo) start TFC analysis using the current paradigm settings
* TFCdisplay -- change the TFC display (e.g. power/amplitude, coherence)
* TFCsave -- save numerical results to an ASCII file, or save a screenshot of the TFC window
* TFCimage -- start beamformer analysis on a selected time-frequency range
* TFCSendToMATLAB -- send TF results or single-trial data to Matlab

==== How to Average Your Data in a Batch ====

Using batch processing, several files from an experiment can be averaged at a time.

Here we summarize the steps required:

'''Before running the batch'''

* Create the paradigm, and save the paradigm file.
* Open each individual data file to check the data:

* <div style="margin-left:1.27cm;margin-right:0cm;">Make sure auxiliary files are defined and loaded properly, and the data are displayed correctly.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">Eyeball the data.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">Define bad (and interpolated) channels.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">Mark artifact time ranges.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">If required, set up artifact correction for the file.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">The data file can be closed again after this step.</div>

'''Preparing the batch'''

* Open at least one file and select ''Process / Batch Scripts''.... The file(s) should be displayed in the file list. Alternatively, just select ''Process / Batch Scripts...,'' and add the files by

* <div style="margin-left:1.27cm;margin-right:0cm;">pressing the '''Add File''' button</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">dragging the files from Windows Explorer</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">Opening a previously saved list with ''Load File List''</div>

* You can delete files from the list (press '''Del''') or edit the file sequence using the right click context menu.
* Select the ''Batch Tab''.
* Add commands to your script. For averaging, these would normally be

* <div style="margin-left:1.27cm;margin-right:0cm;">'''Paradigm''' -- to load the paradigm file</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">'''Artifact Scan''' -- to run the artifact scan</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">'''Average''' -- to perform the average</div>

* Save these commands (press '''Save Batch''').
* Test the commands on the files in the current file list: press '''OK'''
* Look at the log file (press '''View Log File''') to check the results of averaging.
* Look at the data averages to make sure they have been done correctly.
* Repeat these steps until averaging is working properly.

'''Running the batch'''

* Select ''Process / Batch Scripts''....
* Open the files you want to average in the batch in the file list:

* <div style="margin-left:1.27cm;margin-right:0cm;">Any files that were open in BESA are included in the list</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">Files can be added using the '''Add File''' button</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">You may drag one or more files from Windows Explorer to the file list</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">Alternatively, load a previously saved file list.</div>

* Edit the file list, e.g. delete unwanted files (use the '''Del''' key or the right click context menu), or reorder the files (use '''Ctrl + cursor keys''' or context menu).
* Note that the order of files in the list specifies the order in which they will be processed in the batch script. This order will be important if all results are saved to the same target file. Otherwise the file sequence is not important.
* Optionally, save the file list (press '''Save Batch'''
* Select the ''Batch Tab'', and load the previously defined batch script with ''Load Batch''.
* Press '''OK''' to run the batch.

==== How to Merge and Compress raw data ====

Using the Export command in a batch, several data files can be merged into a single data file in BESA's data format ('''<nowiki>*.foc</nowiki>''').

This can be useful if data from one subject have been collected in several data blocks, and you want to analyze all data blocks together.

Optionally, to save space, data can be saved in compressed format.

'''Files can be merged:'''

* if they have identical channel configurations, or
* there are at least 16 EEG channels, and the export format is Standard 81 (i.e. EEG channels are interpolated to 81 standard locations). 

<div style="color:#00000a;"></div>

'''How to merge files:'''

* Select Process / Batch Scripts...
* Add all the files that are to be merged to the file list:

* <div style="margin-left:1.27cm;margin-right:0cm;">Any files that were open in BESA Research are included in the list</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">Files can be added using the''' Add File '''button</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">You may drag one or more files from Windows Explorer to the file list</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">Alternatively, load a previously saved file list (''Load File List'').</div>

* Rearrange the files in the file list to the sequence in which they should be merged.
* Select the ''Batch Tab ''and insert an "''Export"'' command, as described below.

<div style="color:#00000a;"></div>

The following dialog shows a possible configuration of the ''Export'' command:

<div style="color:#00000a;">[[Image:Batch processing (4).gif]]</div>

* The parameters shown in the Information box are the settings chosen in the ''Export Dialog'' when the '''Select Options''' button has been pressed.
* '''Append if file already exists''' must be checked in order to merge the files.
* The '''target file name''' must be fixed, i.e. don't use the '''%basename%''' variable, because that will result in a different target file name for each source file.
* There are two variables that can be used for the segment label:

# '''%filename%''' will insert the basename of the source file into the segment label.
# '''%c%''' will insert the file number into the segment label. The number gives the position of the file in the file list. For instance, "File %c%" will generate the label "File 2" for the second file in the list.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

==== Example: Data averaging in the auditory intensity experiment ====

In this example, two raw data files, '''s1.cnt''' and '''s2.cnt''', from the auditory intensity experiment will be batch averaged.

Please note that there are further tutorials covering this experiment. The first file is contaminated by many eyeblinks, and more epochs would be averaged if eye correction were used (see Viewlet demonstration on artifact correction on the BESA website). However, in this tutorial we will just use artifact rejection.

'''A. Various ways of creating a File List'''

'''1. Files that were open in BESA Research are automatically added to the File List'''. Start BESA Research and open the files '''s1.cnt '''and '''s2.cnt '''in the directory ''Examples\ERP-Auditory-Intensity''.

2. Select ''Process / Batch Scripts''.... You should see the file names in the '''''File List Tab''''' something like this:

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Batch processing (5).gif]]</div>

3. You can resort the files in the file list alphabetically by clicking onto the '''''File List column header''''':

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Batch processing (6).gif]]</div>

Alternatively, you can mark any file, hold down the '''Ctrl '''key and press the '''Up''' or '''Down arrow '''to move the file name up or down the list. This is the sequence in which files will be processed in the batch.

[[Image:Batch processing (7).gif]]

4. Press '''Save File List''' and save the list you have created to '''ERP-Aud-Ex1.flist'''.

5. Highlight both names and press the''' Del '''button to remove them from the list.

6. '''Files can be dragged from Windows Explorer'''. Start Windows Explorer and navigate to the ''ERP-Auditory-Intensity'' subdirectory of your BESA Research examples folder (located in the ''Public Documents'' folder of your computer). Click on '''s1.cnt''' and drag it with the mouse onto the '''''File List Tab'''''. Let go of the mouse. BESA Research opens the file, and displays the name in the File List. Repeat for '''s2.cnt.'''

7. Highlight both names and press the '''Del '''button to remove them from the list.

8. '''Files can be added using the''' '''Add File button'''. Press '''Add File''' and navigate to the ''Examples\ERP-Auditory-Intensity'' subdirectory. Select '''s1.cnt'''. Press '''Ctrl''' and select '''s2.cnt'''. Both names should then be displayed in the ''File Open'' dialog. Press '''OK''' to add the files to the file list.

9. Highlight both names and press the '''Del''' button to remove them from the list.

10. '''Files can be loaded from a previously saved file list'''. Press '''Load File List '''and select '''ERP-Aud-Ex1.flist''', the list you saved in step 6 above.

<div style="color:#00000a;"></div>

'''B. Setting up the batch'''

1. We will add three commands, '''Paradigm''', '''Artifact Scan''', and '''Average''', to create a batch that will be applied to the two files in the file list.

2. Click on the''''' ''Batch Tab'''.

<div style="color:#00000a;"></div>

[[Image:Batch processing (8).gif]]

3. Press the '''Add Command''' button to obtain the ''Select Command'' window:

<div style="color:#00000a;"></div>

[[Image:Batch processing (9).gif]]

4. Click on '''Paradigm''' and then on '''OK''' (alternatively, double-click on '''Paradigm'''). Hit '''Browse''', navigate to the ''Auditory'' folder, and select '''AEP_Intensity.pdg''', the paradigm for the auditory intensity experiment.

<div style="color:#00000a;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Batch processing (10).gif]]</div>

5. Press '''OK '''to obtain the ''Load Paradigm Task'' window.

<div style="color:#00000a;"></div>

[[Image:Batch processing (11).gif]]

6. Press '''OK''', and the first task in the batch is ready, and listed in the Batch Command window. If you want to modify the command, double-click on it to open the above window, that allows to browse for a different paradigm file.

<div style="color:#00000a;"></div>

[[Image:Batch processing (12).gif]]

7. Next, we add the '''Artifact Scan''' command. Click on the '''Add Command''' button, and select ''Artifact Scan.''

<div style="color:#00000a;"></div>

[[Image:Batch processing (13).gif]]

8. Press''' OK''' to open the ''Artifact Scan Task'' window. We want to be able to view the results of the scan, and adjust thresholds and bad channels if necessary. Therefore, check the ''Wait after scan'' checkbox.

<div style="color:#00000a;"></div>

<div style="margin-left:1.136cm;margin-right:0cm;">[[Image:Batch processing (14).gif]]</div>

9. Press '''OK''' to close the ''Artifact Scan Task'' window. Our batch now contains two commands.

<div style="color:#00000a;"></div>

[[Image:Batch processing (15).gif]]

10. Finally, we will add an '''Average''' command. Press the '''Add Command''' button and select ''Average''. Press '''OK''' to open the ''Average Task ''window.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Batch processing (16).gif]]

11. With the default settings, the average would be saved to the same directory as the data. The file name mask is set by default so that in this example the two averages would be saved to '''s1-av.fsg '''and '''s2-av.fsg'''. We will save the averaged files to subdirectory ''"Averages''" of the data directory. Uncheck the ''Use default target'' check box, change the File name mask to '''%basename%_av-test''' in order not to overwrite the predefined files.

<div style="color:#00000a;margin-left:1.136cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.136cm;margin-right:0cm;"></div>

[[Image:Batch processing (17).gif]]

12. Press '''OK '''to close the ''Average Task'' window. Our batch is now complete.  

<div style="color:#00000a;"></div>

[[Image:Batch processing (18).gif]]

13. We will now save the batch so that it can be used again. Press the '''Save Batch''' button, and save to the file '''ERP-Aud-ex1.bbat'''. Note that an easy way to generate new averaging batches is to load a previously save batch and edit the commands -- it may only be necessary to edit the '''Paradigm''' command to select the relevant paradigm file, and maybe to adjust the target directory in the '''Average''' command.

14. Press '''OK''' in the ''Batch'' Window to start the batch running. As requested, the batch pauses after the artifact scan:. 

<div style="color:#00000a;"></div>

[[Image:Batch processing (19).gif]]

You may now adjust the number of rejected trials, e.g. by moving the vertical red bar to the left, or exclude bad channels.  

15. Press '''OK''' to continue with averaging.

<div style="color:#00000a;"></div>

<div style="margin-left:1.136cm;margin-right:0cm;">[[Image:Batch processing (20).gif]]  </div>

16. Note that, in the background, the ''Batch Running'' window is providing feedback about the current file and current task.  

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Batch processing (6).jpg]]

17. The batch will stop again after the next artifact scan. Press '''OK''' to allow the batch to run to the end.  

<div style="color:#00000a;"></div>

[[Image:Batch processing (21).gif]]

18. Press '''View Log''' to view the batch protocol. If you are using Internet Explorer or Netscape family (Mozilla, Firefox) browsers, and JavaScript is enabled, you will first see just batch titles defined by the date and time the batch was started. The most recent title is at the top of the list. For other browsers, or if JavaScript was not enabled, all protocol texts are expanded as in 19 (below).

<div style="margin-left:1.136cm;margin-right:0cm;">[[Image:Batch processing (22).gif]]</div>

19. Click on the first title to expand its protocol. Here, for example, the protocol gives feedback about the number of epochs that were averaged for each file.

<div style="color:#00000a;"></div>

[[Image:Batch processing (23).gif]]

20. Finally, press '''OK''' to return to the main BESA Research display. Open the averages in the ''Averages'' subdirectory to confirm that they were generated properly.

<div style="color:#00000a;"></div>

==== Example: Merging files using the Export Command ====

Here we will demonstrate the use of the '''Export '''command to merge two files. We will combine the two averages from the previous example (Data averaging in the auditory intensity experiment) into one target file.

'''A. Generate the file list'''

# Start BESA Research and load the two data files '''S1_av-test.fsg''' and '''S2_av-test.fsg''' that were saved in the previous example.
# Select ''Process / Batch Scripts....''The two file names should be displayed in the file list.
# In the file list, make sure that '''s1_av-test.fsg '''is the first file in the list. If it is not, highlight the file, and move it up using '''Ctrl+up''', or right click and select ''Move Up'' in the context menu.

'''B. Generate the batch'''

1. Press the '''Add Command''' button, and select the '''Export''' command.

2. Press '''OK''' to open the ''Export Task'' window.

[[Image:Batch processing (24).gif]]

3. Press the '''Select Options'''... button to open the ''Export Dialog''.

[[Image:Batch processing (25).gif]]

4. Since we are combining averages, select ''Hires (no compression)'' in the '''Target data format''' drop-down list (If we were merging raw data files, it is better to select compression. Press '''OK '''to close the dialog. Check'' Append if file already exists'', so that the files will be merged. Enter '''s1+s2''' in the target file name mask edit box. This ensures that both files will be saved to the same target: '''S1+S2.fsg'''.

[[Image:Batch processing (26).gif]]

5. Press '''OK '''to close the ''Export Task'' window. The '''Export '''command is displayed.  

[[Image:Batch processing (27).gif]]

6. Optionally, you may save the batch file by pressing '''Save Batch'''.

7. Press '''OK''' to run the batch, and '''OK''' in the ''Batch Completed'' window to return to the BESA main window.

8. Finally, open the file '''S1+S2.fsg''' to confirm that it contains the two merged files.

'''C. Merge raw data'''

# Repeat the above task to merge the two raw data files '''S1.cnt''' and '''S2.cnt''' into a single target file '''S1+S2.foc'''. In this case, select one of the compression options as the target data format. Note that you would not normally want to merge two files from different subjects. However, several data blocks from the same subject can conveniently be merged using this method.

Note that ''<nowiki>*.fsg</nowiki>'' files can also be merged using the ''Combine Conditions'' dialog. 

=== Combine Conditions, Channels ===

==== Combine Condition Scripts ====

With the Combine-Conditions module you can do a variety of operations on BESA averages (files with the extension '''<nowiki>*.fsg</nowiki>''', and other segment files, such as '''<nowiki>*.mul</nowiki>''', '''<nowiki>*.avr</nowiki>''', '''<nowiki>*.swf</nowiki>'''):

* Create grand averages
* Combine averages (add, subtract, weighted/unweighted)
* Merge files
* Exclude unwanted averages
* Rename conditions
* Rename or resort channels
* Generate averages or differences over selected channels
* Transform the data: standard interpolated 81 electrodes, change sampling rate, change interval
* Determine peaks, mean amplitudes, or integrals on data averages
* These operations can be performed on one or more files simultaneously. Results of an operation are stored in a single target file.

The module includes four tabbed windows:

* File List: Define a list of files on which the operations will be performed.
* Condition List: List the condition names, define target condition names, and how input conditions are combined into target conditions.
* Channel List: List the channel names, define target channel names, and how input channels are combined into target channels.
* Run Scripts: Define global options for the output (e.g. spatial interpolation, resampling, copy/merge or average, peak analysis). Start the operation.
* Note that in all four tabs, configurations can be saved for future use, and the '''Load Previous''' button restores the most recently used configuration.

==== Condition List Tab ====

List the condition names, define target condition names, and how input conditions are combined into target conditions.

The first column of the list box shows a list of all the condition names found in the source files.

Rows of the list box define the source conditions. Columns define the target conditions.

'''Initial setting'''

When first selecting the tab, each column shows each condition name found in the source files (as in the example below). In the list box, there is a "+1" along the diagonal. The result of this selection is that target conditions will have the same name as source conditions. Right click on source condition labels to view properties (e.g. no. of samples, time range, sampling rate).

[[Image:Batch processing (28).gif]]

'''Editing the condition list'''

* Target condition names can be edited, inserted or deleted by clicking on the label at the top of each column.
* Click on a box within the list to toggle between "+1", "-1" and blank. These correspond to the operations:

* <div style="margin-left:1.259cm;margin-right:0cm;"> "+1" = add</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">"-1" = subtract</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">blank = do nothing</div>

* Right click on a box for further operations: conditions can be weighted by a given factor other than 1.

'''Divide result by sum of PLUS factors'''

* Normally, when creating an average over conditions, the sum is divided by the number of conditions, or a weighted average is generated (see below).  If "''Divide result by sum of PLUS factors''" is unchecked, the conditions will be summed rather than averaged.
* Note that, when making differences between conditions, no such division is required. BESA Research will uncheck the checkbox automatically if subtraction ("-1") is specified somewhere in the condition list.

'''Weighting of averages'''

* Below the list, click on the ''Weighted Average'' row to toggle "YES" and "NO". "YES" means that averages will be weighted by the number of epochs contributing to the average. For instance, if average A contained 100 epochs and average B contained 200 epochs, the weighted average will be computed as

<div style="margin-left:1cm;margin-right:0cm;">(100 * A +  200 * B) / (100 + 200)</div>

<div style="margin-left:1cm;margin-right:0cm;">Select "NO" for an unweighted average. For the above example, the average is computed as</div>

<div style="margin-left:1cm;margin-right:0cm;">(A + B) / 2</div>

<div style="margin-left:1cm;margin-right:0cm;">Weighted averages are not permitted if one of the boxes contains a negative value.</div>

* Values other than +1 or -1 in the boxes apply a different kind of weighting. For instance, we want to compute the difference between the means of conditions A, B, C and D, E. Use a right click to specify the fraction 1/3 for each of A, B, and C, and -1/2 for each of D and E (see example below).

[[Image:Batch processing (29).gif]]

'''Save the current condition list'''

* Press the '''Save Condition List''' button.

'''Load a condition list'''

* Press the '''Load Condition List''' button.

'''Load previous settings'''

* Press the '''Load Previous''' button

'''Feedback'''

* Conditions that have different numbers of electrodes (averaging across different files) can only be combined if channels are interpolated to a standard set of electrodes.
* Conditions that have different durations or sampling rates can only be combined if the sampling rate and durations are made the same.
* Feedback about the above situations is displayed by the presence of tick marks above the list box.

==== Channel List Tab ====

List the channel names, define target channel names, and how input channels are combined into target channels.

Note that this tab is very similar in usage to the '''Condition List Tab'''. Note also that some of the functions performed in this tab could also be done in the Montage Editor. It may be a matter of convenience whether you choose to perform these operations here or in the Montage Editor.

The first column of the list box shows a list of all the channel names found in the source files.

Rows of the list box define the ''source'' channel. Columns define the'' target'' channel.

'''Initial setting'''

When first selecting the tab, each column shows each channel name found in the source files (as in the example below). In the list box, there is a "+1" along the diagonal. The result of this selection is that target channel will have the same name as source channel.

'''Combining files'''

If files with different channel configurations are included in the File List, the rows and columns of the Channel List Tab will only contain the labels for the channels that are in common among the files.

If the files in the File List have a different sequence of channels, the sequence of the first file in the list will be adopted in the Channel List.

Thus, for the initial setting, unless the "''Ignore Settings in this Tab''" checkbox is checked, the target grand average or peak/amplitude analysis, etc. will be applied using only channels that are in common among the input files, and using the channel sequence of the first file in the File List. By changing the target channels or by changing the entries in the Channel List, new channels consisting of averages or differences can be generated.

'''What can the Channel List be used for?'''

Some examples:

* Reorder or relabel channels
* Create channel differences
* Create averages over channel groups, e.g. for peak analysis
* Extract a selection of channels for peak analysis or mean amplitudes
* Create grand averages across files with different channel configurations, just using channels in common among the files

[[Image:Batch processing (30).gif]]

'''Editing the channel list'''

* Target channel names can be edited, inserted or deleted by clicking on the label at the top of each column.
* Click on a box within the list to toggle between "+1", "-1" and blank. These correspond to the operations:

* <div style="margin-left:1.259cm;margin-right:0cm;">"+1" = add</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">"-1" = subtract</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">blank = do nothing</div>

* Right click on a box for further operations: channels can be weighted by a given factor other than 1.

'''Divide result by sum of PLUS factors'''

* Normally, when creating an average over channels, the sum is divided by the number of channels, or a weighted average is generated (see below).  If "Divide result by sum of PLUS factors" is unchecked, the channels will be summed rather than averaged.
* Note that, when making differences between channels, no such division is required. BESA Research will uncheck the checkbox automatically if subtraction ("-1") is specified somewhere in the channel list.

'''Save the current channel list'''

* Press the '''Save Channel List''' button.

'''Load a channel list'''

* Press the '''Load Channel List '''button.

'''Load previous settings'''

* Press the '''Load Previous''' button

==== Run Scripts Tab ====

Define global options for the output (e.g. spatial interpolation, resampling, copy/merge or average, peak detection. Start the operation.

[[Image:Batch processing (7).jpg]]

'''Load or Save Settings'''

* You can save the current settings of this tab to a file (*.run) which can be loaded later.
* When you run the script, the current settings are saved automatically to a file "'''PreviousSettings.run'''".

'''Load Previous'''

* Press this button to load the previous settings (from "'''PreviousSettings.run'''").

'''Averages to Generate'''

* '''Generate separate averages for each source file'''. Averages are performed over conditions within the source file, and are then appended to the target file.
* '''Combine data from source files'''. Conditions are combined over all source files into a single target average.
* '''No averages, just copy'''. Files are copied and merged to the target file. Use this option for renaming conditions, merging files, removing unwanted averages (see below), changing the sampling rate and interval.
* '''Peaks and mean amplitudes'''. Specify time ranges for peaks, mean amplitudes, or integrals (areas).
* Note: When generating or copying averages (first three options), filters and baseline settings are turned off. For Peaks and mean amplitudes, filters and baseline settings are specified in the dialog.

'''Spatial Interpolation'''

* '''Interpolate to Standard 81 electrodes'''. The target file will contain only electrodes (other channels are omitted), using the Standard 81 configuration (as in other export functions within BESA Research). This cannot be selected if the source data contain less than 16 EEG channels.
* '''Interpolate Bad Channels'''. Bad electrode channels in the source file will be interpolated. If the above option is deselected and bad channels exist in one or more of the source files, this option is always on.

BESA Research can interpolate EEG, and MEG if the sensors are axial gradiometers or magnetometers. If other channels are marked as bad in one or more of the source files, these will be defined as bad in the target file. This applies to MEG planar gradiometers, to polygraphic data, and to ICR channels.

'''Temporal Interpolation'''

* '''Spline to New Sampling Rate and Interval'''. Data can be converted to a new sampling rate, and the interval can be changed.

* <div style="margin-left:1.259cm;margin-right:0cm;">If the sampling rate is reduced, the data will be low-pass filtered at 1/3 sampling frequency before reduction.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">If the sampling interval is changed, the prestimulus and poststimulus intervals are limited by the smallest intervals in the conditions contributing to the averages. These limits are shown below the edit boxes.</div>

'''Peaks and Mean Amplitudes'''

[[Image:Batch processing (31).gif]]

'''Peaks:'''

* Select the time range between which peaks are to be determined.
* Select the montage on which the peaks are to be determined.
* Define the filter settings.
* Define the baseline settings.
* Specify whether peaks are to be defined at one latency: if so, select the channel on which peaks are to be detected.
* Specify whether you want to find positive or negative peaks.

'''Mean amplitudes and areas:'''

* Select the time range over which the mean amplitudes or areas are to be determined.
* Select the montage on which the mean amplitudes or areas are to be determined.
* Define the filter settings.
* Note that when computing areas, data are first rectified (made positive) and then summed over the time range.

'''Output options of the analysis:'''

* A single ASCII file that contains the result of the analysis for all data sets, conditions, and channels including header and information lines.
* A sparse output suitable for import in SPSS. Each variable (e.g. a latency, a channel amplitude) constitutes one column of the output file.
* Direct transfer to MATLAB into a struct besa_peak. For more information on the data transfer from BESA Research to MATLAB, please refer to help chapter ''“The MATLAB interface”.''

'''Starting the Operation'''

* Press '''OK''' to start the operation. After the operation is completed, and the "Open target file in BESA" box is checked, BESA Research will open the target file.  "Open target file in BESA" cannot be checked if "Peaks and mean amplitudes" was selected - then the result of the operation will be an ASCII file or a MATLAB transfer.
* You will be asked for the name of the target file (unless a MATLAB transfer of peak data has been performed).

'''Restrictions'''

* Depending on source file configurations, not all options above are selectable. For instance, if two files contain different numbers of electrodes, and the "''Ignore Settings in this Tab''" checkbox is checked in the '''''Channel List''''' Tab, spatial interpolation to Standard 81 is enforced in the target. Similarly, if different sampling rates are used in different files, temporal interpolation is enforced.
* You are not allowed to add files to the file list if the channel configuration is different, and the data cannot be combined with Standard 81 interpolation. Since Standard 81 interpolation is only possible for EEG, multiple files without EEG can only be loaded if they have the same number of channels.

==== How to Create Grand Averages ====

* Open the files you want to average in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...).''
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions. To average across different conditions, click in the list boxes to obtain "+1" for each source condition to combine, and rename the target condition to define a meaningful name for the average.
* Click on the '''Run Scripts Tab'''.
* If you have more than one file, specify whether averages should be generated across files ('''Combine data from source files''') or within files ('''Generate separate averages for each source file''').
* Select other options if required (spatial or temporal resampling).
* Press '''OK'''.

==== How to Generate Differences Between Conditions ====

* Open the files you want to operate on in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...).''
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions. To create differences, click in the list boxes to obtain "+1" for one of the source conditions, and "-1" for the source condition to subtract, and rename the target condition to define a meaningful name for the difference.
* Click on the '''Run Scripts Tab'''.
* If you have more than one file, specify whether averages should be generated across files ('''Combine data from source files''') or within files ('''Generate separate averages for each source file''').
* Select other options if required (spatial or temporal resampling).
* Press '''OK'''. An average of the differences is generated. If only one example of each condition exists, e.g. in a grand average file, the result is the difference between conditions.

==== How to Merge Files ====

* Open the files you want to merge in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions''...).
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions.
* Click on the '''Run Scripts Tab'''. Select "''No averages, just copy''".
* Press '''OK'''.

'''Notes'''

* If the source files have different electrode configurations, use the Standard 81 configuration for the target.
* If the source files have different sampling rates or intervals, use Temporal Interpolation.

==== How to Remove Unwanted Averages ====

'''Removing one or more unwanted segments'''

* Normally, all conditions are read from a source file. To exclude one or more segments from operations in the Combine Conditions module, mark the segments as artifacts in the main program display. It is sufficient for the beginning or the end of an artifact interval to be within the segment for the segment to be excluded.
* Open the file you want to operate on in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...).''
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions.
* Click on the '''Run Scripts Tab'''. Select "''No averages, just copy''".
* Press''' OK'''.
* The target file contains the copied data without the conditions that were marked as averages.

'''Removing one or more unwanted conditions (by label)'''

* Open the file you want to operate on in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...).''
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions.
* Deselect the target conditions you want to omit (replace the "+1" by a blank).
* Click on the '''Run Scripts Tab'''. Select "''No averages, just copy''".
* Press''' OK'''.
* The target file contains the copied data without the conditions that were marked as artifacts.

==== How to Rename Conditions ====

* Open the file you want to operate on in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions''...).
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions. Click on column headings to rename the target conditions.
* Click on the''' Run Scripts Tab'''. Select "''No averages, just copy''".
* Press '''OK'''.
* The target file contains the copied data with the renamed conditions.

==== How to Change the Sampling Rate ====

* Open the file(s) you want to change in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...'').
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions.
* Click on the '''Run Scripts Tab'''. Select "''No averages, just copy''".
* Select "''Spline to New Sampling Rate and Interval''" and type the new sampling rate into the edit box.
* Press '''OK'''.

==== Example: Create grand average and combinations of conditions ====

In this example, we will generate a grand average of the results of the Auditory Intensity Experiment. The experiment includes averages from five different stimulus intensities. We will create a grand average over each intensity, but also include means over the two lowest and the two highest intensities, and the difference between these two combinations.

'''A. File selection'''

# Start BESA Research and open files '''S1_av.fsg - S10_av.fsg''' in the ''Examples\ERP-Auditory-Intensity'' folder. The files contain the individual averaged data of the 10 subjects who participated in this study.
# Select ''ERP / Combine Conditions...'' The file list should display the two files, with feedback about the number of averages and conditions. 8 epochs are found. See the ''“Data averaging in the auditory intensity'' ''experiment”'' example for examples how to manipulate the file list.

[[Image:Batch processing (32).gif]]

'''B. Define conditions'''

1. Click on the '''Condition List Tab'''. The initial window defines target conditions with the same name as the source conditions. To generate the grand average over these conditions we could proceed without further changes to the '''Run Scripts Tab'''. However, we want to modify the condition list and create a condition that contains the grand averaged difference between the''' High''' and '''Low''' conditions.

[[Image:Batch processing (8).jpg]]

2. Click on the '''All '''column label. In the resulting window, rename condition '''All''' to''' Difference'''. Then press '''OK'''.

[[Image:Batch processing (33).gif]]

3. The last column is now labeled '''Difference.''' Left-click twice onto the ‘'''+1’''' entry that links this condition to the '''All '''input condition. This will remove the link and leave the field blank. To define the ‘Difference’ condition as the average of ‘High’ minus ‘Low’ over subjects, left-click once into the field linking input '''High''' with target '''Difference''' to generate an entry ‘'''+1’''' in this field. Left-click twice into the field linking input '''Low '''with target '''Difference''' to generate an entry '-'''1'''’.

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Batch processing (35).gif]]</div>

4. Press '''Save Condition List''' and save the list to '''ERP-aud-ex1.clist'''. This condition combination can thus be loaded later using the '''Load Condition List''' button.

'''C. Run the script'''

# Click on the '''Run Script Tab'''.
# The default tab settings are ready for generating the grand average ('''Combine data from source file''' and '''Open target file in BESA''' should be checked). Just press '''OK'''. Enter '''All_Subjects_cc-test.fsg''' as file name and press''' Save'''.

The resulting file contains the 8 target conditions, 60db, 70dB, 80dB, 90dB, 100dB, Low, High, and Difference.

==== Example: Average files from different experiments ====

This example is intended to illustrate several features of the ''Combine Conditions'' Dialog, such as electrode interpolation and resampling. We will combine an average from the Auditory Intensity experiment with one from the P300 auditory experiment. In this particular case, it is not a very meaningful thing to do, but it shows what is possible. For instance, the same experiment may have been performed using different sampling rates or electrode combinations. This example shows how such data may be combined.

'''A. File selection'''

# Start BESA Research and open the file '''All_Subjects_GA.fsg''' in the ''Examples\ERP-Auditory-Intensity'' folder. The file contains the grand average data from the auditory intensity experiment.
# Open the file '''RareFrequentResponseLeft.fsg''' in the ''Examples\ERP-P300-Auditory'' folder. This file contains averages from the P300 auditory experiment.
# Select ''ERP / Combine Conditions... ''Note that the files have different sampling rates and different numbers of electrodes.

[[Image:Batch processing (36).gif]]

'''B. Define conditions'''

1. Click on the '''Condition List Tab'''. Note that the feedback text at the bottom of the window displays the text "Standard 81 interpolation required to generate average; Across files: resampling or change in time range required to generate average". The condition labels show all the names from both files.

[[Image:Batch processing (37).gif]]

2. We will exclude most conditions, and just combine the most similar conditions from the two experiments: the "Standard" and the "80dB" conditions. Click on the title of the first column,''' Blink'''. Select “''Delete all conditions to the right of this column”'', and press '''OK'''.

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Batch processing (38).gif]]</div>

3. Click on the title again, and rename the target condition to "Standard".

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Batch processing (39).gif]]</div>

4. Click twice in the first line to remove the "+1" entry there. Click once in the third row ("Frequent"), and in the 7th row ("80dB"), to display "+1" at each entry. Thus, just two of the conditions will be combined into one target condition.

[[Image:Batch processing (40).gif]]

'''C. Run the script'''

1. Click on the '''Run Script Tab'''.

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Batch processing (41).gif]]</div>

2. Note that '''Interpolate to Standard 81 electrodes''' is checked and grayed: since two different electrode sets are to be combined, we can only do this by interpolating electrodes. Also, both '''Spline to new sampling rate''' and '''Clip interval '''are checked and grayed. Again, these settings are required in order to be able to average the two data files together. The sampling rate is set to the higher of the two selections. The time range is set to the largest possible range that can be clipped from the two data sets. For now, leave these settings as they are, and press '''OK'''. Save the target to '''TestCombineExpts_CC-std81.fsg'''.

{{BESAManualNav}}

BESA Research ICA

2017-04-07T13:05:47Z

Alexa:

BESA Research ICA

2017-04-07T12:53:40Z

Alexa:

BESA Research ERP Processing

2017-04-07T12:52:25Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
== ERP Processing and Averaging ==

=== The Event-Related Potentials (ERP) Module - Introduction ===

The Event-Related Potentials (ERP) module provides many features that assist you with the analysis of event-related and evoked potentials and fields. These features, which are explained below, include

* defining triggers and conditions on the basis of experimental paradigms
* simultaneous averaging of multiple conditions
* viewing and analyzing averaged results in a Top Viewer window, e.g. for peak finding and measurement of amplitudes
* Grand Average and combining of conditions
* a Schmitt Trigger tool which makes it easy to convert EMG/EEG artifacts into trigger events
* a tool for editing triggers
* import and export of triggers from/to ASCII file

Coherence analysis is covered in the chapter on ''Source Coherence''.

A comprehensive review of the features is given in the online help chapter ''"ERP / Reference". ''Detailed tutorials can be found in help chapter ''" ERP / Functions of the ERP module"'' under the corresponding section.

=== Paradigms for Averaging ===

==== Introduction ====

Paradigms allow to use scripting techniques for averaging of multiple recordings.

They keep track of all relevant settings for averaging and make it easy to perform all necessary steps for optimal averaging of the data with a few mouse clicks. Each experimental task is described by a condition, in which trigger events are selected for averaging on the basis of user-defined boolean statements. Conditions can later be combined, e.g. to create grand averages or to form difference conditions.

The process of editing paradigm definitions is started using the menu entries '''ERP / Open Paradigm''' or '''ERP / Edit Paradigm''', or the''' ERP''' push button in the main window, as shown in the figure below.

[[Image:ERP Processing (1).gif ]][[Image:ERP Processing (2).gif ]]

''ERP menu. Select Open Paradigm BESA Research browses to the folder of pre-defined paradigms ''

''to open a pre-defined paradigm file. automatically. From the 'Directories' drop-down menu, the current ''

''data directory can be quickly accessed as well.''

Whereas '''''Open Paradigm''''' asks for a pre-defined paradigm file, '''''Edit Paradigm''''' opens the last used paradigm file for the current data set. If no paradigm is present, a new paradigm with default settings is created automatically. The '''ERP''' push button tries to open the last used paradigm file. If it does not exist, the '''''File Open''''' box appears.

The paradigm is defined using 6 (with Source Coherence Module 7) different dialog tabs. Each summarizes one aspect of the paradigm:

* Trigger: define trigger codes by assigning names and other attributes. Attributes (e.g. "intensity") help to group triggers.
* Condition: define a condition which selects trigger events from the experiment. Logical expressions can be combined to filter, for example, only the correct responses to a given task.
* Epoch: define epochs for averaging, baseline, artifact rejection, stimulus artifacts, and possibly a delay in trigger administration
* Filter: edit filter settings for averaging
* Artifact: reject artifacts by means of an interactive graphical rejection tool
* Average: select conditions for averaging and perform the average
* Coherence: specify settings for the time-frequency transformation (Source Coherence Module required)

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

'''Trigger'''

By default, triggers are defined by the trigger code. However, this definition is arbitrary and working with numbers instead of names is error-prone. The Trigger dialog tab in the Paradigm property sheet enables naming triggers and grouping triggers by making use of attributes. These attributes can be freely assigned, and each trigger obtains a unique definition for its attributes.

Generally, the suggested order in which to proceed for trigger definition is:

# Define the attributes which cover all the different sub-groups of triggers
# For each attribute, define the different values the attribute can take
# Define the triggers by selecting the code and the appropriate attribute values, and using the '''Set '''button

<div style="color:#00000a;"></div>

The ''Trigger ''dialog tab contains two main sections: The upper part is used to define attributes and attribute values for the triggers, whereas the lower part shows the current definitions.

For example, to assign names to the trigger codes:

* Enter names in the edit boxes of the ''Attribute Values'' section (below the attribute “name”)
* Add them to the list using the '''Add to List''' button.
* Define them by selecting code and name in the list box under the attribute “name” and clicking the '''Set''' button.

<div style="color:#00000a;"></div>

[[Image:ERP Processing (3).gif ]]

''Trigger tab. The trigger codes are shown. The attribute “name” is defined automatically.''

'''Condition'''

A condition holds all information connected with a task or a specific event type.

In the ERP module, averaging is performed on the basis of conditions. A condition is given by a logic expression that defines which trigger events are accepted for averaging. The "condition" tab makes it possible to define complex logic expressions and to see immediately how many matching trigger events result.

The example conditions shown in the figure below are defined in Tutorial 1: ''‘Using a P300 Paradigm for'' ''Averaging ''' in help chapter ''“ERP / Functions… / Paradigms for Averaging”,'' which gives a comprehensive overview of the features of the averaging module.

<div style="color:#00000a;"></div>

[[Image:ERP Processing (2).png ]]

''Editing a paradigm: Conditions can be defined by combining trigger definitions using boolean logic. This example shows definitions of three conditions (Rare, Standard, Hit) with a different number of matching events (40, 160, 134).''

'''Epoch'''

The dialog tab'' Epoch'' is used to set the epochs which define the averaging interval. For each condition, an individual set of epochs can be defined for averaging by the edit boxes at the top of the dialog tab. At the bottom of the tab, the current settings for all conditions can be viewed.

The push buttons in the center of the tab control the editing process. Two push buttons at the bottom right are for loading and saving a paradigm file.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (3).png]]

''Epoch tab. 4 different epochs can be defined for each condition. A stimulus delay time can also be specified.''

'''Filter'''

The ''Filter ''dialog tab allows you to change filter settings prior to averaging the data. The low and high pass filters can be chosen differently for the artifact scan and the average. '''Note''': If the paradigm is edited for the first time, default filter settings are used. These can differ from the filter settings which you set in the review window. If a paradigm file was opened which does not contain filter settings, the filter settings which were chosen in the base module are displayed in the dialog tab.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (4).png]]

''Filter tab. Low cutoff, high cutoff, and band pass filters can be applied.''

'''Artifact'''

The ''Artifact'' dialog tab provides an easy way to define artifact rejection thresholds and to exclude bad channels and bad sweeps from the analysis. This is achieved by scanning the data file and then using the graphics display presented in the center of the dialog tab, which shows channels and sweeps sorted according to user-defined criteria.

If the user does not check any of the options ''Fixed Thresholds'' and ''Artifact Scan Tool'', only regions which were explicitly marked as artifacts by the user will be excluded from the averages. If the option ''Fixed Thresholds'' is checked, the thresholds given in the edit boxes for amplitude and gradient are used to reject sweeps contaminated by artifacts.

The option ''Artifact Scan Tool'' provides an interactive tool for the comprehensive detection and rejection of both artifact-loaded channels and sweeps.

The figure below shows the result of an artifact scan. The trials are depicted in the columns of the display, sorted according to the highest amplitudes. Trials are rejected by mouse drag of the vertical cursor or by adjusting the rejection threshold for maximum amplitude, gradient, or minimum variance within a trial. The channels are depicted in the rows of the display, sorted according to the mean amplitude values over the trials. Similarly to excluding trials, a mouse drag of the horizontal cursor at the top of the display excludes channels.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (5).gif ]]

''Artifact scan result. The channel at the top shows significantly higher amplitudes than the rest, indicated by the lighter color. Trials in the rightmost columns have been excluded from averaging.''

'''Average'''

The ''Average'' dialog tab is used to define

* which conditions are averaged
* which range of the data file is searched for trigger events matching the conditions
* whether automatic or query search is performed

<div style="color:#00000a;"></div>

The left part of the'' Average ''tab contains radio buttons to select the search range within the data file.

The central part contains a list of available conditions and of available constraints for averaging.

The list box array at the bottom shows the active and inactive conditions, the total number of matches, and the selected constraints. It provides an overview about the conditions which are selected. To add a condition to the list, select the condition and the constraint in the list boxes at the top, and click the '''Add to''' '''List '''button.

The right part contains additional sections for defining statistics and toggling between query averaging and automatic averaging.

Two push buttons at the bottom right are for loading and saving a paradigm file.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (6).gif ]]

''Averaging tab. Range, conditions, and constraints for split-half averaging can be adjusted.''

The tutorial in help chapter ''"ERP / Functions...  / Paradigms... / Tutorial 1: Using a P300 Paradigm for'' ''Averaging"'' gives an introduction to the available features. Different conditions can be combined to analyze experimental paradigms of high complexity.

A detailed description of the features can be found in electronic help chapter ''"ERP / Reference / Using Paradigms to Average".''

==== Tutorial 1: Using a P300 Paradigm for Averaging ====

This example illustrates how to define and evaluate experimental paradigms using the ERP module. We will work on an experiment with an auditory oddball paradigm. The paradigm involves frequent and rare tones of different pitch and a motor response. The following list shows the encoding of the three different events to triggers:

{| style="border-spacing:0;width:16.374cm;"
|- style="background-color:#ffffff;border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| '''File name'''

|| '''Triggers'''
| style="color:#00000a;" |
|| '''Motor response to'''
|- style="background-color:#ffffff;border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| Freq-1200Hz-Resp-L.cnt
|| Frequent tone (1200Hz)

Rare tone (800Hz)

Motor response (left hand) 
|| Trg. 1

Trg. 2

Trg. 128 
|| frequent tone
|-
|}
<div style="color:#00000a;"></div>

The electrode positions were digitized. The file with the extension Freq-1200Hz-Resp-L.sfp contains the digitized 3D coordinates for the EEG.

Follow the steps in the next section to see how the ERP module allows to customize the paradigm and to evaluate and average conditions.

<div style="color:#00000a;"></div>

'''A. Open a pre-defined paradigm'''

'''1. Load data'''

* Load data file "'''Freq-1200Hz-Resp-L.cnt'''" in the folder "''Examples\ERP-P300-Auditory''".
* Select'' File/Head Surface Points ''and ''Sensors/Load Coordinate Files''... Browse for the coordinate files ''''P300-Aud.ela'''' and '''P300-Aud.sfp '''in the first two rows. They contain the type and location of the recorded electrodes. Enter ' 8mm' as electrode thickness, because in this example the coordinates specified in the sfp-file were measured 8mm away from the head surface.

<div style="color:#00000a;"></div>

[[Image:ERP Processing (7).gif ]]

'''2. Open a pre-defined paradigm definition'''

<div style="color:#00000a;">[[Image:ERP Processing (2).gif ]]</div>

* Choose the menu entry '''ERP/Open Paradigm'''. A file selection box appears.
* Choose the folder ''"Auditory"'' and open the paradigm file "'''P300.PDG'''". Note that the combo box at the bottom of the file selection box enables a fast change between the default paradigm directory, and the directory where the data is stored.

The dialog box that appears consists of several pages (" tabs"). The tab which you see is divided into three sections. The list box on the left shows the current number of matches for all defined conditions. In this case, 3 conditions are defined:
* Rare
* Standard
* Hit

[[Image:ERP Processing (2).png ]]

Upon reading the paradigm, the conditions were automatically evaluated. For all three conditions, matches were found.

* In the list box in the center of the page, the currently defined conditions are displayed. The right part contains the command buttons. We will learn more about them later.
* Leave the page by selecting the tab "Epoch" at the top.

<div style="color:#00000a;"></div>

'''B. Average conditions'''

'''1. Edit Averaging Epochs'''

[[Image:ERP Processing (3).png]]

All three lines are highlighted, since they all hold the same epoch settings which were entered into the edit boxes in the top half of the tab.

The epoch which is used for calculating the baseline is set to -100ms (start position) and 0ms (end position) by default.

* Select the last condition "Hit" in the list by a single click with the left mouse button. The settings are automatically copied to the edit boxes. In the edit section, change the averaging epoch to -800ms (start position) and +100ms (end position). Click the button '''"Assign to Selected"''' which changes the epoch settings for this condition only. This allows you to average the pre-stimulus potentials for the motor response selectively. You will notice that the artifact rejection interval was also updated, to fit into the newly defined averaging interval. Before you move on to the tab "Filter", adjust the Baseline Definition Epoch to [-800ms, -700ms] and click the button "'''Assign to Selected".'''

<div style="color:#00000a;"></div>

'''2. Filter Settings'''

In the "Filter" tab, the low frequency cutoff filter and the high frequency cutoff filter can be edited.

* If the high cutoff filter is enabled for either artifact scan or averaging, disable it by clicking off the check boxes. Switch to the "Artifact" tab.

<div style="color:#00000a;"></div>

'''3. Artifact Rejection'''

The artifact rejection tool offers two methods of artifact rejection. If the check box "''Fixed Thresholds''" is checked, the thresholds given at the right of the tab are used as limits which must not be exceeded in a trial. If the check box "''Artifact Scan Tool''" is checked, a scan of the data set is used to find artifacts.

* Press the green "'''Start Scan'''" button. The data file is scanned for artifacts. After the scan is completed, a color-coded representation of maximum signal in channels and trials appears. This scan only has to be performed once for a data file, unless conditions are changed. The next time the paradigm is opened with the "''Edit Paradigm"'' command (cf. part C of this tutorial), the scan result will be available.

<div style="color:#00000a;"></div>

[[Image:ERP Processing (5).png]]

* The trials of the three active conditions are sorted according to their maximum amplitude from left to right. The red bar at the bottom indicates which of the trials are currently marked as artifacts due to their high amplitude. The channels are sorted according to the mean of the maximum amplitudes of the trials from bottom to top. Move the mouse pointer to the top of the display. The cursor changes to an up-down arrow. Click and drag the cursor down with the left mouse button to exclude the topmost channel, which carries an EKG artifact.
* Click on the button "'''Gradient'''" at the bottom of the dialog tab. The display changes to show the maximum gradients in the trials. The gradient is defined as the amplitude difference between two neighboring samples. Move the mouse pointer to the right edge of the display. When the cursor changes to a left-right arrow, click and drag the cursor to the left with the left mouse button to exclude the sweeps with the highest gradients, which are due to eye artifacts.
* At the new position of the dividing line which separates artifacts from good trials, press the right mouse button. A popup menu with information about the channel and trial at the cursor position appears.

<div style="color:#00000a;">[[Image:ERP Processing (9).gif ]]</div>

* Choose the menu entry "'''Show Trial".''' The trial is displayed in the EEG. If it still carries an artifact, more sweeps should be excluded.
* For more information about the artifact scan tool, please refer to the corresponding reference section in the electronic help. Switch to the "Average" tab now.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

'''4. Averaging'''

* At the bottom of the Average dialog tab, a list of currently selected conditions for averaging is shown. It already contains the three conditions for which matches were found in the EEG file. The right-most column indicates that all trigger events which matched the conditions will be averaged ("A").
* Double-click on the condition "Hit" in the list box at the bottom. The cross in front of the condition name disappears, which indicates that this condition will not be averaged. Double-click it again to activate averaging of the condition again.
* Click the green button '''"Average"''' on the right to start averaging. The progress is shown in an information window.

<div style="color:#00000a;"></div>

[[Image:ERP Processing (6).gif ]]

To cancel the averaging process, press any key. A message box appears. If you choose "'''No'''" averaging is continued. Choosing "'''Yes'''" stops the averaging process and asks you for a file name for each condition. After saving, the new averaged file is opened and the averaged segments are automatically displayed in the Top Viewer window. If you choose "'''Cancel'''", the results for the condition are not saved.

'''C. Edit a pre-defined paradigm'''

'''1. Load data and paradigm file'''

* With file "'''Freq-1200Hz-Resp-L.cnt'''" open, choose menu entry '''ERP/Edit Paradigm''', which opens the paradigm again (the copy of the paradigm file that was stored in the data directory), including the changes which were made in the last session.

<div style="color:#00000a;"></div>

'''2. Edit trigger definition'''

* Choose the tab "Trigger" on the top left. You now see the definition of triggers in the list view box at the bottom.

<div style="color:#00000a;"></div>

[[Image:ERP Processing (8).png]]

* The top half of the tab contains the edit section. In the top row, attributes which describe experimental categories can be defined or deleted. The next row shows the attribute values which are available. The values which are currently active for the selected trigger code (left) are highlighted.
* Trigger code 128 does not have a proper definition for the attribute "frequency". To change the definition:

* <div style="margin-left:1.259cm;margin-right:0cm;">In the list box below the attribute "code" (left), choose code 128.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">In the edit box below the attribute "frequency", type in "undefined". Click the pushbutton "'''Add to List"''' on the righthand side, which adds the new value into the list box and selects it automatically.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Click the button '''"Set"''' to set the new definition for trigger code 128.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Alternatively: right-click with the mouse directly on the value which you want to change in the list view box at the bottom of the tab. See what happens... (more information about defining triggers can be found in the electronic help reference section).</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">The definition for trigger 128 has changed. Choose the tab "Condition" (top of the page) to get back to the condition page.</div>

<div style="color:#00000a;"></div>

'''3. Edit conditions'''

* Switch to the 'Condition' tab. Select the last line of the condition edit list box (center of page) by a single click with the left mouse button. The name of the condition appears in the top left corner of this section of the page.

<div style="color:#00000a;"></div>

You can edit the name in the name edit field, and rename the condition by clicking the "'''Replace"''' button.

Now we will add a new condition that links the standard stimulus with a response time:
A new condition is defined as follows: In the name field, type in a new name, e.g. "Resp_Time".

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Qualifier", select "CURRENT".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Attribute", select "type".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Operator", select "IS".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Value", select "auditory".</div>

<div style="margin-left:0.cm;margin-right:0cm;">Click the '''"Insert"''' button to start up the new condition. The name is automatically assigned to the new condition.</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Qualifier", select "NEXT".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Attribute", select "Interval".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Operator", select "IS LESS THAN".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the edit box that appeared under "Value", type 500.</div>

<div style="margin-left:0cm;margin-right:0cm;">Click the "'''AND"''' button to extend the condition.</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Qualifier", select "NEXT".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Attribute", select "name".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Operator", select "IS".</div>

<div style="margin-left:0cm;margin-right:0cm;">In the list box "Value", select "response".</div>

<div style="margin-left:0cm;margin-right:0cm;">Finish off the condition by clicking the '''"AND"''' button again.</div>

* The new condition is automatically evaluated. 160 matches are found, i.e. in all cases, the response was within 500ms.
* Select the line "Next.Interval IS LESS THAN 500ms" in the condition. Enter the value "300" in the edit box at the top right of the tab and click the '''"Replace"''' button. The condition changes accordingly and is re-evaluated. Only 142 matches are found now.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (9).png]]

* If you leave the dialog box with the "'''OK" '''button, the settings are automatically stored in the data directory if the directory is writeable. If you choose the menu entry '''ERP/Edit Paradigm''' in the future, this specific definition will be opened.
* Choose ''ERP/Average ''again. You will see that four conditions are selected for averaging. The newly defined condition is active. If you just want to compare the condition "Resp_Time" with the one that did not have a time limit ("Standard"), select the other two entries (by holding down the '''CTRL '''button on the keyboard while selecting) and click the button''' "Remove from List" '''to remove these conditions from the averaging list. Only two conditions are now active for averaging.

=== Top View of Data Segments ===

Any EEG or MEG data segment can be viewed and analyzed in the Top View window. Waveforms are arranged according to their position on the head. The various options include peak finding, analysis and annotation, 3D mapping of amplitude or current source density, overplot of several conditions, and many more.

A detailed description of the features is given in online help chapter “''ERP / Reference / Viewing and Analyzing Data in the Top View”.''

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (10).png]]

''Topographic view of averaged data in a 32-channel auditory auditory evoked ERP experiment. Two conditions are overplotted. A map of the N100 in one condition is shown. Channel amplitudes at the N100 latency are displayed''

To view a segment or a set of segments in the Top View window, right-click on the segment waveforms and select '''''Top View''''' from the popup menu that appears. The Top Viewer window comes up, displaying the first segment in the data file. To switch to another segment, click on the segment name in the top line; select several segments for overplot by holding down the '''<CTRL>''' key while clicking on the segment names. Note that even if several conditions are shown, only one condition is active for analysis. The active condition is indicated by bold print in the top line, and in the title bar of the window.

'''Measuring peaks and amplitudes'''

'''Note: There are powerful tools for peak and amplitude analysis and export in the''' '''Combine Conditions, Channels, Find Peaks Module.'''

'''''Peaks'''''

To measure peaks and peak areas in the Top Viewer, right-click into a waveform between the baseline and the peak, and select the option '''''Find and Mark Peak''''' from the popup menu. If the peak is small, operate on the zoomed waveform: Right-click onto the waveform, select '''''Zoom Waveform''''' from the popup menu and then proceed to mark the peak. The ''Peak Finding'' dialog box appears and shows the result of the peak search:

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (14).gif ]]

''Result of a peak search in the waveform of electrode T3 of a single epileptic spike. The peak ''

''amplitude is -50.7 µV. The peak latency is 5 milliseconds after the mid-latency of the search pattern.''

A peak search can also be initiated from the menu entry '''Analysis / Find Peaks'''. The search channel and time range can then be specified in the top row of the dialog box. Click the '''Find '''button to start the search.

Please refer to the online help'' Reference ''chapter for a detailed description of the peak finding tool.

'''''Waveform amplitudes'''''

To display amplitudes at specific latencies, double-click on a waveform and drag the cursor to the desired latency or use the '''left-right arrow keys''' on the keyboard. The latency is displayed at the bottom of the window, and a 3D map appears in the top right corner. From the '''View '''menu, select the '''''Preferences''''' option. In the dialog box which appears, select the tick marks '''''Show Labels''''' and '''''Show Amplitudes''''':

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (15).gif ]]

'''Please note:''' Peak latencies and amplitudes can be determined over multiple files in a quick automatized way using scripts. Please refer to Chapter "''Batch Processing'' ''and Combining Conditions / Combine Conditions".''

'''Montages'''

The displayed montage in the Top Viewer can be any arbitrary montage. Peak amplitudes are automatically adapted to the currently applied montage. When the Top Viewer window opens, the montage selected in the BESA Research main window is selected by default. Use the '''Montage '''menu or click on the text at the bottom left to switch to another montage.

'''Advanced viewing options'''

Further options include:

* <div style="margin-left:1.259cm;margin-right:0cm;">Moving waveforms in the display, zooming individual channels, hiding channels, zooming the whole display.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Selecting only a part of the epoch for display.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">3D whole head mapping of voltage or current source density.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Changing display options such as tick marks, channel labels, baseline information, font sizes, colors, and more.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Display of standard deviations, and event-related (de-)synchronization (this requires band pass filtering of the data during averaging, see the corresponding help chapter).</div>

<div style="color:#00000a;"></div>

Please refer to the online help chapter “''ERP / Reference / Viewing and Analyzing Data in the Top View'' for more information.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

=== Grand Averaging and Combining Conditions ===

[[Image:ERP Processing (16).gif ]]

The ERP Module allows for quick combination of averaged segments, e.g. to create Grand Averages over subjects or to compute weighted sums and differences of conditions.

Conditions from different recordings/subjects can be combined in a convenient way using scripts. The menu entry "'''ERP/Combine Conditions, Channels, Find Peaks'''" allows for grand averaging and creating sums and differences between conditions. It also provides a tool for spatial and temporal resampling, and allows to perform an automatic peak analysis of multiple averaged files. For a detailed description of the 'Combine Conditions, Channels, Find Peaks' functions, please refer to the help chapter "''Batch Processing and Combining Conditions / Combine Conditions''".

[[Image:ERP Processing (17).gif ]]

=== Managing Triggers ===

==== Creating Triggers from EMG/EEG Channels ====

It is possible to create new trigger events from any of the recorded channels. This is achieved by defining parameters that characterize the features of the event. After the parameters are defined, the whole EEG /MEG is searched for events which match the parameters, and new trigger events are created. The steps to be taken are illustrated in the help tutorial chapter ''"ERP / Functions... / Managing Triggers / Tutorial 2'' ''Creating Triggers from EMG".''

Briefly, the procedure to create triggers for a recurring pattern is as follows:

1. Mark a typical occurrence of the pattern by a left mouse drag.

2. Use menu item '''ERP / Create Triggers from EMG/EEG''' to open the ''Schmitt Trigger'' dialog box.

3. In the dialog box, select the channel you want to scan for triggers under'' Chan+.'' In most cases, it is advisable to go through section ''Trigger Channel Prefiltering'' and check the tick marks ''Differentiate, Rectify, Smooth After Rect'' and enter a value between 50 Hz and 100 Hz for the smoothing frequency (see figure below).

4. Set the Schmitt Trigger parameters. The Schmitt Trigger is characterized by 4 parameters:

* <div style="margin-left:1.9cm;margin-right:0cm;">upper threshold: the threshold that the signal has to exceed</div>
* <div style="margin-left:1.9cm;margin-right:0cm;">lower threshold: the threshold that the signal must not exceed during the dead time before the trigger</div>
* <div style="margin-left:1.9cm;margin-right:0cm;">dead time: the time interval before the trigger where the signal must be lower than the lower thresholds</div>
* <div style="margin-left:1.9cm;margin-right:0cm;">return time: the time during which the signal has to return below the threshold</div>

Click the button '''View Current Settings'''. In the window that pops up, use the mouse drag to adjust the edges of the yellow block so that the lower threshold is above the pre-trigger baseline, and that the higher threshold stays well under the peak (vertical mouse dragging). Adjust the pre-trigger dead time (length of block left of the red line) which prevents recognizing each threshold crossing in a burst as trigger event, and the return time (horizontal mouse dragging).

5. Click '''OK'''. The parameters are updated in the ''Schmitt Trigger'' dialog box.

6. Click the buttons '''Add to List''' and '''Search Selected''' to start the trigger search.

Triggers can be deleted again by calling the ''Schmitt Trigger'' dialog box again, selecting the corresponding entry in the list box, and clicking the''' Delete Selected '''button. Triggers can also be deleted using the'' Edit'' ''Triggers'' command (see next section).

A complete reference of the features is given in the online help chapter ''"ERP / Reference / Managing Triggers / Creating Triggers''". An advanced topic explains the use of different filter settings using a myoclonic burst as an example (Strategies for Schmitt Trigger definition).

'''Tutorial 2: Creating Triggers from EMG'''

[[Image:ERP Processing (18).gif ]]

''The waveform of a trigger channel can be rectified and filtered to define trigger events. In the example above, the EMG channel FDIL is scanned for myoclonic discharges. The small window shows the waveform of the marked epoch after appropriate filtering.''

==== Editing Triggers ====

Patterns and tags can be converted into trigger events using the '''''Edit Triggers''''' tool. After conversion, tags found in a pattern search can be used in conditions: they can be analyzed by the paradigm tool which controls and stores the complete pre-averaging process. This facilitates for example the averaging of epileptic spikes which were hand-marked or found by a pattern search (cf. chapter ''"Review / Searching and Averaging"'').

The '''''Edit Triggers''''' tool is also useful to delete triggers which were created earlier, to change trigger codes, or to create triggers for FFT averaging with graphical artifact rejection on the basis of the paradigm tool.

A detailed description of the features is given in the online help chapter ''"ERP / Reference / Managing Triggers / Editing Triggers".''

[[Image:ERP Processing (19).gif ]]

''The Edit Triggers dialog box is divided into different sections to convert tags to triggers, delete triggers, change trigger codes, and to create triggers for FFT averaging using the artifact scan tool of the ERP paradigm.''

==== Event Files ====

BESA Research stores events in a binary event file in the program data base. However, it can be useful to be able to export, edit, or import events. The ERP module allows to export and import event files in ASCII format with the menu commands '''ERP / Save Events As '''and '''ERP / Open Event File'''. These event files can hold all types of events which occur during EEG or MEG recordings, e.g. triggers, comments, epochs, or tags. They can also be edited to change the type, latency, or number of events. For example, trigger events may be read in from an ASCII file, or the frequency of events of a certain type may be analyzed in a statistics software after exporting events.

A detailed description of the features and the format of ASCII event files is given in the online help chapter ''"Help / ERP / Reference / Managing Triggers / Working with Event Files".''

==== Tutorial 2: Creating Triggers from EMG ====

In this tutorial, myoclonic activity that was recorded via polygraphic channels is converted into trigger events.

* Open the MEG+EEG file segment "'''myo_sect.foc'''" in the folder "''Examples\EEG -MEG -Myoclonic-Jerks''". We will only inspect EEG channels during this tutorial and select the two relevant EMG channels as additional channels. Press the "'''Scp'''" button to display only EEG channels. Set the time interval to 4s and switch off the high cutoff filter (choose menu entry '''"Filters/High Cutoff Filter / High Cutoff Filter Off"''' or use the ''''HF'''' button). Press the ''''Add' '''button at the top right of the window and select the additional channel montage 'FDI-EMG'. The channels FDIL/FDIR which can be seen at the bottom of the window are the EMG channels recorded from the FDI muscles of the left and right hand.
* By clicking on the scaling button on the bottom right of the screen, adjust the voltage of the additional channels to 20 µV.

<div style="color:#00000a;"></div>

Mark a block that encloses a time interval where the feature occurs, e.g. an EMG discharge (jerk) in channel FDIL:

[[Image:ERP Processing (20).gif ]]

* From the '''ERP''' menu, select '''"Create Triggers from EMG/EEG'''". The '''Schmitt Trigger settings''' dialog box appears.
* Press the ''''Load' '''button and open the pre-defined trigger definition ''''EMG-Jerks.smt''''.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (21).gif]]

Two definitions for triggers have already been set for comparison. They are listed in the list box at the bottom.

Apart from the definition list, the box comprises three main sections.

* In the section ''"Trigger Channel''s" choose a trigger code which you want to assign to the EMG artifact. As a default setting, the code 403 is suggested. In this example, accepted this default.
* Select the channel that contains the information (FDIL) in the "''Chan. +"'' dropdown list.
* If you want to reference the channel against another channel, choose a reference channel from the "''Chan. –"'' dropdown list. This is not necessary here.
* In the section "''Trigger Channel Prefiltering''" check the respective options if you want the channel pre-filtered according to the current filter settings ("''Initial Filtering"),'' differentiated, rectified, and smoothed with an additional low-pass filter after rectification. Check the options 2, 3, and 4 (all except "Initial Filtering"). The cut-off frequency for the smoothing can be adjusted manually. Try 70 Hz as the smoothing frequency.
* Click the button "'''View Current Settings'''" to view the effect of the current filter settings on the signal in the specified channel. In our example, the result looks like this:

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:ERP Processing (22).gif]]

* The yellow rectangle denotes the parameters which define whether the signal is accepted as a trigger event. Four parameters can be varied:
* The top edge of the rectangle denotes the threshold which must be exceeded by the signal (green line).
* The bottom edge of the rectangle denotes the pre-trigger threshold which must not be exceeded by the signal prior to the trigger event (red line). This ensures that in the case of multiple trigger events, events are excluded which may contain contributions from previous triggers.
* The left edge denotes the "dead time" prior to the trigger event during which no other event is allowed to occur.
* The right edge denotes the "return time" during which the signal must return below the bottom edge. If the event shows a slow decay, it is excluded. This prevents merged multiple events to be included.
* Drag the bottom and the top of the rectangle up with the left mouse button to increase the thresholds. The result can look like this:

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

[[Image:ERP Processing (23).gif]]

* Clicking the '''OK''' button leads back to the dialog box, where the four parameters (shown in the section "''Trigger Settings''") have now been adjusted. By typing in the values manually, adjust the threshold to 40 µV, the limit during dead time to 25 µV, the dead time to 70 ms, and the return time to 30 ms.
* Click the button "'''Add to List'''" to complete the definition of the trigger event. 
* Click the button "'''Search Selected'''" to search the file for occurrences of the trigger event. After the end of the search, the number of detected trigger events is given in the list box. In this example, 39 trigger events were found.
* Leave the dialog box with "'''OK'''". The current settings are automatically saved in a file with the filename of the data file with the extension "SMT".
* Press the ''''SCP'''' button again and page forward in the file using the space bar. In the screen that appears, mark a relatively small myoclonic signal in the FDIR channel:

<div style="color:#00000a;"></div>

[[Image:ERP Processing (24).gif]]

* Choose the menu entry '''Create Triggers from EMG/EEG''' again. The dialog box automatically suggests a new trigger code. Choose the channel "FDIR" in the "Chan.+" combo box. Select the title bar in the list box at the bottom of the dialog box to make sure that no already defined trigger definition is selected. Click the button '''"View Current Settings'''". The thresholds have to be lowered to yield a picture like this (corresponding to upper and lower thresholds of 14.8 µV and 8.5 µV):

<div style="color:#00000a;"></div>

[[Image:ERP Processing (25).gif]]

* Click the button "'''Search Selected'''". Since no trigger definition is selected in the list box at the bottom of the dialog box, the settings which you have just entered are copied to the list box, and a search for myoclonic events in the FDIR channel is performed. For the settings quoted above, 17 trigger events are found.

<div style="color:#00000a;"></div>

If the file is opened again later and the menu entry '''Create Triggers from EMG/EEG''' is chosen, the settings made earlier are automatically loaded from file. It is also possible to load different files or to save the settings to a different filename using the "'''Load'''" and "'''Save'''" buttons.

'''Note''': If one of the entries in the list box other than the header line is selected, the button "'''View current''' '''settings'''" shows the settings of this particular entry. Since it is a fixed definition of a trigger, the thresholds cannot be changed graphically.

For further information about conversion of EMG/EEG artifacts into trigger events, please consult the online help section in the Averaging Module Reference on "''Strategies for Schmitt Trigger Definition''".
[[Category:Research Manual]]

BESA Research Spectral Analysis

2017-04-07T12:51:45Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
== Spectral Analysis ==

There are two different types of spectral analysis in BESA Research:

1. A Fast Fourier Transform (FFT) computes the total spectral content of a certain data interval, usually a few seconds or minutes long. This interval can be

* a short data block of interest, typically a few seconds
* an extended time range, e.g. between two markers or the whole data file ('mean FFT')

2. Density spectral arrays (DSA) provide an overview of the temporal evolution of spectral activity over longer epochs (here: 15, 20 or 30 minutes) or the whole data file. DSA is useful for reviewing long recordings, since epochs where changes of frequency distribution or amplitudes occur can be identified at a glance.

=== FFT ===

The Fast Fourier Transformation (FFT) can be applied to a marked region, the data displayed on the screen, over a larger time range in the data between two markers, over marked epochs, or the whole EEG, in order to examine the frequency content of a signal. Results of the FFT can be viewed in a variety of ways, including amplitude and power spectra, amplitude and power in frequency bands, and these results may be printed or written to data files in ASCII format. The previously calculated FFT spectrum may be redisplayed. The current FFT can be saved to a binary file and reloaded. Topographic maps of amplitude, power, and phase can be plotted.

==== FFT Computation and Display ====

Two FFT computations are available in BESA Research:

* The FFT over a short data block of interest
* The Mean FFT over an extended time range

'''FFT over a short data block of interest'''

To start an FFT calculation, highlight a data block by left mouse click and drag. If no block is highlighted, the FFT will be performed over the time range shown on the display. Apply one of the following:

# Right-click into the marked block and select the item ''FFT''.
# Type the HotKey ''''F''''.
# Select the item ''FFT-Spectrum'' in the '''Process '''menu ('''Alt+P F''').

[[Image:Spectral (2).gif ]]

[[Image:Spectral (1).gif ]]

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

'''Note:''' It is not possible to select the FFT process if the region to be processed contains less than 128 samples. This can occur, for instance, if the time range of a highlighted region is too short.

'''Note''': When an FFT is selected, BESA Research displays the results for the current montage on the screen. In the background, the program also performs the FFT on 81 standard interpolated, average referenced channels in the case of EEG and on the average referenced data in the case of MEG. When FFT results are saved to a file, you have the choice of saving either the current montage, or the 81 interpolated, average referenced channels (only for EEG). Maps of the FFT results are always based on the average referenced data. This is necessary to ensure that electrodes are given equal weights in the nonlinear transformation to power or amplitude (=root of power).

For an FFT over a marked block or the whole screen, no parameters have to be specified. Internally, BESA Research preprocesses the selected data segment for the FFT in two steps:

# A window function is multiplied with the data to attenuate the amplitudes at the ends to zero
# The number of samples is increased by interpolation (if necessary) to make it a power of 2.

<div style="color:#00000a;"></div>

This preprocessing of a highlighted data segment is illustrated in the figure below:

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Spectral (3).gif ]]

The highlighted block constitutes 80% of a window of width 100%. A cosine squared (cos²) window of width 20% of the total is applied at the edges, so that the signal amplitude is attenuated to 50% at the edges of the marked block, and zero at the edges of the window. Then we take the number of time samples in the window, and select the next higher power of 2 (up to 8196). Using spline interpolation, the data in the window are converted to this larger number of points, and the FFT is applied. If the number of points is greater than 8196, spline interpolation is used to reduce the number to 8196. In this case, to avoid aliasing, the data are low-pass filtered at a frequency corresponding to ¼ of the new sampling rate.

If the FFT is applied to the data displayed on the screen, windowing is similar to that for the highlighted block, except that no data outside the block are included: the cosine squared window is applied so that the signal amplitude is attenuated to zero at the edges of the display.

'''Mean FFT Spectrum over an extended time range'''

To start a mean FFT over an extended time range, e.g. between markers or over the whole data file, select the item ''Mean FFT-Spectrum'' in the '''Process''' menu ('''Alt+P M''').

<div style="color:#00000a;">[[Image:Spectral (4).gif ]]</div>

In the upper section of the ''Mean FFT'' dialog box the range on which the FFT is performed can be set:

# <div style="margin-left:1.259cm;margin-right:0cm;">on the whole EEG</div>
# <div style="margin-left:1.259cm;margin-right:0cm;">on all marked epochs within the EEG</div>
# <div style="margin-left:1.259cm;margin-right:0cm;">on all marked epochs with a specific label</div>
# <div style="margin-left:1.259cm;margin-right:0cm;">on a time range delimited by two markers</div>
# <div style="margin-left:1.259cm;margin-right:0cm;">on all epochs delimited by two markers</div>
# <div style="margin-left:1.259cm;margin-right:0cm;">over triggers generated by the ERP module; mean FFT over triggers is only available if the mean FFT is called from the ERP module</div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

Ranges which are not currently available (e.g. if no epochs or no markers are defined) are grayed out.

The mean FFT consists of a set of FFTs from overlapping data segments spanning the selected time range. Each data segment has a fixed width, defined as a power of 2 sampling points, that can be selected under '''Block Size / Points per Block''': In the center of the options window, the number of points per FFT block is selected. Selection can be 128, 256, 512, or 1024 points. The block width influences in particular the contribution to the spectrum of low frequencies: the wider the block, the lower the frequencies that can be represented. The lowest frequency is given by 2/(block width in seconds). Thus, if you have recorded data with a high sampling rate, a wider window is necessary to compute low frequencies. Note: For each block size in samples the corresponding width in seconds is specified in brackets.

The lower section of the options window determines amplitude and gradient thresholds for including a block in the mean FFT. If signal amplitudes exceed the amplitude threshold or the difference of two consecutive signal amplitudes exceeds the gradient threshold, the block will be omitted. Different thresholds may be set for each channel type (in the above example, scalp and polygraphic channels).

Press '''OK''' in the options window to start computation of the mean FFT. Computation can be interrupted by pressing any key. The interrupt has to be confirmed and may be canceled to resume mean FFT calculation.

Note on computational steps: Each data segment overlaps 50% with the next segment, and is multiplied by a cosine squared (cos² window, as shown at the bottom of the figure below. This combination of overlap and windowing ensures that each time point contributes equally to the mean spectrum (since cos² (x) + sin²(x) = 1). Because mean spectra are computed, phase information is not available.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Spectral (5).gif ]]

Note that time ranges marked as artifacts are not included in the computation of the mean FFT. These time ranges are not excluded when computing the FFT of a marked block or of the displayed data.

'''Redisplaying the previous FFT'''

The results of the previously calculated FFT spectrum can be redisplayed by selecting the item ''Previous FFT-Spectrum'' in the '''Process '''menu or by typing the hotkey ‘'''CTRL-F’'''. It is not possible to recall the previous FFT if there was a change in

* the montage for which the FFT was calculated
* additional or artifact channels
* bad or interpolated channels
* the channel configuration

<div style="color:#00000a;"></div>

after the last FFT was calculated.

==== Mapping the Results of the FFT ====

Amplitude, power, mean band amplitude or power, and phase delays can be mapped. How to map FFT results is described in the chapter ''"Mapping / FFT Mapping''".

==== FFT 'View' Menu: Adjusting the FFT Display ====

[[Image:Spectral (6).gif ]]

The FFT spectrum of each channel in the '''current montage''' is displayed in a window on the left of the screen. At the bottom is the frequency scale. To the right, the dominant frequency is shown for each channel, together with the amplitude or power at this frequency. The dominant frequency is determined between the lower boundary of the first frequency band and the maximum displayed frequency.

<div style="color:#00000a;"></div>

[[Image:Spectral (7).gif ]]

''FFT result window with display of amplitude spectrum with sum of amplitudes in bands, color coding, and frequency range 1-30 Hz. The montage is TR_Temporal Region.''

Using the '''View''' Menu, the following options can be selected:

* <div style="margin-left:1.259cm;margin-right:0cm;">Results can be displayed as '''Amplitude''' ('''Alt+V A''') or '''Power''' ('''Alt+V P)''' spectra. At the top of the display (cf. example below) is the text ''"Amp. Spectrum"'' or'' "Power Spectrum". ''Click on the text to toggle between the two types of display.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">The graphical display of amplitude or power spectra can be '''Normalized''' ('''Alt+V N'''), such that all displayed values are scaled relative to the dominant frequency separately for each channel (i.e. amplitudes cannot be compared between channels). Without this option set, values in each channel group (scalp, source, MEG, Pgr, ICR) are scaled to the channel in this group which has the largest amplitude in its dominant frequency (i.e. amplitude relationships among channels within one channel group are upheld).</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Amplitude or power values can be displayed on a '''Logarithmic scale''' ('''Alt+V L'''). Amplitude values are displayed over two log units, power values over four log units. Thus, for amplitudes, values less than 1/100 (two log units) of the maximum are set to zero. For power, values less than 1/10000 (4 log units) of the maximum are set to zero.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">The sum of '''amplitudes''' or '''powers''' in each frequency band can be displayed ('''Alt+V M''', or '''Alt+V''' '''O''').</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Spectra are shown as a curve of amplitude/power vs. frequency. If '''Color coding''' is selected ('''Alt+V C'''), then the areas underneath the curve are colored differently for each frequency band. Colors can be changed in the FFT Options menu ('''FFT/FFT Options Menu''').</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">The frequency scale can be set to one of the three predefined display frequencies '''1-30 Hz, 1-50''' '''Hz''', ('''Alt+V 3''', or '''Alt+V 5''') '''or 1-half of the sampling frequency''', e.g. 1-100 Hz in the above screenshot of the '''View''' menu. Alternatively, any user-defined '''Frequency Band '''('''Alt+V B''') can be displayed. The upper and lower boundary of the frequency band is set to the next whole-numbered multiple of the frequency resolution. The DC component is always set to zero.</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">'''Info-box'''. Click with the right mouse button on a particular frequency in the spectrum of one of the channels to obtain a box with the following information: Channel name, frequency, and amplitude/power at that frequency.</div>

<div style="color:#00000a;"></div>

'''Note:''' The number of channels shown in the FFT display is the same as the number shown in the EEG display. If you change the EEG display (e.g. by changing the number of scalp electrodes or switching off polygraphic channels), the FFT display is updated automatically. The update can be performed without recalculation. If additional channels or artifact channels reconstructed by BESA Research artifact correction are switched on/off, or the status of bad or interpolated channels changes, the FFT is recalculated. Recalculation is only possible if the FFT was calculated over a block or the whole screen. The mean FFT window has to be closed in this case. Recalculation is also not possible if the FFT was loaded from file. If you change the montage in the EEG display, the FFT window will always be removed: different montages require recalculation of the FFT.

'''Note''': Bad channels in the original montage are displayed in an attenuated color. The spectrum of bad channels is zero for each frequency. As the dominant frequency, its amplitude and the sum of amplitudes or powers in each frequency band cannot be determined, a horizontal bar is shown for each missing value.

'''Notes about display resolution: frequencies and pixels'''

When plotting the results of the FFT on the screen, there is a subtle interaction with the screen resolution which can affect the frequency and amplitude/power values displayed when generating maps or looking in the Info-box. Note that two types of situation can arise, depending on whether the number of frequency steps (= half the no. of sampling points in the data window) is greater or less than the number of screen pixels.

If the number of frequency steps is less than or equal to the number of screen pixels, the amplitude at each frequency can be displayed correctly.

If the number of frequency steps is greater than the number of screen pixels, then there are not enough pixels to display each amplitude. In this case, the amplitude displayed at each pixel is the maximum amplitude in the range of frequencies covered by that pixel. For a given pixel, this '''maximum''' amplitude can differ among channels. Thus, depending on the channel to which the mouse is pointing, the frequency displayed in maps (left click) or in the Info-box (right click) can vary, even if the horizontal position of the mouse is the same.

==== FFT 'File' Menu: Saving, Loading and Printing Results of the FFT ====

[[Image:Spectral (8).gif ]]

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

'''Loading and Saving FFT'''

Select''' Load'''... ('''Alt+F L''') to load an FFT file that has been saved to a binary file using '''Save'''... ('''Alt+F S'''). An FFT spectrum should be redisplayed with the file from which it was calculated. An FFT file cannot be loaded if electrode configuration and bad channels of the current file do not match with the electrode configuration and bad channels of the saved FFT spectrum. The montage of the current EEG is changed

to the montage of the loaded FFT. Filter settings that were active at the time when the FFT was calculated are not reset, but are indicated correctly in the FFT printout.

The heading of the printout shows the name of the loaded FFT file and the name of the EEG for which the FFT was calculated. If the loaded file contains a mean FFT spectrum, the mean FFT options are adjusted to the settings used to calculate the loaded mean FFT spectrum.

'''Averaging FFT spectra'''

Select '''Load and Average'''... ('''Alt+F V''') to compute averages of previously saved FFT spectra. In the appearing window, select an FFT spectrum ('''<nowiki>*.fft</nowiki>''') from the list on the left and press the [[Image:|top]] button to copy it to the list of FFTs to be averaged on the right. Press''' OK''' to calculate and display the averaged FFT spectrum.

[[Image:Spectral (2).png ]]

'''Note:''' Averaging of FFT spectra is only possible if the spectra were computed using the same epoch length (marked block or whole screen), montage, and sampling rate.

'''Exporting FFT spectral data'''

Select '''Export FFT Data''' in the '''File''' menu ('''Alt+F F'''). You can select two different output montages:

* Output '''81 Interpolated''' average referenced data (to a standard configuration of 81 electrodes, only available for EEG data) ('''Alt +F FI'''), or
* Output '''Current Montage''' data ('''Alt+F FM''')

<div style="color:#00000a;"></div>

Select one of two output formats:

* Write the data in''' Vectorized '''format: Line 1 of the output file contains the number of frequency steps (Npts), a starting value for BESA Research’s time scale (TSB), the frequency step (DI), scaling in bins per microvolt (SB), a scaling value for the BESA Research display (SC), and the number of channels (Nchan) as shown in the following example:

<div style="color:#00000a;"></div>

<div style="margin-left:0cm;margin-right:0cm;">"Npts= 1023 TSB= 0.10 DI= 0.100 SB= 1.000 SC= 100.0 Nchan= 23".</div>

<div style="margin-left:0 cm;margin-right:0cm;">Line 2 lists the channel labels. Each successive line contains the amplitude/power values at each frequency for one channel.</div>

* Write the data in''' Multiplexed''' format: Line 1 contains the frequency step size in Hz. Line 2 lists the channel labels. Each subsequent line contains amplitude/power values for all channels (in the sequence given in line 2) for one frequency.

<div style="color:#00000a;"></div>

Both vectorized and multiplexed files may be reread into BESA Research in the same way as time-domain averages. Vectorized files may be read directly using the '''File / Open''' menu. Multiplexed files may be read using the ASCII import menu item '''File / Import ASCII file'''.

For each of these output formats and montages, different data can be saved:

* '''Amplitude Spectrum''' ('''Alt+F FA'''),
* '''Power Spectrum''' '''(Alt+F FP'''), or
* '''Real + Imaginary Part''' ('''Alt+F FR'''). In this case, amplitudes of the real and imaginary components are written to two separate files.

<div style="color:#00000a;"></div>

DOS file name extensions for each type of output file are given in the following table:

[[Image:Spectral (11).gif]]

'''Exporting band amplitudes and power'''

Select '''Export Power in Bands''' ('''Alt+F P''') or '''Export Amplitude in Bands''' ('''Alt+F A'''). An ASCII file is produced with one channel per line, and each line contains the value for each frequency band.

'''Sending FFT data to MATLAB'''

Select''' Send to MATLAB '''('''Alt+F M''') to transfer the current FFT data to MATLAB. This menu entry is available only when MATLAB is installed. Details on the MATLAB interface are provided in Help Chapter ''“MATLAB”.''

[[Image:Spectral (12).gif]]

A dialog window opens that allows to specify:

* the type of data to be transferred (Amplitude, Power, or Complex FFT data)
* whether each frequency bin should be transferred or frequencies should be pooled in bands
* the montage for which the FFT should be sent

When hitting '''OK''', the sent data will be made available in MATLAB in struct variable '''besa_fft'''. For details on the data transfer from BESA Research to MATLAB, please refer to Help Chapter ''“The MATLAB interface”.''

'''Printing results of the FFT'''

Select '''File / Print''' to print the FFT display and FFT maps. BESA Research uses the standard WINDOWS printer output. You may change your printer settings temporarily for your current BESA Research session. In the printer setup, you can choose the orientation (landscape or portrait) and the resolution. If you have any problems with printing, try to set the resolution to 300*300. If you want to change the printer setup permanently, please select the Printer Control from the WINDOWS main control group.

A preview of the printout can be generated with '''File / Print Preview'''. Click on the ''''OK'''' button to return to the program.

'''Closing FFT'''

To remove the FFT window (without saving the results), select ''Close'' in the''' File''' menu ('''Alt+F C'''), or simply type the '''<Esc> '''key.

==== FFT ‘Options’ Menu ====

[[Image:Spectral (13).gif]]

The''' Options '''menu allows to define FFT mapping options, to set colors for the display of each frequency band, and to define and name up to 7 bands. When working with BESA Research, the band colors, names, and frequency ranges of the last session are stored in the file '''BESA.set'''. These values are then used in the next BESA Research session.

'''Mapping options'''

In the Mapping submenu two entries toggle different mapping modes:

<div style="color:#00000a;">[[Image:Spectral (14).gif]]</div>

* The entry '''3D Whole Head Mapping''' toggles between 3D and 2D mapping.
* The entry '''Top Meridian Projection''' toggles between top meridian projection and whole head mapping.

'''Defining band colors'''

[[Image:Spectral (15).gif]]

Select '''Options / Band Color''' ('''Alt+O C'''), and then the name of the band to define (e.g. '''Theta''': '''Alt+O CT'''). A window is presented with a palette of colors, allowing the choice of a color for the display.

Select''' Default Colors''' ('''Alt+O CD''') to select the default colors for the bands (predefined in '''BESA.ini''').

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

'''Defining band names and widths'''

Select '''Options / Band Name and Width''' to define up to 7 band names and frequency ranges. A window showing names and frequency limits is displayed, allowing redefinition of the frequency bands. Overlapping frequency ranges can be defined. Upper/lower limits of FFT bands can be set up to the maximum frequency that can be displayed in the current FFT (which is usually half of the sampling rate). Press the '''Default''' button to select the default definitions as predefined in the file BESA.ini and shown in the following table:

[[Image:Spectral (16).gif]]

==== FFT Mouse Controls ====

'''Single left click'''* on the '''displayed peak frequency''' or peak amplitude values of a channel or on the channel labels or head symbols at the left of the FFT window: Sets a cursor at the peak (dominant) frequency of the selected channel and displays a map of the topography at the marked frequency (only if the channel is not defined as bad).

* on the string indicating the '''spectrum type '''(Amp. Spectrum or Power Spectrum): Toggles between display of amplitude and power spectrum.
* on the string indicating the map type (EEG or MEG): Toggles between EEG and MEG FFT maps (only for combined MEG and EEG measurements). 
* on the '''displayed spectrum''': Sets a cursor and draws a FFT map of the topography at the marked frequency. The availability of this function by single left mouse click depends on the settings in the main window’s '''Options / Mapping''' submenu ('''Options / Mapping / Enable Direct Mapping by Single Click''').

<div style="color:#00000a;"></div>

'''Note:''' The mouse pointer changes to a hand in areas of the FFT window where left mouse clicks initiate an action.

'''Double left click'''
* on the '''displayed spectrum''': Sets a cursor and draws a map of the topography at the marked frequency. The availability of this function by single left mouse click depends on the settings in the main window’s''' Options / Mapping''' submenu ('''Options / Mapping / Enable Direct Mapping by Double Click''').

'''Right click'''
* on the '''displayed spectrum''': Opens an info-box indicating channel name, frequency, and amplitude/power at that frequency.

=== Density Spectral Arrays (DSA) ===

==== Introduction ====

The Density Spectral Arrays (DSA) module displays a compressed two-dimensional time-frequency display of the activity in the data file. It focuses on the frequency range of 1 Hz - 25 Hz which includes the commonly observed oscillatory rhythms in the human brain. This allows for a quick overview of the sections where events of interest occur, e.g. in the analysis of epileptic seizures or in sleep research. DSA values are computed for every second in the data file using a windowed FFT with a window length of 2s. By default, the DSA module uses a standardized brain source montage to separate the activities of both hemispheres and the different brain regions using 15 regional sources. This spatial filtering prior to the application of the time-frequency transformation helps to identify brain regions where oscillatory activity originates. The DSA can be invoked by hitting the [[Image:Spectral (17).gif]] button or from the '''Process''' menu.

[[Image:Spectral (18).gif]]

[[Image:Spectral (19).gif]]

''Standard DSA display of an EEG containing four seizures. For each brain hemisphere, the sum of activities is shown.''

'''Using DSA to navigate'''

With a '''left mouse click''' into the DSA display, you can navigate to the selected EEG event. The data review window display jumps to the selected time in the record.

'''DSA display modes'''

Three modes of DSA display are possible:

# Hemispheric Comparison, which sums up all the lateral activities of each hemisphere
# Regional Comparison, which gives account of the activity within five gross brain regions
# Current Montage, which shows the activity in each channel of the selected montage at the time the DSA window was opened. For MEG data, only the Current Montage option is available.

<div style="color:#00000a;"></div>

For the first two modes, the signals are first transformed to the standardized brain source montage ''BR_Brain Regions'' (see chapter ''"Review / Remontaging"'') before the summation of the spectral parameters is performed. This transformation of the data to a source montage optimally separates the activities from the different brain regions that generate overlapping signals at the scalp surface. DSA of scalp channels can be seen by selecting a recording (traditional) montage and selecting mode 3, current montage.

The way in which signals are sub-sampled to obtain the density display can be modified, from the fastest sub-sampling to an averaged or maximum signal display. The color-coded display of the spectral values in frequency bins can be normalized to the percentage value relative to the sum over all frequency bins of each channel.

The current position in the data file is indicated by the vertical dashed lines in the display.

[[Image:Spectral (20).gif]]

The time scale shows minutes as small gray ticks (in real time - not time measured from file start). In the "''Hemispheric Comparison''" mode, the time scale appears in the middle, whereas it is displayed below the channels otherwise. Thicker gray ticks indicate five-minute marks, larger black ticks ten-minute-marks, and segment borders are displayed in red.

==== Setting the DSA Display Mode ====

The data can be remontaged for display in three different ways using the first three toolbar buttons.

[[Image:Spectral (21).gif]] '''Hemispheric Comparison (default option)'''  

Hemispheric comparison is activated by clicking on the '''leftmost''' toolbar button. The integrated activity of each hemisphere is shown. In this mode, the DSA window aligns with the event bar at the bottom of the main window to relate activity to the events marked in the event bar. The integrated activity of each hemisphere is calculated by first transforming the data to the standardized source montage ''BR_Brain'' ''Regions'', which is also available from the "'''Src'''" button in the BESA Research main window (see chapter ''"Review / Remontaging").'' Then the signals of all source channels in the left ('''L''') and the right ('''R''') hemispheres are summed up separately. This transformation of the data to a source montage optimally separates the activities from the different brain regions that are overlapped and smeared at the scalp surface.

For MEG data, this option is not available.

[[Image:Spectral (22).gif]]''' Regional Comparison  '''

This option is activated by clicking on the''' second''' toolbar button. The integrated activity of five brain regions is shown. The regions are:

* '''FcpL, FcpR''', which sum all lateralized activity in the upper parts of the brain
* '''TmpL, TmpR''', which sum all activity in the temporal regions of the brain
* '''SagM''', which sum all activity in the sagittal midline regions of the brain (only shown if tick mark ''"Midline Channels"'' is on in '''Montage Options''').

<div style="color:#00000a;"></div>

In this mode, the DSA window is displayed in the right portion of the BESA Research main window. The integrated activity of each region is calculated by first transforming the data to the standardized source montage ''BR_Brain Regions'', which is also available from the '''"Src" '''button in the BESA Research main window (see chapter ''"Review / Remontaging''").

Then the signals of the source channels which belong to the corresponding region are summed up.

For MEG data, this option is not available.

<div style="color:#00000a;"></div>

[[Image:Spectral (23).gif]] '''Current Montage'''

With the '''third''' toolbar button, the Current Montage option is selected to display the spectra of the channels of the montage that was selected when the DSA window was opened. In this mode, the DSA window is displayed in the right portion of the BESA Research main window. If the current montage is changed in the BESA Research main window, the DSA display remains unchanged -''' Ändern'''.

<div style="color:#00000a;"></div>

[[Image:Spectral (24).gif]] '''Source Montage'''

The four following buttons, which appear only in the hemispheric comparison window, allow for the selection of the montage underlying the display, based on the source montage ''BR_Brain Regions''. One of the buttons is always down, with '''BR''' as default.

In the case of '''BR''' (''Brain Regions''), the averages of all left-hand and right-hand side channels of the montage ''BR_Brain Regions'' are shown in the upper and lower channel, respectively, as indicated by the labels''' L''' and '''R'''.

For '''TL''' (''Temporal Lobe''), the averages of the most important channels of the source montage ''TR_Temporal Regions'' are calculated and displayed in the upper and lower channels labelled '''L''' and '''R'''. The channels in question are TAL and TPL for the left-hand side and TAR and TPR for the right-hand side.

'''FP''' (''Frontoparietal'') is based on the source montage ''BR_Brain Regions'' and averages the source channels FL, CL, PL and FR, CR, PR, respectively, displaying them in channels '''L''' and '''R.'''

'''SG''' (''Sagittal'') also uses the source montage ''BR_Brain Regions''. The mean of the frontal sagittal channels FpM, FM and CM is displayed in the upper channel F, the mean of the posterior sagittal channels CM, OpM and CM is shown in the lower channel '''P'''.

<div style="color:#00000a;"></div>

[[Image:Spectral (25).gif]] '''Visualizing Differences'''  

Many features of interest are lateralized in the brain and show up clearly when hemispheric regions are compared directly. This is achieved using the '''Delta''' toolbar button:

This button enables subtraction of hemispherically homologue regions and is available for the standardized montage options "''Hemispheric Comparison"'' and "''Regional Comparison".''

'''Hemispheric Difference'''

<div style="margin-left:1.27cm;margin-right:0cm;">The integrated activities of the hemispheres (calculated as in the ''Hemispheric Comparison'' option) are subtracted from one another. The differences between the activities are displayed. The channel '''L+''' shows signal at the frequencies and latencies where activity was higher in the left hemisphere. Frequencies and latencies where activity was higher in the right hemisphere show up in channel '''R+.'''</div>

'''Regional Difference'''

<div style="margin-left:1.27cm;margin-right:0cm;">The integrated activity of four brain regions is calculated as in the ''Regional Comparison'' option excluding the midline sagittal region. Then the activities of homologous regions are subtracted from one another and this difference is displayed on the side where the activity is larger: Thus, the channel '''FcpL+''' only shows signal at frequencies and latencies where activity was higher in ''FcpL'' than in ''FcpR''. The signals in the other channels are calculated accordingly.</div>

<div style="color:#00000a;"></div>

[[Image:Spectral (26).gif]]''' Epochs'''

The epoch buttons allow the choice of time interval for browsing through the data.''' '''Either the whole file ("''All")'' or intervals of 15, 20 or 30 minutes, with one additional''' '''minute of overlap with the following window, are shown. The default is 20 minutes,''' '''which corresponds best to the length of the standard EEG. For continuous data files,''' '''interval start times are chosen in relation to the full hour (e.g. 18:00, 18:20 and''' '''18:40 for the 20-minute window). Only the first and last window are positioned such''' '''as to start and end with file start and end, respectively.

The default epoch is "All" for files shorter than 20 minutes and "20" for longer files. For files no longer than 15 minutes, all buttons are grayed (with "All" automatically selected). Otherwise, "All" and those buttons which allow paging are enabled.

In the case of "All" and files of long duration, a progress bar may appear. Hitting "'''Abort'''" will result in the display of those portions of the data that have already been calculated.

The epoch buttons are grayed in the zoom mode.

[[Image:Spectral (27).gif]] '''Paging'''

Page backward / forward one interval of the currently selected length. The page buttons are enabled only if the position in the file, and the file length, allow to browse to an earlier / later interval.

The page buttons are grayed in the zoom mode.

==== Display Options ====

To emphasize features of interest, the DSA display can be optimized to normalize and scale the spectral data in different ways.

[[Image:Spectral (28).gif]] '''Percentage Button'''

The status of the''' percentage '''button on the toolbar determines how the color-coded display of the intensity values in frequency bins is normalized. The options are:

'''Absolute Value''' (button is up):

<div style="color:#00000a;"></div>

<div style="margin-left:0cm;margin-right:0cm;">If this option is selected, the absolute amplitude or power intensity values are displayed.</div>

'''Percentage''' (default option, button is down)

<div style="color:#00000a;"></div>

<div style="margin-left:0 cm;margin-right:0cm;">If this option is selected, the intensity value for each sampling time and frequency is normalized to the summed intensities over all frequency bins averaged over all channels for that sampling time. Thus, the displayed DSA amplitude/power for one frequency bin is its contribution (in %) to the overall activity at that sampling time.</div>

The effect when applying the percentage normalization to data is shown in the example below, where hemispheric difference with and without percentage normalization is shown:

[[Image:Spectral (29).gif]]

<div style="color:#00000a;"></div>

[[Image:Spectral (30).gif]]

''Hemispheric difference display without percentage normalization (top) and with percentage normalization (bottom). The decreasing 9 to 7-Hz seizure activity in the right hemisphere emerges better from the background with percentage normalization.''

[[Image:Spectral (31).gif]]]''' Amplitude Button  '''

The amplitude button toggles between display of amplitude and power. The default setting is on amplitude (button is pressed).

If amplitude is selected, displayed intensities are in µV/Hz, fT/Hz, fT/(cmHz), or nAm/Hz.

If power is selected, displayed intensities are in µV²/Hz, fT²/Hz, fT²/(cm²Hz), or nAm²/Hz.

[[Image:Spectral (32).gif]]] '''Original Data and Baseline Normalization'''

By default, the original data are shown (button D down). If option B (baseline normalization) is chosen, amplitude/power for each sampling time and frequency and each remontaged channel is normalized by the sum over all sampling times for the given frequency.

This can sometimes help to suppress or intermittent or continuous signals of constant frequency.

[[Image:Spectral (33).gif]]]

[[Image:Spectral (34).gif]]]

''Hemispheric comparison display without (top) and with (bottom) additional baseline normalization, which enhances the contrast between seizures and background for this example.''

<div style="color:#00000a;"></div>

[[Image:Spectral (35).gif]]]''' Setting the Display Sampling  '''

Since the data file features far more sampling times than pixels available for DSA display, a sub-sampling is required to compress data file sections into the pixels shown in the DSA. The method how this is achieved can be chosen with the sampling popup menu. Using the sampling button in the toolbar, the type of sampling of data for the display can be chosen.

Three options are possible:

* '''Sub-sample Epochs:'''

<div style="color:#00000a;"></div>

<div style="margin-left:0.635cm;margin-right:0cm;">For each displayed pixel, one sample second in the middle of the represented time interval is selected. For this sample second, the activities are displayed. This is the fastest way to obtain the DSA display. The principle is illustrated in the graphics. In this example, only every fourth sample is computed for the DSA display.</div>

<div style="margin-left:0.635cm;margin-right:0cm;">[[Image:Spectral (36).gif]]]</div>

* '''Average Epochs''' (default option):

<div style="color:#00000a;"></div>

<div style="margin-left:0.635cm;margin-right:0cm;">For each displayed pixel, the average over all seconds which are summarized in that pixel is calculated for each frequency bin. In this way, it is ensured that sudden bursts of activity are not accidentally missed out. The principle is illustrated in the graphics.</div>

[[Image:Spectral (37).gif]]]

* '''Select Maximum:'''

<div style="color:#00000a;"></div>

<div style="margin-left:0.635cm;margin-right:0cm;">For each displayed pixel, the maximum over all seconds which are summarized in that pixel is calculated for each frequency bin. This enhances the impact of sudden bursts of activity in the display. The principle is illustrated in the graphics.</div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Spectral (38).gif]]]

<div style="color:#00000a;"></div>

[[Image:Spectral (39).gif]]] '''Scaling Buttons  '''

The left button (+) scales intensities up, the right one (-) scales them down. Each time one of the buttons is pressed, scaling is increased/decreased by a factor of ³√2. This means that pressing the same button 3 times results in doubling / halving the normalization intensity.

'''Zooming the Display'''

You can use the left mouse button to drag a rectangle anywhere in the display. A popup menu containing the entries "Zoom In" and "Zoom Out" appears, from which you can choose to zoom into the selected area. In the zoom mode, the epoch and page buttons are up and grayed.

[[Image:Spectral (40).gif]]] Zooming out can be done using the Zoom Out button, which is shown only if the display is zoomed. The display then returns to the former view. Otherwise, dragging another rectangle reopens the popup menu.

'''Note:''' for further details on Spectral Analysis (FFT and DSA) in BESA Research, please refer to the Help Chapter ‘''Spectral Analysis’''.

==== Tutorial ====

This tutorial will introduce the main features of the DSA module. A detailed description of all features can be found in the reference section.

The tutorial uses a data file with four concatenated EEG segments of epileptic seizure data (by courtesy of Prof. J. Ebersole, U Chicago). We will learn how to identify events in the data file quickly using the DSA display and how to find epochs with prominent rhythmic activities that differ between hemispheres.

1. Use the '''File / Open''' menu to browse to the folder '''Examples\Epilepsy\Seizures'''. Select the data file ''''Seizure-Right-Temporal.foc'''' and open it. The data are shown in the originally recorded montage. By default, a time constant of 0.3 sec (i.e. Low Filter: 0.53 Hz) is enabled (unless you changed the settings in your '''.ini''' file).

2. In the main window, press pushbutton ''''Src'''' and select the source montage '''TR_Temporal Region'''. This displays the left and right temporal lobe channels in the top 8 traces and reveals strongly lateralized right temporo-basal seizure activity. Press the '''high filter''' pushbutton '''HF''' and select '''35 Hz''' to reduce the EMG artifact.

3. Press the push button "'''DSA"''' at the top of the main window. The DSA window opens. In the DSA display, the horizontal axis represents time, whereas the vertical axis represents frequency (from 1 to 25 Hz). 

With the '''Amplitude button''' [[Image:Spectral (31).gif]]] down, and the '''Percentage button''' [[Image:Spectral (28).gif]]] released, the following image is obtained:

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;">[[Image:Spectral (41).gif]]]</div>

Four seizures can be distinguished in the display (red blocks of large EEG activity). Only two source channels, L and R, are shown, one for each hemisphere. These channels are obtained by calculating the mean left and right source activities using the 5 left and 5 right regional sources of brain source montage BR_BrainRegions to reduce overlap by volume conduction.

4. '''Scale the DSA display''' up using the '''Scaling button''' in the toolbar ([[Image:Spectral (42).gif]]). Pressing it three times decreases the threshold for maximum intensity by a factor of 2. The color map caption text changes correspondingly. '''Scale''' the display down again, either using the next toolbar button, or the ''''Cursor-Down'''' key on the keyboard to set the amplitude scale to 79.4 nAm. This will reveal the dark 'nose-tips' at the beginning of the second and fourth seizure with frequencies decreasing from about 8 to 5 Hz and obvious lateralization to the right hemisphere.

5. '''Move the mouse cursor''' over the data display. Current time and frequency are shown below the color bar and next to the mouse cursor, respectively. '''Click''' on the red-nose tip (~6.5 Hz) around +00:02:09 (12:02:09 AM) in the right source channel (R) to move the EEG display to this epoch at the beginning of the second seizure. A comparison of the traces of the left (traces 1-4) and right (traces 5-8) temporal lobe sources (''Src/TR_Temporal Region'') confirms the lateralization of the seizure onset to the right hemisphere.

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:0.635cm;margin-right:0cm;">[[Image:Spectral (43).gif]]</div>

6. '''Press''' the '''second-left''' toolbar button ([[Image:Spectral (44).gif]]) to switch to the display mode ''''Regional Comparison''''. The DSA display moves to the right of the main window and displays the spectral densities of five regions by summarizing the activities in the lateralized upper parts of the brain, in the temporal regions bilaterally, and in the midline regions.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Spectral (45).gif]]

7. '''Press''' the '''third''' toolbar button ([[Image:Spectral (46).gif]]) to switch to the display mode ''''Current Montage'. '''The DSA display on the right of the main window now displays the spectral densities of all channels in the current montage. Enlarge the DSA window by using the full-screen symbol at the top right. It is very apparent now that the seizures start with an interval of increased activity in the 8-5 Hz range. This activity is most noticeable in the anterior three source channels of the right temporal lobe (TBvr_TR, TApr_TR, and TArR_TR).    

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Spectral (47).gif]]

8. Use the overlapping window icon at the top right of the window to get the window back to its original position at the right of the screen. Then press the '''Sampling '''toolbar button ( [[Image:Spectral (48).gif]] ) to select the menu entry ''''Select Maximum'''' from the dropdown menu which appears. This results in pronouncing maxima of intensities: for each frequency bin, the maximum over the epoch that is related to one pixel of the display is computed. In this case, the noise is enhanced by the procedure. Press the button again to go back to 'Average Epochs', which displays the average over the epoch related to one displayed pixel for each frequency bin.

9. '''Close the DSA window''' using the close symbol at the top right. Press pushbutton ''''Vir'''' to select the virtual '''Horizontal Bipolar''' montage. Press the pushbutton '''DSA''' to recalculate DSA for the new current montage, then press the Amplitude button ( [[Image:Spectral (31).gif]] ) and the third toolbar button ([[Image:Spectral (23).gif]]). You can now see that the scalp montage, although optimized for temporal-basal activity shows a poor separation between hemispheres.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Spectral (49).gif]]

10. '''Press''' the '''second-left''' toolbar button ( [[Image:Spectral (44).gif]] ) to select the menu entry ''''Regional Comparison''''. '''Press''' the ''''Delta'''' button ( [[Image:Spectral (25).gif]] ) to switch to regional difference. The channels now show the difference between activities in the homologous brain regions. Then '''press''' the '''Display '''button ([[Image:Spectral (50).gif]]) to switch to the display mode''' 'Percentage''''. Now, the relative spectral amplitude in each frequency bin and time point is displayed.''' Switch''' to displaying '''spectral power''' by releasing the '''Power''' button ( [[Image:Spectral (31).gif]] ). Adjust the scaling to 16% at maximum intensity using the '''scaling''' toolbar buttons or the '''cursor up-down''' keys.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Spectral (51).gif]]

This display mode takes away most of the unwanted activity which is not lateralized, and clearly shows the dark clusters in the right hemisphere in the 7 Hz range immediately before the second and fourth seizure.

11. Use the '''left mouse button''' to drag a rectangle around the beginning of the fourth seizure in channel "TmpR+". From the popup menu that appears, select "Zoom In". The display is zoomed to show just the selected area. The seizure onset of the 4th seizure is visible as a decelerating 7Hz oscillation in the right temporal region. Use the right mouse button to zoom out again.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Spectral (52).gif]]

This concludes the tutorial on density spectral arrays. It gave a brief introduction into the ways in which the DSA can be used in combination with traditional and brain source montages, and demonstrated its abilities to quickly identify epochs and regions of interest in EEG data files.
[[Category:Research Manual]]

BESA Research Artifact Correction

2017-04-07T12:51:05Z

Alexa:

BESA Research Mapping

2017-04-07T12:50:17Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}

== Mapping ==

=== Mapping Window ===

The 3D mapping window displays whole-head 3D maps that reflect the voltage topography of the ongoing EEG using the current filter settings. The mapping procedure interpolates the EEG voltage or current source density (CSD) values over the whole head on the basis of the spherical splines method with moderate smoothing (Perrin et al. 1989). Maps are projected onto a 3D standardized head surface for a more realistic display of the voltage topography. The head surface was generated by averaging the MRI images of 50 normal subjects after transformation into Talairach space.

A single 3D map is displayed automatically at the detection peak of a clustered event when selecting an event or cluster in the cluster or hyper cluster displays. The single 3D map is rotated automatically to set the view point to the center of gravity in the map to provide for immediate optimal inspection of dipolar topography. To adjust the viewpoint for more detailed inspection, use the standard rotation buttons introduced below or use the mouse drag over the head.

[[Image:Mapping (1).gif ]]

''2D (left) and 3D (right) voltage maps in single head view at one time point. The EEG shows a detected event in the Av33 user-defined montage.''

The mapping window appears also when a cursor is set in the EEG data display by clicking onto the EEG.

The mapping window can appear in four different layouts: Single map, 6 maps in standard view, 15 serial maps, or customized series of maps. For details on 3D maps see the section ''"3D Maps".''

=== 3D Maps ===

'''Introduction'''

Maps are projected onto a 3D standardized head surface for a more realistic display of voltage topography. The head surface was generated by averaging the MRI images of 24 normal subjects after transformation to the Talairach space using the BrainVoyagerTM software. The standard 10-10 electrodes were adjusted to each individual head using the nasion, pre-auricular points (T9, T10), the inion and the eye canthii as landmarks. Using the spherical spline interpolation over the whole head, reference-free maps are calculated.

'''Controls'''

Use the mouse and the keyboard as follows:

* Click on a map in the standard whole head view with 6 preset viewpoints to display 15 serial maps in the selected view.
* Click on a serial map to select a specific time for the display of the 6 standard whole-head maps.

[[Image:Mapping (1).png ]]

''3D whole head maps at one latency using 6 standard viewpoints (left) and at a sequence of 15 latencies in serial view (right)''

* Double-click on a standard or serial map to obtain a single enlarged map.

[[Image:Mapping (3).gif ]]

* Drag over the head to rotate or use standard rotation buttons (for more details see below).
* Click or double click on the single head to obtain the 15 serial maps.
* Click on the EEG-Voltage label (bottom left) to display CSD maps. Click on the EEG-C.S.D. label which appears to redisplay voltage maps,
* or type''''' M''''' or '''''V''''' for voltage maps and '''''C''''' for CSD maps.
* When you move the mouse pointer over an electrode, the electrode label (and voltage if in voltage mode) is displayed.
* Left and right cursor keys plot new maps one time unit before or after the current time point. The time units can be adjusted using the '''Timing Interval''' toolbar button. [[Image:Mapping (4).gif ]]
* Up and down cursor keys raise or lower the scaling units of the map display. 3 steps change the scaling by a factor of 2.
* In the sequential and single map views, the head can be rotated, zoomed, or moved, by clicking and dragging with the mouse, depending on which of the '''3D Rotate''', '''3D''''''Magnify''', '''3D Move''' buttons in the toolbar has been depressed (see below). In addition, the three mouse dragging functions can be controlled directly by holding down the '''Shift''',''' Ctrl''', or '''Ctrl+Shift''' keys:

* <div style="margin-left:1.259cm;margin-right:0cm;">'''Shift-Drag''': Rotate</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">'''Ctrl-Drag''': Move</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">'''Shift+Ctrl-Drag''': Magnify/Zoom</div>

* Hit the '''Escape '''key to close the map window.

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

'''Toolbar'''

[[Image:Mapping (5).gif ]]

The toolbar offers a convenient way to modify the mapping display. The buttons are grouped as follows:

[[Image:Mapping (6).gif ]]

The '''3D Rotate''', '''3D Magnify''', and '''3D Move '''buttons select what happens when you click and drag with the mouse on a map:

Maps can be rotated (left button pressed), zoomed (middle button pressed), or moved (right button pressed).

The buttons are only enabled when 3D maps series or single heads are displayed. They are grayed in the standard 6-head view.

[[Image:Mapping (7).gif ]]

The '''3D Fast Rotation''' buttons rotate maps in steps of 45°, to the left (left button pressed), to the right (middle button pressed), or vertically (right button pressed).

The buttons are only enabled when maps series or single heads are displayed. They are grayed in the standard 6-head view.

[[Image:Mapping (8).gif ]]

These buttons control mapping layout and options.

The left button, '''Seq-Std Display''', toggles between the standard 6-head view (6 maps from different viewpoints) and the standard sequential top view display with 15 serial maps.

The middle button, '''Serial Arrangement''', opens a dropdown menu that allows for selection of either 5 x 7, 5 x 3 serial maps, a single map (1 x 1), or a custom array of serial maps:

[[Image:Mapping (9).gif ]]

The right button, '''Options''', opens the Options popup menu that allows for general settings of the maps:

[[Image:Mapping (10).gif ]]

* Toggle between 3D or 2D mapping
* Toggle between whole head mapping and top meridian projection
* Toggle between voltage and CSD display
* Toggle between serial and standard maps
* Toggle whether maps cover the entire head or are cut off at the lower part of the head
* Toggle display of electrodes on the maps
* Open the online Help

<div style="color:#00000a;"></div>

[[Image:Mapping (11).gif ]]

These buttons control the timing of maps: Pressing the left button, '''Timing Left''', generates maps one time unit earlier than the current map. Pressing the middle button, '''Timing Right''', generates maps one time unit later than the current map. In serial maps, clicking on the '''Timing Left/Right''' buttons in the toolbar moves the center latency to the first or last latency displayed, i.e. by 7 intervals in the standard 15 serial view.

Pressing the right button, '''Timing Interval''', opens a dropdown menu, allowing for the definition of the time interval between sequential maps or the frequency spacing between FFT maps. Voltages and CSD are interpolated to allow for the following standard and custom interval settings:

<div style="color:#00000a;">[[Image:Mapping (12).gif ]]</div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Mapping (13).gif ]]

The final two buttons, '''Scaling''', raise (left) or lower (right) the scaling of the

maps. 3 steps change the scaling by a factor of 2.

'''Right Click Popup Menu'''

A right click on the voltage or CSD maps displays the Options popup menu that allows for general settings of the maps:

[[Image:Mapping (10).gif ]]

A right click on FFT maps displays the '''Options '''popup menu with specific settings for FFT and phase maps:

[[Image:Mapping (14).gif ]]

=== 2D Maps ===

2D Maps are generated by '''spherical spline interpolation''' and are projected onto a spherical head outline. The display shows contour lines. Red contour lines denote positive voltage, whereas blue contour lines stand for negative voltage. In addition, areas of negative voltage are denoted by a dotted pattern.

The user interaction in 2D maps is essentially the same as in 3D maps. 

Only the differences are listed here:

# [[Image:Mapping (7).gif ]] In sequential time view, dragging with the left mouse button over the heads rotates them by 90 degrees. The same is achieved using the '''standard rotation''' toolbar buttons 
# The buttons '''3D Rotate''', '''3D Magnify''', '''3D Move''', are disabled in 2D maps.

<div style="color:#00000a;"></div>

A top meridian projection of the heads can be selected either using the options menu (available from the '''Options''' toolbar button), or by right click with the mouse onto a map. Top meridian projected maps are cut off at a theta value of 110°.

The 2D maps use equipotential line mapping instead of color maps to avoid bias due to the selection of the color scale and in order to emphasize the shape of the voltage or CSD distribution rather than peak areas. The noise in the EEG tends to produce arbitrary shapes in the maps around zero. Therefore, we have spaced the equipotential lines symmetrically around zero at levels of ±1/2, ±3/2, ±5/2....., and shaded negativities below -1/2 of the scaling between lines. This produces maps which are less biased by EEG noise, especially when larger scales are used. In 3D maps, an additional color shading is shown for each of the potential compartments.

A minimum of 12 scalp channels is required to calculate the spline maps. However, a larger array of electrodes is recommended, including electrodes at inferior lateral sites (see help chapter ''"Special Topics / Working with Electrodes... / Electrodes / Recommendations for Electrode Placement"'').

=== Mapping of the FFT ===

FFT spectra can be mapped in a similar way as the voltage maps of the ongoing EEG. The maps are initiated from the FFT window (see the chapter ''"Spectral Analysis / FFT"'' for more information on FFT analysis).

The results can be shown in three different ways, which are described in detail below:

# FFT maps of amplitude or power showing the topography at a single frequency
# FFT maps of amplitude or power showing the mean over a preset frequency band
# Phase maps showing the voltage amplitude topography at a selected frequency and at a specific or different phase angles. Serial phase maps are encoded to show phase delay (in ms) for better comparison with EEG voltage maps, since phase shift is proportional to time delay. Phase maps are only available if the FFT was computed over a single data block.

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

The type of map and further mapping options can be selected from the menus '''Map''' and '''Options/Mapping''' in the FFT window.

<div style="color:#00000a;">[[Image:Mapping (15).gif ]]</div>

''Map menu of the FFT window''

Note: Mapping of FFT spectra is only possible if there are at least 12 electrodes!

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

'''Topographies at a given frequency and at a series of frequencies'''

The topography of the amplitude/power at any frequency can be viewed by clicking (single or double click) on an FFT spectral plot at that frequency. As with the voltage/source maps, maps are then plotted on the right of the screen.

[[Image:Mapping (16).gif ]]

''3D amplitude maps at a single frequency (left) and at a sequence of frequencies (right) ''

''for one viewing angle''

Analogous to voltage maps, clicking on a map will toggle between views from six sides of the head at one frequency (as above left), and a display showing a series of maps at 15 consecutive frequencies in one view (as above right). In the serial view, click on the left/right arrows in the toolbar to page 7 frequencies backward or forward. Pressing the arrow keys on the keyboard pages only one frequency.

The frequency spacing between consecutive maps can be adjusted using the [[Image:Mapping (4).gif ]] symbol on the toolbar. Clicking on the''' Timing Left/Right '''buttons in the toolbar shifts the consecutive frequency maps analogous to the serial voltage maps.

'''Topography at the peak frequency'''

In the FFT window, double click on the peak amplitude or click on the peak frequency value at the right of the FFT spectrum of a prominent channel to view the topography of the peak (dominant) frequency. For bad channels mapping of the peak frequency is disabled.

'''Topography of a frequency band'''

To view the topography of the amplitude/ power density within a given frequency band from 6 different views, select the band in the '''Map''' menu (for example, to view maps of the theta band, press '''Alt+M T''' on the keyboard). To view the topography of the summed amplitude/power over the total frequency range, select the menu item '''Map/Total'''. Click on one of the maps to view maps of each frequency band in one head view, together with a map showing the mean over the total frequency range.

If a frequency band is grayed out, its upper or lower limit is out of range for the current FFT. Use the item '''Band Name''' and '''Width''' in the '''Options '''menu of the FFT window to redefine frequency band settings.

'''Phase maps at a given frequency'''

Frequency maps visualize the frequency specific distribution of absolute amplitude or power over the scalp. However, these maps do not reveal phase lags caused by multiple underlying processes. Therefore, a series of spherical spline maps (phase maps) is calculated at successive phase angles α, according to

H(f, α) = cos(α) Re(f) + sin(α) Im(f)

where Re(f) and Im(f) are the real and imaginary voltage amplitude topographies at frequency f over the marked block which was transformed by FFT.

A '''change of topography''' in consecutive maps indicates '''multiple underlying processes'''. Only if there is '''no change''' in topography with phase, a '''single generator process''' may be assumed. The phase shifts can directly be translated into time lags between the different topographies that are displayed in the phase maps.

To view phase maps at a specific frequency, double click on the FFT signals or click on the peak amplitude value to generate amplitude or power maps at the selected frequency in the standard 6-head view. Then right click onto the map with the best viewpoint to obtain the '''Options '''popup menu for FFT maps:

[[Image:Mapping (14).gif ]]

Select ''Switch to Phase Mapping'' to obtain a series of 15 serial phase maps in 5 ms intervals. Changes to this interval and other mapping options are described above in section ''"3D Maps".'' Clicking on the '''Timing''' '''Left/Right''' buttons in the toolbar shifts the phase similar to the serial voltage and consecutive frequency maps.

Phase maps can also be initiated from the FFT window using the '''Map''' menu.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;">[[Image:Mapping (17).gif ]]</div>

''3D phase maps: This sequence shows a change in topography, indicating that more than one process generates the EEG signals.''

Phase maps cannot be generated for mean spectra: generating means over frequencies or over a set of FFTs causes phase information to be lost. Thus, phase maps cannot be shown for frequency bands or for the result of mean FFTs between markers.

'''Toggling between EEG/MEG FFT maps'''

For a combined EEG and MEG measurement, the type of map (either EEG or MEG) that is currently selected is displayed in the left upper corner of the FFT window. Initially EEG is displayed. Click on the text to toggle between EEG and MEG FFT maps. A currently open map window will be updated immediately.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

=== Source Images ===

Source images show the activation of brain regions which are represented by individual channels in source montages (for more information on source montages, see the chapter ''"Review / Remontaging"'').

To start a source image, first set a cursor on the pattern of interest by double clicking with the mouse. Use the '''IMG '''push button in the control ribbon or hit the ''''I'''' key on the keyboard to display a source image.

<div style="color:#00000a;"></div>

[[Image:Mapping (18).gif ]]

When a cursor is set in the waveforms display, you can toggle between voltage maps and source images by pressing or releasing the '''IMG''' button. Note that the montage switches automatically to a source montage when the '''IMG''' button is pressed. The last active source montage is displayed. If no source montage has been specified for the current EEG data set, the montage ''TR_Temporal Region'' is used.

For each dipole channel in the current montage, the activation is shown inside the approximate brain region which is modeled by the dipole source. Regional sources are not included in the image. As in maps, it is possible to toggle between six different views at one latency, and a sequence of 15 images. The activation is shown in 7 shades. The amplitude range is measured in nAm, since the current flow inside the brain is depicted.

Using the arrow buttons at the top, you can change the latency range which is displayed, and the interval between subsequent maps:

* Left group of arrow buttons: These buttons jump 7 maps forward (or backward) in time (i.e. the last (or first) map in the sequence becomes the central map.
* Right group of arrow buttons: These buttons increase (or decrease) the interval between the maps in the sequence 

<div style="color:#00000a;"></div>

Using the arrow buttons at the bottom, you can adjust the scaling of the source images. They change the amplitude range of the individual shades. The amplitude range between minimum and maximum color is shown at the bottom. In the example below, it is 0 ... 158 nAm.

[[Image:Mapping (19).gif ]]

''Images of brain activation during spike propagation in the left temporal lobe from the basal (-20 ms) to the polar (-5 ms) and antero-lateral aspects (0 ms). Each dipole source in the source montage is represented by an ellipsoid which covers the approximate volume modeled by the source. As in maps, different views at the same latency, or a sequence of maps in one view can be shown.''

=== Spherical Spline Maps ===

''Why use spherical spline interpolation?''

Spherical spline maps present an interpolation of the potential distribution at the scalp with zero integral over the whole head and maximum smoothness (Pascual et al. 1988; Pernier et al. 1989). Based on these assumptions, the spherical spline method provides an optimal interpolation within the area covered by electrodes on the scalp as well as an optimal extrapolation to the part of the sphere not covered by electrodes. The strength of the spherical spline method stems from the underlying physical boundary

condition: The voltages at the lower part must sum with those at the upper part to zero. Provided that the electrode coordinates are appropriately assigned to equivalent locations on a sphere, maximum smoothness is achieved by the intrinsic properties of splines which can be compared to bending an elastic bar around multiple supporting poles:

[[Image:Mapping (20).gif ]]

''Comparison of the effects of spherical splines (left) and linear interpolation (right).''

The spherical spline method allows to interpolate and integrate the scalp voltage differences across the entire sphere or whole head. Therefore, it can be used to provide a reference free estimate of the scalp voltages (Rfr-montage), and an estimate of the mean voltage at the ears (Ears-montage). We have compared the spherical spline maps with voltage maps generated by simulated dipole fields due to sources within a multi-shell spherical head model. Even with a small number of scalp electrodes located at the upper half of the head, a very accurate estimate of the reference signal can be obtained. In the worst case of vertical dipole fields (compare example '''eeg2.eeg''') the negative peak at the lower half of the head could be estimated with fair accuracy.

Traditional mapping and source derivations are based on interpolation of the voltages at selected nearby electrodes. This causes problems at electrodes at the boundary of the array and discontinuities within the electrode array. Further, if a voltage maximum lies between electrodes it will not be recognized. In contrast, the spherical spline method provides a maximally smooth interpolation between all electrodes and is capable of extrapolating voltage maxima within and outside of the electrode array. Intrinsically, the spherical splines also provide the optimal estimation of current source density (CSD) which reflects the current flow out of the brain through the skull.

BESA uses an implementation of the spherical splines method as described in the publication 'Spherical splines for scalp potential and current density mapping' by Perrin et al. (Electroencephalogr. Clin. Neurophysiol. 72:184-187, 1989). BESA uses 4th order spherical splines, including Legendre polynomials up to 50th degree. The smoothing constant l can be specified from the menu entry '''Options / Mapping / Spline Interpolation Smoothing Constant.'''

=== Current Source Density (CSD) ===

''What is Current Source Density (CSD)?''

'''The surface Laplacian operator '''(second spatial derivative of the voltage distribution in tissue) calculates the volume current flow out of the brain through the skull into the skin. That is why we use the term '''Current Source Density '''(CSD). The CSD montage will show a large signal if the cortical surface (convexity) is active. This corresponds to a radial superficial dipole.

If the brain activity is in a fissure (tangential dipole) the CSD signal is much weaker. The current flows in a tangential direction, so you will see two peaks of opposite polarity in the CSD maps, corresponding to where the volume current is leaving (+) and entering (-) the skull. The two zones of maximum current are closer together than in voltage maps, because voltage is an integral over current source density.

Units of current source density are voltage per unit distance per unit distance (e.g. µV/cm²) or current per unit area (e.g. µA/cm²). Conversion from the second derivative of the voltage to current units is a complex issue because this requires knowledge about conductivities of the skull and scalp surfaces. Therefore, µV/cm² is used, i.e. just the second derivative of the voltage distribution.

=== Mapping/Tutorial ===

The aim of this section is to generate map and source image displays. It is assumed that you have loaded EEG2 (data: sub-folder '''Examples\EEG_Focus\eeg2.eeg''', electrode file: '''eeg2.elb''', filters variable 1.6-35 Hz, ''Org ''montage).

'''Basic steps'''

* 1. Move to the '''periodic pattern''' in EEG2 by clicking on the event marked at the middle of the event bar. 

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Mapping (21).gif]]</div>

* 2. Double click on any of the peak deflections to set a mark at the cursor position. A '''vertical bar''' (dark red on a yellow background) will be set, and '''Voltage maps''' will be displayed automatically. The latency will be shown at the bottom of the map window.

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Mapping (22).gif]]</div>

* 3. Repeat double clicking on several different peaks to view the maps at different latencies. Type the '''Esc''' key to close the map window.
* 4. Press the '''SRC''' button, and from the dropdown menu select the'' TR-Temporal Region ''montage. Double-click on one of the peaks to display voltage maps again.
* 5. Press the '''IMG '''button, so that it remains down. The map display changes to '''source images''' calculated from the magnitude of the source channels at the marked latency.

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="color:#00000a;margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Mapping (23).gif]]</div>

* 6. Repeat double clicking on several different peaks to view the source images at different latencies. Click on the up/down arrows to the right or left of the scaling bar below the images to increase or decrease scaling.
* 7. Select a prominent peak and double click to display the source images. On the keyboard press the '''left and right arrows''' to display source images at the next/previous sampling point or 5 ms later/earlier. Click on the up/down arrows right or left of the scale bar to increase or decrease scaling.
* 8. The latency should still be marked from the previous step. Type M to display voltage maps instead of the source images at the currently marked latency, and type 'i' again if you want to view the source images.
* 9. Press the '''IMG''' button again. Source images are switched off and 3D amplitude maps are displayed. Click on a map to convert the display from''' standard''' to '''sequential''' view.
* 10. Click and drag on a map to rotate the head to a new position. Note how all the maps in the sequential view are redrawn in the new position.
* 11. Try out the various controls on the 3D map toolbar (at the top of the map window. See chapter ''“3D Maps”'' for descriptions of the toolbar controls. Finally, switch back to 2D maps by disengaging the '''3D''' button.
*12. You may also select '''Voltage maps''' or any other process from the '''Process '''menu when a latency is marked and a source montage is displayed. Note that voltage maps can be displayed in all montages by clicking anywhere on the EEG, if the '''IMG''' button is not down.
* 13. Select average reference montage '''''Avr''''', and repeat double clicking on several different peaks (Note that typing 'i' will change to the last active source montage again and display source images).
* 14. Display voltage maps and make sure that electrodes are shown (if not, right-click on one of the heads, and select '''Show Electrodes''' from the popup menu. If selected, the electrode locations, projected on the 6 different views of the head model, will be displayed. Select '''Top Meridian Projection''' from the '''Options/Mapping''' menu to display a sequence of maps in equidistant steps relative to the marked latency. Note that the sequential maps present top views in meridian projection down to the level of F9, T9, P9, F10, T10, P10. By using spline interpolation, the maps are capable of covering this wider range as compared to traditional maps. Deselect top view sequential maps again.

<div style="color:#00000a;"></div>

'''Map and source image sequences'''
* 1. Select file '''segm1.eeg''' and select the ''TA_Temporal Lobe ''source montage. Engage the '''IMG '''button. The '''''TA '''''montage includes basal, anterior, and lateral temporal brain regions. Note how this montage suggests the onset of the spike in the left basal temporal lobe, with subsequent components in the anterior tip and lateral surface of the left temporal lobe.
* 2. Double click on the positive (upward-going) peak on the third channel from the top of the screen (left lateral temporal lobe). The source image will be displayed.
* 3. Click on the left lateral head view (top left source image). Note how the cursor changes to a hand over areas where clicks initiate an action. A series of 15 equidistant source images around the cursor latency will be displayed.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="margin-left:0.635cm;margin-right:0cm;">[[Image:Mapping (24).gif]]</div>

* 4. Click on the left/right arrows at the left at the top of the map display to page 7 maps backward or forward.
* 5. Click on the left/right arrow at the right at the top of the map display to decrease or increase the interval between the sequential maps. Alternatively, you may set the interval in '''Interval between Sequential Maps''' in the '''Options/Mapping''' menu.
* 6. Type 'm' or 'v' to view a sequence of amplitude maps in the same time range (click the rotate-left button and the rotate-up-down button twice each to arrive at the head positions shown below): 

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="margin-left:0.635cm;margin-right:0cm;">[[Image:Mapping (25).gif]]</div>
[[Category:Research Manual]]

BESA Research Montage Editor

2017-04-07T12:49:39Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
== Montage Editor ==

=== Montage Editor - Introduction ===

The Montage Editor provides information about the current montage and the available standard montages.

The Montage Editor also offers the possibility to create new user-defined montages, modify a standard montage, or combine channels from different montages.

Edited Montages can be saved and selected in the main window of the BESA Research program using the montage push buttons or the montage menu.

The Montage Editor opens after clicking on the''' EdM''' push button in the BESA Research ''control ribbon.''

The following chapters will guide you through the most important features and the layout of the Montage Editor.

=== Layout of the Montage Editor ===

The Montage Editor window is subdivided into three main parts which will be explained briefly in the following sections.

[[Image:Montage Editor (4).jpg]]

[[Image:Montage Editor (5).jpg]]

The '''title bar''' shows the name of the ''current montage'' (the montage which is currently displayed).

Most of the functions and commands can be chosen from the main '''menu bar''' and the '''toolbar''' below the title bar. However, many commands are also available via a right mouse click. If you right-click, a context-sensitive popup menu may appear containing the available commands.

The functions of the toolbar and the popup menus are described in the next section. A detailed description of the commands of the menu bar is given in electronic help chapter ''"Montage Editor / Reference".''

==== 2D View ====

The 2D view displays a scheme of the ''current montage''. Additionally, available electrodes which are not used in the current montage can be shown.

The name of the current montage is given at the top. Note: If the montage name starts with '''"Add:"''', an ''additional channel montage'' is displayed. Additional channel montages are described in the chapter ''"Predefined Additional Channel Montages".''

[[Image:Montage Editor (1).png]]

[[Image:Montage Editor (2).png]] Use the '''One 2D Head toolbar button''' if you want to switch between the available 2D head views: the top meridian projection, or the top, bottom, back, front, left and right views.

[[Image:Montage Editor (1).jpg]]

The top meridian projection shows all electrodes of the current montage. Other 2D head views only show the electrodes which are visible from the corresponding side.

[[Image:Montage Editor (4).png]] Use the '''Four 2D Heads toolbar button''' to switch between the available four head layouts.

The following objects are displayed:

[[Image:Montage Editor (5).png]] '''Recorded electrodes''' which are available for the current data file, not interpolated and not marked as 'bad'.

[[Image:Montage Editor (6).png]] '''Interpolated electrodes''' which have been set as 'to be interpolated' in the main program.

[[Image:Montage Editor (7).png]] '''Bad electrodes''' or '''bad MEG sensors''' which have been marked as 'bad' in the main program.

[[Image:Montage Editor (8).png]] '''Virtual electrodes''' at predefined locations. The interpolated 81 electrodes are always available for EEG data files.

[[Image:Montage Editor (9).png]] '''MEG sensors''' which are available for the current data file.

[[Image:Montage Editor (11).png]][[Image:Montage Editor (12).png]][[Image:Montage Editor (10).png]] '''Montage channels''' with the underlying recorded/virtual electrode or MEG sensor as primary channel and no reference channel or a reference channel which is not visible for the current 2D head view or which is no single channel reference – may be a reference calculated by several channels, e.g.'' avr'' or ''ears''. If a montage channel is selected, the inner circle becomes darker.

[[Image:Montage Editor (14).png]][[Image:Montage Editor (13).png]]'''Montage channels''' with underlying recorded/virtual electrode as primary channel (left electrode) and the right electrode as reference, connected with the montage channel line. If a montage channel is selected, the blue/red circle and the montage channel line become darker.

Additional objects are visible if the 'Edit' montage is displayed. The chapter "Montage Editor / Editing a Montage / Editing in the 2D View and Icr/Pgr View" gives a description of these objects and explains how the 'Edit' montage can be modified.

A right mouse click on a montage channel in the 2D view opens a context-sensitive popup menu for fast access to the most important commands.

==== Montage Channel List ====

The montage channel list is displayed to the right of the '''2D View'''. It displays all montage channels of the ''current montage''.

[[Image:Montage Editor (15).png]]

A montage channel consists of a (primary) channel and may be a reference channel against which the primary channel data are calculated. In the example shown above (which really does not make much sense but shows most of the available channel types) the recorded electrode Pz and the virtual electrode Cz are used as references.

Distinctions are made between channel and reference types and states as follows:

'''Recorded electrodes'''

Recorded electrodes which are available for the current data file are displayed in blue. They may be used as primary and reference channels.

'''Recorded references'''

A combined reference based on the recorded electrodes, e.g. avr. They are also displayed in blue.

'''Interpolated electrodes'''

Interpolated electrodes are recorded electrodes that have been set as 'to be interpolated' in the main program. They are displayed in light purple. Interpolated electrodes may be used as primary and reference channels.

'''Bad channels'''

Recorded channels which have been marked as 'bad' for the current data file are displayed in gray. You may use them as primary or reference channels, but the corresponding data waveform will not be displayed in the main program. However, if you switch to a new data file and the channel is no longer marked as 'bad', the corresponding data waveform will be displayed.

'''Unavailable channels'''

Channels which are not available for the current data file are also displayed in gray and the suffix “[NA]” is appended. You may use them as primary or reference channels but the corresponding data waveform will not be displayed in the main program. However, if you switch to a new data file and the channel becomes available, the corresponding data waveform will be displayed.

'''Virtual electrodes'''

Virtual electrodes at predefined locations. They are always available for any (EEG) data file, displayed in red. They may be used as primary and as reference channels.

'''Virtual references'''

A combined reference based on virtual electrodes, e.g. ears. They are also displayed in red.

'''Source montage channels'''

Source montage channels consist of a single dipole or a regional source as primary channel and cannot have a reference. The source labels are displayed in green. The individual source color is given as a small colored bar to the left.

'''MEG channels'''

Recorded MEG channels which are available for the current data file and which are not marked as 'bad' are displayed in dark purple.

'''Polygraphic channels'''

Available polygraphic channels are written in '''black.'''

'''Intracranial electrodes'''

Available intracranial electrodes are given in brown.

'''Selected montage channels'''

Labels of selected montage channels are highlighted with a black background. A montage channel can be selected by a left mouse click on the channel label. Hold down the '''Control '''key to select more than one montage channel simultaneously.

'''Highlighted montage channel'''

The highlighted montage channel is marked by a yellow rectangle around its label. A montage channel is highlighted if the mouse cursor moves slowly over its label or over the corresponding plot in the '''2D view'''. Only one montage channel can be highlighted at a time.

A right mouse click somewhere in the montage channel list opens a context-sensitive '''popup menu''' for fast access to the most important commands.

The chapter "''Editing a Montage in the Montage Channel List"'' gives an explanation of how to modify the''' 'Edit' montage '''in the montage channel list.

==== 3D View ====

The 3D view is used to visualize the equivalent locations of source channels inside the head in the ''current montage'' and to display the recorded EEG channel montage on the 3D head surface.

* If a source montage channel is selected, the 3D view is centered to the source location and the 3D source location is highlighted by a golden halo. If you click on a source in the 3D view, the corresponding montage channel will be selected.
* If scalp electrodes are part of the montage, the 3D whole-head view displays the corresponding electrodes on the head surface.

[[Image:Montage Editor (17).png]][[Image:Montage Editor (16).png]]

Editing is not possible in the 3D view. Use the''' 2D view '''or the '''montage channel list''' instead.

==== Pgr/Icr View (Polygraphic / Intracranial Channels) ====

This view displays a scheme of the available polygraphic / intracranial Channels.

[[Image:Montage Editor (18).png]]

[[Image:Montage Editor (19).png]] Use the Intracranial Channels button to switch on/off the display of intracranial channels.

[[Image:Montage Editor (20).png]] Use the Polygraphic Channels button to switch on/off the display of polygraphic channels.

The following objects are displayed:

[[Image:Montage Editor (21).png]] '''Intracranial electrodes''' (brown color) which are available for the current data file.

[[Image:Montage Editor (22).png]] '''Polygraphic channels''' (black color) which are available for the current data file.

=== Creating and Editing a Montage ===

==== Creating a New Montage ====

[[Image:Montage Editor (23).png]] Press the''' New 'Edit' Montage '''toolbar button. 

[[Image:Montage Editor (24).png]] This clears and opens the '''Edit' montage'' as indicated by the highlighted ''''Edit' Montage '''toolbar button. 

[[Image:Montage Editor (25).png]] Then select the '''Recorded Electrodes''',

[[Image:Montage Editor (26).png]] '''Virtual Electrodes''',

[[Image:Montage Editor (27).png]] '''MEG Sensors''',

[[Image:Montage Editor (20).png]] '''Polygraphic Channels''',

[[Image:Montage Editor (19).png]] or '''Intracranial Channels'''

toolbar buttons depending on which type of channels you want to add.

You can add new montage channels now in three different ways:

1. Add new montage channels in the '''2D view''' and '''Pgr/Icr view''' by selecting channels and dragging to the reference electrode (T7 to P7 in the example below)

[[Image:Montage Editor (28).png]]

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

<div style="margin-left:1cm;margin-right:0cm;"></div>

2. Click on the ''Set chan. & ref''. text box. This box will start flashing to indicate that new channels can be added. Click alternately on the next channel to be added (in the 2D view, the Pgr/Icr view, or the montage channel list), followed by its reference electrode. Each new click will alternately define a new montage channel and its reference. When done adding new channels, click on the ''Set chan. & ref.'' text box again,'' ''which will stop flashing.

[[Image:Montage Editor (29).png]]

3. Select one or more channels (see “''Editing in the 2D View'' ''and Pgr/Icr View”'' and “''Editing in the Montage Channel List”'') and add them using the '''right-click popup menu'''.

To add '''source '''channels, switch to the desired source montage using the''' Standard Source''' '''Montages''' toolbar button [[Image:Montage Editor (30).png]], select montage channels in the Montage Channel List (see ''“Editing in the Montage Channel List”''), and copy and paste to the 'Edit' Montage.

For more details see the sections “''Editing in the 2D View and Pgr/Icr View”'' and ''“Editing in the Montage Channel List''” below.

==== Editing a Montage ====

In the Montage Editor, only one montage can be edited at a time. This is referred to as the ''''Edit' montage'''. The most convenient ways to edit recorded or virtual scalp montages are described below in the sections “''Editing in the 2D View'' ''and Pgr/Icr View”'' and “''Editing in the Montage Channel List“.''

Whenever you want to modify a predefined standard montage, an available '''user montage''', or an '''additional channel montage''', you have to select the montage you want to modify and copy it to the 'Edit' montage. If you have not yet edited a montage after starting the montage editor, the 'Edit' montage is empty.

When you switch from the selected current montage to the 'Edit' montage using the ''''Edit' Montage toolbar button''' [[Image:Montage Editor (31).png]], then the selected '''current montage''' is automatically copied to the 'Edit' montage. In addition, the Montage Editor copies the current montage to the 'Edit' montage automatically if you start dragging or deleting montage channels when viewing a selected montage.

If the 'Edit' montage is not empty, you can clear it by clicking again on the ''''Edit' Montage toolbar button''' or by clicking on the '''New 'Edit' Montage button''' [[Image:Montage Editor (23).png]] . Then switch''' '''to the montage you want to modify using the '''Standard User''', or '''Additional Montage buttons''' and switch back to the 'Edit' montage using the toolbar buttons. This copies''' '''the selected montage to the 'Edit' montage.

==== Changing the Reference of Montage Channels ====

In the ''''Edit' montage''', select one montage channel by clicking on the related electrode in the 2D View or select the channel from the montage channel list. Select more channels by holding down the '''Control key'''.

To change the reference of the selected channels, use the ''Set Reference ''text box in one of the following ways:

* Either drag from the ''Set Reference'' text box to an electrode in the 2D view, to a channel box in the Pgr/Icr view, to any of the standard reference text boxes at the top of the 2D view (see also ''“Editing a Montage in the 2D View and Pgr/Icr View”),'' or onto a montage channel in the montage channel list as shown below.

<div style="margin-left:0cm;margin-right:0cm;"></div>

<div style="margin-left:0cm;margin-right:0cm;">[[Image:Montage Editor (32).png]]</div>

* Or click on the ''Set Reference ''text box (it will start flashing), and then click on the desired reference channel in the Montage Channel List, in the 2D view, or in the Pgr/Icr view.

[[Image:Montage Editor (33).png]]

<div style="margin-left:0cm;margin-right:0cm;"></div>

'''Note:''' If you want to modify the viewing reference of the '''recorded Referential''' or the '''virtual Referential''' montage, you don’t have to edit a montage. To change the viewing reference in the referential montages simply switch to the corresponding montage and drag from the ''Set Reference ''box to the desired new reference electrode in the 2D view (as shown in the section after next).

==== Creating New Average Channel Groups ====

Average channel groups can be used as references in montage channels. They are computed for each time point as the mean voltage over the amplitudes of included channels. If one channel is bad or not available, average channel groups including this channel are also not available.

For the creation of a new average channel group, at least two channels must be selected (see chapter “''Editing a Montage in the 2D View and Pgr/Icr View”'' for information about how channels are selected). Channels must be of the same type. Source channels and MEG sensors are not allowed in average channel groups.

Channels that have been selected multiple times will enter the average only once.

To create a new average channel group, activate the corresponding menu entry (see chapters “''Montage Channel List Popup Menu”'' and “''Edit Menu”'').

Note that you can get information about average channel groups which are currently available using the ''Average Channel Group Information'' dialog box.

==== Changing the Viewing Reference in Referential Montages ====

If the '''recorded Referential''' or the '''virtual Referential''' montage is displayed, an additional ''Set Reference'' text box is displayed in the '''2D view'''. In the example below, the viewing reference of the''' virtual Referential '''montage is changed from Cz to A2. The'' Set Reference ''box can be used to change the viewing reference in one of the following ways:.

* Place the mouse cursor on the ''Set Reference ''text box and press and hold the left mouse button. Start to move the mouse while the left mouse button is still held down (“dragging”). The mouse cursor changes to a black cross as soon as dragging has begun. Move the mouse cursor to one of the visible electrodes in the 2D view or to a montage channel in the montage channel list. If the cursor is on top of an electrode or montage channel which can be set as viewing reference, the cross-color changes to green. Release the left mouse button while the cursor cross is green. A new viewing reference is set.

[[Image:Montage Editor (34).png]]

* Alternatively, click on the ''Set Reference'' text box. It will start blinking. Then click onto the new reference channel either in the Montage Channel List, in the 2D view, or in the Pgr/Icr view.

[[Image:Montage Editor (35).png]]

Press the''' Exit''' and '''Set toolbar button''' [[Image:Montage Editor (36).png]] to return to the main window of the BESA Research program.

==== Editing a Montage in the 2D View and Pgr/Icr View ====

'''Reference Boxes'''

If the ''''Edit' montage''' is displayed, additional reference boxes are displayed at top of the '''2D view''' showing available multiple channel references or average channel groups (see “''Create New Average Channel Group”''). If not all available reference boxes can be shown, an additional text box [[Image:Montage Editor (37).png]]  is displayed. If the mouse cursor is positioned over this box, remaining reference boxes will be displayed temporarily. Reference text boxes may be used to define references for new montage channels (see below).

Additional references displayed in blue are recorded references. Additional references shown in red are virtual references. The recorded (virtual) '''ears''' reference, for example, is the mean voltage of the amplitudes at recorded (virtual) electrodes A1 and A2. The recorded (virtual)''' mast''' reference is the mean voltage of the amplitudes at recorded (virtual) mastoid electrodes M1 and M2. If the electrodes A1/A2 or M1/M2 are not present in the current electrode configuration, or if the electrode locations have been digitized (i.e. the electrodes are not exactly at the default position), a recorded '''ears''' or recorded''' mast''' reference may be available. This reference is built of the two recorded electrodes that are closest to the standard positions of A1/A2 or M1/M2 if they are within 12 degrees of these standard positions. Note that this assignment of the reference is independent of the actual electrode label in this case. The '''mast''' reference in the example below is calculated as mean voltage of the amplitudes at P7 and P8, for example. A recorded ears reference is not available in this example as there are no recorded electrodes within 12 degrees of the standard positions of A1/A2.

Note that you can right-click on a reference box of an average channel group to display the ''Average Channel Group Information'' dialog box showing detailed information about available average channel groups.

[[Image:Montage Editor (38).png]]

'''Selecting Montage Channels'''

Montage channels can be selected by clicking on the montage channel line or the channel circle/box. If a montage channel is selected, other selected montage channels will be deselected unless you also hold down the '''Control key'''. With the '''Control key''', the new montage channel is added to the current selection.

You may also drag a box with the left mouse button to select all channels within the rectangle box. Press the '''Control''' key when releasing the mouse button to add the channels to the current selection.

All montage channels are deselected by clicking beneath any montage channel while the''' Control key '''is not pressed, or by hitting the '''Escape key.'''

[[Image:Montage Editor (40).png]][[Image:Montage Editor (39).png]]

'''Deleting Montage Channels'''

To delete montage channels, select them and activate the corresponding entry in the '''Edit menu''' or in the right-click '''popup menu''', or press the corresponding hot key (default: '''Delete''').

Note: If you want to clear the 'Edit' montage completely, use the corresponding entry in the ''''Edit' Montage popup menu'''.

'''Adding Montage Channels'''

There are four ways of adding new montage channels:

* If you previously copied or cut montage channels using the corresponding menu entry in the '''Edit menu''', you can paste them using the same menu or using the associated hot key (default: '''Control-V'''). The montage channels are inserted before the first selected montage channel in the 'Edit' montage. If no montage channel is selected, they are appended at the end of the '''montage channel list'''.
* Drag from a visible electrode or polygraphic/intracranial channel to another visible electrode or polygraphic/intracranial channel, to one of the additional reference boxes plotted at the top of the 2D view, or to a montage channel in the montage channel list. If the mouse cross becomes green, release the mouse button. The new montage channel will be added at the end of the montage channel list.

Use the '''Recorded Electrodes''' [[Image:Montage Editor (25).png]] ,

'''Virtual Electrodes''' [[Image:Montage Editor (26).png]] ,

'''MEG Sensors''' [[Image:Montage Editor (27).png]] ,

'''Polygraphic Channels''' [[Image:Montage Editor (20).png]] ,

or '''Intracranial Channels''' [[Image: Montage Editor (19).png]] 

toolbar buttons to display or hide the corresponding electrodes/channels.
You can hit the '''Escape''' key while dragging if you want to abort the drag operation.

* Click on the Set chan. & ref. text box. This box will start blinking to indicate that new channels can be added. Click alternatively on the next electrode/channel to be added (in the 2D view, The Pgr/Icr view, or the montage channel list), followed by its reference electrode (if required). Each new click will alternatively add a new montage channel and its reference. When done adding new channels, click again on the Set chan. & ref. text box, which will stop blinking.
* Select channels from the 2D view, the Pgr/Icr view, and the montage channel list and right click on a selected channel to display a '''popup menu''', to add the selected channels.

'''Sorting Montage Channels'''

In the 2D view or the Pgr/Icr view, there is no way to modify the sequence of montage channels. Use the '''montage channel list''' instead as described in the section “''Editing'' ''a Montage in the Montage Channel List”.''

'''Changing the Reference'''

Select the montage channel(s) for which you wish to change the reference. If no montage channel is selected, you can modify the reference for all montage channels simultaneously.

Drag from the ''Set Reference'' text box at the bottom of the 2D view to another visible electrode/channel or to one of the additional reference boxes at top of the 2D view. Alternatively, click on the ''Set Reference'' text box (it will start blinking), and then click on the desired reference channel in the montage channel list, in the 2D view, or in the Pgr/Inc view.

Note that you can hit the''' Escape '''key if you want to abort the drag operation.

==== Editing a Montage in the Montage Channel List ====

If the ''''Edit' montage''' is currently displayed, this montage may be modified in the '''montage channel list''' as follows:

'''Selecting Montage Channels'''

Montage channels can be selected by clicking on the primary channel label box or on the reference label box. If a montage channel is selected, other selected montage channels will be deselected unless you also hold down the''' Control''' key. With the '''Control '''key pressed, the new montage channel is added to the current selection.

All montage channels are deselected by clicking beneath any montage channel while the '''Control''' key is not pressed, or by hitting the '''Escape''' key.

'''Deleting Montage Channels'''

To delete montage channels, select them and activate the corresponding entry in the '''Edit menu''' or in the right click '''popup menu''', or press the corresponding hot key (default: '''Delete''').

Another possibility is to drag them over the left border of the montage channel list – the mouse cursor changes to a litter box icon.

Note: If you want to clear the 'Edit' montage completely, use the corresponding entry in the ''''Edit' Montage popup menu'''.

'''Adding New Montage Channels'''

There are two ways to add new montage channels:

* If you previously copied or cut montage channels using the corresponding menu entry in the '''Edit menu''', you can paste them using the same menu or using the associated hot key (default: '''Control-V).''' The montage channels are inserted before the first selected montage channel in the 'Edit' montage. If no montage channel is selected, they are appended at the end of the '''montage channel list.'''
* Drag the selected montage channels to a position you want to insert them and press the '''Control''' key while you release the mouse button. The selected montage channels are copied and inserted at the current mouse position.

Other ways of adding new montage channels are possible in the '''2D view or Pgr/Icr view.'''

'''Sorting Montage Channels'''

Drag the selected montage channel(s) with the mouse to the new list position. When releasing the mouse button, the selected montage channels are cut from their current positions and inserted at the new position.

'''Changing the Reference'''

Changing the reference of a montage channels is not possible in the montage channel list. Please use the 2D view instead as described in the section ''"Changing the'' ''Reference of Montage Channels".''

==== Editing a Montage in the 3D View ====

It is currently not possible to edit a montage in the 3D view. Please use the '''2D''' '''view '''and the '''montage channel list''' instead and refer to the corresponding chapters.

=== Loading and Saving Montages ===

'''Saving Montages'''

In the Montage Editor, the ''''Edit' montage''', '''user montages,''' and '''additional channel''' '''montages''' can be saved. If the 'Edit' montage has been saved using the default settings, it is saved in the User Montages folder and is available from the '''Usr''' button (user montages) in the main window of the BESA Reasearch program.

If a montage is saved under a filename which is already used by another montage, the other montage is unloaded. A message box will inform the user before this happens.

If a montage is saved (or loaded) using the same file base name as an existing montage (e.g. '''Besa Research \ Montages \ UserMontages \ Test.mtg''' and '''C: \ Temp''' '''\ Test.mtg'''), the montage label will receive the appendix “(2)” (''Test (2)'') etc.

Please note that the file selector dialog box which is displayed if a montage is going to be saved (or loaded) provides an additional selection list at the bottom of the dialog box. The ''Folders'' selection list can be used to switch to predefined folders, e.g. the current data file folder, to the ''User Montages'' folder or to the ''Additional Channels'' folder. The list also shows recently used folders.

By default, the extension '''.mtg''' and the User Montages folder is proposed for saving edited montages.

'''Saving Additional Channel Montages'''

If you specify the extension '''.sel''' when selecting the montage filename, you define that the saved montage belongs to the '''additional channel montages'''. Any other extension will result in adding the montage to the '''user montages''' after saving. Please make sure that you save additional channel montages either in the standard Additional Channel Montages folder or in the current data folder, if you want to use the montage only for a specific data file.

Note that you can use the filter selection list close to the bottom of the file selector dialog box to switch between “common” montages and additional channel montages.

'''Loading Montages'''

To load a montage that is not located in the current data folder or in the User Montages or Additional Channel Montages folders, press the '''Open Montage push button''' on the toolbar or use the '''File / Open Montage''' menu item. Montages that have already been loaded at program start or by the user can be selected for viewing or editing via the '''User Montages'''  and '''Additional Channel Montages'''  toolbar buttons or via the '''User Montages menu''' or the '''Additional Channel Montages menu''' (please see online help chapter ''"Montage Editor / Reference / Popup Menus"'' for detailed information).

If a montage has already been loaded, it is not reloaded unless the file has been modified – e.g. by saving a montage file in the BESA Source Analysis module.

Note that several montages can be selected in the file selector dialog box to be loaded simultaneously.

'''Automatic Loading of Montages'''

The Montage Editor loads montages found at default locations automatically:

* At program start, all montages found in the ''User Montages folder'' or the ''Additional'' ''Channel Montages folder'' (and first-level subfolders) are loaded. They are displayed in the first section of the '''User Montages menu''' or the '''Additional Channel Montages '''menu.
* If the current data file in the main program is switched or a new data file is loaded, all montages''' '''found in the new data folder are loaded. They are displayed in the second section of the''' User Montages menu'''.
* If a source montage file is stored in the BESA Source Analysis module, it is automatically loaded and displayed in the '''User montages menu.'''

=== Standard Montages ===

The Montage Editor provides several standard montages which can be applied to all EEG data files. The standard montages are subdivided into three groups:

* '''Recorded Standard Montages''' which are based on the recorded electrodes of the current
* '''Virtual Standard Montages''' which are based on virtual electrodes at predefined locations, and
* '''Standard Source Montages''' which are used to remontage the measured data to show the estimated underlying brain activity.

Additionally, several predefined '''additional channel montages''' are available which can be applied to all EEG data files or to data files which contain the corresponding channels, e.g. EKG.

* '''Predefined Additional Channel Montages''' are used to display eye activity and EKG or sphenoidal channels below the main montage channels.

See the next sections for details on the different standard montages.

==== Recorded Standard Montages ====

Recorded standard montages are sets of predefined channel configurations based on the recorded electrodes of the current data file. In the Montage Editor, recorded standard montages can be selected

using the '''Recorded Standard Montages popup menu''' which opens after clicking onto the '''Recorded Standard Montages''' toolbar button or activating the corresponding menu entry in the '''Montage menu.'''

The '''Original Recording''' and '''Original Average Reference''' '''montage''' have the same sequence of electrodes as the original recorded data. The other recorded standard montages (as well as the '''virtual standard montages''') are derived from predefined montage lists based on a standard set of 27 10-10 electrodes (Std-27):

Fp1 Fpz Fp2

F9 F7 F3 Fz F4 F8 F10

A1  T7  C3  Cz  C4  T8  A2

P9 P7 P3 Pz P4 P8 P10

O1 Oz O2

The Std-27 set includes the 21 electrodes of the 10-20 standard with some traditional labels replaced by the newer 10-10 standard (e.g. T3=T7, T5=P7). If the traditional 10-20 labeling is not set after program installation, it can be restored by entering the following lines in the BESA initialization file '''BESA.ini''' under

section [Electrodes]:

[Electrodes]

T7=T3

P7=T5

T8=T4

P8=T6

This will relabel the names of these electrodes everywhere in the program. Thus, the standard-27 electrode set will be displayed as:

Fp1 Fpz Fp2

F9 F7 F3 Fz F4 F8 F10

A1  T3  C3  Cz  C4  T4  A2

P9 T5 P3 Pz P4 T6 P10

O1 Oz O2

A predefined montage channel is only displayed in the '''2D view''', if the recording electrode set contains an electrode that is equal to or close to its location (e.g. A1, T9, TP9 or P9 will be indicated). If the predefined montage channel is bipolar, e.g. A1-Cz, the recording electrode set has to contain electrodes with locations equal or close to the location of both channel (here A1) and reference (here Cz). Otherwise, the montage channel is not displayed in the 2D view. It is grayed in the '''montage channel list''' and the suffix “[NA]” is appended (“not available”).

If the common reference used for recording is a known single electrode, the common reference electrode is regarded as part of the recording electrode set. Predefined montage channels using the common reference can be displayed. The common reference will be included in the computation of the average reference. This is not possible, however, for EEG systems using a combination of electrodes as the common reference.

The following recorded standard montages are available:

* <div style="margin-left:1.259cm;margin-right:0cm;">Average Reference</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Double Banana</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Triple Banana</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Horizontal Bipolar</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">A1/A2 Reference</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Referential</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Original Recording</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">Original Average Reference</div>

For more details on the different recorded standard montages see help chapter ''"Montage Editor /'' ''Standard Montages / Recorded Standard Montages".''

'''Recorded Standard Montage - Average Reference'''

In this traditional montage, the available channels of the Std-27 electrode set are displayed against average reference. The average reference is computed for each time point as the mean voltage over the amplitudes of all scalp electrodes that are not bad. If the common reference used for recording is a known single electrode, it will be included in the computation of the average reference.

[[Image:Montage Editor (41).png]]

'''Recorded Standard Montage - Double Banana'''

This is a longitudinal bipolar montage containing two left hemispheric, two right hemispheric and one midline longitudinal row of montage channels. Longitudinal rows are arranged from front to back. Predefined montage channels are only displayed if both channel and reference are available (i.e. recorded and not bad).

[[Image:Montage Editor (42).png]]

'''Recorded Standard Montage - Triple Banana'''

The Triple Banana montage is an extended longitudinal bipolar montage. It has an additional inferior row on each side as compared to the '''Double Banana''' montage. Predefined montage channels are only displayed if both channel and reference are available (i.e. recorded and not bad). The Triple Banana montage is not available if less than 2 inferior electrodes are recorded or defined as ‘good’ on each side.

[[Image:Montage Editor (43).png]]

'''Recorded Standard Montage - Horizontal Bipolar'''

The horizontal bipolar montage contains three transversal rows of montage channels. Transversal rows are arranged from left to right. Predefined montage channels are only displayed if both the channel and reference are available (i.e. recorded and not bad).

[[Image:Montage Editor (44).png]]

'''Recorded Standard Montage - A1/A2 Reference'''

In this traditional montage, the available left-hemispheric channels of the Std-27 electrode set (except inferior electrodes F9, A1, P9) are displayed against the electrode A1 (or, if A1 is not available, a nearby channel such as P9 > T9 > TP9 > M1). The available right-hemispheric channels of the Std-27 electrode set (except inferior electrodes F10, A2, P10) are displayed against the electrode A2 (or a nearby channel such as P10 > T10 > TP10 > M2). The available midline electrodes of the Std-27 electrode set (except Fpz and Oz) are displayed twice, referenced a) to A1 and b) A2 (or a nearby channel). If neither A1 nor A2 nor one of the nearby channels are recorded or defined as ‘good’, the A1/A2 Reference montage is not available.

[[Image:Montage Editor (45).png]]

For this example, the electrodes A1 and A2 are not available. Therefore, the electrodes T9 and T10 have been used instead.

'''Recorded Standard Montage - Referential'''

In this traditional montage, the available channels of the Std-27 electrode set are displayed against a common 'viewing reference'. The default viewing reference is Cz. Any of the recording electrodes in the EEG file may be used as viewing reference.

For details on how to change the viewing reference, see chapter ''"Changing the Viewing Reference”''

Note that the viewing reference is independent of the common reference used for recording.

[[Image:Montage Editor (46).png]]

'''Recorded Standard Montage - Original Recording'''

This montage displays the data as recorded. Note that channels defined as 'bad' are displayed in the '''2D view''' and '''Pgr/Icr view''' with grey color. In this case, the montage channel label is grayed in the '''montage channel list.'''

[[Image:Montage Editor (47).png]]

'''Recorded Standard Montage - Original Average Reference'''

In this montage, the scalp electrodes are displayed in the recording sequence, versus average reference. The average reference is computed for each time point as the mean voltage over the amplitudes of all scalp electrodes that are not bad.

If the common reference is a known single electrode, it will be included in the computation of the average reference.

This montage is not available if the current data file contains no electrodes (e.g. a pure MEG data file).

[[Image:Montage Editor (48).png]]

==== Virtual Standard Montages ====

Virtual standard montages are sets of predefined channel configurations based on virtual electrodes. In the Montage Editor, virtual standard montages can be selected using the '''Virtual Standard Montages popup menu''' which opens after clicking onto the '''Virtual Standard Montages''' toolbar button or activating the corresponding menu entry in the '''Montage menu'''.

The virtual montages except ''Reference Free'' (10-10) and ''CSD-Laplacian'' (10-10) use predefined montage lists based on the same standard set of 27 10-10 electrodes (Std-27) as the recorded standard montages:

Fp1 Fpz Fp2

F9 F7 F3 Fz F4 F8 F10

A1  T7  C3  Cz  C4  T8  A2

P9 P7 P3 Pz P4 P8 P10

O1 Oz O2

The Std-27 set includes the 21 electrodes of the international 10-20 electrode standard with four traditional labels named according to the newer 10-10 standard (T3=T7, T4=T8, T5=P7, T6=P8). For the standard coordinates of the 27 electrode locations on the sphere see help chapter ''“Electrode'' ''Conventions / Recommendations for Electrode Placement”''. ''Reference Free'' (10-10) and ''CSD-Laplacian'' (10-10) use predefined montage lists based on a standard set of 81 10-10 electrodes.

Virtual montages estimate the voltage at the idealized locations of the standard 27 (81) electrodes on a sphere using spherical spline interpolation. This method is described in Perrin et al. (Electroenceph. clin. Neurophysiol. 72:184-187, 1989); for more details please refer to chapter “''Mapping / Spherical Spline'' ''Maps”''. Using this interpolation, EEG traces can also be displayed for missing or bad electrodes. The use of interpolation is indicated by the keyword ‘virtual’ displayed in the upper left corner of the waveform window above the montage channel labels. In principal, spherical spline interpolation is possible outside the area covered by the recording electrodes. Over the lower half of the head, interpolation benefits greatly from the presence of inferior lateral electrodes (F9, A1,P9, F10,A2,P10). Although only a minimum of 2 separate channels with lower lateral electrodes is required, for example A1/A2 or M1/M2, the use of 6 or 4 inferior lateral electrodes is recommended.

'''Note''': If the number of scalp electrodes is less than 12, virtual standard montages are not available since spline interpolation and interpolated montages cannot be computed.

The following virtual standard montages are available:

* Reference Free
* 10-10 Average
* CSD-Laplacian
* Double Banana
* Triple Banana
* Horizontal Bipolar
* A1/A2 Reference
* Combined Ears
* Referential
* Reference Free (10-10)
* CSD-Laplacian (10-10)

For more details on the different virtual standard montages see help chapter ''"Montage Editor / Standard Montages / Virtual Standard Montages".''

'''Virtual Standard Montage - Reference Free'''

In this montage, the standard 27 interpolated channels are displayed against a reference free average reference. The reference is estimated as the mean voltage over 642 equidistant locations covering the whole head sphere. Voltages are calculated by spherical spline interpolation. According to physics, the voltage integral over the outer surface of the head is zero. By using the mean voltage over the whole head as the reference a close approximation of the true zero reference is obtained.

[[Image:Montage Editor (49).png]]

'''Virtual Standard Montage - 10-10 Average'''

In this montage, the standard 27 interpolated channels are displayed against a virtual average reference. The average reference is computed for each time point as the mean voltage over the interpolated amplitudes of the extended 81 standard virtual scalp electrodes. Since this standard covers inferior electrodes, the 10-10 virtual average reference is not much different from the reference-free montage.

[[Image:Montage Editor (50).png]]

'''Virtual Standard Montage - CSD-Laplacian'''

In this montage, current source density (Laplacian) for each of the standard 27 interpolated electrodes is displayed. The CSD waveforms and maps are computed as the second spatial derivative by spherical spline interpolation and are implicitly reference-free. Because this method intrinsically uses information from all electrodes, it provides a more accurate estimation of the source current leaving and entering the skull than source derivations using only 3 or 4 neighboring electrodes. This is particularly true for electrodes at the boundary of the electrode array.

[[Image:Montage Editor (51).png]]

'''Virtual Standard Montage - Double Banana'''

This is a longitudinal bipolar montage containing two left hemispheric, two right hemispheric and one midline longitudinal row of montage channels. Longitudinal rows are arranged from front to back. All channels are interpolated.

[[Image:Montage Editor (52).png]]

'''Virtual Standard Montage - Triple Banana'''

The Triple Banana montage is an extended longitudinal bipolar montage. It has an additional inferior row on each side as compared to the Double Banana montage. All channels are interpolated.

[[Image:Montage Editor (53).png]]

'''Virtual Standard Montage - Horizontal Bipolar'''

The horizontal bipolar montage contains three transversal rows of montage channels.

Transversal rows are arranged from left to right. All channels are interpolated.

[[Image:Montage Editor (54).png]]

'''Virtual Standard Montage - A1/A2 Reference'''

In this montage, the left-hemispheric channels of the standard 27 interpolated channels (except inferior electrodes F9, A1, P9) are displayed against the interpolated voltage at electrode A1. The right-hemispheric channels of the standard 27 interpolated channels (except inferior electrodes F10, A2, P10) are displayed against the interpolated voltage at electrode A2. The midline electrodes of the standard 27 interpolated channels (except Fpz and Oz) are displayed twice, referenced a) to the interpolated voltage at electrode A1 and b) to the interpolated voltage at electrode A2.

[[Image:Montage Editor (55).png]]

'''Virtual Standard Montage - Combined Ears'''

In this montage, the standard 27 interpolated channels are referenced to a computed virtual linked ears reference. The reference is calculated as the mean voltage of the interpolated amplitudes at A1 and A2 determined by spherical spline interpolation. The calculation of the average potential at the ears balances both sides correctly in contrast to the unknown bias when linking the ears or mastoid electrodes directly.

[[Image:Montage Editor (56).png]]

'''Virtual Standard Montage - Referential'''

In this montage, the standard 27 interpolated channels are displayed against a common virtual 'viewing reference'. The default viewing reference is Cz virtual. Any of the extended 81 standard virtual electrodes may be used as viewing reference.

For details on how to change the viewing reference, see the help chapter'' "Montage Editor / Editing a Montage / Changing the Viewing Reference".''

[[Image:Montage Editor (57).png]]

'''Virtual Standard Montage - Reference Free (10-10)'''

In this montage, the extended standard 81 electrode channels are displayed using spherical spline-interpolation and the reference-free mode. The reference is estimated as described for the ''Reference Free'' montage. This montage yields more detailed spatial information as compared to the reference free 27 channel montage described above.

[[Image:Montage Editor (58).png]]

'''Virtual Standard Montage - CSD-Laplacian (10-10)'''

In this montage, current source density (Laplacian) for each of the standard 81 interpolated electrodes is displayed. The CSD is computed as described for the ''CSD-Laplacian'' montage. This montage may yield more spatial information than the 27 channel CSD-Laplacian montage described above.

[[Image:Montage Editor (59).png]]

==== Standard Source Montages ====

BESA Research provides several standard brain source montages for EEG review. They were derived from a set of 15 regional sources covering lateral and midline frontal, central and parietal cortex, midline fronto-polar and occipito-polar cortex as well as anterior and posterior temporal lobes bilaterally. The following standard sources montages are provided:

* BR_Brain Regions
* FR_Frontal Region
* CR_Central Region
* PR_Parietal Region
* TR_Temporal Region
* Evoked Potentials and MEG
* Resting State Montages

The frontal, central and parietal brain source montages (FR, CR, PR) were derived from the montage BR_Brain Regions in order to emphasize the respective regions in the display. They show the three source activities of each right and left lateral brain region separately along with the 13 other regional sources. The three source activities of each selected region are represented by three '''single dipoles''' with radial and tangential orientations. The activities of the right and left dipoles are displayed in the top six source channels of these montages.

The montage focusing onto the temporal lobe have 4 dipoles in each temporal lobe to reveal temporal-basal, polar, antero-lateral and postero-lateral source activities. The basal and polar sources are oriented tangentially, the lateral sources radially. The montage TR_Temporal Region separates these 4 aspects of the temporal lobe against the source currents in the other 11 regions irrespective of their orientation.

The resting state montages contain regional sources in brain regions associated with the Default Mode Network (DMN), fronto-parietal task control system as well as the dorsal attention system and the ventral attention system. They allow investigating resting state EEG and MEG data in a swift and straight-forward manner. For a more detailed description of the resting state montages, see Resting State Source Montages.

Brain source montages are provided to facilitate the detection of focal source processes in the brain by reversing the overlap from different brain regions seen at the scalp. If brain activity is focal, i.e. represented predominantly in one source waveform, a large amount of the recorded scalp activity reflected in this trace will originate in the related brain region. If source activity is distributed over several traces, the origin is likely to be more widespread or in areas not precisely modeled by the combination of sources in the selected source montage. Each channel in a brain source montage can be viewed as a 'gross virtual electrode' placed onto a particular brain region.

Standardized brain source montages are defined for the 81 standard 10-10 electrodes. Therefore, the recording montage is first interpolated onto the 81 standard electrodes. Then the source waveforms are calculated using the source montage file.

Source montages are labeled using a specific naming scheme to characterize the location, orientation, and type of the underlying source.

'''Note''': If the number of scalp electrodes is less than 12, source montages cannot be computed.

For more details on the different standard source montages see help chapter ''"Montage Editor / Standard Montages / Standard Source Montages".''

'''Naming Scheme of Standard Sources'''

The label of a source channel used in a standard source montage is a combination of the source label itself and the abbreviation of the montage label (separated by an underscore '_').

The source label starts with an abbreviation of the '''brain region '''in which the source is located.

The following abbreviations are available:

* '''C''' ('''c'''entral),
* '''F''' ('''f'''rontal),
* '''Fp''' ('''f'''ronto-'''p'''olar),
* '''Op''' ('''o'''ccipito-'''p'''olar),
* '''P''' ('''p'''arietal),
* '''TA''' ('''t'''emporal '''a'''nterior),
* '''TB''' ('''t'''emporal '''b'''asal), and
* '''TP''' ('''t'''emporal '''p'''osterior)

If the source is a '''single dipole''' (and no '''regional source'''), the '''dipole orientation''' is given in the next lower case character. The orientations are specified as follows:

* '''p''' ('''p'''olar),
* '''r''' ('''r'''adial),
* '''ta''' ('''t'''angential '''a'''nterior), 
* '''tm''' ('''t'''angential '''m'''edial),
* '''tv''' ('''t'''angential '''v'''ertical), and 
* '''v''' ('''v'''ertical).

The last letter before the underscore ('_') which separates the abbreviation of the montage name specifies the '''hemisphere''':

* '''L''' ('''l'''eft hemisphere),
* '''M '''('''m'''idline), and 
* '''R''' ('''r'''ight hemisphere).

Examples:

* TAL_BR:  '''t'''emporal '''a'''nterior regional source, '''l'''eft hemisphere, source montage '''''BR'''_Brain Regions''
* FprM_TA: '''f'''ronto-'''p'''olar '''r'''adial single dipole source, '''m'''idline, source montage '''''TA'''_Temporal Lobe''

'''Standard Source Montage - BR_Brain Regions'''

This source montage uses a set of 15 regional sources covering lateral and midline frontal, central and parietal cortex, midline fronto-polar and occipito-polar cortex as well as anterior and posterior temporal lobes bilaterally. It separates the activities of the 15 different brain regions and provides for fast comparison and quantification of the different activities.

Note: If the data contains '''MEG channels''', the corresponding MEG montages ''BRM ''(for magnetometers and axial gradiometers) and ''BRG'' (for planar gradiometers) are located in subfolder '''MEG'''.

[[Image:Montage Editor (60).png]]

''Highlight on the left temporal anterior (TAL) regional source.''

[[Image:Montage Editor (61).png]]

''Highlight on the left frontal (FL) regional source. The two temporal sources in the foreground are still visible.''

[[Image:Montage Editor (62).png]]

''Highlight on the central midline (CM) regional source. The left-side sources in the foreground are also visible.''

'''Standard Source Montage - CR_Central Region'''

This source montage displays the radial and tangential activities of the central brain region bilaterally in the first 6 '''single dipole''' channels. The other 13 '''regional sources''' separate the source activities arising from the other brain regions.

'''Note:''' If the data contains '''MEG channels''', the corresponding MEG montages ''BRM'' (for magnetometers and axial gradiometers) and ''BRG'' (for planar gradiometers) are located in subfolder '''MEG.'''

[[Image:Montage Editor (63).png]]

'''Standard Source Montage - FR_Frontal Region'''

This source montage displays the radial and tangential activities of the frontal brain region bilaterally in the first 6 '''single dipole''' channels. The other 13 '''regional sources''' separate the source activities arising from the other brain regions.

'''Note:''' If the data contains '''MEG channels''', the corresponding MEG montages ''BRM'' (for magnetometers and axial gradiometers) and ''BRG'' (for planar gradiometers) are located in subfolder '''MEG'''.

[[Image:Montage Editor (64).png]]

'''Standard Source Montage - PR_Parietal Region'''

This source montage displays the radial and tangential activities of the parietal brain region bilaterally in the first 6 '''single dipole''' channels. The other 13 '''regional sources''' separate the source activities arising from the other brain regions.

'''Note:''' If the data contains '''MEG channels''', the corresponding MEG montages ''BRM'' (for magnetometers and axial gradiometers) and ''BRG'' (for planar gradiometers) are located in subfolder''' MEG'''.

[[Image:Montage Editor (65).png]]

'''Standard Source Montage - TR_Temporal Region'''

This source montage displays the activities of four different aspects of the temporal lobe bilaterally in the first 8 dipole traces. There are 4 equivalent dipole sources in each temporal lobe to reveal temporal-basal, polar, antero-lateral and postero-lateral source activities. The basal and polar sources are oriented tangentially, the lateral sources radially. The montage TR_Temporal Region separates these 4 aspects of the temporal lobe from the source currents in the other 11 regions irrespective of their orientation. Head schemes illustrate location and orientation of each virtual electrode.

The ''Temporal Lobe'' and ''Temporal Region'' montages may be used to facilitate the detection of lateralized temporal lobe activities and of the differences of the activities at the various spatial aspects of both temporal lobes. Note that eye movement artifacts may be well represented by the sources at the tip of the temporal lobe due to similarities in the scalp distribution of the related source activities.

'''Note:''' If the data contains '''MEG channels''', the corresponding MEG montages ''BRM ''(for magnetometers and axial gradiometers) and ''BRG'' (for planar gradiometers) are located in subfolder '''MEG'''.

[[Image:Montage Editor (66).png]]

'''Evoked Potentials'''

BESA Research provides three standard source montages designed specifically for use with auditory (AEP), somatosensory (SEP), and visual (VEP) evoked data. Brain regions that are specifically relevant for the auditory, somatosensory, and visual pathway, respectively, are modeled with equivalent current dipoles. Remaining brain regions are modeled with regional sources. The Evoked Potentials source montages are available for EEG only.

'''Standard Source Montage - Resting State Montages'''

'''''Introducing Resting State Networks'''''

The default mode network (DMN) is the most commonly known brain network associated with resting state activity. It comprises brain regions that become less active, when the subject is engaged with a task, and in turn more active when the subject is resting (Raichle, MacLeod et al. 2001; Buckner, Andrews-Hanna et al. 2008). Thinking of the DMN as a “baseline” state of the brain would be misleading, as DMN brain regions have been linked with remembering the past, envisioning future events, and considering the thoughts and perspectives of other people (Buckner, Andrews-Hanna et al. 2008). This internal reflection is likely to happen when the brain is not otherwise engaged and the corresponding network thus becomes active in resting state. Recent research (Power, Cohen et al. 2011; Bressler and Menon 2010) has shown that several other brain networks known to become active during certain tasks can also be identified in resting state. Among them are the fronto-parietal task control system as well as the dorsal and ventral attention system (Power, Cohen et al. 2011). These networks seem to be stable systems that are internally connected even when no particular task is given. The resting state networks DMN, fronto-parietal task control system as well as the dorsal attention system and the ventral attention system are available in BESA Research as source montages. They allow investigating resting state EEG and MEG data in a swift and straight-forward manner.

'''''How the Resting State Source Montages were created'''''

BESA resting state source montages are based on source solutions, for which regional sources were placed at the MNI locations of the brain regions of interest. Source locations were derived from the following publications:

[[Image:Montage Editor (67).png]]

Bilateral Sources representing the same brain regions that were not perfectly symmetrical were symmetrized favoring the position of the less superficial source.

Additional noise sources were placed to increase the sensitivity of the sources of interest.

Noise sources are easily identified by their name.

[[Image:Montage Editor (68).png]]

'''''Applying Resting State Source Montages on your data'''''

'''EEG'''

For EEG data, the resting state source solutions were saved as source montages and are automatically available from the Menu Montage / Source / Resting State Montages'''.'''

[[Image:Montage Editor (69).png]]

All sources are regularized with a regularization constant of 1%.

'''MEG'''

For MEG data, source montages are not pre-saved as there are varying MEG sensor types depending on the MEG system and manufacturer. MEG users should send a segment of their raw data to source analysis and load the desired source solution in the source analysis module. 

Source solutions for resting state networks can be found here: 

'''“C:\Program Files (x86)\BESA\Research_6_0\Montages\SourceMontages\Resting State Montages”.'''

After loading the source solution, it is possible to save it as a source montage with '''File / Save Source Montage As.''' The source montage will now be applied on the data in the main window and is also available from the menu option '''Montage / User-Defined'''.

'''Mean FFT Analysis in Resting State Source Space'''

Before applying the desired resting state source montage on the raw data, artifacts should be dealt with either by artifact correction and / or artifact rejection (as part of the mean FFT scan). 

After applying the resting state source montage, a mean FFT can be calculated on the source waveforms associated with the source channels, i.e. the ongoing brain activity in the resting state network. Mean FFT performs block-wise FFTs on the whole dataset and the mean output is created when the end of the file is reached. Hereby, information can be drawn on the frequency content of the whole dataset. 

Mean FFT can be started from the menu '''Process / Mean FFT Spectrum'''. The dialogue allows specifying the data range (by default all data) and the block length, BESA Research will use for calculating individual FFTs. Artifact thresholds for the source channels can also be defined. Mean FFT’s output will give an overview of the frequency content of the individual source channels.

'''TFC Analysis in Resting State Source Space'''

For TFC analysis in BESA Research, it is required to insert triggers in the raw resting state data. This can be done by pressing '''ERP / Insert Triggers'''. After insertion of the triggers, a paradigm must be created ('''ERP / Edit Paradigm''') that will allow the calculation of the time-frequency plots based on the inserted triggers in the final tab. Please make sure that any filters are only applied for artifact scanning

in the filter tab and not for “averaging”, as this would also reduce the frequency domain for time-frequency analysis. 

For TFC analysis of resting state data it is recommendable to not use any baseline correction in the paradigm window. If possible, however, a control resting condition should be used (e.g. eyes open / eyes closed) that can be contrasted with the resting state condition of interest in the time-frequency window.

In the time-frequency display, the results should be displayed as absolute values (the ABS button [[Image:Montage Editor (70).png]] )

If a control condition is available the two resting state conditions can also be contrasted by pressing the according subtraction button ( [[Image:Montage Editor (71).png]] ). 

Coherence can be calculated between any resting state source channel and all other channels:

[[Image:Montage Editor (72).png]]

''This example shows resting state connectivity between the right-frontal source (red label) and the left-frontal source, as well as the right dorso-lateral prefrontal cortex. No strong coherence is found with the other network sources or the noise sources.''

It is possible to apply beamformer and / or DICS analysis on the time-frequency range of interest, suggesting the following possible workflow:

[[Image:Montage Editor (73).png]]

'''References'''

1 .Bressler, S. L. and V. Menon (2010). "Large-scale brain networks in cognition:

emerging methods and principles." Trends Cogn Sci 14(6): 277-290.

2. Buckner, R. L., J. R. Andrews-Hanna, et al. (2008). "The brain's default network:

anatomy, function, and relevance to disease." Ann N Y Acad Sci 1124: 1-38.

3. Corbetta, M. and G. L. Shulman (2002). "Control of goal-directed and stimulus-driven

attention in the brain." Nat Rev Neurosci 3(3): 201-215.

4. Dosenbach, N. U., D. A. Fair, et al. (2007). "Distinct brain networks for adaptive

and stable task control in humans." Proc Natl Acad Sci U S A 104(26): 11073-11078.

5. Power, J. D., A. L. Cohen, et al. (2011). "Functional network organization of

the human brain." Neuron 72(4): 665-678.

6. Raichle, M. E., A. M. MacLeod, et al. (2001). "A default mode of brain function."

Proc Natl Acad Sci U S A 98(2): 676-682.

==== Predefined Additional Channel Montages ====

Predefined '''additional channel montages''' may be used to display eye activity and EKG or sphenoidal channels in addition to the main montage channels.

In the Montage Editor, additional channel montages can be selected using the '''Additional Channel''' '''Montages''' popup menu. Open this menu by clicking onto the '''Additional Channel Montages toolbar''' '''button '''or activate the corresponding entry in the '''Montage''' menu.

The following predefined additional channel montages are available:

* EKG
* EOG-HB
* EOG-HV
* EOG-HVB
* EKG+EOG-HB
* EKG+EOG-HV
* EKG+EOG-HVB
* Sphenoidals_Avr
* Sphenoidals_Bip

For more details on the different additional channel montages see help chapter ''"Montage Editor / Standard Montages / Predefined Additional Channel Montages"''.

'''Additional Channel Montage - EKG'''

This additional channel montage defines several polygraphic EKG channels. Depending on the recorded channels of your data file, the available EKG channel or channel combination is used.

Note that this montage is not available if the current data file does not contain any EKG channels.

<div style="color:#00000a;">[[Image:Montage Editor (74).png]]</div>

If you use different conventions for defining EKG channels, you may edit this montage in the Montage Editor using copy and paste from the ''Original Recording'' montage.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

'''Additional Channel Montage - EOG-HB'''

This virtual additional channel montage automatically generates a horizontal EOG channel (H_EOG) and an eye blink channel (B_EOG) from the recorded EEG scalp electrodes using spherical splines interpolation to the standard 81 electrodes and a source montage that contrasts brain and eye activity. It is recommended to reference all electrodes including electrodes near the eyes, e.g. F11, F12, LO1, LO2, IO1, IO2, to the common reference, because this virtual montage can then better separate eye and brain activities (cf. Berg and Scherg, 1994). Special bipolar EOG channels cannot be used in this calculation and are, therefore, not recommended.

<div style="color:#00000a;"></div>

[[Image:Montage Editor (75).png]]

''The display shows the equivalent centers of the spatial components reflecting the topographies of horizontal eye movements (black) and eye blinks (green).''

This automatic virtual montage is currently available for EEG data files only.

'''Additional Channel Montage - EOG-HV'''

This virtual additional channel montage automatically generates a horizontal (''H_EOG'') and a vertical (''V_EOG'') EOG channel from the recorded EEG scalp electrodes using spherical splines interpolation to the standard 81 electrodes and a source montage that contrasts brain and eye activity. It is recommended to reference all electrodes including electrodes near the eyes, e.g. ''F11, F12, LO1, LO2'', ''IO1, IO2,'' to the common reference, because this virtual montage can then better separate eye and brain activities (cf. Berg and Scherg, 1994). Special bipolar EOG channels cannot be used in this calculation and are, therefore, not recommended.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Montage Editor (76).png]]

''The display shows the equivalent centers of the spatial components reflecting the topographies of horizontal (black) and vertical (blue) eye movements.''

This automatic virtual montage is currently available for EEG data files only.

'''Additional Channel Montage - EOG-HVB'''

This '''additional channel montage''' is a combination of the '''EOG-HB''' and the '''EOG-HV''' additional channel montages. Please see there for a detailed description.

'''Additional Channel Montage - EKG+EOG-HB'''

This '''additional channel montage''' is a combination of the '''EKG''' and the '''EOG-HB''' additional channel montages. Please see there for a detailed description.

'''Additional Channel Montage - EKG+EOG-HV'''

This '''additional channel montage''' is a combination of the '''EKG''' and the '''EOG-HV''' additional channel montages. Please see there for a detailed description.

'''Additional Channel Montage - EKG+EOG-HVB'''

This '''additional channel montage''' is a combination of the '''EKG, '''the '''EOG-HB''', and the '''EOG-HV''' additional channel montages. Please see there for a detailed description.

'''Additional Channel Montage - Sphenoidals_Avr'''

This '''additional channel montage''' allows to display sphenoidal electrodes referenced against the common average reference in parallel with any recorded, virtual, or source montage for comparison.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Montage Editor (77).png]]

If the current data file has no channels labeled'' SP1'' and ''SP2'', this montage is not available.

'''Additional Channel Montage - Sphenoidals_Bip'''

This '''additional channel montage''' allows to display sphenoidal electrodes using a bipolar reference in parallel with any recorded, virtual, or source montage for comparison. The reference is ''T3/T4'' (or ''T7/T8'') to enhance the hemispheric difference of vertical activity resulting from the activation of the inferior surface of the temporal lobe. Note that the standard source montage ''TR_Temporal Region'' provides for a better hemispheric separation of right and left temporal lobe activities (see e.g. example '''EEG-Focus\EEG2.eeg''').

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Image:Montage Editor (78).png]]

If the current data file has no channels labeled ''SP1'' and'' SP2'', this montage is not available.

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

<div style="color:#00000a;"></div>

[[Category:Research Manual]]

Review

2017-04-07T12:48:14Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
= BESA Research Review =

== The Review Window ==

BESA Research incorporates many features of the EEGFOCUS program. Therefore, it is a comprehensive EEG review program combining traditional EEG review with new and unmatched tools for digital EEG analysis. The user interface of BESA Research has been designed to allow for very efficient and quick EEG review. BESA Research can store information, i.e. file names, paths and settings of up to 20 EEGs, from one or several subjects. Once you have selected an EEG file, you can use the control push-buttons to:

* switch back and forth between the different selected EEG files
* page forward and backward through the EEG, automatically or manually
* use the event or scroll bar to jump to any marked event or anywhere else in the EEG
* change instantaneously between recorded, virtual, source and user defined montages
* mark, tag, analyze and store any EEG event or segment
* change scales and timing rapidly using toolboxes
* select combinations of scalp, polygraphic, intracranial, and additional channels

Note that BESA Research can also work with MEG. Most of the functions described for EEG are also valid for the processing of MEG signals.

The review window is the main window in BESA Research. It provides access to all important review and analysis features with one or two mouse clicks. The main features are illustrated in the layout figure below. The central part of the window shows the EEG waveforms of the current montage. Around the central display, the menu bar and buttons are grouped for an easy access to the program features.

[[Image:Review (1).jpg]]

''Overview of the review window''

== Controls and Push Buttons ==

'''Menu bar: '''

The menu bar is situated at the '''top''' of the window. All commands can be selected from one of the submenus which open when you click on one of the headings. Each heading summarizes a set of features for a specific aspect, e.g. artifact correction. All menu items and sub-items are explained in section '''Menus''' and in online help chapter ''"Review / Reference / Menus"''.

'''Control ribbon: '''

<div style="margin-left:1.55cm;margin-right:0cm;">The push button controls '''below the menu bar''' allow for a fast selection of commands and settings which are often used. They are grouped in sections which feature file manipulation, mapping display, data analysis, remontaging, and filtering. The functions of the push buttons in the control ribbon are explained below and in online help chapter ''"Review / Reference / Menus"''. </div>

<div style="margin-left:1.55cm;margin-right:0cm;">[[Image:Review (2).jpg]]</div>

'''Channel group selection: '''

<div style="margin-left:1.288cm;margin-right:0.09cm;">The controls at the '''top right''' of the waveforms display enable showing or hiding channels which belong to a specific channel group. These can be scalp, polygraphic, or intracranial channels. Additional channels can be chosen for display below the current montage, e.g. EKG channels and/or virtual eye electrodes that are automatically calculated. </div>

'''Scaling and channel selection controls: '''

<div style="margin-left:1.288cm;margin-right:0.09cm;">For each selected channel group, e.g. '''Scp, Pgr''' etc., two push buttons and a scaling symbol are available on the '''righthand side''' of the window. By means of these buttons, a subset of channels can be selected for display, and the scaling of the channel group can be adjusted. For additional channels (the blue channels at the bottom of the display), the scaling can be adjusted individually. </div>

'''Timing push button: '''

<div style="margin-left:1.288cm;margin-right:0.09cm;">The timing push button at the '''bottom right''' of the window adjusts the time resolution of the data segment which is displayed on the screen. </div>

'''Event bar: '''

<div style="margin-left:1.288cm;margin-right:0.09cm;">The event bar at the '''bottom''' of the waveforms display summarizes the position of events within the data file. By clicking on an event, you can jump to the corresponding position in the data. </div>

'''Scroll bar: '''

<div style="margin-left:1.288cm;margin-right:0.09cm;">By using the scroll bar which is situated '''just below''' the event bar, you can quickly move through the data file - either by clicking into the scroll bar, by dragging the scroll button, or by using the arrows for small adjustments. </div>

'''Status bar: '''

<div style="margin-left:1.288cm;margin-right:0.09cm;">The status bar at the very '''bottom''' of the window provides information about the current settings. The information displayed depends on the context, e.g. on whether a cursor is set or not, or whether an average buffer or raw data are viewed. </div>

'''Paging controls: '''

<div style="margin-left:1.288cm;margin-right:0.09cm;">These push buttons are placed at the '''bottom left''' of the window. They enable fast forward and backward paging, either by using the arrows at the left for a whole page, or by using the arrows at the right for a half page. The '''Auto''' button is used for automatic paging and searching / averaging. </div>

For more details about controls and push buttons see online'' ''help chapter'' "Review / Reference / Controls".''

== Using the Mouse ==

Easy to use mouse operations facilitate working with data files. You can mark specific items by a single click, initiate a map by a double click, or use a right click to open context-optimized menus. The figure below illustrates the main mouse functions. In this example ('''EEG2.eeg'''), right temporal-basal seizure onset is shown using the source montage TR_Temporal Region. An automatic eye artifact correction was performed that added two virtual EEG channels for vertical and horizontal eye movements below the montage channels (more information on artifact correction is found in the chapter "''Artifact Correction''"). The source montage displays the signals from four aspects of the left and right temporal lobes (head symbols: basal, polar, antero-lateral, postero-lateral aspects) and 11 other brain regions (more information on remontaging is found in the chapter "''Montage Editor''").

The most important mouse functions in the different areas of the review window are:

[[Image:Review (3).jpg]]

''Basic mouse functions in the review window.''

'''Channel label area: '''

'''Left mouse click:''' Mark channels for analysis or pattern search (see figure below)

'''Right mouse click:'''
* In source montages, a click on the channel label (or head symbol) at the left of the display opens an image which shows the brain region corresponding to the source channel. Learn more about images in the chapter “''Mapping''”.
* In the original montage, the right click on the channel label opens a popup menu to define a channel as bad, or to interpolate its signal using the other channels.

'''Waveform area: '''

<div style="margin-left:1.289cm;margin-right:0.09cm;">'''Left mouse double click:''' Opens the mapping window and shows the voltage topography at the selected position. Maps can be displayed either as 2D or 3D whole head maps, or as top meridian projection maps. For more details see the chapter “''Mapping''”. </div>

<div style="margin-left:1.288cm;margin-right:0.09cm;">'''Left mouse click:''' Remove cursor and maps or images, if displayed. </div>

<div style="margin-left:1.288cm;margin-right:0.09cm;">'''Right mouse click:''' Opens a popup menu for marking, adding or deleting events and to start specific processes related to the selected position in the EEG. In the example shown here, a comment was added to indicate seizure onset. </div>

<div style="margin-left:1.289cm;margin-right:0.09cm;">'''Left mouse drag:''' Mark a block for analysis, e.g. FFT or correlation analysis. Right click into the marked block to obtain the special popup menu for processing of marked data blocks. </div>

<div style="margin-left:1.289cm;margin-right:0.09cm;">'''Right mouse drag:''' Measure peaks and frequency of marked channels segment (cf. figure below) </div>

<div style="margin-left:-0.009cm;margin-right:0cm;">'''Event bar: '''</div>

<div style="margin-left:1.289cm;margin-right:0cm;">'''Left mouse click:''' Jump to events. </div>

<div style="margin-left:1.289cm;margin-right:0.09cm;">'''Right mouse click:''' Display information about events. </div>

<div style="margin-left:-0.009cm;margin-right:0cm;">'''Control buttons: '''</div>

<div style="margin-left:1.288cm;margin-right:0cm;">'''Left mouse click:''' Use button. </div>

<div style="margin-left:1.288cm;margin-right:0.09cm;">'''Right mouse click:''' Display information on use of button. </div>

[[Image:Review (4).jpg‎]]

''Mouse drag functions in the review window.''

The example above illustrates how amplitude peaks and frequencies can be measured using the right mouse drag, and how a block can be marked using the left mouse drag, e.g. for correlation analysis. Please refer to the sections “''Measuring Peaks and Frequency” ''and ''"Correlation" ''for detailed explanations.

== Paging ==

Paging through the EEG with BESA Research has several advantages over paging through paper EEG. For example, the default setting in BESA Research is paging with a 10% overlap, which ensures that events at the edge of a page are not overlooked. Larger or smaller paging steps are achieved by just two mouse clicks. You can also jump to any part of the EEG recording by a click into the event bar, switch among various montages using the push buttons, etc.

'''Paging Using Buttons '''

You can page through the data using the control push buttons at the bottom left of the review window, as illustrated in the figure below:

[[Image:Review (5).jpg ]]

The arrows page forward or backward by a whole page. If ''Paging with Overlap ''is selected in the program options, paging occurs with a 10% overlap (maximum 1 second). To page through the display automatically, click on the automatic button between the arrow buttons. Then click on the page forward or page backward button, or press the '''<Space>''' bar on the keyboard to start paging. Automatic paging may be stopped by clicking the Auto button again, or by pressing the '''<Space>''' bar or any key on the keyboard. You can speed up or slow down automatic paging using the menu '''Options/Paging/Timing of Auto-Page Mode'''''. ''The arrows at the right are used for paging half a page forward or backward.

Press the arrows on the scrollbar at the bottom of the window (cf. figure below) to step forward or backward by just one second. Clicking into the scrollbar area pages forward or backward in whole page steps (this is also achieved by using the mouse wheel).

[[Image:Review (6).jpg]]

These controls are described in more detail in online help chapter '''''"'''[mk:@MSITStore:C:\Users\Alexa\Documents\work\Manual\BESA%20Help\Data-Review.chm::/Controls_Moving_through_the_EEG_file.htm Review / Reference / Menus / Paging Controls]'''.'''''

'''Paging Using the Keyboard'''

A useful and efficient way to work with BESA Research is to keep the left hand on the keyboard and the right hand on the mouse (see the figure below). You can page through the EEG using the '''<Space>''' bar (left hand). Stop paging by pressing the '''<Space>''' bar again and press the ''''B' '''key to page back in half page steps, for example, until you see the pattern that made you stop paging. Use the right hand on the mouse to work on the displayed signals, e.g. view maps (left mouse double click), set tags or define epochs and artifacts (right click for popup menu), and perform FFT or linear correlation (drag to mark block and right click for popup menu), etc. To move back by a half page (useful e.g. if a pattern was detected during automatic paging), press the ''''B'''' key. Move forward by a half page with the ''''N' '''key.

For detailed information on additional keyboard paging commands, please refer to online help

Chapter ''"Reference / Controls / Mouse and Keyboard / Keyboard Controls".''

[[Image:Review (9).jpg]]

== Events and Tags ==

Tagging of the EEG is like making notes on an EEG-printout. Tagged events in a digital EEG are more powerful, since they can be used, for example, for selected viewing of a group of similar events (see online help chapter'' "Review / Reference / Menus / View / Selected View").''

Tags of different kinds can be used to mark time points or ranges of interest, add comments, and define artifact time ranges. All types of tag can be set using the popup menu that appears when the right mouse button is pressed.

'''Types of Events '''

There are different types of events that can be tagged manually: * '''Markers'''. These define time points that are used to divide the EEG into gross time ranges, for functions such as: FFT or average between markers.
* '''Comments.''' These are text notes that can be placed at any time point in the EEG.
* '''Epochs'''. Time ranges of interest with optional labels. These can be selectively viewed excluding all the remaining EEG. This allows for a fast overview over similar epochs.
* '''Artifacts'''. Time ranges containing artifacts. These are similar to epochs, with the additional property that they are excluded from averaging and FFT.
* '''Patterns'''. These define time points in one of five categories (Pattern 1-5). They may be used for averaging in 5 different buffers and can be defined by the pattern search.
* '''Triggers'''. These are defined by an external trigger input or are created from recorded channels by converting pattern tags into triggers from the ERP menu (see help chapter "''ERP / Functions... / Managing Triggers / Editing Triggers''").

'''Event Bar '''

<div style="margin-left:0.042cm;margin-right:0.09cm;">The event bar is located at the bottom of the review window. It shows all events in the data file as vertical lines. Different event types are indicated by different colors. You can view an event description by right click on the corresponding line. Jump to any event by left click on the line. </div>

<div style="margin-left:0.042cm;margin-right:0.09cm;">[[Image:Review (11).jpg]]</div>

'''Setting Events'''

Most tags are defined at single time points by moving the mouse pointer over the position in the waveforms display, performing a right click, and selecting the tag type from the menu that appears.

Epochs and artifacts are defined when a block has been marked by dragging over a portion of the EEG and pressing the right mouse button. Left and right borders of an epoch/artifact can also be defined at single times by pressing the right mouse button and selecting epoch or artifact. You can page and terminate the pending epoch/artifact by right clicking at another time to mark longer segments.

{| style="border-spacing:0;width:15.256cm;"
|- style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.164cm;padding-bottom:0cm;padding-left:0.265cm;padding-right:0.164cm;"
|| [[Image:Review (1).gif]]
|| [[Image:Review (2).gif]]
|-
| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.164cm;padding-bottom:0cm;padding-left:0.265cm;padding-right:0.164cm;" | ''Popup menu after right click somewhere in the EEG. ''
| style="background-color:#ffffff;border:0.75pt solid #000001;padding-top:0.164cm;padding-bottom:0cm;padding-left:0.265cm;padding-right:0.164cm;" | ''Popup menu after right click when a block is marked ''
|-
|}

'''Viewing Events'''

You can view the type and description of an event in two ways:
# Right click on the vertical line in the event bar which represents the event.
# Jump to the position of the event in the data file by a left click in the event bar (or by using the '''Goto''' menu). The event is indicated in the waveform display by a vertical line. Right click into the display just above the event bar with the mouse positioned at the latency of the event.

== Remontaging ==

BESA Research offers three types of montages:* '''Recorded (traditional) montages''' using combinations of the recorded channels
* '''Virtual (interpolated) montages''' using combinations of 27, 33 or 81 standard virtual
* '''Brain source montages''' using transformations onto virtual electrodes in the brain

Remontaging in BESA Research is conveniently performed by pressing one of the push buttons '''Rec, Vir, Src or Usr'',''''' which provide a shortcut to the '''Recorded,''' '''Virtual, Source '''and '''User-Defined '''submenus of the '''Montage''' menu. The push buttons''''' ''Opt''' and '''EdM '''allow for setting montage options and editing of user-defined and additional montages.

{{clear}}
[[Image:Review (7).png]]

The following standardized montages are provided in BESA Research and can be selected using the '''Montage''''' ''menu or the montage push buttons:

'''Rec: Recorded (traditional) montages'''* Original EEG data: '''Original Recording'''.
* Average reference montages: '''Average Reference''', '''Original Average Reference'''.
* Longitudinal/horizontal bipolar montages: '''Double Banana''', '''Triple Banana''', '''Horizontal Bipolar'''.
* Montages with a single channel reference: '''A1/A2 Reference''', '''Referential'''.

'''Vir: Virtual (interpolated) montages'''

Spherical spline interpolation over the recorded electrodes is used to calculate the voltage at a standard set of 81 virtual electrodes of the 10-10 international electrode system. The average potential over these 81 electrodes is used as the 10-10 average. Combinations between these virtual electrodes are used to calculate standardized montages which are also available if some electrodes are missing or bad:* Average reference montage: '''10-10 Average'''.
* Longitudinal/horizontal bipolar montages: '''Double Banana''', '''Triple Banana, Horizontal Bipolar'''.
* Montages with a single channel reference: '''A1/A2 Reference''', '''Referential'''.
* Combined (=averaged) ears reference: '''Combined Ears'''.
* Reference-free montage: '''Reference Free''', '''Reference Free (10-10)'''.
* Current source density montage: '''CSD-Laplacian''', '''CSD-Laplacian (10-10)'''.

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

'''Src: Brain source montages'''* Standard brain source montages. See below for further explanation.

'''Usr: User-defined montages'''* Specific user-defined montages created in the Montage Editor or the Source Analysis window. See below for further explanation.

'''Opt: Montage Options'''

Recorded, virtual and source montages can be arranged in different systematic orders and groupings using the '''Opt'' '''''push button, which provides a shortcut to the '''Montage / Options''''' ''menu (see the online help chapter ''"Review / Reference / Menu / Montage / Options"''). Montages can be ordered from:

* '''left to right '''depicting lower left, intermediate left, midline, intermediate right and lower right rows of channels with a sequence from anterior to posterior.
* '''right to left '''depicting lower right, intermediate right, midline, intermediate left and lower left rows of channels with a sequence from anterior to posterior.

Additionally, montages can be grouped by hemisphere for easier hemispheric comparison or by regions for easier regional comparison.

This allows for convenient comparison of lateralization and location of focal activity across the different montages. This systematic arrangement of traditional, virtual and brain source montages yields a completely new perspective that was not available previously during digital EEG review.

More details on the montage options for regional sources see below.

'''EdM: Edit Montage'''

Press this button to open the montage editor. In the Montage Editor, the montage channels can be viewed, edited and combined to new user-defined montages.

'''Note:''' You can switch among montages quickly by clicking on the montage push-buttons '''Rec, Vir, Src, Usr''' at the top of the main window below the menus. Clicking on the '''Rec''''' ('''''Vir, Src, Usr''''')'' button once switches to the last displayed montage of this category. Clicking again, the popup menu opens to select another montage of this category. BESA Research provides several predefined recorded, virtual and source montages and allows the user to define new montages. User-defined montages are created in the Montage Editor and are stored in binary files. User-defined montage files located in the program subfolder ''Montages\UserMontages ''or in the data directory are automatically available from the '''Montage / User-Defined''' menu. User-defined montage files located elsewhere can be loaded in the Montage Editor. After loading they are available from the '''Usr '''push button too.

'''The Montage menu'''

The Montage menu provides the same functionality as the push buttons described above, plus the option to show additional channels below the current montage. A brief description of the available montages is given below. For more details see chapter Standard Montages in the help chapter "''Montage Editor''".

'''Recorded montages'''

{{clear}}
Press the push button''''' ''Rec''' twice or use the menu Montage/Recorded to select a recorded (traditional) montage.

[[Image:Review (3).gif]]

'''Average Reference'''

In this traditional montage, the available channels of the Std-27 electrode set are displayed against average reference. The average reference is computed for each time
point as the mean voltage over the amplitudes of all scalp electrodes that are not bad. If the common reference used for recording is a single electrode and has been
specified, it will be included in the computation of the average reference.

'''Double Banana'''

This is a longitudinal bipolar montage containing two left hemispheric, two right hemispheric and one midline longitudinal row of montage channels. Longitudinal rows
are arranged from front to back. Predefined montage channels are only displayed if both the channel and reference are available (i.e. recorded and not bad).

'''Triple Banana'''

The Triple Banana montage is an extended longitudinal bipolar montage. It has an additional inferior row on each side as compared to the Double Banana montage. Predefined montage channels are only displayed if both the channel and reference are available (i.e. recorded and not bad). The Triple Banana montage is not available if less than 2 inferior electrodes are recorded or defined as ‘good’ on each side.

'''Horizontal Bipolar'''

The horizontal bipolar montage contains three transversal rows of montage channels. Transversal rows are arranged from left to right or right to left depending on the
settings in Options. Predefined montage channels are only displayed if both the channel and reference are available (i.e. recorded and not bad). In the Horizontal Bipolar
montage, available midline electrodes are always displayed even if ''Midline Channels'' is set to ''Off'' in ''Montage / Options.''

'''A1/A2 Reference'''

In this traditional montage, the available left-hemispheric channels of the Std-27 electrode set (except inferior electrodes F9, A1, P9) are displayed against the electrode
A1 (or, if A1 is not available, a close channel such as P9 -> T9 -> TP9 -> M1). The available right-hemispheric channels of the Std-27 electrode set (except inferior
electrodes F10, A2, P10) are displayed against the electrode A2 (or a close channel such as P10 -> T10 -> TP10 -> M2). The available midline electrodes of the Std-27
electrode set (except Fpz and Oz) are referenced to A1 and A2 (or a close channel), respectively. If neither A1 nor A2 nor any of the close channels are recorded or
defined as ‘good’, the A1/A2 Reference montage is not available.

'''Referential'''

In this traditional montage, the available channels of the Std-27 electrode set are displayed against a common ‘viewing reference’. The default viewing reference is
Cz. The viewing reference can be changed in the Montage Editor (which can be opened using the''''' ''EdM'' '''''button in the control ribbon). Any of the electrodes in the EEG file may be used as viewing reference. Note that the common viewing reference is independent of the common reference used for recording.

'''Original Recording'''

This montage displays the data as recorded. Note that channels defined as 'bad channels' are shown as a flat grey line. In the other recorded montages, bad channels are not displayed.

If the common reference has been defined, it will be displayed as a flat line as well, since Com minus Com equals zero. The label of the common reference is appended to each channel label.

In this montage, push buttons appear at the upper right of the EEG window for selecting '''''All '''''channel groups or one of the possible channel groups ('''Scp'' '''''<nowiki>= scalp EEG, </nowiki>'''Pgr'' '''''<nowiki>= polygraphic, </nowiki>'''Icr'' '''''<nowiki>= intracranial, </nowiki>'''MEG'' '''''<nowiki>= magnetoencephalographic channels). These buttons and the group buttons above the calibration marks may be used to change conveniently between displays of a few selected channels of one group and all groups and channels.</nowiki>

'''Original Average Reference'''

In this montage, the scalp electrodes are displayed in the recording sequence, versus common average reference. The average reference is computed for each time point as the mean voltage over the amplitudes of all scalp electrodes that are not bad.

If the common reference is a known single electrode, it will be included in the computation of the average reference. The voltage at the common reference electrode against average reference will be displayed. Note that this is not a flat line!

The ''Original Recording ''and ''Original Average Reference ''montage have the same sequence of electrodes as the original recorded data. The other recorded montages (as well as the virtual montages) are derived from predefined montage lists based on a standard set of 27 electrodes (Std-27) of the international 10-10 electrode system.

If the common reference used for recording is a known single electrode and has been specified in ''Edit/ Channel Configuration'', the common reference electrode is regarded as part of the recording electrode set. Predefined montage channels using the common reference can be displayed. The common reference will be included in the computation of the average reference. This is not possible, however, for EEG systems using a combination of electrodes as the common reference. e.g. F3/F4.

Note: A predefined recording montage channel is not displayed if either channel or reference are defined as bad in ''Edit / Bad Channels''. Due to missing or bad channels, a predefined recorded montage may be empty. If this is the case, the montage will not be available for selection in the menu. For more details see the help chapter ''"Montage Editor / Recorded Standard Montages''".

'''Virtual montages'''

{{clear}}
Press the push button '''Vir '''twice or use the menu '''Montage/Virtual to''' select a virtual (interpolated) montage.

[[Image:Review (4).gif]]

'''Reference Free'''

<div style="margin-left:1.55cm;margin-right:0cm;">In this montage, the standard 27 interpolated channels are displayed against a computed zero reference. The reference is estimated as the mean voltage over 642 equidistant locations covering the whole head sphere. Voltages are calculated by spherical spline interpolation. According to physics, the voltage integral over the outer surface of the head is zero. By using the mean voltage over the whole head as the reference a close approximation of the true zero reference is obtained.</div>

'''10-10 Average'''

<div style="margin-left:1.55cm;margin-right:0cm;">In this montage, the standard 27 interpolated channels are displayed against a virtual average reference. The average reference is computed for each time point as the mean voltage over the interpolated amplitudes of the extended 81 standard virtual scalp electrodes. Since this standard covers inferior electrodes, the 10-10 virtual average reference is not much different from the reference-free montage.</div>

'''CSD-Laplacian'''

<div style="margin-left:1.55cm;margin-right:0cm;">In this montage, current source density (Laplacian) for each of the standard 27 interpolated electrodes is displayed. The CSD waveforms and maps are computed as the second spatial derivative by spherical spline interpolation and are implicitly reference-free. Because this method intrinsically uses information from all electrodes, it provides a more accurate estimation of the source current leaving and entering the skull than source derivations using only 3 or 4 neighboring electrodes. This is particularly true for electrodes at the boundary of the electrode array.</div>

'''Double Banana'''

<div style="margin-left:1.55cm;margin-right:0cm;">This is a longitudinal bipolar montage containing two left hemispheric, two right hemispheric and one midline longitudinal row of montage channels. Longitudinal rows are arranged from front to back. All channels are interpolated.</div>

'''Triple Banana'''

<div style="margin-left:1.55cm;margin-right:0cm;">The Triple Banana montage is an extended longitudinal bipolar montage. It has an additional inferior row on each side as compared to the Double Banana montage. All channels are interpolated.</div>

'''Horizontal Bipolar'''

<div style="margin-left:1.55cm;margin-right:0cm;">The horizontal bipolar montage contains three transversal rows of montage channels. Transversal rows are arranged from left to right. All channels are interpolated. In the Horizontal Bipolar montage, available midline electrodes are always displayed even if ''Midline Channels ''is set to Off in ''Montage/Options''.</div>

'''A1/A2 Reference'''

<div style="margin-left:1.55cm;margin-right:0cm;">In this montage, the left-hemispheric channels of the standard 27 interpolated channels (except for the inferior electrodes F9, A1, P9) are displayed against the interpolated voltage at electrode A1. The right-hemispheric channels of the standard 27 interpolated channels (except inferior electrodes F10, A2, P10) are displayed against the interpolated voltage at electrode A2. The midline electrodes of the standard 27 interpolated channels (except Fpz and Oz) are displayed twice, referenced a) to the interpolated voltage at electrode A1 and b) to the interpolated voltage at electrode A2. The midline channels are only displayed if ''Midline Channels ''is set to On in ''Montage/Options''.</div>

'''Combined Ears'''

<div style="margin-left:1.55cm;margin-right:0cm;">In this montage, the standard 27 interpolated channels are referenced to a computed virtual linked ears reference. The reference is calculated as the mean voltage of the interpolated amplitudes at A1 and A2 determined by spherical spline interpolation. The calculation of the average potential at the ears balances both sides correctly in contrast to the unknown bias when linking the ears or mastoid electrodes directly.</div>

'''Referential'''

<div style="margin-left:1.55cm;margin-right:0cm;">In this montage, the standard 27 interpolated channels are displayed against a common virtual ‘viewing reference’. The default viewing reference is Cz (virtual). The viewing reference can be changed in the Montage Editor (which can be opened using the '''EdM''''' ''button in the control ribbon). Any of the extended 81 standard virtual electrodes may be used as viewing reference.</div>

'''Reference Free (10-10)'''

<div style="margin-left:1.55cm;margin-right:0cm;">In this montage, the extended standard 81 electrode channels are displayed using spherical spline interpolation and the reference-free mode. The reference is estimated as described for the Reference Free montage. This montage yields more detailed spatial information as compared to the reference free 27 channel montage described above.</div>

'''CSD-Laplacian (10-10)'''

<div style="margin-left:1.55cm;margin-right:0cm;">In this montage, current source density (Laplacian) for each of the standard 81 interpolated electrodes is displayed. The CSD is computed as described for the CSD-Laplacian montage. This montage may yield more spatial information than the 27 channel CSD-Laplacian montage described above.</div>

Virtual montages estimate the voltage at the idealized locations of the standard 27 (81) electrodes on a sphere using spherical spline interpolation. This method is described in Perrin et al. (Electroenceph. clin. Neurophysiol. 72:184-187, 1989); please see chapter “''Mapping/ Spherical Spline Maps''” for more details. Using this interpolation, EEG traces can also be displayed for missing or bad electrodes. The use of interpolation is indicated by the keyword ‘virtual’ displayed in the upper left corner of the waveform window above the montage channel labels. In principal, spherical spline interpolation is possible outside the area covered by the recording electrodes. Over the lower half of the head, interpolation benefits greatly from the presence of inferior lateral electrodes (F9, A1, P9, F10, A2, P10). Although only a minimum of 2 separate channels with lower lateral electrodes is required, for example A1/A2 or M1/M2, the use of 6 or 4 inferior lateral electrodes is recommended.

For more details regarding virtual montages and virtual electrodes see help chapter "''Montage Editor /'' ''Virtual Standard Montages''".

'''Note: If the number of scalp electrodes is less than 12, spline interpolation and interpolated montages cannot be computed.'''

'''Source montages'''

Press the push button '''Src''' twice or use the menu '''Montage/Source '''to select a pre-defined

source montage. These source montages are available for EEG or MEG, except for the

Evoked Potentials montages (EEG only).

<div style="margin-left:0cm;margin-right:0.263cm;">[[Image:Review (5).gif]]</div>

'''BR_Brain Regions'''

<div style="margin-left:1.55cm;margin-right:0cm;">This source montage uses a set of 15 regional sources covering lateral and midline</div>

<div style="margin-left:1.55cm;margin-right:0cm;">frontal, central and parietal cortex, midline fronto-polar and occipito-polar cortex</div>

<div style="margin-left:1.55cm;margin-right:0cm;">as well as anterior and posterior temporal lobes bilaterally. It separates the activities</div>

<div style="margin-left:1.55cm;margin-right:0cm;">of the 15 different brain regions and provides for fast comparison and quantification</div>

<div style="margin-left:1.55cm;margin-right:0cm;">of the different activities.</div>

'''CR_Central Region'''

<div style="margin-left:1.55cm;margin-right:0cm;">This source montage displays the radial and tangential activities of the central</div>

<div style="margin-left:1.55cm;margin-right:0cm;">brain region bilaterally in the first 6 dipole traces. Head schemes illustrate location</div>

<div style="margin-left:1.55cm;margin-right:0cm;">and orientation of each virtual electrode. The other 13 regional sources separate</div>

<div style="margin-left:1.55cm;margin-right:0cm;">the source activities arising from the other brain regions.</div>

'''FR_Frontal Region'''

<div style="margin-left:1.55cm;margin-right:0cm;">This source montage displays the radial and tangential activities of the frontal</div>

<div style="margin-left:1.55cm;margin-right:0cm;">brain region bilaterally in the first 6 dipole traces. Head schemes illustrate location</div>

<div style="margin-left:1.55cm;margin-right:0cm;">and orientation of each virtual electrode. The other 13 regional sources separate</div>

<div style="margin-left:1.55cm;margin-right:0cm;">the source activities arising from the other brain regions.</div>

'''PR_Parietal Region'''

<div style="margin-left:1.55cm;margin-right:0cm;">This source montage displays the radial and tangential activities of the parietal</div>

<div style="margin-left:1.55cm;margin-right:0cm;">brain region bilaterally in the first 6 dipole traces. Head schemes illustrate location</div>

<div style="margin-left:1.55cm;margin-right:0cm;">and orientation of each virtual electrode. The other 13 regional sources separate</div>

<div style="margin-left:1.55cm;margin-right:0cm;">the source activities arising from the other brain regions.</div>

'''TA_Temporal Lobe'''

<div style="margin-left:1.55cm;margin-right:0cm;">This source montage displays the activities of four different aspects of the temporal</div>

<div style="margin-left:1.55cm;margin-right:0cm;">lobe bilaterally and largely separates them from the radial activities in the other</div>

<div style="margin-left:1.55cm;margin-right:0cm;">11 brain regions. There are 4 equivalent dipole sources in each temporal lobe to</div>

<div style="margin-left:1.55cm;margin-right:0cm;">reveal temporal-basal, polar, antero-lateral and postero-lateral source activities.</div>

<div style="margin-left:1.55cm;margin-right:0cm;">The basal and polar sources are oriented tangentially, the lateral sources radially.</div>

<div style="margin-left:1.55cm;margin-right:0cm;">Head schemes illustrate location and orientation of each virtual electrode. </div>

<div style="margin-left:1.55cm;margin-right:0cm;">The montage TA_Temporal Lobe is equivalent to the montage T-A in previous </div>

<div style="margin-left:1.55cm;margin-right:0cm;">versions of BESA Research. However, the use of the TR_Temporal Region source</div>

<div style="margin-left:1.55cm;margin-right:0cm;">montage is more recommended because it provides a better separation of the </div>

<div style="margin-left:1.55cm;margin-right:0cm;">activities of other brain regions.</div>

'''TR_Temporal Region'''

<div style="margin-left:1.55cm;margin-right:0cm;">This source montage displays the activities of four different aspects of the temporal</div>

<div style="margin-left:1.55cm;margin-right:0cm;">lobe bilaterally in the first 8 dipole traces. There are 4 equivalent dipole sources</div>

<div style="margin-left:1.55cm;margin-right:0cm;">in each temporal lobe to reveal temporal-basal, polar, antero-lateral and postero-lateral source activities. The basal and polar sources are oriented tangentially, the lateral sources radially. The montage TR_Temporal Region separates these 4 aspects of the temporal lobe from the source currents in the other 11 regions irrespective of their orientation.</div>

'''Evoked Potentials'''

<div style="margin-left:1.55cm;margin-right:0cm;">This submenu contains three source montages designed specifically for use with auditory (AEP), somatosensory (SEP), and visual (VEP) evoked data. Brain regions that are specifically relevant for the auditory, somatosensory, and visual pathway, respectively, are modeled with equivalent current dipoles. Remaining brain regions are modeled with regional sources. The Evoked Potentials source montages are available for EEG only.</div>

BESA Research can transform the scalp EEG into signals of source activity which predominantly reflect the electrical activity of specific regions in the brain. These 'brain source montages' are calculated using specific weighted combinations of the recorded scalp EEG signals. The weights are selected on the basis of multiple dipole models to enhance the activity from one brain region while suppressing the contributions from other brain regions, for example from the contralateral hemisphere. Each new waveform is an optimized linear combination of the measured EEG channels in order to provide a focus onto a particular brain region of interest. On the scalp, the electrical activities of the different brain regions overlap. The brain source montages provide a substantial separation, or deconvolution, of this overlap. Due to the limited number of scalp electrodes, this separation can never be complete. However, separation can be strong enough to make focal activity in the brain visible, by depicting this activity predominantly in the source trace(s) associated with the brain region generating the focal electrical activity.

Brain source montages are provided to facilitate the detection of focal source processes in the brain by reversing the overlap from different brain regions seen at the scalp. If brain activity is focal, i.e. represented predominantly in one source waveform, a large amount of the recorded scalp activity reflected in this trace will originate in the related brain region. If source activity is distributed over several traces, the origin is likely to be more widespread or in areas not precisely modeled by the combination of sources in the selected source montage. Each channel in a brain source montage can be viewed as a 'gross virtual electrode' placed onto a particular brain region.

Standardized brain source montages are defined for the 81 standard 10-10 electrodes. Therefore, the recording montage is first interpolated onto the 81 standard electrodes. Then the source waveforms are calculated using the source montage file.

The standardized source montages are optimized for different brain regions (central, frontal, parietal, temporal). The source montages are composed of dipoles, which predominantly model the activity of the different aspects of the selected brain region, and of regional sources, which largely suppress the source activity arising from other brain regions.

The option ''Midline Channels ''in ''Montage/Options ''may be used to turn on/off midline source channels. A source channel is considered to be midline if abs(x)<0.2, i.e. if it is located at the midsagittal plane or left/right of the midsagittal plane within 20% of the head radius.

The regional source display type can be changed in ''Montage/Options''. Note that dipoles are indicated by head symbols if ''Options/Display/Show Heads in Source Montage ''is selected while regional sources always have green channel labels.

Use the 3D view in the Montage Editor (which can be opened using the '''EdM''''' ''button in the control ribbon) to visualize the locations of the dipoles and regional sources in the different source montages or right click on the head symbol/channel label of a source channel to view the brain region and its orientation associated with the selected dipole channel.

For a more detailed description of brain source montages see help chapter "''Montage Editor / Standard Source Montages''".

Brain source montages show a much better separation of focal brain activities than scalp montages. For example, if we remontage an EEG showing a temporal lobe seizure best in the horizontal bipolar montage (below left) to a brain source montage (below right, montage TR_Temporal Region), focal source activity is visible at the base and at the tip of the right temporal lobe. Due to the limited spatial resolution of the scalp EEG, a small amount of the activity also appears in other source channels. Nevertheless, the largest activity appears at the base and tip of the right temporal lobe as seen in the source channels. The activity is similar to the activity recorded at the sphenoidal electrodes (SP2-T3 & SP1-T4, below right), but the separation between right and left temporal lobe is larger in the source montage.

<div style="margin-left:0.284cm;margin-right:0cm;">[[Image:Review (6).gif]]</div>

<div style="margin-left:0.286cm;margin-right:0.28cm;">''Left: Horizontal bipolar montage of the file '''''eeg2.eeg'''''<nowiki>; Right: TR_Temporal Lobe source montage of the same data segment.</nowiki>''</div>

The patches of activity shown in color coding in the schematic head views reflect the brain regions onto which the source channels are focused. In other words, each source channel represents a gross 'virtual electrode' placed over the corresponding cortical surface. The size of the patches indicates that the location and extent of the source activity cannot be precisely determined because of the limited spatial

resolution. However, the patches reflect a high probability that source activity exists in this brain region provided that one brain region is predominantly active. If multiple patches appear to be active, the distribution of source activity in the brain may be more complex, i.e. more distributed or multifocal, and the distribution has to be interpreted with care.

'Brain source montages' are different from traditional 'source derivations', which subtract the amplitudes of the signal at the adjacent electrodes from the data at a given electrode. Thus, a 'source derivation' shows an approximation of the 'current source density (CSD)' flowing in and out from the skull below a given electrode. BESA Research provides improved 'source derivations' on the basis of 'Laplacian' or current source density montages: CSD-Laplacian and CSD-Laplacian (10-10) montages. In BESA Research, the Laplacian is calculated by spherical spline interpolation. This method provides a more accurate estimate of CSD at any given electrode than the subtraction method using 3-4 surrounding electrodes, especially at the outer electrodes of the scalp electrode array.

Note: If the number of scalp electrodes is less than 12, brain source montages cannot be computed.

'''User-Defined Montages'''

Press the push button '''Usr'' '''''twice or use the menu '''Montage/User-Defined''''' ''to select a user-defined source montage.

User defined montages can be created, edited, saved and reopened in the Montage Editor. For more details see chapter “''Montage Editor''”.

User montages may contain recorded, virtual and source channels, also in combination. The montage can be saved to file in the Montage Editor in binary format. When saving, the user can decide to put the montage into the folder ''Montages\UserMontages ''as a generally available montage or into the data folder as a file specific montage.

Available user montages are displayed by filename in the''' Montage/User-Defined '''popup menu. General user montages (stored in '''Montages\UserMontages''') are displayed above the separator in the menu. File specific user montages (stored in the data directory) are displayed below the separator. The latter montages are only displayed if the corresponding data file is currently displayed. It is recommended to use a naming convention similar to the standard brain source montages: '''AB_Full Name.mtg'''. AB is abbreviation, which will appear after the label of each channels, e.g. source montage BR_Brain Regions, 1st montage channel = FL_BR.

'''Additional Channels'''

<div style="margin-left:0cm;margin-right:0.284cm;">Press the push button''' Add '''at upper right of the review window or use the menu ''Montage/Additional Channels ''to select an additional channel montage.</div>

<div style="margin-left:0.268cm;margin-right:0.284cm;">[[Image:Review (7).gif]]</div>

A set of additional channels can be displayed along with the current montage channels at the bottom of the screen. This is useful, for example, for displaying ECG and other polygraphic channels, and for comparing depth channels with the scalp EEG. Additional channels may be individually filtered (see online help chapter "''Review / Reference /Menus / Filters / Polygraphic / Additional Chns''") and scaled.

BESA Research ships with a predefined set of additional channel montages which can be selected from the dropdown menu. The corresponding files are stored in the folder ''Montages\AdditionalChannels''. Note that additional channel montages are only available if the labels of the (traditional) additional channels are available or if the (virtual) additional channels can be calculated for the current file.

A detailed description of the predefined additional channel montages is given in the section Standard Montages in the help chapter "''Montage Editor''".

Further additional channel montages may be defined and saved to a file in the Montage Editor. They can also be selected from this menu if they are available for the current file. Use this menu, too, to switch off the currently displayed additional channels.

A commonly used additional channel file can be assigned in the initialization file '''BESA.ini''' (entry AdditionalChannelFile in the section [Defaults]). The additional channels will be displayed automatically if they are available, if the entry AdditionalChannelStatus in '''BESA.ini''' is set to On and if there is no other additional channel file assigned via the entries in the program database.

Note that this menu can also be conveniently reached from the''' Add''' button in the upper right corner of the main window or by a right mouse click on the label of an additional channel.

'''Options'''

<div style="margin-left:0.483cm;margin-right:0cm;">Press the push button '''Opt'' '''''twice or use the menu '''Montage/Options''''' ''to</div>

<div style="margin-left:0.483cm;margin-right:0cm;">[[Image:Review (8).gif]]</div>

#* display montages in a sequence from left to right or right to left
#* display montages in a sequence for regional comparison
#* display montages in a sequence for hemispheric comparison
#* switch on/off midline channels
#* change the display type of regional source channels

'''Left to Right'''

<div style="margin-left:1.55cm;margin-right:0cm;">This item selects the sequence of montage channels in recorded (except ''Original Recording ''and ''Original Average Reference ''montage), virtual and standard brain source montages. If ''Left to Right ''is selected (default), montage channels are displayed in a systematic order from left to right. If left to right is not selected, the sequence is reversed from right to left. This option can be combined with ''Regional Comparison ''or ''Hemispheric Comparison''.</div>

'''Regional Comparison'''

<div style="margin-left:1.55cm;margin-right:0cm;">This item selects the grouping of montage channels in recorded (except ''Original Recording ''and ''Original Average Reference ''montage), virtual and standard brain source montages. If ''Regional Comparison ''is selected, channels are grouped regionally to ease regional comparison. ''Regional Comparison ''is off by default. ''Regional Comparison ''and ''Hemispheric Comparison ''cannot be set together.</div>

'''Hemispheric Comparison'''

<div style="margin-left:1.55cm;margin-right:0cm;">This item selects the grouping of montage channels in recorded (except ''Original Recording ''and ''Original Average Reference ''montage), virtual and standard brain source montages. If ''Hemispheric Comparison ''is selected, channels are grouped pairwise by hemisphere to ease hemispheric comparison. ''Hemispheric Comparison ''is off by default. ''Hemispheric Comparison ''and ''Regional Comparison ''cannot be set together.</div>

'''Midline Channels'''

<div style="margin-left:1.55cm;margin-right:0cm;">The option ''Midline Channels ''decides if midline channels (recorded, virtual, source) are displayed or not. Note: for recorded and virtual horizontal bipolar montages, midline channels cannot be switched off. ''Midline Channels ''are displayed by default (tick marked).</div>

'''Regional Sources Oriented'''

<div style="margin-left:1.55cm;margin-right:0cm;">If this menu item is selected, the 3 waveforms of a regional source are combined to a single waveform by calculating the maximum PCA component of the 3 waveforms. With this option, the regional source is oriented such that the source waveform depicts most of the variance in the currently displayed data. When paging through the data, the orientation of the source waveform changes depending on the data. Note that this regional source display type also focused on high-amplitude artifacts like blinks and eye movements.</div>

'''Regional Sources Radial'''

<div style="margin-left:1.55cm;margin-right:0cm;">If this menu item is selected, only the radially oriented waveform of the 3 regional source waveforms is displayed. Note that source waveforms will be small if source activity in the associated brain region is not oriented radially. For MEG, this menu item is grayed.</div>

'''Regional Sources First Trace'''

<div style="margin-left:1.55cm;margin-right:0cm;">If this menu item is selected, only the first of the 3 regional source waveforms is displayed. This orientation can be user-defined if the montage has been created from a source model in the Source Analysis window that contains oriented regional sources. Otherwise, a default orientation is displayed (radial in EEG source montages, tangential towards the vertex in MEG source montages)</div>

'''Regional Sources All Traces'''

<div style="margin-left:1.55cm;margin-right:0cm;">If this menu item is selected, all 3 waveforms of a regional source are displayed, one below the other. The 1st waveform is oriented radially (pointing inwards), the 2nd waveform is oriented vertically (orthogonal to 1st, pointing upwards), the 3rd waveform is oriented horizontally (orthogonal to 1st and 2nd, pointing forward or from right to left if the source lies in the sagittal plane).</div>

<div style="margin-left:1.55cm;margin-right:0cm;">For MEG, only 2 waveforms are displayed. Both depict activity in the plane tangential to the location of the regional source.</div>

'''Regional Sources Magnitude'''

<div style="margin-left:1.55cm;margin-right:0cm;">If this menu item is selected, the 3 waveforms of the regional source are combined to a single waveform by calculating the root mean square magnitude of the 3 waveforms. </div>

'''Sequence of Channels in Montages'''

All montages can be displayed in 6 different systematic orders: ''Left to Right, Right to Left, Left'' ''to Right (or Right to Left)'' + ''Hemispheric Comparison, Left to Right (or Right to Left) + Regional'' ''Comparison''. Select'' '''''Montage / Options''''' ''to set the montage order.

If ''Midline Channels'' is On in '''Montage / Options''', available midline electrodes are displayed (from Fpz to Oz) in the sequences ''Left to Right, Right to Left ''or ''Regional Comparison''. They are not displayed when ''Hemispheric Comparison'' is On. In the Horizontal Bipolar montage, available midline electrodes are always displayed.

'''Color Coding of Montage Channels'''

Montage channels are systematically colored in BESA Research. Left channels are displayed in dark blue, right channels in dark red. Midline channels are displayed in black. A recorded or virtual montage channel is considered to be midline if channel and reference are at the midline (e.g. Fz-Fcz) or if the reference has no side (e.g. Fz-avr). If the channel is midline but the reference is on the left (right) side, e.g. Fz-A1 (Fz-A2), the montage channel is considered as left (right)-sided, i.e. it is colored in dark blue (red). The same rule applies if the reference is midline but the channel is on the left (right) side, i.e. Fp1-Cz (Fp2-Cz) is displayed in dark blue (red).

In source montages, left channels are displayed in dark blue, right channels in dark red. Midline channels are also displayed in black. A source channel is considered to be midline if abs(x)<0.2, i.e. if it is located in the sagittal plane or left/right of the sagittal plane within 20% of the head radius.

== Scaling ==

The scaling of amplitudes and time intervals is performed using the buttons which are grouped at the righthand side of the waveform display.

'''Time Scaling'''

[[Image:Review (9).gif]]

The displayed time can be scaled by clicking the Timing button at the bottom right of the display. The button shows the time interval displayed on the screen. Pressing the button opens the Timing dialog box where epochs between 0.1 s and 60 s can be selected.

'''Channel Group Selection'''

[[Image:Review (10).gif]]

The controls at the top right of the window allow to display '''All '''channels of the recording montage or to toggle between subgroups of channels ('''Scp''' = scalp,''' Icr '''<nowiki>= intracranial,</nowiki>''' Pgr''' = polygraphic,''' MEG'''). Click on the '''Add '''button to display additional channels below the recorded channels. A popup menu appears from which you can choose sets of additional channels. For example, if you choose 'EOG_HV', two virtual eye channels, horizontal and vertical, are calculated from the data and displayed.

'''Channel Selection and Amplitude Scaling'''

[[Image:Review (11).gif]]For each channel group, there are two controls at the right side of the window. The upper one controls the subset of channels which is displayed, the lower one controls the scaling. To select a subset of a channel group for display, click on the upper of the two buttons. It shows the number of channels which are currently shown, and the total number of channels in that channel group (e.g. Scp, 32/32). In the dialog box that appears, you can make a fast selection using one of the buttons, or make a precise selection using the rulers.

The lower of the two buttons for each channel group controls the amplitude scaling. The scaling bar between the buttons shows the scale of the current value, which is shown on the button. To change, for example, the scaling of the EEG channels to 100 µV, click on the lower button of the ''''Scp'''' channel group, and select 100 µV in the dialog box that appears.

For more details about timing, scaling and channel selection controls see the online help chapter ''"Review / Reference / Controls / Timing, Scaling, and Channel Selection".''

== Filtering ==

The digital filters in BESA Research are used in addition to the filters set during recording of the digital EEG. It is therefore useful to record the EEG with the largest bandwidth compatible with the sampling rate (e.g. 70 Hz high cutoff at 200 Hz sampling rate), and to use the digital filters in BESA Research to suppress unwanted low and high frequency noise during review, or to enhance the resolution of a periodic pattern by setting the band-pass filter around the frequency of interest.

When a data file is first opened, the filter settings as defined in the initialization file ('''BESA.ini''') are used.

BESA Research supports 4 different filter types: low cutoff, high cutoff, band pass, and notch filter. Filters can conveniently be changed using the push buttons at the top of the waveform display:

[[Image:Review (12).gif]]

'''Low Filter Button'''

The '''LF '''button opens a popup menu with the available settings for the '''low cutoff filter'''. You can choose between time-constant filters and variable filters, where different filter types can be selected (forward, backward, zero phase shift), as well as the slope.

'''High Filter Button'''

The popup menu for the''' HF '''button provides a selection of frequently used '''high cutoff''' '''filters.''' Again, it is also possible to use the option 'Variable High Cutoff Filter', where frequency, type, and slope can be selected freely.

'''Notch Filter Button'''

A notch filter for suppression of noise in narrow frequency bands is available from the''' NF '''button. Click the button to choose between 50 Hz or 60 Hz suppression.

'''Edit Filters Button'''

The''' EdF''' button starts the dialog box to edit the variable filter settings and to select special band pass and notch filter settings.

In the '''Filter '''menu, further commands are available to view the filter response with the current settings, and to adjust baseline settings. In the Filter menu, it is also possible to apply special filtering to polygraphic and additional channels.

For more details see the online help chapter ''"Review / Reference / Menus / Filters".''

== Measuring Peaks and Frequency ==

Amplitude maxima, peak-to-peak differences and the frequency of oscillations of a channel can be measured simply by right clicking and dragging the mouse over the waveform and interval of interest:

[[Image:Review (13).gif]]

The red box indicates the dragging interval and selected channel. The popup window shows the channel label and the measured values for negative peak, positive peak, peak-to-peak amplitude difference, and frequency. If no frequency dominates inside the interval, the frequency is classified as undefined.

To display the amplitude of a channel at a certain time point, place the mouse cursor over the point of interest. The corresponding amplitude will be displayed in the status bar at the bottom of the BESA Research main window.

== Correlation Analysis ==

Correlation analysis provides information about the similarity, relative amplitudes and time delays between one reference channel and the other concurrent waveforms. Using source montages, it can give valuable information about the relationships among the activities of different brain regions. For example, we may want to measure whether a certain pattern in one brain region appears with some time lag and a certain similarity in shape in a different brain region. We can measure the relationship by correlating a segment of interest in a selected channel with all the other channels. BESA Research provides linear and non-linear regression methods (Pijn 1990). These methods can be applied to any montage, but they are '''most meaningful with source or intracranial''' '''waveforms,''' since scalp waveforms can pick up activity from remote brain regions due to volume conduction effects. When a block of EEG data is marked, you can '''click the''' '''right mouse button''' and select '''Linear Correlation''' from the popup menu. By selecting

the menu item '''Process / Nonlinear Regression''', the non-linear regression is calculated for the marked block.

[[Image:Review (14).gif]]

When Linear Correlation is selected, BESA Research computes a correlation function between a reference channel and all the displayed channels, including the reference channel (=autocorrelation). If no specific channel is selected, the channel with the largest signal over the marked block is used as the reference for computing the correlation functions. You may select a different reference channel by clicking on the label or head symbol at the left of the desired reference channel waveform. The correlation window is immediately updated if a new channel is selected as reference.

Correlation is calculated by shifting the reference channel by 30 data sampling points in both directions relative to the other channels. At each shifted point (total 61 points) one value of the correlation function is computed. The squared correlation functions are displayed as waveforms in the correlation window, and their maxima are used to define the time lag or lead of each channel with respect to the reference channel.

A block is marked by holding the''' left mouse button down '''to''' drag''' over a portion of the EEG in order to mark a specific pattern, or by right-clicking on a '''peak latency''' of interest, and selecting ''“Default block”'' from the popup menu that appears. If you use the right-click, the default epoch will be marked around the current cursor. The default epoch can be set using the menu '''Edit / Default Block Epoch'''. To compute '''non-linear''' correlation, use the menu '''Process / Nonlinear Correlation'''. The computation of non-linear regression may be slow if the marked epoch is long. You may type''' any''' '''key''' to stop computing.

Press '''<Space>''' to remove the block marking or the cursor. Press '''<Space>''' again to continue paging through the EEG.

In the correlation window the following values are displayed (See figure below).:

* The squared linear correlation function r², or the non-linear regression coefficient h². The pattern of the marked/largest channel is shifted forward and backward by 30 samples (corresponding to a time lag of ± 150 ms at a sampling rate of 200 Hz).

* The relative value of the maximum signal amplitude in the various channels (amp). 100% is assigned to the amplitude of the largest scalp/source montage channel. Normally, 100% is assigned to the reference channel unless a polygraphic or intracranial channel was used as reference.

* The maximum of the squared correlation coefficient r² or h² (c[%]; 0 - 100%).

* The time lag (positive) or lead (negative) of the maximum of the correlation function relative to the reference channel in milliseconds (lag).

== Pattern Search and Averaging ==

BESA Research offers several possibilities to search for similar events or patterns in the EEG and to average them. Pattern search is initiated by marking a specific block, e.g. from 200 ms before a sharp wave until the following trough, to define a template over one or more selected channels or all displayed channels (spatio-temporal search). Then you decide over which range (whole EEG, between markers etc.) the search will be conducted and which of the pattern tags shall be used. Patterns are detected and tagged automatically, if their correlation with the template exceeds a predefined threshold and if the amplitudes are below artifact threshold or if artifact detection is set to off during search. The correlation threshold and the rejection threshold for artifacts can be adjusted in the menu '''Search/Options '''(for more details, see online help chapter'' "Review / Reference / Menus / Search").''

Tags, defined by pattern search or manually, as well as triggers can be used for averaging. Tagged segments or epochs around triggers can be averaged repeatedly while setting different artifact detection thresholds and filters. Search and average can be set to automatic or manual, thus enabling visual inspection of segments prior to tagging or averaging. Search and average offers the following choices:

* Pattern search: uses the signal pattern template in a selected channel or the spatio-temporal pattern over the marked epoch and several marked channels or all displayed channels to search for similar events.

* Tagged event search: used to average similar patterns tagged manually or by pattern

* Trigger events: used to average epochs around external triggers or internally created triggers stored in a separate event file or in the EEG data file

If you want to perform a pattern search, you should mark an epoch first to be used as template. The search can be performed in two ways:

* Spatio-temporal search over all channels: This search type is the default. All channels which are displayed on the screen are used.

* Search for the pattern of one or several specific channels: Mark the channel(s) to be used for the template with a left mouse click on its label (hold down the '''Ctrl'''-key to mark more than one channel; cf. section ''"Using the Mouse").''

Before you start searching, you should

* select the type of search –'' Pattern'', ''Tagged Events'', or'' Triggers ''– in the '''Search '''menu,

* define the '''Buffer''' number either in the '''Tags''' menu, or more simply by typing the buffer

* set the toggle items in the''' Search''' menu (query search, artifact rejection), and the range in the data file which is searched

* for '''Pattern Search''' set correlation threshold in '''Search / Options''' to approx. 80-85%, if using a single channel template, and to 70-75%, if using a spatio-temporal template with several channels.

Note that even though the search is performed with the template data block size, BESA Research always uses the settings of the ''Default Block Epoch'' (set using the '''Edit''' menu) to define the length of the average buffer.

The search and/or average starts when a range is selected in the''' Search''' menu, or

the button''' SAW''' ('''S'''earch-'''A'''verage-'''W'''rite) on the control ribbon is pressed.

== Selecting Data Files ==

If you start reviewing from a patient data base that connects to BESA Research, simply select the recordings you want to review and press the BESA Research icon to open the files.

Otherwise, you may open a data file directly from the menu '''File / Open'''. This uses a standard Windows File Open dialog that is enhanced by an extra selection box for fast switching between frequently used data folders.

The only special aspect to note is the name extension of the type of data that your own EEG system generates: files are displayed using filters that only show names with particular extensions. These are selected using the dropdown list under "Files of type:". The most commonly used file extensions are summarized under the file type "EEG files". Depending on your EEG system, you may have to switch to a different file type (by selecting one of the entries in the list) the first time you use BESA Research. Your file type setting is remembered for the next time you open a data file.

By holding down the '''Shift''' or the '''Ctrl''' key you can select several files.

[[Image:Review (15).gif]]

BESA Research allows to open several data files at once. You can switch among the opened files using the file list in the '''File '''Menu or the '''F+''' and '''-F''' buttons. When a file is closed, the most recently used display settings (filter, no. of secs in the display, etc.) are saved in the database, and restored the next time the file is opened.

'''Recent Files'''

The Recent File List (Menu '''File/Recent Files'''...) can be used to open recent files. Note also that the files from the previous session can be opened using '''File/Recent''' '''Files.../Open All Files''' from Previous Session. A keyboard short-cut for this operation is to hold down the '''Ctrl''' key and press the '''-F''' button.

When BESA Research is started, and no data files have been opened, pressing '''-F''' will open the most recent file. If only one file is open, pressing the button again will open the second most recent file.

'''Data Readers'''

Data comes in a variety of file formats. Several data formats are controlled by Reader Dlls that are located in the ''System/Readers ''subdirectory of the BESA Research installation. Some readers, although supported, are not installed by default. They can be installed by navigating to the ''Utilities\Additional'' Readers subdirectory of the BESA Research installation with the Windows Explorer, and double-clicking

on Install '''Additional Readers.htm.''' Here you will find a list of additional readers, and a link to install each reader.

== Defining the Channel Configuration ==

In order to map the data, for source analysis or to transform to virtual montages or source montages, the correct electrode labels or the electrode positions on the head must be known. In the case of MEG, fiducials and, preferentially, additional surface points on the head must be digitized. This information is often not supplied or is incomplete in the original data, although it is strongly recommended to define the correct names and electrode labels to all recording channels during acquisition.

For the case that the channel information is not provided adequately or erroneous, different mechanisms are supplied to enable you to redefine the channel assignment or to read in the required information.

The simplest way to define electrode locations is in terms of the international 10-20 or 10-10 electrode naming system. BESA Research uses a location table to specify where these locations are on a spherical head (see help chapter ''"Special'' ''Topics / Working with Electrodes").'' For electrodes at locations deviating from this standard, you can define specific spherical coordinates using the menu '''Edit / Channel'''

'''Configuration / Advanced'''. Make sure that you check the correct relative location of deviating electrodes using the 3D whole head maps.

More advanced electrode location information is provided with a 3D digitizer.  See online help chapter ''"Special Topics / Working with Electrodes" ''for a more detailed description how to read digitizer coordinates and other 3D locations (e.g. for MEG).

The following three menu entries can be used to define channel configurations and

electrode names and locations:

* '''Edit / Channel Configuration '''

Opens a dialog allowing to name channels, define their type (e.g. EEG, Polygraphic, Intracranial), and assign an electrode label or to specify spherical coordinates for EEG electrodes deviating from standard. Channels are listed in the order in which they were recorded. If standard names are supplied for scalp channels, spherical coordinates are assigned automatically by BESA Research

* '''File / Load Channel Configuration'''

Loads a file containing a predefined configuration.

* '''File / Head Surface Points and Sensors / Load Coordinate Files (CTRL-L) '''

Opens a dialog allowing to select channel configurations and digitized coordinates. This dialog is opened automatically when you open a file for the first time and important

information is missing. For more details, see help chapter ''"Special Topics / Working''

''with Electrodes ... / Working with Auxiliary Files".'' For the rules about when this dialog is opened automatically, see help chapter ''"Special Topics / Working with Electrodes... / General Reading Rules for Data Files and Auxiliary Files".''

'''Caveat:''' It is important to check the labels and sequence of channels in the original recorded montage (''Montage/Recorded/Original Recording'') to make sure that the recording electrode configuration has been correctly protocoled and read from the file header. There may be EEG systems which do not provide this information correctly. Errors may also occur if this information has been entered incorrectly into the recording software. In these cases, you may want to read an electrode file from disk containing your standard or some specific electrode configuration. Such configurations can be edited and stored on disk using the '''Edit / Channel Configuration''' menu. It is strongly recommended that you read the ''ELECTRODES'' section in the help chapter "''Special Topics"'' carefully, to make sure that each EEG is associated with the correct labels and sequence of channels, and that the common reference is correctly defined. Otherwise, maps, source images and source montages may be incorrect, and source analysis cannot work properly.

[[Category:Research Manual]]

BESA Research Manual

2017-04-07T12:47:18Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}

= BESA Research Manual =

== Review ==
[[Review]]

[[BESA Research Montage Editor]]

[[BESA Research Mapping]]

[[BESA Research Artifact Correction]]

[[BESA Research Spectral Analysis]]

[[BESA Research ERP Processing]]

[[BESA Research ICA]]

[[BESA Research Batch Processing]]

== Source Analysis ==
[[Source Analysis Introduction]]

[[Source Analysis Functions of the Window]]

[[Source Analysis Head Models]]

[[Source Analysis 3D Imaging]]

== Integration with MRI and fMRI ==
[[Integration with MRI and fMRI ]]

== Source Coherence ==
[[Source Coherence Introduction and Concepts]]

[[Source Coherence How to...]]

== Export ==
[[Export]]

== MATLAB Interface ==
[[MATLAB Interface]]

== Special Topics ==
[[Electrodes and Surface Locations]]

[[The Initialization File: BESA.ini]]

[[Working With Additional Files]]

[[Category:Research Manual]]

BESA Research Manual

2017-04-07T12:43:01Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}

= BESA Research Manual =

== Review ==
[[Review]]
[[BESA Research Montage Editor]]

[[BESA Research Mapping]]

[[BESA Research Artifact Correction]]

[[BESA Research Spectral Analysis]]

[[BESA Research ERP Processing]]

[[BESA Research ICA]]

[[BESA Research Batch Processing]]

== Source Analysis ==
[[Source Analysis Introduction]]

[[Source Analysis Functions of the Window]]

[[Source Analysis Head Models]]

[[Source Analysis 3D Imaging]]

== Integration with MRI and fMRI ==
[[Integration with MRI and fMRI ]]

== Source Coherence ==
[[Source Coherence Introduction and Concepts]]

[[Source Coherence How to...]]

== Export ==
[[Export]]

== MATLAB Interface ==
[[MATLAB Interface]]

== Special Topics ==
[[Electrodes and Surface Locations]]

[[The Initialization File: BESA.ini]]

[[Working With Additional Files]]

[[Category:Research Manual]]

BESA Research Manual

2017-04-07T12:42:20Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}

= BESA Research Manual =

== Review ==
[[Review]]
[[BESA Research Montage Editor]]
[[BESA Research Mapping]]
[[BESA Research Artifact Correction]]
[[BESA Research Spectral Analysis]]
[[BESA Research ERP Processing]]
[[BESA Research ICA]]
[[BESA Research Batch Processing]]

== Source Analysis ==
[[Source Analysis Introduction]]
[[Source Analysis Functions of the Window]]
[[Source Analysis Head Models]]
[[Source Analysis 3D Imaging]]

== Integration with MRI and fMRI ==
[[Integration with MRI and fMRI ]]

== Source Coherence ==
[[Source Coherence Introduction and Concepts]]
[[Source Coherence How to...]]

== Export ==
[[Export]]

== MATLAB Interface ==
[[MATLAB Interface]]

== Special Topics ==
[[Electrodes and Surface Locations]]
[[The Initialization File: BESA.ini]]
[[Working With Additional Files]]

[[Category:Research Manual]]

BESA Research Manual

2017-04-07T12:39:30Z

Alexa: Created page with "{{BESAInfobox |title = Module information |module = BESA Research Basic or higher |version = 6.1 or higher }} = BESA Research Manual = == Review == Review BESA Researc..."

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}

= BESA Research Manual =

== Review ==
[[Review]]
[[BESA Research Montage Editor]]
[[BESA Research Mapping]]
[[BESA Research Artifact Correction]]
[[BESA Research Spectral Analysis]]
[[BESA Research ERP Processing]]
[[BESA Research ICA]]
[[BESA Research Batch Processing]]

== Source Analysis ==
[[Source Analysis Introduction]]
[[Source Analysis Functions]]
[[Source Analysis Head Models]]
[[Source Analysis 3D Imaging]]

== Integration with MRI and fMRI ==
[[Integration with MRI and fMRI ]]

== Source Coherence ==
[[Source Coherence Introduction and Concepts]]
[[Source Coherence How to...]]

== Export ==
[[Export]]

== MATLAB Interface ==
[[MATLAB Interface]]

== Special Topics ==
[[Electrodes and Surface Locations]]
[[The Initialization File: BESA.ini]]
[[Working With Additional Files]]

[[Category:Research Manual]]

Integration with MRI and fMRI

2017-04-07T12:27:16Z

Alexa:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}
= BESA Research Integration with MRI and fMRI =

Both for developing and evaluating dipole source models of EEG or MEG activity, it is useful to have access to structural MRI or fMRI data.

The BESA MRI software allows to preprocess structural MRI data so that the individual anatomical information contained in the MRI can be utilized in BESA Research. BESA MRI makes it possible ...
* ... to align the EEG and MEG sensors with the structural MRI data.
* ... to read and display the aligned, individual Talairach structural MRIs directly in the BESA Research Source Analysis module. In this way, source analysis results can be presented on top of the aligned MRIs, which allows us to evaluate the anatomical regions to which the reconstructed sources may correspond.
* ... to use an individual, realistically shaped FEM head model for source analysis in BESA Research. FEM head models take into account the individual volume conduction properties of the subject's head derived from the structural MRI data. This allows for more accurate source analysis (Yvert 1997, Lanfer 2012).

To offer an easy integration with fMRI data we have, in collaboration with Rainer Goebel, optimized the interface between BESA Research and BrainVoyagerQX.

With these tools, we can ...
* ... use fMRI BOLD regions or MRI structures to initialize dipole models.
* ... visualize dipoles from BESA Research models together with the structural MRI in BrainVoyager in order to evaluate the regions to which the dipoles may correspond.
* ... combine the localization advantages of (f)MRI with the high temporal resolution of EEG and MEG, for instance by using (f)MRI to place the sources, and the source waveforms of BESA Research to provide feedback about the time course of the source activity.
* ... overlay source analysis results obtained in BESA Research with fMRI data.

'''Note:''' For simpler coregistration, we recommend to use BrainVoyagerQX rather than the older BrainVoyager, but BESA Research will work with both program versions.

The chapters below describe the steps necessary to integrate the MRI and fMRI data with BESA Research. Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website (http://brainvoyager.com/Downloads.html).

'''Aligning Coordinate Systems'''

* For a given BESA data set, the electrode and other head surface points need to be aligned to the MRI coordinates.
* The basic steps necessary to align the EEG electrode locations, the MEG sensors and the MRI are described in Section “''How Coregistration is done”''.
* Detailed instructions on how to align EEG / MEG and MRI data using BESA MRI can be found in the coregistration quick guide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).
* Detailed instructions on how to align EEG / MEG and MRI data using BrainVoyager are described in Section “''How To set up Coregistration between BESA and BrainVoyager”.''
* In BESA Research all necessary settings with regard to the alignment are made in the ''Coregistration Dialog.''
* Requirements with respect to the MRI data for a good coregistration can be found in Section “''MRI Requirements for Good Coregistration”.''
* Requirements with respect to EEG and MEG data for a good coregistration can be found in Section “''EEG/MEG Data Requirements for Good Coregistration”.''

'''Generating an individual, realistically shaped FEM head model'''

* The generation of a FEM head model that can be used in BESA Research is done in BESA MRI as an additional step following the EEG / MEG to MRI coregistration.
* Detailed instructions on how to generate the FEM head model can be found in the coregistration quick guide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).

'''Co-locating dipoles and MRI locations'''

* After aligning the EEG / MEG and the MRI data it is possible to co-locate dipoles and MRI locations. This means, it is possible to visualize the dipoles and to specify the dipole parameters in the MRI coordinate system.
* ''“How to Co-locate sources'' ''and MRI”'' in the BESA Research Source Module describes how in the BESA Research Source Analysis module dipoles can directly be visualized in the space of the individual MRI.
* ''“How to Send a Dipole from BESA Research to BrainVoyager”'' describes how to send a source model from BESA Research to BrainVoyager for further inspection.
* ''“How to Define a Dipole in BESA Research at a Location Defined in the MRI”'' describes how to insert a dipole at a location defined in the MRI in BrainVoyager.

'''References'''

Lanfer, B., I. Paul-Jordanov, M. Scherg, and C. H. Wolters. “Influence of Interior Cerebrospinal Fluid Compartments on EEG Source Analysis.” In Proceedings BMT 2012, Vol. 57. Jena: De Gruyter, 2012. doi:10.1515/bmt-2012-4020.

Yvert, B., O. Bertrand, M. Thévenet, J. F. Echallier, and J. Pernier. “A Systematic Evaluation of the Spherical Model Accuracy in EEG Dipole Localization.” Electroencephalography and Clinical Neurophysiology 102, no. 5 (May 1997): 452–59. doi:16/S0921-884X(97)96611-X.

== How Coregistration is done ==

This section outlines the basic steps to coregister the EEG / MEG data to an individual MRI. These steps are necessary to load an individual MRI into BESA Research.

'''What happens:'''

* EEG / MEG sensor locations and the MRI data are defined in different coordinate systems. Setting up coregistration is the process of aligning the two coordinate systems.
* BESA Research uses the ''Coregistration Dialog'' to coordinate the alignment procedure.
* Alignment is done with the ''AC-PC-transformed MRI''.
* BESA Research displays the ''Talairach-transformed MRI'' in the source analysis module.
* A coregistration file (with the extension "'''.sfh'''") is used to mediate between BESA Research and BESA MRI (or BrainVoyagerQX):
* BESA Research writes the coregistration file which contains the coordinates of head surface points (fiducials, electrodes, other digitized surface points).
* The coordinates are read into BESA MRI (or BrainVoyager), and aligned with the AC-PC-transformed MRI. The alignment information is then appended to the ''coregistration file''. The names of the AC-PC MRI ('''<nowiki>*.vmr</nowiki>''') and the surface mesh ('''<nowiki>*.srf</nowiki>'''), and, if available, the Talairach transformation, are also appended.
* BESA Research reads the coregistration file and appends the name of the Talairach-transformed MRI and head surface. If a brain surface has been created, this is also appended.
* Subsequently, BESA Research reads the coregistration file automatically when loading the data file.
* In the BESA Research source module, the individual MRI is displayed instead of the standard MRI. Talairach coordinates of dipoles are the "real" Talairach coordinates as defined, e.g., in BrainVoyager.

'''The steps you have to take (once for each data set):'''

* From the BESA Research ''Coregistration Dialog'', write a coregistration file. Switch to BESA MRI (or BrainVoyagerQX).
* If BESA MRI is used follow the steps in the coregistration quickguide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).
* If BrainVoyager is used follow the steps in Section “''How to set up coregistration between BESA and BrainVoyager”.''
* Back in BESA Research, reload the altered '''coregistration file'''. When using BESA MRI the file names of the generated surface and volume data files will be automatically filled in. When using BrainVoyager file names are only filled in automatically when the files are named according to the file naming conventions. Otherwise, file names have to be set manually.
* The coregistration file is now associated with the data file in the BESA Research database and will be used automatically the next time the file is opened in BESA Research. If the database entry is cleared, and the data are reloaded, you must make sure the coregistration file is also loaded (either using the ''Coregistration Dialog'' or the ''Channel and digitized head surface point information Dialog'').

== Alignment of BESA and MRICoordinate Systems ==

=== The Coregistration Dialog ===

The dialog is opened either from the ''Channel and digitized head surface point information'' ('''Ctrl-L''') ''dialog ''by pressing the '''Edit/Coreg''' button, or from the main menu ("'''File/MRI Coregistration...'''").

'''Note:''' If the coregistration dialog is invoked from an EEG data set in which no digitized electrode coordinates are available (i.e. standard electrode positions located on a sphere are assumed), BESA Research presents a warning message, saying that for MRI coregistration realistic electrode coordinates produce better results. BESA Research has a list of such realistic standard coordinates (i.e. located on a pre-defined standard head surface) for various electrodes available in file '''Default.sfp''', which is located in the Standard Electrode folder. If all electrodes in the dataset are listed in this file, a dialog window suggests to apply this file to the current data set, i.e. to switch from standard sphere coordinates to the standard realistic electrode coordinates in file '''Default.sfp'''. If the suggestion is accepted, '''default.sfp''' is assigned to the dataset (see Channel and digitized head surface point information ('''Ctrl-L''') dialog).

'''The Dialog:'''

[[Image:MRI Integration (1).gif ‎]]

* Press the '''Select MRI prog''' button to select your preferred MRI program. The current choice is between ''BESA MRI.exe'' and ''BrainVoyagerQX.exe''. The path to the MRI program is saved (in ''System\BESA.set'') and will be remembered by BESA Research. The top right hand button (now showing '''BESA MRI''') shows the current selection.
* Press the '''BESA MRI''' button to start the process of aligning the BESA Research and MRI coordinate systems. If no coregistration ('''<nowiki>*.sfh</nowiki>''') file is defined in the dialog (empty ''Surface coregistration file edit box''), BESA Research will first prompt for a file name. We recommend saving this file to the folder where the MRIs are kept. The MRI program will then be started. When you return to the ''Coregistration Dialog'', BESA Research checks if the ''Coregistration File'' has changed. If so, the dialog is updated with the new information.
* Press the top '''Browse... '''button to select a preexisting ''Coregistration File''.
* The entries in the edit boxes below show the files that will be used in the BESA Research Source Analysis module when the individual MRI is loaded. When using BESA MRI the file names will be automatically filled in. If you are using BrainVoagerQX and you are following our (and the BrainVoyagerQX) recommended naming conventions for files, and the files exist, then the names will be filled in automatically after you have completed the alignment procedure in BrainVoyagerQX. Otherwise you may have to browse for the files.
* Below the edit boxes the FEM field states whether all necessary information for the individual FEM head model were found in the coregistration file. If the field says ''Individual FEM for EEG'' ''defined!'' then all necessary data was found and the individual FEM EEG head model can be used in the BESA Research Source Analysis module. A similar message indicates whether the FEM MEG head model is available.
* Note that the MRI and the surfaces are Talairach-transformed! Alignment between BESA Research and the individual MRI is done with the MRI transformed to the AC-PC coordinate system, but the BESA Research Source Analysis module uses the Talairach-transformed image data and surfaces.

<div style="color:#ff0000;"></div>

=== Setting Up Coregistration Using BrainVoyager ===

It is assumed that you know how to load an MRI as a 3D data set into BrainVoyagerQX, and how to clean the image so that regions outside the head are black. We also assume knowledge of how to create AC-PC-aligned and Talairach-transformed MRIs.

Perform the following steps:

* BESA Research. Start the ''Coregistration Dialog''. Export the Coregistration File (head surface points) from your data by pressing the''' BrainVoyagerQX''' button in the dialog. Save the file to the directory where your MRI is located. BrainVoyagerQX is started.
* BrainVoyagerQX. Load the MRI corresponding to the EEG/MEG data. For optimal performance, the MRI should be cleaned so that regions outside the head are black. Prepare an AC-PC-transformed MRI and a Talairach MRI. For each, generate a surface mesh. Save these files following our recommended naming conventions (see chapter “''MRI File Name Conventions''”). Save the Talairach coordinate file ('''<nowiki>*.tal</nowiki>'''). If these steps have already been performed, load the ACPC MRI and load the ACPC mesh. If you want to generate a brain surface mesh, see chapter “''How to Generate a Brain Surface Mesh''”.
* BrainVoyagerQX. Load the Coregistration File (''EEG-MEG BESA/Load Surface Points''). The points will be displayed, but they are not aligned to the head:

<div style="color:#ff0000;"></div>

[[Image:MRI Integration (2).gif ‎]]

* BrainVoyagerQX. Define fiducial points on the head surface. Right click on the 3D head display and select the ''Fiducials Dialog'' in the drop-down menu:

[[Image:MRI Integration (3).gif ‎]]

 [[Image:MRI Integration (4).gif ‎]]

* BrainVoyagerQX. Rotate the head (by holding the '''Shift '''button down and clicking and dragging with the mouse) so that the Nasion is clearly visible. Move the mouse to the Nasion, and press '''Ctrl+Left Click'''. The coordinates of the Nasion are inserted into the dialog. Repeat for the left preauricular point, and then for the right preauricular point.

[[Image:MRI Integration (5).gif ‎]]

Note: if you have defined your fiducials differently in your BESA Research data (e.g. ear holes), click on the corresponding points in the MRI. If you have additional head surface points (step 8), accuracy in pinpointing the fiducials is not critical.

* BrainVoyagerQX. In the Fiducials Dialog, press the '''Fit fiducials''' button. The head surface points are now more or less aligned to the head.

[[Image:MRI Integration (6).gif ‎]]

* BrainVoyagerQX. Now select '''''EEG-MEG BESA/Fit Surface Points...'''''

[[Image:MRI Integration (7).gif ‎]]

If you do not see the right half of the dialog, press the '''Advanced >>''' button.

* Specify the distances of the digitization points from the skin. In the illustration above, the digitization points for electrodes are estimated to be 8 mm from the surface of the head. For the purpose of accurate alignment, the distance of digitization points from skin section of the dialog needs to be filled in correctly. We recommend that "Restrain solution around fiducials" is checked, and a reasonable limit (here 3 mm) of the restraint is defined. Then press '''OK'''.

[[Image:MRI Integration (8).gif ‎]]

BrainVoyager fits the points to the head, stretching x, y, and z coordinates to obtain a better fit than before.

Note: The fit performed during this step accounts for scaling inequalities between the x, y, and z axes in the MRI. Coregistration gains in accuracy over the use of fiducials alone a) because more head surface points are used, and b) because the scaling inequalities are accounted for.

* Alignment is now completed. If you only want to display the structural MRI in the BESA Source Module, you can return to the BESA Coregistration Dialog.
* BESA Research. When you switch back to the Coregistration Dialog, BESA Research will try to fill in the names of the Talairach MRI and surface meshes. If the names are not filled in, use the '''Browse...''' buttons to select the MRI and surface meshes. Press '''OK''' to save the Coregistration File. Alignment is completed!

The alignment steps need only be performed once for a given MRI and EEG/MEG data set. Otherwise, after starting BrainVoyager, just load the MRI, the surface mesh, and the surface points (see “''How to Set Up Coregistration with BrainVoyager after Alignment'' ''has been Done”''). Now the following actions are possible: see chapters “''How to Co-Locate Sources and MRI in the BESA Research Source Module”, '' ''“How to Send a Dipole from BESA Research to BrainVoyager”, “How to Define a Dipole in BESA Research at a Location Defined in the MRI”). ''

=== MRI file Name Conventions ===

If you follow the naming conventions for file names as described here, BESA Research detects the file names it requires, and the ''Coregistration Dialog'' is filled in automatically.

Please note that BESA MRI automatically uses these naming conventions for the generated files.

* '''The AC-PC MRI file name''' should end with "'''_ACPC.vmr'''", and the corresponding surface mesh name should end with "'''_ACPC.srf'''". After alignment, BrainVoyagerQX writes these names to the Coregistration File.
* '''The Talairach MRI file name '''should end with "'''_TAL.vmr'''", and the corresponding surface mesh name should end with "'''_TAL.srf'''". If defined, the brain surface mesh should end with "'''_TAL_WM.srf'''" ('''WM''' = '''w'''hite '''m'''atter).
* '''How BESA Research finds the Talairach files.''' When BESA Research rereads the Coregistration File after alignment of the coordinate systems, it finds the ACPC file names and defines the corresponding TAL file names. If these files exist, the names are entered into the Coregistration Dialog. For instance, if the Coregistration File contains the name "'''MRI''' '''PB_ACPC.vmr'''", BESA Research will look for the files "'''MRI_PB_TAL.vmr'''", "'''MRI_PB_TAL.srf'''", and "'''MRI_PB_TAL_WM.srf'''". If these files exist, they are entered into the dialog.
* '''Older BrainVoyager version.''' If you use BrainVoyager.exe to align coordinate systems, the file names are not saved with the Coregistration File. In this case, browse for the Talairach or the ACPC MRI from the Coregistration Dialog. BESA Research will use the rules as described above to insert the correct file names into the dialog.
* '''Missing Talairach coordinates.''' If, after aligning coordinate systems, the Talairach coordinates are missing from the Coregistration File (you forgot to load the Talairach coordinates in BrainVoyagerQX, or you used BrainVoyager.exe), BESA Research will look for a file ending with "'''_ACPC.tal'''", and read the coordinates from this file. You can also browse for a '''<nowiki>*.tal</nowiki>''' file in the Coregistration Dialog. For instance, if the MRI file is named "'''MRI_PB_ACPC.vmr'''" or "'''MR_''' '''PB_TAL.vmr'''", BESA Research will look for "'''MRI_PB_ACPC.tal'''" to find the Talairach coordinates.
* '''File names in the Coregistration File are saved relative to the Coregistration File location, if they are in the same folder.''' If the MRIs are in the same folder as the Coregistration File they will be recorded as ".\filename" (e.g. "'''.\MRI PB_tal.vmr'''"). This means that you can copy the Coregistration File together with the MRIs and meshes to a different folder, and BESA Research will be able to locate the files when the Coregistration File is opened. If the MRIs are saved in a different folder from the Coregistration File, the absolute paths are saved in the file. If the files are moved to new locations, you will have to restart the Coregistration Dialog and redefine the file locations.

=== How to Generate a Brain Surface Mesh ===

BESA Research is able to compute surface images, such as (Cortical LORETA, Cortical CLARA, Minimum Norm) using an individual cortex surface as the source space. A suitable cortex surface for this purpose can be effortlessly created using BESA MRI. Alternatively, BrainVoyager can be used for the creation of the brain surface mesh.

'''BESA MRI'''
* The brain surface generation is performed as one work step of the BESA MRI segmentation workflow.
* The cortex surface reconstruction is done using a robust and accurate automatic segmentation procedure.
* Details on how to generate the brain surface mesh in BESA MRI can be found in the coregistration quickguide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).

'''BrainVoyager'''
* BrainVoyagerQX provides a semiautomatic procedure to generate meshes for the brain surface of the Talairach MRI. Please refer to the BrainVoyager Help to find out how to do this.
* The result of the BrainVoyager procedure is two meshes, one for the left and one for the right hemisphere.
* BESA Research requires a single mesh. Therefore, load first one mesh (''Meshes/Load Mesh..''.), and append the other mesh (''Meshes/Add Mesh...''). Merge these two meshes (''Meshes/Merge'' ''meshes in surface window'') and then save the result (''Meshes/Save Mesh...''). If possible, use the recommended name conventions for the resulting file (file name ends in "'''_TAL_WM.srf"). '''For instance, if the Talairach MRI is named "'''MRI PB_TAL.vmr'''", name the brain surface mesh "'''MRI PB_TAL_WM.srf'''".
* See also the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website (http://brainvoyager.com/Downloads.html).

== Co-locating Dipoles and MRI Locations ==

=== Co-locating Sources and MRI in the BESA Research Source Module ===

If the alignment procedure using BESA MRI (or BrainVoyager) has been completed then you can load the individual structural MRI in the Source Module by pressing ''''A'''' or using a mouse right click and selecting '''''Display MRI'''''.

Sources in the current model are then overlayed onto the individual MRI.

A double-click at any location in the MRI will define a new source at the corresponding location in the BESA Research head model.

[[Image:MRI Integration (9).gif ‎]]

=== Coregistration with BrainVoyager after Alignment has been Done ===

Alignment between BESA Research and BrainVoyager is only required once for a given BESA Research data set and the corresponding MRI. At a later time, if you want to Co-locate sources between BESA Research and BrainVoyager, perform the following steps in BrainVoyager:
* Load the MRI.
* Load the head surface mesh (''Meshes/Load Mesh..''.).
* Load the Coregistration File (''EEG-MEG BESA/Load Surface Points..''.).

BrainVoyager is now ready for Co-location.

=== Send a Dipole from BESA Research to BrainVoyager ===

First, start BrainVoyager(QX). This can be done from the BESA Research Source Module by pressing the '''BrainVoyager '''button. Note that in the Source Module, the ''Options / Preferences / BrainVoyager'' tab allows to define the path to BrainVoyager.

In BrainVoyager, set up coregistration.

In the BESA Research Source Module, highlight the dipole of interest.

In the BESA Research Source Module, click on the '''BrainVoyager''' button.

Program control will automatically switch to BrainVoyager. The head will be cut at the section corresponding to the dipole of interest.

[[Image:MRI Integration (10).gif ‎]]

Note that all dipoles in the current model are sent to BrainVoyager. The highlighted dipole (here, the red dipole) determines the plane at which the head will be cut.

Note that the dipoles are visible in both the surface module and in the 2D view:

[[Image:MRI Integration (11).gif ‎]]

=== Define a Dipole in BESA Research at a Location Defined in the MRI ===

First set up coregistration (see chapter ''“Coregistration with BrainVoyager after Alignment has been'' ''Done”'').

In the BrainVoyager 2D MRI view, place the mouse over the point at which you would like to define a dipole. Right click at this point. If this point lies within an fRMI cluster, BrainVoyager will automatically determine its center and use it as a seeding point instead. Press '''Send Seed Point To BESA....'''

[[Image:MRI Integration (12).gif ‎]]

The following Dialog is opened:

[[Image:MRI Integration (13).gif ‎]]

Press '''Send to BESA'''.

The BESA Source Analysis window appears. The new dipole or regional source (depending on the setting in the ‘Options’ dialog in the Source Analysis window is now displayed at the corresponding location. If a dipole is seeded, BESA automatically fits its orientation. For further adjustment of the model, you may need to refit the orientation, e.g. at a certain time range, or in the presence of other sources.

Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website ([http://brainvoyager.com/Downloads.html http://brainvoyager.com/Downloads.html]).
[[Category:Research Manual]]

Integration with MRI and fMRI

2017-04-07T12:25:11Z

Alexa: /* Integration with MRI and fMRI */

= BESA Research Integration with MRI and fMRI =
{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.1 or higher
}}

Both for developing and evaluating dipole source models of EEG or MEG activity, it is useful to have access to structural MRI or fMRI data.

The BESA MRI software allows to preprocess structural MRI data so that the individual anatomical information contained in the MRI can be utilized in BESA Research. BESA MRI makes it possible ...
* ... to align the EEG and MEG sensors with the structural MRI data.
* ... to read and display the aligned, individual Talairach structural MRIs directly in the BESA Research Source Analysis module. In this way, source analysis results can be presented on top of the aligned MRIs, which allows us to evaluate the anatomical regions to which the reconstructed sources may correspond.
* ... to use an individual, realistically shaped FEM head model for source analysis in BESA Research. FEM head models take into account the individual volume conduction properties of the subject's head derived from the structural MRI data. This allows for more accurate source analysis (Yvert 1997, Lanfer 2012).

To offer an easy integration with fMRI data we have, in collaboration with Rainer Goebel, optimized the interface between BESA Research and BrainVoyagerQX.

With these tools, we can ...
* ... use fMRI BOLD regions or MRI structures to initialize dipole models.
* ... visualize dipoles from BESA Research models together with the structural MRI in BrainVoyager in order to evaluate the regions to which the dipoles may correspond.
* ... combine the localization advantages of (f)MRI with the high temporal resolution of EEG and MEG, for instance by using (f)MRI to place the sources, and the source waveforms of BESA Research to provide feedback about the time course of the source activity.
* ... overlay source analysis results obtained in BESA Research with fMRI data.

'''Note:''' For simpler coregistration, we recommend to use BrainVoyagerQX rather than the older BrainVoyager, but BESA Research will work with both program versions.

The chapters below describe the steps necessary to integrate the MRI and fMRI data with BESA Research. Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website (http://brainvoyager.com/Downloads.html).

'''Aligning Coordinate Systems'''

* For a given BESA data set, the electrode and other head surface points need to be aligned to the MRI coordinates.
* The basic steps necessary to align the EEG electrode locations, the MEG sensors and the MRI are described in Section “''How Coregistration is done”''.
* Detailed instructions on how to align EEG / MEG and MRI data using BESA MRI can be found in the coregistration quick guide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).
* Detailed instructions on how to align EEG / MEG and MRI data using BrainVoyager are described in Section “''How To set up Coregistration between BESA and BrainVoyager”.''
* In BESA Research all necessary settings with regard to the alignment are made in the ''Coregistration Dialog.''
* Requirements with respect to the MRI data for a good coregistration can be found in Section “''MRI Requirements for Good Coregistration”.''
* Requirements with respect to EEG and MEG data for a good coregistration can be found in Section “''EEG/MEG Data Requirements for Good Coregistration”.''

'''Generating an individual, realistically shaped FEM head model'''

* The generation of a FEM head model that can be used in BESA Research is done in BESA MRI as an additional step following the EEG / MEG to MRI coregistration.
* Detailed instructions on how to generate the FEM head model can be found in the coregistration quick guide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).

'''Co-locating dipoles and MRI locations'''

* After aligning the EEG / MEG and the MRI data it is possible to co-locate dipoles and MRI locations. This means, it is possible to visualize the dipoles and to specify the dipole parameters in the MRI coordinate system.
* ''“How to Co-locate sources'' ''and MRI”'' in the BESA Research Source Module describes how in the BESA Research Source Analysis module dipoles can directly be visualized in the space of the individual MRI.
* ''“How to Send a Dipole from BESA Research to BrainVoyager”'' describes how to send a source model from BESA Research to BrainVoyager for further inspection.
* ''“How to Define a Dipole in BESA Research at a Location Defined in the MRI”'' describes how to insert a dipole at a location defined in the MRI in BrainVoyager.

'''References'''

Lanfer, B., I. Paul-Jordanov, M. Scherg, and C. H. Wolters. “Influence of Interior Cerebrospinal Fluid Compartments on EEG Source Analysis.” In Proceedings BMT 2012, Vol. 57. Jena: De Gruyter, 2012. doi:10.1515/bmt-2012-4020.

Yvert, B., O. Bertrand, M. Thévenet, J. F. Echallier, and J. Pernier. “A Systematic Evaluation of the Spherical Model Accuracy in EEG Dipole Localization.” Electroencephalography and Clinical Neurophysiology 102, no. 5 (May 1997): 452–59. doi:16/S0921-884X(97)96611-X.

== How Coregistration is done ==

This section outlines the basic steps to coregister the EEG / MEG data to an individual MRI. These steps are necessary to load an individual MRI into BESA Research.

'''What happens:'''

* EEG / MEG sensor locations and the MRI data are defined in different coordinate systems. Setting up coregistration is the process of aligning the two coordinate systems.
* BESA Research uses the ''Coregistration Dialog'' to coordinate the alignment procedure.
* Alignment is done with the ''AC-PC-transformed MRI''.
* BESA Research displays the ''Talairach-transformed MRI'' in the source analysis module.
* A coregistration file (with the extension "'''.sfh'''") is used to mediate between BESA Research and BESA MRI (or BrainVoyagerQX):
* BESA Research writes the coregistration file which contains the coordinates of head surface points (fiducials, electrodes, other digitized surface points).
* The coordinates are read into BESA MRI (or BrainVoyager), and aligned with the AC-PC-transformed MRI. The alignment information is then appended to the ''coregistration file''. The names of the AC-PC MRI ('''<nowiki>*.vmr</nowiki>''') and the surface mesh ('''<nowiki>*.srf</nowiki>'''), and, if available, the Talairach transformation, are also appended.
* BESA Research reads the coregistration file and appends the name of the Talairach-transformed MRI and head surface. If a brain surface has been created, this is also appended.
* Subsequently, BESA Research reads the coregistration file automatically when loading the data file.
* In the BESA Research source module, the individual MRI is displayed instead of the standard MRI. Talairach coordinates of dipoles are the "real" Talairach coordinates as defined, e.g., in BrainVoyager.

'''The steps you have to take (once for each data set):'''

* From the BESA Research ''Coregistration Dialog'', write a coregistration file. Switch to BESA MRI (or BrainVoyagerQX).
* If BESA MRI is used follow the steps in the coregistration quickguide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).
* If BrainVoyager is used follow the steps in Section “''How to set up coregistration between BESA and BrainVoyager”.''
* Back in BESA Research, reload the altered '''coregistration file'''. When using BESA MRI the file names of the generated surface and volume data files will be automatically filled in. When using BrainVoyager file names are only filled in automatically when the files are named according to the file naming conventions. Otherwise, file names have to be set manually.
* The coregistration file is now associated with the data file in the BESA Research database and will be used automatically the next time the file is opened in BESA Research. If the database entry is cleared, and the data are reloaded, you must make sure the coregistration file is also loaded (either using the ''Coregistration Dialog'' or the ''Channel and digitized head surface point information Dialog'').

== Alignment of BESA and MRICoordinate Systems ==

=== The Coregistration Dialog ===

The dialog is opened either from the ''Channel and digitized head surface point information'' ('''Ctrl-L''') ''dialog ''by pressing the '''Edit/Coreg''' button, or from the main menu ("'''File/MRI Coregistration...'''").

'''Note:''' If the coregistration dialog is invoked from an EEG data set in which no digitized electrode coordinates are available (i.e. standard electrode positions located on a sphere are assumed), BESA Research presents a warning message, saying that for MRI coregistration realistic electrode coordinates produce better results. BESA Research has a list of such realistic standard coordinates (i.e. located on a pre-defined standard head surface) for various electrodes available in file '''Default.sfp''', which is located in the Standard Electrode folder. If all electrodes in the dataset are listed in this file, a dialog window suggests to apply this file to the current data set, i.e. to switch from standard sphere coordinates to the standard realistic electrode coordinates in file '''Default.sfp'''. If the suggestion is accepted, '''default.sfp''' is assigned to the dataset (see Channel and digitized head surface point information ('''Ctrl-L''') dialog).

'''The Dialog:'''

[[Image:MRI Integration (1).gif ‎]]

* Press the '''Select MRI prog''' button to select your preferred MRI program. The current choice is between ''BESA MRI.exe'' and ''BrainVoyagerQX.exe''. The path to the MRI program is saved (in ''System\BESA.set'') and will be remembered by BESA Research. The top right hand button (now showing '''BESA MRI''') shows the current selection.
* Press the '''BESA MRI''' button to start the process of aligning the BESA Research and MRI coordinate systems. If no coregistration ('''<nowiki>*.sfh</nowiki>''') file is defined in the dialog (empty ''Surface coregistration file edit box''), BESA Research will first prompt for a file name. We recommend saving this file to the folder where the MRIs are kept. The MRI program will then be started. When you return to the ''Coregistration Dialog'', BESA Research checks if the ''Coregistration File'' has changed. If so, the dialog is updated with the new information.
* Press the top '''Browse... '''button to select a preexisting ''Coregistration File''.
* The entries in the edit boxes below show the files that will be used in the BESA Research Source Analysis module when the individual MRI is loaded. When using BESA MRI the file names will be automatically filled in. If you are using BrainVoagerQX and you are following our (and the BrainVoyagerQX) recommended naming conventions for files, and the files exist, then the names will be filled in automatically after you have completed the alignment procedure in BrainVoyagerQX. Otherwise you may have to browse for the files.
* Below the edit boxes the FEM field states whether all necessary information for the individual FEM head model were found in the coregistration file. If the field says ''Individual FEM for EEG'' ''defined!'' then all necessary data was found and the individual FEM EEG head model can be used in the BESA Research Source Analysis module. A similar message indicates whether the FEM MEG head model is available.
* Note that the MRI and the surfaces are Talairach-transformed! Alignment between BESA Research and the individual MRI is done with the MRI transformed to the AC-PC coordinate system, but the BESA Research Source Analysis module uses the Talairach-transformed image data and surfaces.

<div style="color:#ff0000;"></div>

=== Setting Up Coregistration Using BrainVoyager ===

It is assumed that you know how to load an MRI as a 3D data set into BrainVoyagerQX, and how to clean the image so that regions outside the head are black. We also assume knowledge of how to create AC-PC-aligned and Talairach-transformed MRIs.

Perform the following steps:

* BESA Research. Start the ''Coregistration Dialog''. Export the Coregistration File (head surface points) from your data by pressing the''' BrainVoyagerQX''' button in the dialog. Save the file to the directory where your MRI is located. BrainVoyagerQX is started.
* BrainVoyagerQX. Load the MRI corresponding to the EEG/MEG data. For optimal performance, the MRI should be cleaned so that regions outside the head are black. Prepare an AC-PC-transformed MRI and a Talairach MRI. For each, generate a surface mesh. Save these files following our recommended naming conventions (see chapter “''MRI File Name Conventions''”). Save the Talairach coordinate file ('''<nowiki>*.tal</nowiki>'''). If these steps have already been performed, load the ACPC MRI and load the ACPC mesh. If you want to generate a brain surface mesh, see chapter “''How to Generate a Brain Surface Mesh''”.
* BrainVoyagerQX. Load the Coregistration File (''EEG-MEG BESA/Load Surface Points''). The points will be displayed, but they are not aligned to the head:

<div style="color:#ff0000;"></div>

[[Image:MRI Integration (2).gif ‎]]

* BrainVoyagerQX. Define fiducial points on the head surface. Right click on the 3D head display and select the ''Fiducials Dialog'' in the drop-down menu:

[[Image:MRI Integration (3).gif ‎]]

 [[Image:MRI Integration (4).gif ‎]]

* BrainVoyagerQX. Rotate the head (by holding the '''Shift '''button down and clicking and dragging with the mouse) so that the Nasion is clearly visible. Move the mouse to the Nasion, and press '''Ctrl+Left Click'''. The coordinates of the Nasion are inserted into the dialog. Repeat for the left preauricular point, and then for the right preauricular point.

[[Image:MRI Integration (5).gif ‎]]

Note: if you have defined your fiducials differently in your BESA Research data (e.g. ear holes), click on the corresponding points in the MRI. If you have additional head surface points (step 8), accuracy in pinpointing the fiducials is not critical.

* BrainVoyagerQX. In the Fiducials Dialog, press the '''Fit fiducials''' button. The head surface points are now more or less aligned to the head.

[[Image:MRI Integration (6).gif ‎]]

* BrainVoyagerQX. Now select '''''EEG-MEG BESA/Fit Surface Points...'''''

[[Image:MRI Integration (7).gif ‎]]

If you do not see the right half of the dialog, press the '''Advanced >>''' button.

* Specify the distances of the digitization points from the skin. In the illustration above, the digitization points for electrodes are estimated to be 8 mm from the surface of the head. For the purpose of accurate alignment, the distance of digitization points from skin section of the dialog needs to be filled in correctly. We recommend that "Restrain solution around fiducials" is checked, and a reasonable limit (here 3 mm) of the restraint is defined. Then press '''OK'''.

[[Image:MRI Integration (8).gif ‎]]

BrainVoyager fits the points to the head, stretching x, y, and z coordinates to obtain a better fit than before.

Note: The fit performed during this step accounts for scaling inequalities between the x, y, and z axes in the MRI. Coregistration gains in accuracy over the use of fiducials alone a) because more head surface points are used, and b) because the scaling inequalities are accounted for.

* Alignment is now completed. If you only want to display the structural MRI in the BESA Source Module, you can return to the BESA Coregistration Dialog.
* BESA Research. When you switch back to the Coregistration Dialog, BESA Research will try to fill in the names of the Talairach MRI and surface meshes. If the names are not filled in, use the '''Browse...''' buttons to select the MRI and surface meshes. Press '''OK''' to save the Coregistration File. Alignment is completed!

The alignment steps need only be performed once for a given MRI and EEG/MEG data set. Otherwise, after starting BrainVoyager, just load the MRI, the surface mesh, and the surface points (see “''How to Set Up Coregistration with BrainVoyager after Alignment'' ''has been Done”''). Now the following actions are possible: see chapters “''How to Co-Locate Sources and MRI in the BESA Research Source Module”, '' ''“How to Send a Dipole from BESA Research to BrainVoyager”, “How to Define a Dipole in BESA Research at a Location Defined in the MRI”). ''

=== MRI file Name Conventions ===

If you follow the naming conventions for file names as described here, BESA Research detects the file names it requires, and the ''Coregistration Dialog'' is filled in automatically.

Please note that BESA MRI automatically uses these naming conventions for the generated files.

* '''The AC-PC MRI file name''' should end with "'''_ACPC.vmr'''", and the corresponding surface mesh name should end with "'''_ACPC.srf'''". After alignment, BrainVoyagerQX writes these names to the Coregistration File.
* '''The Talairach MRI file name '''should end with "'''_TAL.vmr'''", and the corresponding surface mesh name should end with "'''_TAL.srf'''". If defined, the brain surface mesh should end with "'''_TAL_WM.srf'''" ('''WM''' = '''w'''hite '''m'''atter).
* '''How BESA Research finds the Talairach files.''' When BESA Research rereads the Coregistration File after alignment of the coordinate systems, it finds the ACPC file names and defines the corresponding TAL file names. If these files exist, the names are entered into the Coregistration Dialog. For instance, if the Coregistration File contains the name "'''MRI''' '''PB_ACPC.vmr'''", BESA Research will look for the files "'''MRI_PB_TAL.vmr'''", "'''MRI_PB_TAL.srf'''", and "'''MRI_PB_TAL_WM.srf'''". If these files exist, they are entered into the dialog.
* '''Older BrainVoyager version.''' If you use BrainVoyager.exe to align coordinate systems, the file names are not saved with the Coregistration File. In this case, browse for the Talairach or the ACPC MRI from the Coregistration Dialog. BESA Research will use the rules as described above to insert the correct file names into the dialog.
* '''Missing Talairach coordinates.''' If, after aligning coordinate systems, the Talairach coordinates are missing from the Coregistration File (you forgot to load the Talairach coordinates in BrainVoyagerQX, or you used BrainVoyager.exe), BESA Research will look for a file ending with "'''_ACPC.tal'''", and read the coordinates from this file. You can also browse for a '''<nowiki>*.tal</nowiki>''' file in the Coregistration Dialog. For instance, if the MRI file is named "'''MRI_PB_ACPC.vmr'''" or "'''MR_''' '''PB_TAL.vmr'''", BESA Research will look for "'''MRI_PB_ACPC.tal'''" to find the Talairach coordinates.
* '''File names in the Coregistration File are saved relative to the Coregistration File location, if they are in the same folder.''' If the MRIs are in the same folder as the Coregistration File they will be recorded as ".\filename" (e.g. "'''.\MRI PB_tal.vmr'''"). This means that you can copy the Coregistration File together with the MRIs and meshes to a different folder, and BESA Research will be able to locate the files when the Coregistration File is opened. If the MRIs are saved in a different folder from the Coregistration File, the absolute paths are saved in the file. If the files are moved to new locations, you will have to restart the Coregistration Dialog and redefine the file locations.

=== How to Generate a Brain Surface Mesh ===

BESA Research is able to compute surface images, such as (Cortical LORETA, Cortical CLARA, Minimum Norm) using an individual cortex surface as the source space. A suitable cortex surface for this purpose can be effortlessly created using BESA MRI. Alternatively, BrainVoyager can be used for the creation of the brain surface mesh.

'''BESA MRI'''
* The brain surface generation is performed as one work step of the BESA MRI segmentation workflow.
* The cortex surface reconstruction is done using a robust and accurate automatic segmentation procedure.
* Details on how to generate the brain surface mesh in BESA MRI can be found in the coregistration quickguide which is available on the BESA homepage (http://www.besa.de/tutorials/quickguides/).

'''BrainVoyager'''
* BrainVoyagerQX provides a semiautomatic procedure to generate meshes for the brain surface of the Talairach MRI. Please refer to the BrainVoyager Help to find out how to do this.
* The result of the BrainVoyager procedure is two meshes, one for the left and one for the right hemisphere.
* BESA Research requires a single mesh. Therefore, load first one mesh (''Meshes/Load Mesh..''.), and append the other mesh (''Meshes/Add Mesh...''). Merge these two meshes (''Meshes/Merge'' ''meshes in surface window'') and then save the result (''Meshes/Save Mesh...''). If possible, use the recommended name conventions for the resulting file (file name ends in "'''_TAL_WM.srf"). '''For instance, if the Talairach MRI is named "'''MRI PB_TAL.vmr'''", name the brain surface mesh "'''MRI PB_TAL_WM.srf'''".
* See also the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website (http://brainvoyager.com/Downloads.html).

== Co-locating Dipoles and MRI Locations ==

=== Co-locating Sources and MRI in the BESA Research Source Module ===

If the alignment procedure using BESA MRI (or BrainVoyager) has been completed then you can load the individual structural MRI in the Source Module by pressing ''''A'''' or using a mouse right click and selecting '''''Display MRI'''''.

Sources in the current model are then overlayed onto the individual MRI.

A double-click at any location in the MRI will define a new source at the corresponding location in the BESA Research head model.

[[Image:MRI Integration (9).gif ‎]]

=== Coregistration with BrainVoyager after Alignment has been Done ===

Alignment between BESA Research and BrainVoyager is only required once for a given BESA Research data set and the corresponding MRI. At a later time, if you want to Co-locate sources between BESA Research and BrainVoyager, perform the following steps in BrainVoyager:
* Load the MRI.
* Load the head surface mesh (''Meshes/Load Mesh..''.).
* Load the Coregistration File (''EEG-MEG BESA/Load Surface Points..''.).

BrainVoyager is now ready for Co-location.

=== Send a Dipole from BESA Research to BrainVoyager ===

First, start BrainVoyager(QX). This can be done from the BESA Research Source Module by pressing the '''BrainVoyager '''button. Note that in the Source Module, the ''Options / Preferences / BrainVoyager'' tab allows to define the path to BrainVoyager.

In BrainVoyager, set up coregistration.

In the BESA Research Source Module, highlight the dipole of interest.

In the BESA Research Source Module, click on the '''BrainVoyager''' button.

Program control will automatically switch to BrainVoyager. The head will be cut at the section corresponding to the dipole of interest.

[[Image:MRI Integration (10).gif ‎]]

Note that all dipoles in the current model are sent to BrainVoyager. The highlighted dipole (here, the red dipole) determines the plane at which the head will be cut.

Note that the dipoles are visible in both the surface module and in the 2D view:

[[Image:MRI Integration (11).gif ‎]]

=== Define a Dipole in BESA Research at a Location Defined in the MRI ===

First set up coregistration (see chapter ''“Coregistration with BrainVoyager after Alignment has been'' ''Done”'').

In the BrainVoyager 2D MRI view, place the mouse over the point at which you would like to define a dipole. Right click at this point. If this point lies within an fRMI cluster, BrainVoyager will automatically determine its center and use it as a seeding point instead. Press '''Send Seed Point To BESA....'''

[[Image:MRI Integration (12).gif ‎]]

The following Dialog is opened:

[[Image:MRI Integration (13).gif ‎]]

Press '''Send to BESA'''.

The BESA Source Analysis window appears. The new dipole or regional source (depending on the setting in the ‘Options’ dialog in the Source Analysis window is now displayed at the corresponding location. If a dipole is seeded, BESA automatically fits its orientation. For further adjustment of the model, you may need to refit the orientation, e.g. at a certain time range, or in the presence of other sources.

Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website ([http://brainvoyager.com/Downloads.html http://brainvoyager.com/Downloads.html]).

Source Coherence Introduction and Concepts

2017-04-07T10:08:09Z

Alexa:

= Source Coherence =

== Source Coherence Module - Introduction ==

The Source Coherence Module provides new insights into interaction between brain regions using brain source montages. These are derived from multiple source models of the data. Transforming the scalp surface into the brain signals using source montages greatly enhances the spatial resolution and largely removes one of the major drawbacks of traditional coherence analysis, the widespread overlap at the scalp due to volume conduction.

The Source Coherence Module provides a variety of tools for time-frequency based event-related data analysis.
* Time-frequency diagrams based on brain source or surface channels
* Display of temporal-spectral evolution (TSE) in percent
* Separation of evoked and induced activity  
* Joint display of time-frequency or coherence plots with the evoked potential of individual channels
* Coherence estimate between any combination of surface or source channels (coherence or phase coherence)
* Computation and display of phase delay and latency difference between channels in a graphically defined time and frequency window
* Display of the inter-trial phase locking (ITPL)
* Comparison of two conditions
* Probability plots transforming all time-frequency parameters into statistical p-values
* Export of analysis results into ASCII text files
* Time-frequency transforms are obtained in a very fast implementation based on complex demodulation. Apart from source channels, intracranial channels, and scalp channels, also other polygraphic channels, e.g. rectified EMG, can be included into the analysis.
* A highly optimized graphical user interaction enables a fast testing of hypotheses, and quick focusing onto the features of interest.

For an introduction and an outline of the underlying concepts of source coherence, please continue with the next topic, "''Concepts of Source Coherence''"

For more details check the following topics:
* Layout of the Source Coherence Window
* Reference (in the online help)

Please also refer to our website at http://www.besa.de for the latest tutorial on source coherence and related topics.

== Concepts of Source Coherence ==

Recently, an increasing number of papers on oscillatory coupling between brain regions in animal studies and on time-frequency analysis of human EEG and MEG data has been published. BESA Research introduces several tools for fast and user-friendly time-frequency analysis including source and scalp coherence.

First, let us introduce some terminology in order to clarify the concepts:
* Surface waveform: a time signal recorded from EEG-electrodes or MEG sensors
* Source waveform: a time signal calculated for a specified brain region or cortical surface
* Source montage: transformation of the on-going EEG into the estimated contributions or source waveforms of a set of brain regions

[[Image:SourceCoh Concepts (1).gif ]]

* Time-frequency analysis: analysis or display of the event-related time-locked or induced activity in the time-frequency domain
* Time-locked activity: event-related signal with similar wave shape over trials
* Induced activity: oscillatory activity occurring in a certain event-related time window with varying time lag and phase
* Oscillatory activity: activity occurring with several oscillations in a narrow frequency band; can be time-locked and/or induced

[[Image:SourceCoh Concepts (2).gif ]]

* TSE: temporal spectral evolution, change in amplitude or power over time relative to the baseline interval
* ERD/ERS: event-related (de)-synchronization, used as a synonym for TSE
* ERSP: event-related spectral perturbations, change in power or amplitude over time. This is the more general term and comprises ERD/ERS/TSE that are related to baseline.
* Correlation: correlation between two time signals, i.e. scalar product of normalized signals in time domain

[[Image:SourceCoh Concepts (3).gif ]]

* Spectral-temporal density function S(f,t) = A(f,t)*ei*ϕ(f,t): quantifies amplitude A and phase ϕ of a signal at a certain frequency f and latency t relative to an event
* Coherence: squared correlation of two spectral density functions S1(f,t) and S2(f,t) over trials, i.e. squared scalar product of S1(f,t) and S2(f,t) over trials, normalized across all trials
* Phase coherence: correlation of two normalized spectral density functions S1(f,t) and S2(f,t) over trials, quantified by the phase locking value (PLV)
* Phase locking value (PLV): scalar product of S1(f,t) and S2(f,t) over trials, where S1(f,t) and S2(f,t) are normalized, i.e. they become unit vectors in the complex plane

[[Image:SourceCoh Concepts (4).gif ]]

Phase coherence uses only the phase relationships between channels for the coherence estimate, not the amplitudes. The method implemented here was described by Lachaux et al. (1999). Phase coherence is described by the so-called "phase locking value" (PLV).

Comparison of the formulae for coherence and PLV illustrates that for constant amplitudes, PLV is equivalent to the square root of coherence.

'''Scalp Coherence'''

When coherence is calculated at the surface between 2 EEG channels or 2 MEG sensors, activity from various brain regions is picked up in each of the surface channels. Oscillatory activity in one brain region can already lead to a strong coherence between 2 surface channels because of the wide distribution of focal brain activity at the surface. This is due to the nature of the dipole fields when recording remotely and due to the smearing effect of the volume conduction in EEG. As a consequence, a coherence measure between surface channels cannot distinguish between coherence due to propagation and real coherence between the oscillatory activities in two coupled brain regions.

[[Image:SourceCoh Concepts (5).gif ]]

Whether true coherence can be detected at the scalp, depends mainly on the relative orientation of the source currents in the underlying brain regions and, to a lesser extent, on their distance in location. In the case of the auditory cortex, for example, both the left and right temporal planes produce vertical activity with strong bilateral contributions centrally (e.g. at C3/C4 and F3/F4). The spatial correlation of the radial activities at the lateral surfaces of the superior temporal gyrus is also very large between right and left scalp electrodes, e.g. at T3/T4. A current-source density montage (CSD or Laplacian) can reduce the effects of propagation on scalp coherence to a certain extent, because it enhances the radial current from the underlying cortex relative to more remote sources to some extent.

[[Image:SourceCoh Concepts (6).gif ]]

'''Source Coherence'''

An optimal separation is obtained by a source montage derived from a multiple source model. The model is used to create an inverse spatial filter, i.e. a source montage that separates the different brain activities. Activities that are not accounted for by the model, e.g. from background noise or EEG, are distributed amongst the sources and may therefore lead to 'noise coherence' between source channels. This 'noise coherence' can be large for sources which have very similar spatial topographies. It can be reduced by increasing the regularization constant of the inverse at the expense of a larger cross-talk between the sources or by including specific sources accounting for the 'noise'.

The principal steps to calculate a time-frequency diagram and source coherence are illustrated in the figure below for the real data example of error-related negativity (ERN). A multiple source model is created from averaged ERP data and/or sources in brain regions known to contribute from fMRI/PET studies using a similar task. The source model is then used to calculate a source montage and the source waveforms of the single trials. Next, each single trial is transformed into the time-frequency domain by selecting a certain temporal resolution using complex demodulation (a principle similar to FM radio). From the single trials, time-frequency displays are generated by averaging spectral density amplitude or power over trials. Source coherence is calculated by averaging the cross-spectral density of one reference channel with all other channels over trials and normalizing by the averaged auto-spectral densities (cf. figure above).

[[Image:SourceCoh Concepts (7).gif ]]

In this figure, you can see the separation of the occipital alpha rhythm (top 3 source waveforms) from the frontal midline ERN components (lowest 2 traces) which become prominent in most single trials after transforming from the 128 scalp electrodes onto 9 source areas in the brain. The time-frequency display shows a strong evoked ERN activity in the anterior and posterior cingulate gyrus (CG) sources and an induced suppression and rebound of ~20 Hz activity in the sensori-motor cortex bilaterally. Alpha suppression is most prominent in the midline occipital source. A double click onto the TF display of a selected channel leads to the rapid calculation of the coherence between this channel and all other channels.

For more information, see the following sections ''(Layout of the Source Coherence Window'' and ''Tutorial)''.

== Layout of the Source Coherence Window ==

The source coherence window consists of
* title bar with information on the current display mode and the data file name
* menu bar where the display mode and analysis options are selected
* toolbar for quick access to the menu functions
* display area where time-frequency diagrams of all channels are shown
* information text about the current display mode and units (e.g. Power, Amplitude,
* color map with minimum and maximum normalization values at the center bottom. Any value higher or lower than the normalization value is assigned the color of the normalization value
* information text about the condition which is analyzed at the bottom right
* status bar with information about the channel, frequency, latency, and signal amplitude

[[Image:Coherence (1).gif]]

Source Coherence How to...

2017-04-07T10:05:32Z

Alexa:

= Source Coherence: How to... =

== How to Start the Beamformer from the Time-Frequency Window ==

This chapter shows how to start the BESA Multiple Source Beamformer from the time-frequency window. The displayed screenshots are taken using the file '''BESA5/Examples/Learn-by-Simulations/AC''-''Coherence/AC-Osc20.foc''' (see BESA Tutorial 6: "''Tutorial on source coherence''" on our website http://www.besa.de).

The time-frequency beamformer is especially useful to image induced oscillatory activity in- or decrease. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot.

In the time-frequency diagram of any channel, left-drag to mark a time-frequency region of interest, e.g. a region of power increase. When the left mouse button is released, select '''Image' ''from the popup menu.

[[Image:Image001.gif]]

'''Note:''' The current montage and the type of time-frequency plot currently displayed (TSE, amplitude/power, Coherence) does not affect the output of the beamformer image, because the image is always based on the complex single-trial spectral density of the original recording montage. The status of the 'subtract average signal' button is considered, however. This allows to image either evoked and induced activity or induced activity only.

The 'Image' edit window is displayed. It allows for adjusting the time-frequency range of the target interval and for a re-definition of the baseline interval. If a control condition has been specified, you can choose to reference the power in the target time-frequency interval to the corresponding interval in the control condition instead of the baseline interval by checking 'Compare Conditions'.

[[Image:Image002.gif]]

Note: The text within the window emphasizes that it is recommended to use the same duration for the Baseline Interval and the Target Interval to obtain a reliable beamformer image. The reason is the dependence on the noise estimate on the number of trials that enter the covariance matrix computation. The same recommendation holds if two conditions are compared: It is recommended to define conditions such that they contain approximately the same number of trials. If the baseline interval defined in the Time-Frequency window (the red bar on the x-axis) is larger than the target time interval specified by the dragged rectangle, the baseline interval in the'' 'Image' ''dialog window is automatically shortened to match the duration of the Target Interval. If for some reason these requirements cannot be met, it is recommended to compute a beamformer image with regularization. This is achieved by adjusting the SVD cutoff in the Source Analysis window using the menu entry '''Image/Settings'.''

Press the ''''Go' '''button to start the beamformer computation.

BESA Research now computes mean time-frequency covariance matrices for the target and the reference interval. The source analysis window opens with an enlarged 3D imaging display that compares the power in the target and the reference interval as computed with a bilateral beamformer. The result is superimposed onto the individual or standard MRI.

For more information on the multiple-source beamformer (MSBF), please refer to chapter ''"Source'' ''Analysis".''

[[Image:Image003.gif]]

== How to Start DICS computation from the Time-Frequency Window ==

How to create DICS images you will find in the chapter “''Source Analysis / 3D Imaging / Dynamic Imaging of Coherent Sources (DICS)”.''

== How to Compute Time Lags between oscillations using Phase Diagrams ==

The phase diagram option is used to analyze phase differences between coherent channels. This can give an insight into a possible coupling of brain regions which may be necessary e.g. to integrate input from various specialized neurons to a common perception. However, the measured coupling is also influenced by volume conduction effects (scalp coherence) or the modeling parameters (source coherence).

If brain regions show oscillatory coupling in the same frequency range, the phase relationship should be constant over some time:

[[Image:Image005.gif]]

Since we cannot obtain an ideal frequency resolution using a time-frequency transform, any oscillation frequency is smeared out over several sampling frequencies in the transformed signal. If the delay between the two oscillations is constant, the phase shift between the signals rises linearly with the frequency. We can get a precise estimate of the delay if we use several neighboring frequencies for the calculation. Practically, you can achieve this by the following steps:

1. Enter '''coherence''' mode, either by '''double-clicking''' on the channel of interest, or by right-clicking on it and selecting coherence from the popup menu.

2. In a coherence plot, '''drag''' over an area of interest which comprises the time interval where the oscillation occurs and the relevant frequency range. The left-mouse popup menu appears (see the leftmost channel termed ACsL in the example below):

[[Image:Image006.gif]]

3. Select the menu entry ''''''View Phase Diagram''''''. In all channels where coherence was shown previously, the plot changes to display the phase diagram. Inside the marked time-frequency region, the mean phase difference ϕi within the time window is calculated for each frequency νi, and the values are plotted. The phase is calculated from the cross-spectral matrices of the single trials. The error bars shown in the display are the standard deviations of the phase over the time.

The time lag is calculated from a regression fit to the values. The fitting procedure takes phase shifts of π into account, which can occur due to volume currents, or due to dipole orientations. First, a straight line is fitted to the data. Then, one of two different approaches are used to compute the time lag, depending on the characteristics of the values.
* If extrapolation of the line to ν= 0 Hz yields a phase difference of approximately 0 or approximately π, or if a zero crossing at the origin is within the error margins of the fit, the delay can be calculated directly from the data values. For each data value, the relationship ∆ti <nowiki>= ϕ</nowiki>i/ (2π νi) holds. The time lag is calculated as the weighted mean, where the weights are given by the individual errors of fi (the errors are given by the standard deviation over the time samples).
* If the regression line does not cross the origin, the gradient of the fit is used to calculate the time lag as ∆t=grad(f(ν)) / 2π

'''Note:''' In both cases, any frequency only enters the calculation if the coherence value reaches or exceeds 70% of the current color map maximum for at least one time sample inside the selected time-frequency window. At least 3 valid values are required for the estimation. Channels with less than 3 valid values are not evaluated.

Phase values and fitted lines are only displayed for the channels where the above condition is satisfied. In the example below, the condition was only fulfilled for one channel (ACsL) due to the good separation of activities by the source montage. The calculated delay is displayed beside the channel label (in this case: 5 milliseconds).

[[Image:Image009.gif]]

To get back to coherence, '''right-click '''into the reference channel and select ''''Coherence'''' from the popup menu that appears.

== How to Compute a Probability Map ==

'''Statistical testing with one condition'''

This example uses the simulated data set in the file ''''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''' (see also BESA Research Tutorial on source coherence on www.besa.de).

After the data file is loaded, start coherence analysis by
# selecting the montage "RC0" from the user montages (toolbar button "'''Usr'''")
# loading the paradigm (menu "''ERP/Open Paradigm''", select paradigm file "'''Auditory/AC_Osc.pdg'''")
# performing an artifact scan (paradigm tab "'''Artifact'''", press the "'''Scan'''..." button and adjust the amplitude threshold to about 135µV)
# starting analysis (paradigm tab "Coherence", press the "'''Go'''" button)

The progress bar runs through, and the temporal-spectral evolution (TSE) display is shown.

'''Statistics on TSE'''

In the TSE display, press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu that appears. Alternatively, select "''Statistics/Current Condition"'' from the menu. This starts the bootstrap test. The result looks somewhat like this:

[[Image:Image012.gif]]

''Example for p map of TSE, correction on p=0.05 level. Both significant synchronization and desynchronization is shown (red and blue colors; negative p values indicate desynchronization). The correction yields significant results only at the modelled time-frequency spots, with the exception of the frequency edges in channel PrM, FrR, and the occipital channels. The baseline interval is not tested.''

By default, the results are corrected for multiple testing, and only values with a significance of p < 0.05 after correction are kept. Correction can be switched off using statistics options (''Statistics/Options ''from the menu, or use the toolbar button [[Image:Image010.gif]] and select "''Options''" from the dropdown menu). This '''Options '''menu also enables correcting on the significance level p < 0.01. The text at the bottom left of the window indicates that a correction took place to find the significant sampling points, but the remaining p values were not corrected.

'''Statistics on Coherence and phase coherence'''

Double-click on a channel (e.g. ACsL) to display its coherence with the other channels. Then press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu (or select "''Statistics/Current'' ''Condition''" from the menu). This starts the permutation test, which is quite time-consuming. The result looks somewhat like this:

[[Image:Image013.gif]]

''Example for the p map of source coherence; correction on p=0.05 level. In all channels, alpha band coherence is significant. Furthermore, significant noise coherence can be observed in the proximate source channels, which only recedes where signal is present which is modelled by the reference channel. The oscillatory coupling between ACsL and ACsR is also significant.''

The same procedure applies for a phase coherence analysis. To switch to the p map for phase coherence, simply press the toolbar button [[Image:Image015.gif]] . If statistics mode is already active, the new p map will be computed automatically.

'''Statistical testing comparing conditions'''

This example uses the error-related negativity data set in the file ''''Examples/TFC-Error-Related''' '''Negativity/Correct+Error.foc'''' (see also BESA Research Tutorial on source coherence on [http://www.besa.de www.besa.de]).

After the data file is loaded, start coherence analysis by
# selecting the user montage "ERN9" from the user montages (toolbar button "'''Usr'''")
# Loading the paradigm (menu "'''ERP/Open Paradigm'''", select paradigm file "'''Cognitive/ERN.pdg'''")
# performing an artifact scan (paradigm tab "''Artifact''", press the "'''Scan'''..." button and adjust the amplitude and gradient thresholds to about 180 µV and 75 µV)
# select the conditions with error and correct response for analysis, triggered on the stimulus (tab "''Coherence''", select "''StErr''" as target condition, check the tick mark "''Use Control Condition''", and select "''StCor''" as control condition (see figure below). Press the "'''Go'''" button. The progress bar is displayed, followed by the temporal-spectral evolution (TSE) display for the target condition.

[[Image:Image017.gif]]

''Settings for comparing conditions in the time-frequency analysis.''

'''Statistics on TSE'''

Press the [[Image:Image018.gif]] toolbar button to see the difference between target and control condition.

Then press the toolbar button "" and select "''Compare Conditions''" from the dropdown menu that appears. Alternatively, select "''Statistics/Compare Conditions''" from the menu. This starts the permutation test. The result looks somewhat like this:

[[Image:Image019.gif]]

''Example of TSE p map when comparing conditions; correction on p=0.05 level. Both significant increase and decrease of TSE in target condition with respect to control condition is shown (red and blue colors; negative p values indicate decrease). The baseline interval is not tested.''

As in the case of one condition, the statistics options can be used to switch correction on or off, and to correct on two different significance levels.

'''Statistics on Coherence and phase coherence'''

Double-click on a channel (e.g. CgA) to display its coherence with the other channels. Then press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu (or select "''Statistics/Current Condition''" from the menu). This starts the permutation test, which is quite time-consuming. The result looks somewhat like this:

[[Image:Image021.gif]]

''Example for p-map of coherence comparing conditions; correction on p=0.05 level. The regions where coherence differs significantly between conditions are depicted in red. The main coherent regions are seen in channels CgP and TbR at low frequencies.''

Please note that the problems with noise coherence, which arise when testing within one condition, do not arise when comparing conditions. Computation is also much faster, since a different approach is used.

The same procedure applies for a phase coherence analysis. To switch to the p map for phase coherence, simply press the toolbar button [[Image:Image015.gif]] . If statistics mode is already active, the new p map will be computed automatically.

The Initialization File: BESA.ini

2017-04-07T10:04:14Z

Alexa:

== The Initialization File: BESA.ini ==

=== Introduction ===

'''BESA.ini File'''

BESA Research uses settings provided in the initialization file '''BESA.ini''' whenever BESA Research is started or a new file is opened for the first time. The format of this file conforms with standard initialization files ('''<nowiki>*.ini</nowiki>''') of Windows. You may change the settings in '''BESA.ini''' using NOTEPAD.exe from the ACCESSORIES group, or other plain text editors to adapt BESA Research to '''your own everyday needs'''. The default settings provided in '''BESA.ini''' will be used by BESA Research whenever BESA Research or the launch program is started. It is advised that you make a backup copy of '''BESA.ini''' before you change the default settings.

'''Location of BESA.ini'''

You can place '''BESA.ini''' at three possible locations:

'''a) Private''': each user on a PC should have his/her own private settings. This is normally in ''My'' ''Documents/BESA/Research_6_0''

'''b) Public''':  all users should use one setting, but they can edit '''BESA.ini''' to change the settings. This is normally in ''Shared Documents/BESA/Research_6_0''

'''c) Administrator''': the PC administrator determines the settings. This is normally in ''C:Program'' ''Files/BESA/Research_6_0''

The actual folder names depend on the operating system and the system language.

When BESA starts, it first looks for the''' administrator''' version of '''BESA.ini'''. If this is not found, it looks for the '''private''' version. If this is not found, it looks for the '''public''' version. If this is not found, internal default values are used.

'''There are 13 general sections, and several reader-specific sections:'''

[Defaults]                   -- General settings (filters, scaling, and various other settings)

[Folders]                    -- Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)

[Electrodes]               -- Electrode renaming

[Patterns]                   -- Rename patterns in the '''Tags''' menu

[Artifacts]                   -- Settings for artifact correction

[KEYCONTROLS]     -- Function key definitions

[Search]                     -- Default parameters for search

[FFT]                          -- Frequency band definitions

[Printer]                      -- Printer control

[Calibration]              -- Calibration control

[Video]                      -- Digital video control

[Mapping]                  -- Mapping control

[Matlab]                     -- Settings for the Matlab interface

[Updates]                  -- Options for program updates

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

=== Defaults ===

'''Default settings provided for section [Defaults]:'''

'''DatabaseAllowLocalFiles=Yes''' (If set to "Yes", BESA Research will write filenames "'''datafilename.ftg'''" and "'''datafilename.fst"''' to the data folder, saving current file tag and display settings there. If set to "No", these files are only written to the database. If set to "Yes", you can copy these files along with the data to a new folder, and display settings and tags will be preserved.)

'''DataBuffering=Off''' (If set to "On", an internal buffer of length 180 s of data is kept to speed up paging). This can speed up paging, particularly when the data are in a network folder.

'''DisplayedTime=10''' displayed time window [s] on the screen

'''Montage=Org''' montage used when opening a new file

'''ScpScale=50''' scale of scalp channels in [mV]

'''PgrScale=500''' scale of polygraphic channels in [mV]

'''IcrScale=500''' scale of intracranial channels in [mV]

'''MegScale=500''' scale of MEG/marker channels in [fT]

'''BaselineCorrection=On''' baseline correction, do not switch off in AC systems

'''ClippingPercent= '''set from 100 to 200 if you want to clip artifacts in displayed EEG (not used if empty or 0)

'''LowFilter=''' low filter cutoff frequency [Hz] (variable filter)

'''TimeConstant=0.3''' time constant for low filter cutoff frequency [sec] (fixed forward filter, 0.3 sec is equivalent to 0.53 Hz)

'''HighFilter=70''' high filter cutoff frequency [Hz] (variable filter)

'''NotchFilter=50''' notch filter center frequency [Hz]

'''NotchFilterStatus=Off''' notch filter is off, set=On if you want to use as default

'''BandFilter=12''' band pass filter center frequency [Hz]

'''BandFilterStatus=Off''' band pass is off, set=On if you want to use as default

'''AdditionalChannelFile=''' defines the full path and name of an additional channels montage file, e.g. '''C:\Program Files\BESA\Research_x\Montages\AdditionalChannels\EKG.sel'''

'''ColoredWaveforms=On''' scalp waveforms are (not) colored according to region

'''WriteSegmentPath=''' defines default path for saving segments/averages. If blank, the path of the current data file is used.

'''ShowSubjectInfo=Off''' subject info will (not) be displayed.

The following optional parameters are not defined as default and can be set manually in''' BESA.ini''':

'''TextEditor="Notepad.exe"''' defines the path to your preferred text editor. This will be used when you press the '''Edit''' button the ''Load Coordinate Files dialog box''.

'''NeuroScanDataNumberOfBits=32''' defines the format of NeuroScan data files ('16' for 16-bit, '32' for 32-bit). If this variable is not specified, BESA uses a heuristic to (try to) decide which of the two data formats is used. This variable overrides the heuristic. If you want to specify the NeuroScan data format for specific files, create a file, named "16bit" or "32bit", and place it in the data folder.

'''ScaleAmplitudesForNNChannels=25''' Scale waveforms as if a fixed number of channels were displayed in the window (here: 25). A minimum of 10 channels can be used for the scaling. This parameter is superseded if the parameter "''ScaleAmplitudesFixedPixelHeight"'' is specified.

'''ScaleAmplitudesFixedPixelHeight=70''' Set the scale bar for amplitudes to a fixed pixel height (here: 70). If this parameter is set in the '''.ini''' file, it supersedes the parameter "''ScaleAmplitudesForNNChannels''".

'''Notes'''

Check the Menu descriptions for the various definitions of filters, montages etc. For montage preselection, use the labels as visible on the montage push-buttons.

The additional channels file should contain all polygraphic channels (e.g. EKG, EOG, respiratory) that you want to view regularly along with the scalp channels. The entry AdditionalChannelFile must specify the full path pointing to the location of additional channel files (recommended: ''Montages\AdditionalChannels''). If no drive is specified, the installation drive of BESA is used.

If BaselineCorrection is set to 'On', before displaying a screen of data, BESA subtracts for each channel the mean over its displayed time points. This optimizes viewing, because it ensures that the vertical position of each channel is not shifted upward or downward from the channel label at the left of the screen. There are some cases in which you will not want baseline correction, i.e. when the DC level in the data is already correctly defined. This is usually the case, for instance, when reading in files that have been processed by BESA. In this case, BaselineCorrection should be set to 'Off', because otherwise maps and source montage displays may be distorted.

=== Folders ===

'''The [Folders] section defines where BESA Research places its files. In versions 5.1 and earlier, files were located in various subfolders of the program folder. This led to problems if the user did not have administrator rights, e.g. to create or write to a file. For Vista compatibility, many folders are now located by default in locations where normal users can create and write files. If you wish, you can also specify paths in the [Folders] section to use the previous locations. The previous location is given for each variable.'''

These settings allow some flexibility that can be useful if you want to tune BESA Research for use by several users, or on a network. For instance, the Examples and Montages folders might be located on a network disk. For the current defaults, the database, Examples, Montages, and Scripts are set up for use by all users on the PC on which BESA Research is installed. The settings files ('''Besa.set''', '''Besa.cfg''', etc.) are located in private folders so that each user retains his or her own settings.

The '''default''' settings (i.e. settings that BESA Research uses if the entries are omitted in the '''.ini''' file) are shown for each variable definition.

The folder definitions can use '''placeholders''', labels enclosed by a % sign (e.g. %localapp%), to define paths that vary depending on the language version and on the system (XP or Vista). These are defined below.

'''The Variables'''

'''Database=%localapp%''' The path of the BESA Research database folder (used to be ''%progdir%System\DB'' in BESA versions up to 5.1.x). Unless the provided path ends with ''\DB'' or ''\Database'', BESA Research will automatically create a folder named ''Database'' in the provided path.

'''Settings=%privatprog%Settings''' The path of the BESA Research settings folder (used to be ''%progdir%System'' in BESA versions up to 5.1.x)

'''Montages=%publicprog%Montages''' The path of the BESA Research montages folder (used to be ''%progdir%Montages'' in BESA versions up to 5.1.x)

'''Scripts=%publicprog%Scripts''' The path of the BESA Research Scripts folder (used to be ''%progdir%Scripts'' in BESA versions up to 5.1.x)

'''Examples=%publicprog%Examples''' The path of the BESA Research Examples folder (used to be ''%progdir%Examples'' in BESA versions up to 5.1.x)

'''User=%privatprog%Settings''' The path for user defined settings (used to be ''%progdir%System\Userdirs'' in BESA versions up to 5.1.x)

'''Placeholders'''

The strings enclosed by percent signs (%) are placeholders for the following folders in English-language versions of Windows. Folder names are different for Vista and XP/2000 and for other language settings. BESA Research will substitute the placeholders by the appropriate folder name for the system (W2K, XP, Vista, or Win7) and the system language:

* '''Windows 7(English):'''

'''%localapp%''' = "''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Libraries\Documents\Public'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Libraries\Documents\My'' ''Documents\Research_6_0''" or "''Desktop\[User]\My Documents\BESA\Research_6_0''.

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

* '''Windows Vista (English'''):

'''%localapp% '''<nowiki>= "</nowiki>''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Desktop\Public\Public Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''  

* '''Windows XP (English):'''

'''%localapp% '''<nowiki>= "</nowiki>''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0". ''This folder is directly accessible from the Windows Explorer under "''My Computer\Shared'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''My Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%  '''

* '''Windows 2000 (English):'''

'''%localapp%''' = "''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer '''as "'''''My Documents\BESA\Research_6_0'''''". '''

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

=== Electrodes ===

'''This section allows for automatic relabeling of electrodes. For instance, the 10-20 label "T3" can be replaced by the 10-10 convention "T7".'''

'''Default settings provided for section [Electrodes]:'''

T7=T3 replace 10-10 label with old 10-20 convention

T8=T4 replace 10-10 label with old 10-20 convention

P7=T5 replace 10-10 label with old 10-20 convention

P8=T6 replace 10-10 label with old 10-20 convention

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

Other examples, depending on your electrode input box definition, could be:

PG1=LO1 define X3 as lateral orbital eye electrode left

PG2=LO2 bipolar LO1-LO2 defines horizontal EOG (additional channel)

X3=IO1 infraorbital, e.g. use with FP1 as additional channel for VEOG

X9=Rsp define X9 channel to be a respiratory channel

Relabeling of channel names (as stored in the EEG file header) is helpful to predefine your standard sequence of channels and to avoid the need for reading and/or editing a Channel Configuration file for every EEG file.

'''Note 1''': For polygraphic channels, or if your EKG has been recorded differentially, you should edit and define an ''Additional Channels Montage'' according to your recording channel configuration (e.g. Fp1-IO1=vertical EOG). The Additional Channels group permits to display these channels regularly below the scalp montages with individual scales.

'''Note 2''': EOG channels record both eye and scalp activity. In digital EEG systems, EOG electrodes should be labeled according to their position in the 10-10 system (see "''Electrode Conventions''"). This permits use of these electrodes for mapping and suppression of eye artifacts. The standard definitions above give an example of how to relabel extra channels (X1...X10, PG1, PG2) for the use of EOG, EKG and respiratory (Rsp) channels. Use an ''Additional Channels'' file to define horizontal and vertical EOG channels by using the appropriate electrodes in a bipolar montage (an example is provided in '''eog-ecg.mtg''' in ''Montages\AdditionalChannels''). Differentially recorded EKG and respiratory channel can be defined in the same file.

=== Patterns ===

'''Default settings provided for section [Patterns]:'''

These settings define labels for each of the five patterns. The labels are shown* in the''' Tags''' menu,
* in the '''TAG push-button''' popup menu, and
* when displaying tag info clicking with the right mouse on a tag at the bottom of the EEG or on the event bar.

By default, no labels are defined. Define a label, e.g. for Pattern1 and Pattern2, as in the following example:

Pattern1=Spike

Pattern2=Sharp Wave

=== Artifacts ===

'''Artifact default settings:'''

See the chapter "''Artifact Correction / Reference / Artifact settings in the BESA.ini file''" in the online help.

=== Search ===

Default settings for pattern search.

'''Default Settings for the ''Search/Options ''Dialog box:'''

'''CorrelationThreshold''' = '''75%'''

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

'''Default Settings for the ''Search/Average/View'' (SAV) Dialog box:'''

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

'''HighPassSlope = 12 dB/Octave'''

'''HighPassType = 0 (0 = zero phase, 1 = forward, 2 = backward'''

'''LowPassFreq = 35 Hz'''

'''LowPassSlope = 24 dB/Octave'''

'''LowPassType = 0 (0 = zero phase, 1 = forward, 2 = backward)'''

'''CorrelationThresholdNoMarked = 60%'''

Default correlation threshold if no channel labels are marked when the SAV Dialog is opened.

'''CorrelationThresholdOneMarked = 85%'''

Default correlation threshold if one channel label is marked when the SAV Dialog is opened.

'''CorrelationThresholdFourMarked = 65%'''

Default correlation threshold if between two channel labels are marked when the SAV Dialog is opened.

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

If set to "Yes", a File Save dialog will open, to allow to save the search average to a file (as with the SAW function).

'''WriteAfterSearchCheckBox = No'''

If set to "Yes", an additional checkbox "Write after search" is displayed at the bottom of the SAV Dialog, allowing to choose whether or not to write the search average after a search:

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

If set to "No", the SAV Dialog will open with the same boxes checked as the last time the dialog was opened during the current session.

If set to "Yes", the default frequency, buffer width, selected view after search, and default threshold are always checked when the dialog is opened.

=== KeyControls ===

In the [KeyControls] section you can specify functions that can be allocated to '''function keys''' or to the ''Del'' key. Specify using the form:

'''Fn=function''' or

'''Del=function'''

where "''n''" is a number between 2 and 12 (F1 is reserved for Help). For example:

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

'''Pattern''n''''', where ''n''<nowiki>=1-5: Sets the tag number </nowiki>''n'' at the cursor latency.

'''Epochfast:''' sets one boundary of an epoch at the cursor latency, but does not open the epoch text box to define a label.

'''Marker:'''  sets a marker at the cursor latency.

'''Comment:''' sets a comment at the cursor latency and opens the comment box to enter text.

'''Epoch:''' sets one boundary of an epoch at the cursor latency and opens the epoch text box to enter a label.

'''Artifact:''' sets one boundary of an artifact segment at the cursor latency.

'''Delete:'''  deletes a tag at the cursor latency

'''Batches and Montages:'''

'''Batch''n''''', where n=1-12: Runs a predefined batch file corresponding to the number ''n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a batch, pressing it will open a ''File Open Dialog'' to select a batch. The setting you have chosen will be retained across BESA Research sessions. Holding the '''<shift>''' key while pressing the '''function key''' will always open the dialog. Hold the''' <ctrl> '''key with the function key to open the associated batch in the batch edit dialog.</div>

'''Montage''n''''', where n=1-12: Sets a montage corresponding to the number'' n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a montage, pressing it will generate a message asking you to associate a montage as follows: Holding the '''<shift> '''key while pressing the '''function key''' will remove the current association, and substitute it with the current montage.</div>

The default settings after program installation are listed in the online help chapter ''Review / Reference / Controls / Mouse and Keyboard / Keyboard Controls''.

=== FFT ===

'''Default settings provided for section [FFT]:'''

These settings define the setup in the Spectral Analysis section of the BESA Research program (FFT window, see the chapter "''Spectral Analysis / FFT''"). Up to 7 frequency bands may be defined. Five are defined by default.

'''FFTBand1=On''' FFT Bands 1-5 are defined

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

'''FFTBand6=Off''' FFT Bands 6-7 are not defined

'''FFTBand7=Off'''

'''FFTNameBand1=Delta''' Names of the defined bands

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

'''FFTColorBand1=RGB(0,0,0)'''  Default color of each band

'''FFTColorBand2=RGB(0,128,64)'''

'''FFTColorBand3=RGB(128,0,0)'''

'''FFTColorBand4=RGB(255,0,0)'''

'''FFTColorBand5=RGB(255,128,0)'''

'''FFTColorBand6=RGB(255,192,0)'''

'''FFTColorBand7=RGB(255,255,0)'''

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

'''FFTLowBand3=8''' Alpha from 8-14 Hz

'''FFTHighBand3=14'''

'''FFTLowBand4=14''' Beta from 14-30 Hz

'''FFTHighBand4=30'''

'''FFTLowBand5=30''' Gamma from 30-50 Hz

'''FFTHighBand5=50'''

These values are best set from within BESA Research, using the '''Options''' menu in the FFT window (see the chapter "''Spectral Analysis / FFT / FFT Options Menu''"). Current settings are stored after each session and retrieved in the next session.

=== Printer ===

'''Default settings provided for section [Printer]:'''

'''PrinterMarginPercent=100''' controls size of printout

'''PrinterColors=256''' set to 1/2 for black&white, 0/256 for color printers

'''PrinterLineMode=1''' set to 2 for thicker lines and to save printer memory

'''PrinterMapResolution=1''' set to 2, 3, 4 to save printer memory and increase speed

=== Calibration ===

'''Default settings provided for section [Calibration]:'''

'''AutoCalibration=Off''' On: automatic calibration of signals >= 4 cycles

'''MicrovoltCalibration=50''' peak voltage of calibration signal

If calibration is set to'' On'', the menu item ''Calibration ''will appear in the''' Process '''menu. Position your current screen at an epoch containing at least 4 regular cycles of the calibration signal (in all channels!) and select Calibration.

=== Video ===

'''Default settings provided for section [Video]:'''

'''DVCFilePath=C:\DVC\DVPlay.exe''' holds the path to the digital video player

'''DVCCommandLineArguments=/S:3 /M:P /T:M'''  arguments to be passed to the digital video player

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

'''MappingRepetitionRateWithVideoInMS=100'''  gives the number of milliseconds between two maps if the mapping window is open while the video is running. If the graphics board encounters problems during the display, this value should be increased.

=== Mapping ===

'''Default settings provided for section [Mapping]:'''

'''UseBitmapDrawing=Off'''

Set this to "On" if 3D maps show a strange pattern of black triangular shapes (this is frequently observed with modern Intel On-Board graphics controllers, and is a result of inadequate drivers for Open-GL).

'''Use3DVBlending=Auto'''

Set this to "Off" if the 3D view in the Montage Editor or the Source Analysis window does not show up properly (this may happen with some older graphics cards).

Set this to "On" if the 3D view in the Montage Editor or the Source Analysis window shows a ragged surface boundary.

'''MapSmoothing=0 '''

Set a non-zero value to specify a default map smoothing parameter (normally specified in ''Options/Mapping/Spline Interpolation Smoothing Constant'').

=== Matlab ===

'''Default settings for the [Matlab] section:'''

'''Platform=32'''

'''Set Platform=64''' if you want to use the 64-bit version of Matlab

=== Updates ===

This section is not normally required, but the variables here can be altered or defined to determine how BESA Research checks for dongle and program updates.

'''DaysBetweenUpdateChecks=7'''

Sets the number of days between automatic checks for updates. Set the value to 0 to check every time BESA Research is started. Set to -1 to turn off automatic update checks.

'''CheckNetworkDongle=Off'''

For the network administrator: If set to "On", BESA Research will check the dongle on the network for updates. Otherwise the state of the network dongle will be ignored.

'''LocalPath'''

For the network administrator. This can be set to a path on the local network to the BESA update files, so that users can obtain their updates locally. The path is given to the text file "'''UpdateVersions.txt'''" (e.g. ''LocalPath=\\transtec-sak\zarascratch\BESA\Updates\UpdateVersions.txt''), which contains further details for the program to obtain its updates. If you want to use this feature, please contact us at [mailto:support@besa.de support@besa.de].

The following variables are not required, because BESA Research has the paths hardwired:

'''FTP1 (also FTP2, FTP3)'''

ftp download server

'''Path1 (also Path2, Path3)'''

Path on the server to UpdateVersions.txt.

'''HaspPath1 (also HaspPath2, HaspPath3)'''

Path on the server to HASP (dongle) update files.

'''History'''

Path on the server to general history file

=== Reader-Specific Settings ===

'''BrainLab'''

'''Default settings provided for section [BrainLab]:'''

'''BrainLabFormat=New''' this entry ensures that the newer BrainLab file format can be read by BESA Research.

'''Bio-Logic'''

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:
* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>
* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

'''EDF+/BDF/Trackit'''

'''TriggerScan=On'''

Set '''TriggerScan=Off '''to prevent BESA Research from scanning the file for triggers. This is done separately for EDF+, BDF, and Trackit files in sections '''[EDF+], [BDF],''' and '''[Trackit]''' in the '''BESA.ini''' file.

'''EGI'''

The treatment of DIN events can be modified in the''' [EGI] '''section:

'''CombineDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you want to treat DIN events separately, and not generate combined values.

'''SeparateDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you don’t want to treat DIN events separately.

Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

'''CombineDINeventsPrefix'''<nowiki>=dinComb</nowiki>

<div style="margin-left:0.953cm;margin-right:0cm;">This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

'''Harmonie'''

'''Default settings provided for section [Harmonie] (Stellate Harmonie systems):'''

'''SeizurePreEpoch=60''' length of the epoch preceding a seizure detection in s

'''SeizurePostEpoch=60''' length of the epoch following a seizure detection in s

'''PushButtonPreEpoch=60''' length of the epoch preceding a push button detection

'''PushButtonPostEpoch=60''' length of the epoch following a push button detection

When BESA Research encounters a seizure detection event or a push button detection event in a Stellate Harmonie file, it automatically sets an epoch around the event, which makes it convenient to view just those epochs for analysis. The length of the epochs preceding and following the events can be adjusted in the '''.ini''' file.

'''Neuroscan Keys'''

'''Note that there is a setting "NeuroScanDataNumberOfBits" in the [Defaults] section of BESA.ini that is used for distinguishing the data format of Neuroscan files (16 or 32-bit).'''

'''Default settings provided for section [NeuroScan Keys] (NeuroScan systems):'''

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

'''NKT2100'''

'''Default settings provided for section [NKT2100] (Nihon Kohden EEG 21xx systems):'''

'''TriggerScan=On'''   Set to "Off" to prevent a scan for trigger events.

'''Country=NotKanji''' set to NotKanji for non-Kanji characters else to Kanji

'''KanjiCharSize=16''' Kanji character size

'''KanjiPrinterCharSize=32''' Kanji printer character size

'''EEG_Sensitivity=50''' default sensitivity of Nihon Kohden EEG-2100 system

'''DC_Sensitivity=50''' default sensitivity of Nihon Kohden DAE-2100 system

'''QJ_Sensitivity=100''' default sensitivity of Nihon Kohden QJ-403 system

'''Mark_Sensitivity=100''' default sensitivity of EEG-2100 marker channels

These settings need to be changed only if the manufacturer has specified different gains for your system. Otherwise do not alter these settings.

'''Vangard'''

'''AlwaysOpenFileSelect=Yes'''

If "Yes" is selected, each time a Vangard file is opened, a dialog box will open, asking for a selection of the segment type to display.

If "No" is selected, the selection dialog is opened whenever a Vangard file is opened for the first time, or if the ''Channel and digitized head surface point information dialog box'' is opened (e.g. with '''ctrl-L''' or ''File/Head Surface Points and Sensors/Load Coordinate Files...'' ).

'''XLTEK'''

'''TriggerScan=Off '''Set to "On" to scan the data file for trigger events

'''MontageNo=2''' Set to 1 or 2. If two montages for the data file are defined, this variable determines whether the first or the second alternative should be used.

Working With Additional Files

2017-04-07T10:00:20Z

Alexa:

== Working with Additional Files ==

=== Binary format (*.foc, *.fsg) ===

Select '''Binary High Resolution''' or '''Binary Compressed Format''' to output segments in binary BESA format. If the file already exists, the segment will be appended. Thus, it is possible to create a file combining several segments of interest in a compact form. BESA Research will only allow you to append segments if the number of channels and the sampling interval in source and target files are the same. In Binary Format all channels (scalp, intracranial, polygraphic, MEG) and file events in the selected time range are exported. '''Note:''' The channels are filtered according to the current filter settings.

Select '''Binary High Resolution''' to retain the resolution of the processed data. This is the preferred binary format for small amplitude signals such as averages. Select '''Binary Compressed Format''' to store raw data using the original resolution or to obtain the space savings of compression (see ''File/Export and Append Data/Convert..'' above). This is the preferred binary format for raw data.

=== ASCII vectorized format (*.avr) ===

Select '''ASCII vectorized Format''' to output segments in BESA ASCII format, one channel (all time points) per line.

'''The Format is as follows:'''

The first of two header lines contains the following data descriptors (6 descriptors, the values shown are only examples):

''Npts= 200'' number of sampled points in each channel

''TSB= -500'' time sweep begin [ms]. Time of first data point relative to zero of epoch

''DI= 5'' digitization or sampling interval [ms]

''SB= 2'' scaling bins/microvolt in file = number corresponding to 1 microvolt

''SC= 50'' scaling calibration, used for setting magnitude of display in BESA

''Nchan= 27'' number of channels

''SegmentName= 60dB''  An optional label describing the data.

The second line of the header contains a label for each channel, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each of the subsequent ''Nchan'' lines of the file contains values for all ''Npts'' time points in floating point or scientific format. For more details about scalp electrodes, see chapter "''Working With Electrodes and Surface Locations/Electrodes/Electrode Conventions".''

A second (older) version of the format (written by BESA versions 1, 2 and 3) omits the '''Nchan=xx''' information in the first line, and there is no second header line. Labels must be defined elsewhere. See "''Electrodes/Electrode file conventions and formats''" and “''Reading MEG files in ASCII format”''. In the older versions, only scalp channels were exported, and the data were average referenced.

=== ASCII Multiplexed format (*.mul) ===

Select '''ASCII Multiplexed Format''' to output segments one time point (all channels) per line.  

The '''ASCII Multiplexed Format '''is as follows:

The first of two header lines contains similar information to that of the ASCII vectorized file:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= -500.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 SegmentName=Condition1''

Note that the item 'SegmentName' is missing if no segment comment is specified when writing a segment to file.

If an epoch of a continuous EEG is exported in ASCII multiplexed format, the first header line contains the additional item 'Time', which indicates the daytime of the first sample in the exported segment:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= 0.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 Time=22:02:53 SegmentName=Segment1''

The second line of the header contains labels for each channel, which may be either the original channel names, or the names of the channels of the current montage, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each subsequent line contains values for all 'Channels' at one time point, in floating point or scientific format. Values are given for the current or the original montage, selected as described above.

Labels for '''source montages''' have the following form: '''TAr-L'''.
* The first two letters indicate the head region:

[[Image:ST addfiles (1).gif]]

* The small letter indicates in part the orientation: r=radial, t=tangential, and in part the relative location of the basal temporal source: l=lateral, m=mesial.
* The final letter after the hyphen indicates L=left, M=middle, R=right.

=== Channel definition file conventions and formats ===

BESA Research can read 3 types of file to define channels. These are identified by different extensions:
* channel definition files containing labels and, optionally, channel types (ASCII, 1 label /line): '''<nowiki>*.ela</nowiki>'''
* channel definition files containing coordinates and, optionally, channel types and labels (ASCII): '''<nowiki>*.elp.</nowiki>''' This is the format of the file written by the ''Channel Configuration Dialog.''
* channel definition files stored by older versions of BESA Research (binary format): '''<nowiki>*.elb.</nowiki>''' This format can still be read, but is no longer written by BESA Research.

BESA Research stores and retrieves the channel configuration after editing in binary files. If you open a data file, BESA Research will search for the related channel information in the following sequence:

# For all data files with the extension '''.eeg''', '''.cnt''' and '''.foc''', check in the additional database file in the data directory with the same basename as the data file and the extension '''.fst''', whether a channel file has been associated previously
# Check in the '''''db''''' subdirectory whether a channel file has been associated previously
# Check if labels are defined in the header of the data file
# Search for a corresponding binary channel definition file with the same basename as the data file in the data folder ('''xxxx.elb''')
# Search for a corresponding channel definition file with the same basename as the data file containing labels in the data folder ('''xxxx.ela)'''
# Search for a corresponding channel definition file with the same basename as the data file containing labels and/or coordinates in the data folder ('''xxxx.elp''')
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' (in this order)) in the data folder
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' one directory above the data folder (e.g. '''..\default.elb''')
# Check if the new data file is of the same type and has the same number of channels as the preceding data file in the list. If this is the case, the electrode configuration of the previous file will be assumed. This will avoid having to load or edit the electrode configuration more than once, if you load several data segments of the same subject from separate files.
# If no channel definition file is found, or digitization points (in files '''<nowiki>*.sfp</nowiki>''', '''<nowiki>*.cot</nowiki>''', '''<nowiki>*.pos</nowiki>''', '''<nowiki>*.pmg</nowiki>''') are found in files with the same basename as the data file, the ''"Channel and digitized surface point'' ''information"'' dialog box is opened, allowing you to specify file names.

'''Channel Label Files (*.ela)'''

Files containing a list of channel labels are an alternative to editing electrode configurations. They can be edited using a standard text editor. Electrode label files ('''.ela''') require a sequence of lines corresponding to the sequence of channels in the data. Each line contains one label and an optional identifier. The format is ' [Identifier] {Label} ', ('Identifier' can be omitted if the electrode label defines the type of signal)

'''Identifiers''' can be one of:

EEG -- scalp electrode

SCP -- scalp electrode

POL -- polygraphic channel

PGR -- polygraphic channel

ICR -- intracranial electrode

MEG -- MEG sensor

REF -- reference electrode (this can only occur once, and must be the last item in the file)

For example:

Fz   ('''scalp''' electrode, coordinates assigned by default.ecd)

Cz   ('''scalp '''electrode, coordinates assigned by default.ecd)

......

VEOG   (vertical EOG,''' Polygraphic''' type is assigned by default)

Exx   (xx=01, 02.. electrode number, '''Polygraphic '''type is assigned by default)

......

EEG xx ('''scalp''' electrode, coordinates must be assigned either by '''default.ecd''' or by a surface point (+'''.sfp''') file. An alternative to the "EEG" prefix is "SCP".

......

POL XX  (identifier sets '''Polygraphic''' type -- an alternative to the "POL" prefix is "PGR")

......

ICR A01  (identifier sets '''Intracranial''' type to electrode A01 - do not use A1!)

ICR A02  (identifier sets''' Intracranial''' type to electrode A02 - do not use A2!)

ICR A03  (identifier sets''' Intracranial''' type to electrode A03)

......

MEG M01  (identifier sets '''MEG '''type to electrode M01 - do not use M1!)

MEG M02  (identifier sets '''MEG''' type to electrode M02 - do not use M2!)

......

REF Cz  (the label is assigned to the electrode reference, no channel is associated with this entry. This must be the last line of the file!)

'''Channel spherical coordinate files (*.elp)'''

These files follow the same rules as the channel label files, with the addition of spherical coordinates (theta, phi) that follow the labels of EEG and MEG channels. Labels can also be omitted. In this case, BESA Research will assign labels according to the nearest coordinate defined in the '''default.ecd''' file. To indicate that the coordinates have been assigned, the label will have a tick, e.g. Fz' instead of Fz.

Channels of other types (polygraphic, intracranial) are defined exactly as in the channel label ('''<nowiki>*.ela</nowiki>''') file.

=== cot (Head center) file ===

'''Function''': to redefine the center of the head for the sphere used in dipole models. If the cot file has the same base name as the data file, it is read automatically by BESA Research. If the coordinates deviate by more than 1 mm from the previously defined head center, a window is opened, asking if the new values should be adopted. This mechanism is turned off if the data have been coregistered to MRI (see online help chapter ''"MRI Coregistration''"), and an MRI Coregistration File ('''<nowiki>*.sfh</nowiki>''') has been associated with the data.

BESA Research uses any head surface points (e.g. electrode locations), excluding those on the lower part of the face, to compute the sphere center automatically. The cot file is used if you want to override the automatic calculation. A mechanism is provided which allows to pass a location from the MRI (viewed by BrainVoyager) to the Source Module and save the resulting location as a ''cot ''file.

'''Format''': one set of coordinates (x y z). These are followed by either "'''DC'''" or "'''HC'''", which specify whether these coordinates are in '''D'''evice or '''H'''ead '''C'''oordinates.

'''Units:''' must be in meters!

(Note: In special cases, a fifth value, the '''head radius''', may follow. This is used when reading simulated MEG data from the DipoleSimulator program. When this value is set, BESA Research uses the specified head radius and head center and does not fit a sphere to the head surface points. and does not create an ellipsoid transformation).

Force BESA Research to use a completely spherical model without creating an ellipsoid: Write "'''DipoleSimulator"''' or "'''Phantom'''" on the second line of the file. Under these circumstances, 100% correspondence between DipoleSimulator and BESA Research is achieved. This is also required for dipole fitting on MEG phantom recordings.

The ''cot ''file has also been extended for reading CTF MEG files. Documentation for these extensions is found in the CTF help file.)

=== pos or pmg (MEG sensor coordinate) file ===

'''Function:''' to define coordinates of MEG sensors. Our convention is to save magnetometer information in '''<nowiki>*.pmg</nowiki>''', and gradiometer information in '''<nowiki>*.pos</nowiki>'''. In practice, BESA Research doesn’t mind which extension is used -- the distinction between gradiometers and magnetometers is based on the number of values on each line in the file.

'''Format:''' one sensor per line.

Magnetometers: label (optional), six coordinates per line (location, orientation)

e.g. for BTi:

" Channel 'A1': -0.0019193 0.0304846 0.1081738 0.1188222 0.2394208 0.9636177"

Gradiometers: label (optional), nine coordinates per line (location of primary sensor, location of secondary sensor, orientation). The program decides whether gradiometers are planar or axial based on the distance between the primary and secondary sensor locations and the center of the head.

e.g. for Neuromag:

" 0.108510 -0.000143 -0.044954 0.108510 0.000463 -0.028766 0.999999 0.001450 0.000000 "

Labels in these files are ignored.

See chapter “''3D Coordinates for Precise Analysis/Data reading rules for MEG''”.

=== sfn (surface point name) file ===

'''Function:''' to match up digitized coordinates with channels that are defined as EEG electrodes and to define labels for additional digitized head surface points (e.g. MEG coils, etc.).

'''Format:''' one label per line.

Contains labels of surface points in the order of digitization. If fiducials are defined, these should be on the first three lines, with the labels 'FidT9', 'FidT10', 'FidNz' or 'FidLPA', 'FidRPA', 'FidNAS'.

If electrodes are defined in the data file, the labels of each electrode as defined in the data file (or in its associated ''ela'', ''elp'', or ''elb ''file) must be present!

The case of labels is not important (e.g. 'Fp1' will match with 'fp1').

The ''sfn'' file need not exist if labels are defined in the ''sfp ''file.

See chapter “''3D Coordinates for Precise Analysis / Data reading rules for EEG”.''

=== sfp (surface point coordinate) file ===

'''Function''': to define coordinates of digitized points on the head surface. The order of points must match with the order in the ''sfn ''file, or if no ''sfn'' file is present, labels must be included in the ''sfp'' file.

Note: If the digitized points include electrodes, the channel labels must correspond to the labels of the digitized points. The sequence of labels in channels and surface point coordinate file need not be the same – the allocation is performed by label matching. Channel labels may be defined in the data file, or they may be assigned using channel definition files ('''<nowiki>*.ela, *.elp, *.elb</nowiki>''').

'''Format:''' one set of coordinates (x, y, z) per line. Coordinate units must be either meter, centimeter or millimeter (BESA Research will perform a plausibility check automatically to determine which units are used). If a label is present this can precede or come after the three coordinate values.

If fiducials are defined, these should be on the first three lines. BESA Research will simulate fiducials if none are defined, but it is preferable to record these locations along with the other head surface points.

If there are MEG sensors, the same coordinate systems must be used in the ''sfp'' file and the ''pos/pmg ''file!

If labels are defined in the ''sfp'' file rather than in an ''sfn'' file, labeling rules apply as for the ''sfn'' file.

Example for the ''sfp'' file format:

[[Image:ST addfiles (2).gif ‎]]

BESA Research will check the coordinates for plausibility. If coordinates are more than 30° away from the expected location on the sphere there will be an error message. Such errors are usually due either to incorrect labeling or to a digitization error.

See chapter “''3D Coordinates for Precise Analysis /'' ''Data reading rules for EEG”.''

=== Generic File Format ===

This reader, incorporated into the '''GenericBesa.dll''' file, allows to read simple multiplexed or vectorized data formats, if you know the structure of the data format.

'''What you have to do'''
* With a text editor, write information about the data file you want to read into BESA Research into a text file, the ''Generic Header''.
* Save the edited text in the same subdirectory as the data file.
* '''Mechanism A:''' The generic header contains the data file name. With BESA Research, navigate to the file you just edited, and open it. The data should then be read into BESA Research.
* '''Mechanism B:''' Alternatively, navigate to the data file. The reader will check if there is a generic header in the same subdirectory, and use that to try to open the file. You have two options:

* <div style="margin-left:1.27cm;margin-right:0cm;">'''Specific:''' if the file has the same basename as the data file, and the extension “'''.generic'''”, this file will be used.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">'''Generalized:''' if a specific file is not found, the reader will look for the file “'''BESA.generic'''” in the same subdirectory.</div>

'''Important note:''' We recommend using mechanism A, using a header with the extension "'''.generic'''". When opening the data file in BESA, select the generic header. Mechanism B sometimes fails when opening the data file in BESA Research, because one of the other readers in BESA may erroneously interpret the file as their "own" data format, sometimes leading to a crash.

'''Format of the Generic Header'''

The first line '''must '''consist of the text: “''BESA Generic Data''” (without the inverted commas).

Subsequent lines '''must''' contain the following parameters, in any order (note that the parameters are case insensitive):

'''''nChannels'''''=''nnn'': The number of channels

'''''sRate'''''=''fff'': The sampling rate (samples/sec)

'''''format'''''=''type'': One of ''short'', ''int, float, double, ASCII''. If the format is ''ASCII'', the parameter''' nSamples''' must be specified as well (see below)

The following parameters are optional (values in square brackets denote optional parameters):

'''''nSamples'''''=''nnn'': The number of time samples in the data. If this value is 0, or the line is omitted, then use the file size to estimate the number of samples.

'''''file''''' = '': The data file name, without path information. If this is omitted, you can only read the data with mechanism B (see above). This line '''must''' be included if you want to read the data with mechanism A.

'''''DataOffset''''' = ''nnn'': Offset of data in bytes for binary data, in lines for ASCII data (default = 0).

'''''Factor'''''=''fff [range]'': Data values are multiplied by this factor to obtain µV values (default = 1). Optional parameters can be appended to define a channel range, e.g. ''1-3''. Thus, this command can be used multiply, to define different scaling factors for different channels. If only one channel is specified, use on number only, e.g. ''5''.

'''''SwapBytes''''' = ''ccc'': One of ''off'' or ''on'' (default = off). If the data block originated from Unix or Mac, this will need to be ''on''. (binary data only)

'''''Prestimulus'''''=''fff'': Prestimulus interval in milliseconds.

'''''Label'''''=''ccc'': Segment label.

'''''Trigger''''' = ''chan….'': Channel number containing triggers. Without further parameters, the values are read directly as digital trigger values. Other parameters are described below, for the case where the trigger channel contains analog signals.

'''''nBlocks'''''=''nnn'': The data are epoched. This specifies the number of equal sized blocks in the data. In BESA Research, each block will be separated by a segment boundary. The number of samples in each epoch is computed from the total number of samples divided by ''nBlocks''.

'''''nEpochs'''''=''nnn'': Same as '''nBlocks'''.

'''''EventFile'''''=''name'': Load events from an event file, using BESA's event file ('''<nowiki>*.evt</nowiki>''') format. See below for a description of how to prepare this file.

'''''Order'''''=''type'': One of ''multiplexed'', ''vectorized''. The default is multiplexed (i.e. channels fastest). Specify ''vectorized'' if your data are ordered so that all time samples for channel 1 are followed by all time samples from channel 2, etc.

'''''Orientation'''''=''type'': Same as '''Order'''.

'''''Arrangement'''''=''type'': Same as '''Order'''.

'''Trigger events'''

This section describes how the reader can be used to encode trigger events when the trigger channel contains analog signals. In this case, a '''Trigger '''command is required for each target code in BESA Research.

Syntax:

'''Trigger''' = ''chan  code  fromLevel  toLevel  timerange''  ''deadtime''

'''''chan''' ''is the channel number on which to find the trigger

'''''code''''' is the trigger number that the reader will assign (must be positive!)

'''''fromLevel'' '''is the value in mV defining the lower range for trigger detection

'''''toLevel'' '''is the value in mV defining the upper range for trigger detection. If this is “-“, then only ''fromLevel ''needs to be exceeded for the trigger to be detected.

'''''timerange '''''is the range in milliseconds to define a trigger. The reader will search for the maximum deviation from baseline within the range to find the level that will define the trigger.

'''''deadtime''' ''defines the time after detecting a trigger during which no further trigger with this code can be detected. This does not affect other codes. Also, if the voltage level stays at a level corresponding to a code, the trigger is only defined at the onset of this voltage level.

Multiple lines are required if different trigger codes and different trigger channels are required, one for each new code.

'''Notes'''

'''Channel labels:''' The data channels are labeled ''E1, E2, E3,…,'' and they are initially classified by BESA Research as polygraphic. As with other BESA Research data files, use a '''<nowiki>*.ela </nowiki>'''file (or '''<nowiki>*.elp</nowiki>''', optionally combined with '''<nowiki>*.sfp</nowiki>''') to redefine labels and channel types.

'''Data formats:'''

* Short 16-bit
* Int 32-bit
* Float 32-bit
* Double 64-bit
* ASCII Decimal numbers separated by spaces or tabs (engineering format also permitted)

'''Prestimulus interval and label:''' If either of these are defined, BESA Research reads the data in to define an averaged data segment. The label is displayed, and a vertical dotted line marks timepoint zero. If no prestimulus interval is defined, a zero prestimulus interval is assumed.

'''Future changes'''

Possible developments:
* Read channel labels

If any of these changes are particularly important to you, please contact [mailto:support@besa.de support@besa.de] and let us know.

'''Event File'''

The event file is a text (ASCII) file containing a header line and subsequent lines, with one event description per line.

Each line contains four parameters:

1. latency (units specified by the header, can be µs, ms, s)

2. code (defines the type of event: trigger, comment, marker, pattern, average segment, data break segment)

3. parameter (depends on the event type, e.g. trigger code)

4. label (label assigned to the event)

'''Header Line:'''

The header line contains four values. The first specifies the time units, e.g. '''Tmu '''specifies microseconds.

''    Tmu    Code    TriNo    Comnt''

'''Tms''' specifies milliseconds. '''Tsec''' specifies seconds.

'''Event Code and Parameter 3 (TriNo):'''

'''Code''' specifies the event type:

1 = trigger -- '''TriNo '''specifies the trigger number

2 = comment

3 = marker

11-15 = patterns 1-5

21 = artifact on

22 = artifact off

31 = epoch on

32 = epoch off

41 = segment onset -- '''TriNo '''is a time string that specifies date and time, in the format ''YYYY-MM-DDTHH:MM:SS'', e.g. ''2010-04-26T15:30:20.31'' (note: seconds are a decimal number).

42 = average segment onset -- '''TriNo '''is a number specifying the prestimulus baseline of the subsequent average in microseconds. '''TriNo '''(parameter) is 0 for markers, comments, artifacts, and epochs.

'''Comment'''

The event label. This is not used for markers, artifacts, and epochs.

'''Example of event file:'''

A simple way to generate example files is to export events from BESA (''ERP/Save Events As...'').

Tmu         Code     TriNo     Comnt

0              42     100000    Ave: 25 avs  

10000000  2       0            Comment at 10s

20000000  41     26-04-2010T15:30:20.000   TestSeg2

21000000  3       0

22000000 1        99          Trigger – 99

This specifies an average segment starting at the beginning of the file, with a prestimulus interval of 100 ms, a comment at 10 s, a new segment specifying date and time at 20 s, a marker at 21 s, and a trigger with code 99 at 22 s.

'''Examples'''

The following reads ASCII multiplexed data that were previously exported from BESA Research:

''BESA Generic Data''

''nchannels = 64''

''srate = 100''

''nsamples = 10000''

''dataoffset = 2''

''format = ASCII''

''file = name.mul''

''factor = 1''

With the sampling rate of 100 Hz and 10000 samples, this represents 100 s of 64-channel data. The first two lines of the data are skipped.

Working With Additional Files

2017-04-07T09:58:11Z

Alexa:

Working With Additional Files

2017-04-07T09:48:47Z

Alexa:

== Working with Additional Files ==

=== Binary format (*.foc, *.fsg) ===

Select '''Binary High Resolution''' or '''Binary Compressed Format''' to output segments in binary BESA format. If the file already exists, the segment will be appended. Thus, it is possible to create a file combining several segments of interest in a compact form. BESA Research will only allow you to append segments if the number of channels and the sampling interval in source and target files are the same. In Binary Format all channels (scalp, intracranial, polygraphic, MEG) and file events in the selected time range are exported. '''Note:''' The channels are filtered according to the current filter settings.

Select '''Binary High Resolution''' to retain the resolution of the processed data. This is the preferred binary format for small amplitude signals such as averages. Select '''Binary Compressed Format''' to store raw data using the original resolution or to obtain the space savings of compression (see ''File/Export and Append Data/Convert..'' above). This is the preferred binary format for raw data.

=== ASCII vectorized format (*.avr) ===

Select '''ASCII vectorized Format''' to output segments in BESA ASCII format, one channel (all time points) per line.

'''The Format is as follows:'''

The first of two header lines contains the following data descriptors (6 descriptors, the values shown are only examples):

''Npts= 200'' number of sampled points in each channel

''TSB= -500'' time sweep begin [ms]. Time of first data point relative to zero of epoch

''DI= 5'' digitization or sampling interval [ms]

''SB= 2'' scaling bins/microvolt in file = number corresponding to 1 microvolt

''SC= 50'' scaling calibration, used for setting magnitude of display in BESA

''Nchan= 27'' number of channels

''SegmentName= 60dB''  An optional label describing the data.

The second line of the header contains a label for each channel, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each of the subsequent ''Nchan'' lines of the file contains values for all ''Npts'' time points in floating point or scientific format. For more details about scalp electrodes, see chapter "''Working With Electrodes and Surface Locations/Electrodes/Electrode Conventions".''

A second (older) version of the format (written by BESA versions 1, 2 and 3) omits the '''Nchan=xx''' information in the first line, and there is no second header line. Labels must be defined elsewhere. See "''Electrodes/Electrode file conventions and formats''" and “''Reading MEG files in ASCII format”''. In the older versions, only scalp channels were exported, and the data were average referenced.

=== ASCII Multiplexed format (*.mul) ===

Select '''ASCII Multiplexed Format''' to output segments one time point (all channels) per line.  

The '''ASCII Multiplexed Format '''is as follows:

The first of two header lines contains similar information to that of the ASCII vectorized file:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= -500.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 SegmentName=Condition1''

Note that the item 'SegmentName' is missing if no segment comment is specified when writing a segment to file.

If an epoch of a continuous EEG is exported in ASCII multiplexed format, the first header line contains the additional item 'Time', which indicates the daytime of the first sample in the exported segment:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= 0.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 Time=22:02:53 SegmentName=Segment1''

The second line of the header contains labels for each channel, which may be either the original channel names, or the names of the channels of the current montage, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each subsequent line contains values for all 'Channels' at one time point, in floating point or scientific format. Values are given for the current or the original montage, selected as described above.

Labels for '''source montages''' have the following form: '''TAr-L'''.
* The first two letters indicate the head region:

[[Image:ST addfiles (1).gif]]

* The small letter indicates in part the orientation: r=radial, t=tangential, and in part the relative location of the basal temporal source: l=lateral, m=mesial.
* The final letter after the hyphen indicates L=left, M=middle, R=right.

=== Channel definition file conventions and formats ===

BESA Research can read 3 types of file to define channels. These are identified by different extensions:
* channel definition files containing labels and, optionally, channel types (ASCII, 1 label /line): '''<nowiki>*.ela</nowiki>'''
* channel definition files containing coordinates and, optionally, channel types and labels (ASCII): '''<nowiki>*.elp.</nowiki>''' This is the format of the file written by the ''Channel Configuration Dialog.''
* channel definition files stored by older versions of BESA Research (binary format): '''<nowiki>*.elb.</nowiki>''' This format can still be read, but is no longer written by BESA Research.

BESA Research stores and retrieves the channel configuration after editing in binary files. If you open a data file, BESA Research will search for the related channel information in the following sequence:

# For all data files with the extension '''.eeg''', '''.cnt''' and '''.foc''', check in the additional database file in the data directory with the same basename as the data file and the extension '''.fst''', whether a channel file has been associated previously
# Check in the '''''db''''' subdirectory whether a channel file has been associated previously
# Check if labels are defined in the header of the data file
# Search for a corresponding binary channel definition file with the same basename as the data file in the data folder ('''xxxx.elb''')
# Search for a corresponding channel definition file with the same basename as the data file containing labels in the data folder ('''xxxx.ela)'''
# Search for a corresponding channel definition file with the same basename as the data file containing labels and/or coordinates in the data folder ('''xxxx.elp''')
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' (in this order)) in the data folder
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' one directory above the data folder (e.g. '''..\default.elb''')
# Check if the new data file is of the same type and has the same number of channels as the preceding data file in the list. If this is the case, the electrode configuration of the previous file will be assumed. This will avoid having to load or edit the electrode configuration more than once, if you load several data segments of the same subject from separate files.
# If no channel definition file is found, or digitization points (in files '''<nowiki>*.sfp</nowiki>''', '''<nowiki>*.cot</nowiki>''', '''<nowiki>*.pos</nowiki>''', '''<nowiki>*.pmg</nowiki>''') are found in files with the same basename as the data file, the ''"Channel and digitized surface point'' ''information"'' dialog box is opened, allowing you to specify file names.

'''Channel Label Files (*.ela)'''

Files containing a list of channel labels are an alternative to editing electrode configurations. They can be edited using a standard text editor. Electrode label files ('''.ela''') require a sequence of lines corresponding to the sequence of channels in the data. Each line contains one label and an optional identifier. The format is ' [Identifier] {Label} ', ('Identifier' can be omitted if the electrode label defines the type of signal)

'''Identifiers''' can be one of:

EEG -- scalp electrode

SCP -- scalp electrode

POL -- polygraphic channel

PGR -- polygraphic channel

ICR -- intracranial electrode

MEG -- MEG sensor

REF -- reference electrode (this can only occur once, and must be the last item in the file)

For example:

Fz   ('''scalp''' electrode, coordinates assigned by default.ecd)

Cz   ('''scalp '''electrode, coordinates assigned by default.ecd)

......

VEOG   (vertical EOG,''' Polygraphic''' type is assigned by default)

Exx   (xx=01, 02.. electrode number, '''Polygraphic '''type is assigned by default)

......

EEG xx ('''scalp''' electrode, coordinates must be assigned either by '''default.ecd''' or by a surface point (+'''.sfp''') file. An alternative to the "EEG" prefix is "SCP".

......

POL XX  (identifier sets '''Polygraphic''' type -- an alternative to the "POL" prefix is "PGR")

......

ICR A01  (identifier sets '''Intracranial''' type to electrode A01 - do not use A1!)

ICR A02  (identifier sets''' Intracranial''' type to electrode A02 - do not use A2!)

ICR A03  (identifier sets''' Intracranial''' type to electrode A03)

......

MEG M01  (identifier sets '''MEG '''type to electrode M01 - do not use M1!)

MEG M02  (identifier sets '''MEG''' type to electrode M02 - do not use M2!)

......

REF Cz  (the label is assigned to the electrode reference, no channel is associated with this entry. This must be the last line of the file!)

'''Channel spherical coordinate files (*.elp)'''

These files follow the same rules as the channel label files, with the addition of spherical coordinates (theta, phi) that follow the labels of EEG and MEG channels. Labels can also be omitted. In this case, BESA Research will assign labels according to the nearest coordinate defined in the '''default.ecd''' file. To indicate that the coordinates have been assigned, the label will have a tick, e.g. Fz' instead of Fz.

Channels of other types (polygraphic, intracranial) are defined exactly as in the channel label ('''<nowiki>*.ela</nowiki>''') file.

=== cot (Head center) file ===

'''Function''': to redefine the center of the head for the sphere used in dipole models. If the cot file has the same base name as the data file, it is read automatically by BESA Research. If the coordinates deviate by more than 1 mm from the previously defined head center, a window is opened, asking if the new values should be adopted. This mechanism is turned off if the data have been coregistered to MRI (see online help chapter ''"MRI Coregistration''"), and an MRI Coregistration File ('''<nowiki>*.sfh</nowiki>''') has been associated with the data.

BESA Research uses any head surface points (e.g. electrode locations), excluding those on the lower part of the face, to compute the sphere center automatically. The cot file is used if you want to override the automatic calculation. A mechanism is provided which allows to pass a location from the MRI (viewed by BrainVoyager) to the Source Module and save the resulting location as a ''cot ''file.

'''Format''': one set of coordinates (x y z). These are followed by either "'''DC'''" or "'''HC'''", which specify whether these coordinates are in '''D'''evice or '''H'''ead '''C'''oordinates.

'''Units:''' must be in meters!

(Note: In special cases, a fifth value, the '''head radius''', may follow. This is used when reading simulated MEG data from the DipoleSimulator program. When this value is set, BESA Research uses the specified head radius and head center and does not fit a sphere to the head surface points. and does not create an ellipsoid transformation).

Force BESA Research to use a completely spherical model without creating an ellipsoid: Write "'''DipoleSimulator"''' or "'''Phantom'''" on the second line of the file. Under these circumstances, 100% correspondence between DipoleSimulator and BESA Research is achieved. This is also required for dipole fitting on MEG phantom recordings.

The ''cot ''file has also been extended for reading CTF MEG files. Documentation for these extensions is found in the CTF help file.)

=== pos or pmg (MEG sensor coordinate) file ===

'''Function:''' to define coordinates of MEG sensors. Our convention is to save magnetometer information in '''<nowiki>*.pmg</nowiki>''', and gradiometer information in '''<nowiki>*.pos</nowiki>'''. In practice, BESA Research doesn’t mind which extension is used -- the distinction between gradiometers and magnetometers is based on the number of values on each line in the file.

'''Format:''' one sensor per line.

Magnetometers: label (optional), six coordinates per line (location, orientation)

e.g. for BTi:

" Channel 'A1': -0.0019193 0.0304846 0.1081738 0.1188222 0.2394208 0.9636177"

Gradiometers: label (optional), nine coordinates per line (location of primary sensor, location of secondary sensor, orientation). The program decides whether gradiometers are planar or axial based on the distance between the primary and secondary sensor locations and the center of the head.

e.g. for Neuromag:

" 0.108510 -0.000143 -0.044954 0.108510 0.000463 -0.028766 0.999999 0.001450 0.000000 "

Labels in these files are ignored.

See chapter “''3D Coordinates for Precise Analysis/Data reading rules for MEG''”.

=== sfn (surface point name) file ===

'''Function:''' to match up digitized coordinates with channels that are defined as EEG electrodes and to define labels for additional digitized head surface points (e.g. MEG coils, etc.).

'''Format:''' one label per line.

Contains labels of surface points in the order of digitization. If fiducials are defined, these should be on the first three lines, with the labels 'FidT9', 'FidT10', 'FidNz' or 'FidLPA', 'FidRPA', 'FidNAS'.

If electrodes are defined in the data file, the labels of each electrode as defined in the data file (or in its associated ''ela'', ''elp'', or ''elb ''file) must be present!

The case of labels is not important (e.g. 'Fp1' will match with 'fp1').

The ''sfn'' file need not exist if labels are defined in the ''sfp ''file.

See chapter “''3D Coordinates for Precise Analysis / Data reading rules for EEG”.''

=== sfp (surface point coordinate) file ===

'''Function''': to define coordinates of digitized points on the head surface. The order of points must match with the order in the ''sfn ''file, or if no ''sfn'' file is present, labels must be included in the ''sfp'' file.

Note: If the digitized points include electrodes, the channel labels must correspond to the labels of the digitized points. The sequence of labels in channels and surface point coordinate file need not be the same – the allocation is performed by label matching. Channel labels may be defined in the data file, or they may be assigned using channel definition files ('''<nowiki>*.ela, *.elp, *.elb</nowiki>''').

'''Format:''' one set of coordinates (x, y, z) per line. Coordinate units must be either meter, centimeter or millimeter (BESA Research will perform a plausibility check automatically to determine which units are used). If a label is present this can precede or come after the three coordinate values.

If fiducials are defined, these should be on the first three lines. BESA Research will simulate fiducials if none are defined, but it is preferable to record these locations along with the other head surface points.

If there are MEG sensors, the same coordinate systems must be used in the ''sfp'' file and the ''pos/pmg ''file!

If labels are defined in the ''sfp'' file rather than in an ''sfn'' file, labeling rules apply as for the ''sfn'' file.

Example for the ''sfp'' file format:

[[Image:ST addfiles (2).gif ‎]]

BESA Research will check the coordinates for plausibility. If coordinates are more than 30° away from the expected location on the sphere there will be an error message. Such errors are usually due either to incorrect labeling or to a digitization error.

See chapter “''3D Coordinates for Precise Analysis /'' ''Data reading rules for EEG”.''

=== Generic File Format ===

This reader, incorporated into the '''GenericBesa.dll''' file, allows to read simple multiplexed or vectorized data formats, if you know the structure of the data format.

'''What you have to do'''
* With a text editor, write information about the data file you want to read into BESA Research into a text file, the ''Generic Header''.
* Save the edited text in the same subdirectory as the data file.
* '''Mechanism A:''' The generic header contains the data file name. With BESA Research, navigate to the file you just edited, and open it. The data should then be read into BESA Research.
* '''Mechanism B:''' Alternatively, navigate to the data file. The reader will check if there is a generic header in the same subdirectory, and use that to try to open the file. You have two options:

* <div style="margin-left:1.27cm;margin-right:0cm;">'''Specific:''' if the file has the same basename as the data file, and the extension “'''.generic'''”, this file will be used.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">'''Generalized:''' if a specific file is not found, the reader will look for the file “'''BESA.generic'''” in the same subdirectory.</div>

'''Important note:''' We recommend using mechanism A, using a header with the extension "'''.generic'''". When opening the data file in BESA, select the generic header. Mechanism B sometimes fails when opening the data file in BESA Research, because one of the other readers in BESA may erroneously interpret the file as their "own" data format, sometimes leading to a crash.

'''Format of the Generic Header'''

The first line '''must '''consist of the text: “''BESA Generic Data''” (without the inverted commas).

Subsequent lines '''must''' contain the following parameters, in any order (note that the parameters are case insensitive):

'''''nChannels'''''=''nnn''                 The number of channels

'''''sRate'''''=''fff''                 The sampling rate (samples/sec)

'''''format'''''=''type''                  One of ''short'', ''int, float, double, ASCII''. If the format is ''ASCII'', the parameter''' nSamples''' must be specified as well (see below)

The following parameters are optional (values in square brackets denote optional parameters):

'''''nSamples'''''=''nnn''                 The number of time samples in the data. If this value is 0, or the line is omitted, then use the file size to estimate the number of samples.

'''''file''''' = ''name   ''   The data file name, without path information. If this is omitted, you can only read the data with mechanism B (see above). This line '''must''' be included if you want to read the data with mechanism A.

'''''DataOffset''''' = ''nnn  ''                   Offset of data in bytes for binary data, in lines for ASCII data (default = 0).

'''''Factor''' ''<nowiki>= </nowiki>''fff  [range]''                Data values are multiplied by this factor to obtain µV values (default = 1). Optional parameters can be appended to define a channel range, e.g. ''1-3''. Thus, this command can be used multiply, to define different scaling factors for different channels. If only one channel is specified, use on number only, e.g. ''5''.

'''''SwapBytes''''' = ''ccc  ''           One of ''off'' or ''on'' (default = off). If the data block originated from Unix or Mac, this will need to be ''on''. (binary data only)

'''''Prestimulus''' ''<nowiki>= </nowiki>''fff   ''                   Prestimulus interval in milliseconds.

'''''Label '''''<nowiki>= </nowiki>''ccc   ''                           Segment label.

'''''Trigger''''' = ''chan….''            Channel number containing triggers. Without further parameters, the values are read directly as digital trigger values. Other parameters are described below, for the case where the trigger channel contains analog signals.

'''''nBlocks '''''<nowiki>= </nowiki>''nnn    ''                  The data are epoched. This specifies the number of equal sized blocks in the data. In BESA Research, each block will be separated by a segment boundary. The number of samples in each epoch is computed from the total number of samples divided by ''nBlocks''.

'''''nEpochs'' '''<nowiki>= </nowiki>''nnn        ''                Same as '''nBlocks'''.

'''''EventFile''''' = ''name      ''              Load events from an event file, using BESA's event file ('''<nowiki>*.evt</nowiki>''') format. See below for a description of how to prepare this file.

'''''Order''''' = ''type   ''                         One of ''multiplexed'', ''vectorized''. The default is multiplexed (i.e. channels fastest). Specify ''vectorized'' if your data are ordered so that all time samples for channel 1 are followed by all time samples from channel 2, etc.

'''''Orientation''' ''<nowiki>= </nowiki>''type ''                   Same as '''Order'''.

'''''Arrangement'' '''<nowiki>= </nowiki>''type''                 Same as '''Order'''.

'''Trigger events'''

This section describes how the reader can be used to encode trigger events when the trigger channel contains analog signals. In this case, a '''Trigger '''command is required for each target code in BESA Research.

Syntax:

'''Trigger''' = ''chan  code  fromLevel  toLevel  timerange''  ''deadtime''

'''''chan''' ''is the channel number on which to find the trigger

'''''code''''' is the trigger number that the reader will assign (must be positive!)

'''''fromLevel'' '''is the value in mV defining the lower range for trigger detection

'''''toLevel'' '''is the value in mV defining the upper range for trigger detection. If this is “-“, then only ''fromLevel ''needs to be exceeded for the trigger to be detected.

'''''timerange '''''is the range in milliseconds to define a trigger. The reader will search for the maximum deviation from baseline within the range to find the level that will define the trigger.

'''''deadtime''' ''defines the time after detecting a trigger during which no further trigger with this code can be detected. This does not affect other codes. Also, if the voltage level stays at a level corresponding to a code, the trigger is only defined at the onset of this voltage level.

Multiple lines are required if different trigger codes and different trigger channels are required, one for each new code.

'''Notes'''

'''Channel labels:''' The data channels are labeled ''E1, E2, E3,…,'' and they are initially classified by BESA Research as polygraphic. As with other BESA Research data files, use a '''<nowiki>*.ela </nowiki>'''file (or '''<nowiki>*.elp</nowiki>''', optionally combined with '''<nowiki>*.sfp</nowiki>''') to redefine labels and channel types.

'''Data formats:'''

* Short 16-bit
* Int 32-bit
* Float 32-bit
* Double 64-bit
* ASCII Decimal numbers separated by spaces or tabs (engineering format also permitted)

'''Prestimulus interval and label:''' If either of these are defined, BESA Research reads the data in to define an averaged data segment. The label is displayed, and a vertical dotted line marks timepoint zero. If no prestimulus interval is defined, a zero prestimulus interval is assumed.

'''Future changes'''

Possible developments:
* Read channel labels

If any of these changes are particularly important to you, please contact [mailto:support@besa.de support@besa.de] and let us know.

'''Event File'''

The event file is a text (ASCII) file containing a header line and subsequent lines, with one event description per line.

Each line contains four parameters:

1. latency (units specified by the header, can be µs, ms, s)

2. code (defines the type of event: trigger, comment, marker, pattern, average segment, data break segment)

3. parameter (depends on the event type, e.g. trigger code)

4. label (label assigned to the event)

'''Header Line:'''

The header line contains four values. The first specifies the time units, e.g. '''Tmu '''specifies microseconds.

''    Tmu    Code    TriNo    Comnt''

'''Tms''' specifies milliseconds. '''Tsec''' specifies seconds.

'''Event Code and Parameter 3 (TriNo):'''

'''Code''' specifies the event type:

1 = trigger -- '''TriNo '''specifies the trigger number

2 = comment

3 = marker

11-15 = patterns 1-5

21 = artifact on

22 = artifact off

31 = epoch on

32 = epoch off

41 = segment onset -- '''TriNo '''is a time string that specifies date and time, in the format ''YYYY-MM-DDTHH:MM:SS'', e.g. ''2010-04-26T15:30:20.31'' (note: seconds are a decimal number).

42 = average segment onset -- '''TriNo '''is a number specifying the prestimulus baseline of the subsequent average in microseconds. '''TriNo '''(parameter) is 0 for markers, comments, artifacts, and epochs.

'''Comment'''

The event label. This is not used for markers, artifacts, and epochs.

'''Example of event file:'''

A simple way to generate example files is to export events from BESA (''ERP/Save Events As...'').

Tmu         Code     TriNo     Comnt

0              42     100000    Ave: 25 avs  

10000000  2       0            Comment at 10s

20000000  41     26-04-2010T15:30:20.000   TestSeg2

21000000  3       0

22000000 1        99          Trigger – 99

This specifies an average segment starting at the beginning of the file, with a prestimulus interval of 100 ms, a comment at 10 s, a new segment specifying date and time at 20 s, a marker at 21 s, and a trigger with code 99 at 22 s.

'''Examples'''

The following reads ASCII multiplexed data that were previously exported from BESA Research:

''BESA Generic Data''

''nchannels = 64''

''srate = 100''

''nsamples = 10000''

''dataoffset = 2''

''format = ASCII''

''file = name.mul''

''factor = 1''

With the sampling rate of 100 Hz and 10000 samples, this represents 100 s of 64-channel data. The first two lines of the data are skipped.

Working With Additional Files

2017-04-07T09:40:32Z

Alexa:

== Working with Additional Files ==

=== Binary format (*.foc, *.fsg) ===

Select '''Binary High Resolution''' or '''Binary Compressed Format''' to output segments in binary BESA format. If the file already exists, the segment will be appended. Thus, it is possible to create a file combining several segments of interest in a compact form. BESA Research will only allow you to append segments if the number of channels and the sampling interval in source and target files are the same. In Binary Format all channels (scalp, intracranial, polygraphic, MEG) and file events in the selected time range are exported. '''Note:''' The channels are filtered according to the current filter settings.

Select '''Binary High Resolution''' to retain the resolution of the processed data. This is the preferred binary format for small amplitude signals such as averages. Select '''Binary Compressed Format''' to store raw data using the original resolution or to obtain the space savings of compression (see ''File/Export and Append Data/Convert..'' above). This is the preferred binary format for raw data.

=== ASCII vectorized format (*.avr) ===

Select '''ASCII vectorized Format''' to output segments in BESA ASCII format, one channel (all time points) per line.

'''The Format is as follows:'''

The first of two header lines contains the following data descriptors (6 descriptors, the values shown are only examples):

''Npts= 200'' number of sampled points in each channel

''TSB= -500'' time sweep begin [ms]. Time of first data point relative to zero of epoch

''DI= 5'' digitization or sampling interval [ms]

''SB= 2'' scaling bins/microvolt in file = number corresponding to 1 microvolt

''SC= 50'' scaling calibration, used for setting magnitude of display in BESA

''Nchan= 27'' number of channels

''SegmentName= 60dB''  An optional label describing the data.

The second line of the header contains a label for each channel, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each of the subsequent ''Nchan'' lines of the file contains values for all ''Npts'' time points in floating point or scientific format. For more details about scalp electrodes, see chapter "''Working With Electrodes and Surface Locations/Electrodes/Electrode Conventions".''

A second (older) version of the format (written by BESA versions 1, 2 and 3) omits the '''Nchan=xx''' information in the first line, and there is no second header line. Labels must be defined elsewhere. See "''Electrodes/Electrode file conventions and formats''" and “''Reading MEG files in ASCII format”''. In the older versions, only scalp channels were exported, and the data were average referenced.

=== ASCII Multiplexed format (*.mul) ===

Select '''ASCII Multiplexed Format''' to output segments one time point (all channels) per line.  

The '''ASCII Multiplexed Format '''is as follows:

The first of two header lines contains similar information to that of the ASCII vectorized file:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= -500.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 SegmentName=Condition1''

Note that the item 'SegmentName' is missing if no segment comment is specified when writing a segment to file.

If an epoch of a continuous EEG is exported in ASCII multiplexed format, the first header line contains the additional item 'Time', which indicates the daytime of the first sample in the exported segment:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= 0.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 Time=22:02:53 SegmentName=Segment1''

The second line of the header contains labels for each channel, which may be either the original channel names, or the names of the channels of the current montage, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each subsequent line contains values for all 'Channels' at one time point, in floating point or scientific format. Values are given for the current or the original montage, selected as described above.

Labels for '''source montages''' have the following form: '''TAr-L'''.
* The first two letters indicate the head region:

[[Image:ST addfiles (1).gif]]

* The small letter indicates in part the orientation: r=radial, t=tangential, and in part the relative location of the basal temporal source: l=lateral, m=mesial.
* The final letter after the hyphen indicates L=left, M=middle, R=right.

=== Channel definition file conventions and formats ===

BESA Research can read 3 types of file to define channels. These are identified by different extensions:
* channel definition files containing labels and, optionally, channel types (ASCII, 1 label /line): '''<nowiki>*.ela</nowiki>'''
* channel definition files containing coordinates and, optionally, channel types and labels (ASCII): '''<nowiki>*.elp.</nowiki>''' This is the format of the file written by the ''Channel Configuration Dialog.''
* channel definition files stored by older versions of BESA Research (binary format): '''<nowiki>*.elb.</nowiki>''' This format can still be read, but is no longer written by BESA Research.

BESA Research stores and retrieves the channel configuration after editing in binary files. If you open a data file, BESA Research will search for the related channel information in the following sequence:

# For all data files with the extension '''.eeg''', '''.cnt''' and '''.foc''', check in the additional database file in the data directory with the same basename as the data file and the extension '''.fst''', whether a channel file has been associated previously
# Check in the '''''db''''' subdirectory whether a channel file has been associated previously
# Check if labels are defined in the header of the data file
# Search for a corresponding binary channel definition file with the same basename as the data file in the data folder ('''xxxx.elb''')
# Search for a corresponding channel definition file with the same basename as the data file containing labels in the data folder ('''xxxx.ela)'''
# Search for a corresponding channel definition file with the same basename as the data file containing labels and/or coordinates in the data folder ('''xxxx.elp''')
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' (in this order)) in the data folder
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' one directory above the data folder (e.g. '''..\default.elb''')
# Check if the new data file is of the same type and has the same number of channels as the preceding data file in the list. If this is the case, the electrode configuration of the previous file will be assumed. This will avoid having to load or edit the electrode configuration more than once, if you load several data segments of the same subject from separate files.
# If no channel definition file is found, or digitization points (in files '''<nowiki>*.sfp</nowiki>''', '''<nowiki>*.cot</nowiki>''', '''<nowiki>*.pos</nowiki>''', '''<nowiki>*.pmg</nowiki>''') are found in files with the same basename as the data file, the ''"Channel and digitized surface point'' ''information"'' dialog box is opened, allowing you to specify file names.

'''Channel Label Files (*.ela)'''

Files containing a list of channel labels are an alternative to editing electrode configurations. They can be edited using a standard text editor. Electrode label files ('''.ela''') require a sequence of lines corresponding to the sequence of channels in the data. Each line contains one label and an optional identifier. The format is ' [Identifier] {Label} ', ('Identifier' can be omitted if the electrode label defines the type of signal)

'''Identifiers''' can be one of:

EEG -- scalp electrode

SCP -- scalp electrode

POL -- polygraphic channel

PGR -- polygraphic channel

ICR -- intracranial electrode

MEG -- MEG sensor

REF -- reference electrode (this can only occur once, and must be the last item in the file)

For example:

Fz   ('''scalp''' electrode, coordinates assigned by default.ecd)

Cz   ('''scalp '''electrode, coordinates assigned by default.ecd)

......

VEOG   (vertical EOG,''' Polygraphic''' type is assigned by default)

Exx   (xx=01, 02.. electrode number, '''Polygraphic '''type is assigned by default)

......

EEG xx ('''scalp''' electrode, coordinates must be assigned either by '''default.ecd''' or by a surface point (+'''.sfp''') file. An alternative to the "EEG" prefix is "SCP".

......

POL XX  (identifier sets '''Polygraphic''' type -- an alternative to the "POL" prefix is "PGR")

......

ICR A01  (identifier sets '''Intracranial''' type to electrode A01 - do not use A1!)

ICR A02  (identifier sets''' Intracranial''' type to electrode A02 - do not use A2!)

ICR A03  (identifier sets''' Intracranial''' type to electrode A03)

......

MEG M01  (identifier sets '''MEG '''type to electrode M01 - do not use M1!)

MEG M02  (identifier sets '''MEG''' type to electrode M02 - do not use M2!)

......

REF Cz  (the label is assigned to the electrode reference, no channel is associated with this entry. This must be the last line of the file!)

'''Channel spherical coordinate files (*.elp)'''

These files follow the same rules as the channel label files, with the addition of spherical coordinates (theta, phi) that follow the labels of EEG and MEG channels. Labels can also be omitted. In this case, BESA Research will assign labels according to the nearest coordinate defined in the '''default.ecd''' file. To indicate that the coordinates have been assigned, the label will have a tick, e.g. Fz' instead of Fz.

Channels of other types (polygraphic, intracranial) are defined exactly as in the channel label ('''<nowiki>*.ela</nowiki>''') file.

=== cot (Head center) file ===

'''Function''': to redefine the center of the head for the sphere used in dipole models. If the cot file has the same base name as the data file, it is read automatically by BESA Research. If the coordinates deviate by more than 1 mm from the previously defined head center, a window is opened, asking if the new values should be adopted. This mechanism is turned off if the data have been coregistered to MRI (see online help chapter ''"MRI Coregistration''"), and an MRI Coregistration File ('''<nowiki>*.sfh</nowiki>''') has been associated with the data.

BESA Research uses any head surface points (e.g. electrode locations), excluding those on the lower part of the face, to compute the sphere center automatically. The cot file is used if you want to override the automatic calculation. A mechanism is provided which allows to pass a location from the MRI (viewed by BrainVoyager) to the Source Module and save the resulting location as a ''cot ''file.

'''Format''': one set of coordinates (x y z). These are followed by either "'''DC'''" or "'''HC'''", which specify whether these coordinates are in '''D'''evice or '''H'''ead '''C'''oordinates.

'''Units:''' must be in meters!

(Note: In special cases, a fifth value, the '''head radius''', may follow. This is used when reading simulated MEG data from the DipoleSimulator program. When this value is set, BESA Research uses the specified head radius and head center and does not fit a sphere to the head surface points. and does not create an ellipsoid transformation).

Force BESA Research to use a completely spherical model without creating an ellipsoid: Write "'''DipoleSimulator"''' or "'''Phantom'''" on the second line of the file. Under these circumstances, 100% correspondence between DipoleSimulator and BESA Research is achieved. This is also required for dipole fitting on MEG phantom recordings.

The ''cot ''file has also been extended for reading CTF MEG files. Documentation for these extensions is found in the CTF help file.)

=== pos or pmg (MEG sensor coordinate) file ===

'''Function:''' to define coordinates of MEG sensors. Our convention is to save magnetometer information in '''<nowiki>*.pmg</nowiki>''', and gradiometer information in '''<nowiki>*.pos</nowiki>'''. In practice, BESA Research doesn’t mind which extension is used -- the distinction between gradiometers and magnetometers is based on the number of values on each line in the file.

'''Format:''' one sensor per line.

Magnetometers: label (optional), six coordinates per line (location, orientation)

e.g. for BTi:

" Channel 'A1': -0.0019193 0.0304846 0.1081738 0.1188222 0.2394208 0.9636177"

Gradiometers: label (optional), nine coordinates per line (location of primary sensor, location of secondary sensor, orientation). The program decides whether gradiometers are planar or axial based on the distance between the primary and secondary sensor locations and the center of the head.

e.g. for Neuromag:

" 0.108510 -0.000143 -0.044954 0.108510 0.000463 -0.028766 0.999999 0.001450 0.000000 "

Labels in these files are ignored.

See chapter “''3D Coordinates for Precise Analysis/Data reading rules for MEG''”.

=== sfn (surface point name) file ===

'''Function:''' to match up digitized coordinates with channels that are defined as EEG electrodes and to define labels for additional digitized head surface points (e.g. MEG coils, etc.).

'''Format:''' one label per line.

Contains labels of surface points in the order of digitization. If fiducials are defined, these should be on the first three lines, with the labels 'FidT9', 'FidT10', 'FidNz' or 'FidLPA', 'FidRPA', 'FidNAS'.

If electrodes are defined in the data file, the labels of each electrode as defined in the data file (or in its associated ''ela'', ''elp'', or ''elb ''file) must be present!

The case of labels is not important (e.g. 'Fp1' will match with 'fp1').

The ''sfn'' file need not exist if labels are defined in the ''sfp ''file.

See chapter “''3D Coordinates for Precise Analysis / Data reading rules for EEG”.''

=== sfp (surface point coordinate) file ===

'''Function''': to define coordinates of digitized points on the head surface. The order of points must match with the order in the ''sfn ''file, or if no ''sfn'' file is present, labels must be included in the ''sfp'' file.

Note: If the digitized points include electrodes, the channel labels must correspond to the labels of the digitized points. The sequence of labels in channels and surface point coordinate file need not be the same – the allocation is performed by label matching. Channel labels may be defined in the data file, or they may be assigned using channel definition files ('''<nowiki>*.ela, *.elp, *.elb</nowiki>''').

'''Format:''' one set of coordinates (x, y, z) per line. Coordinate units must be either meter, centimeter or millimeter (BESA Research will perform a plausibility check automatically to determine which units are used). If a label is present this can precede or come after the three coordinate values.

If fiducials are defined, these should be on the first three lines. BESA Research will simulate fiducials if none are defined, but it is preferable to record these locations along with the other head surface points.

If there are MEG sensors, the same coordinate systems must be used in the ''sfp'' file and the ''pos/pmg ''file!

If labels are defined in the ''sfp'' file rather than in an ''sfn'' file, labeling rules apply as for the ''sfn'' file.

Example for the ''sfp'' file format:

[[Image:ST addfiles (2).gif ‎]]

BESA Research will check the coordinates for plausibility. If coordinates are more than 30° away from the expected location on the sphere there will be an error message. Such errors are usually due either to incorrect labeling or to a digitization error.

See chapter “''3D Coordinates for Precise Analysis /'' ''Data reading rules for EEG”.''

=== Generic File Format ===

This reader, incorporated into the '''GenericBesa.dll''' file, allows to read simple multiplexed or vectorized data formats, if you know the structure of the data format.

'''What you have to do'''
* With a text editor, write information about the data file you want to read into BESA Research into a text file, the ''Generic Header''.
* Save the edited text in the same subdirectory as the data file.
* '''Mechanism A:''' The generic header contains the data file name. With BESA Research, navigate to the file you just edited, and open it. The data should then be read into BESA Research.
* '''Mechanism B:''' Alternatively, navigate to the data file. The reader will check if there is a generic header in the same subdirectory, and use that to try to open the file. You have two options:

* <div style="margin-left:1.27cm;margin-right:0cm;">'''Specific:''' if the file has the same basename as the data file, and the extension “'''.generic'''”, this file will be used.</div>
* <div style="margin-left:1.27cm;margin-right:0cm;">'''Generalized:''' if a specific file is not found, the reader will look for the file “'''BESA.generic'''” in the same subdirectory.</div>

'''Important note:''' We recommend using mechanism A, using a header with the extension "'''.generic'''". When opening the data file in BESA, select the generic header. Mechanism B sometimes fails when opening the data file in BESA Research, because one of the other readers in BESA may erroneously interpret the file as their "own" data format, sometimes leading to a crash.

'''Format of the Generic Header'''

The first line '''must '''consist of the text: “''BESA Generic Data''” (without the inverted commas).

Subsequent lines '''must''' contain the following parameters, in any order (note that the parameters are case insensitive):

'''''nChannels''' ''<nowiki>= </nowiki>''nnn''                 The number of channels

'''''sRate''''' = ''fff    ''                          The sampling rate (samples/sec)

'''''format''''' = ''type''        One of ''short'', ''int, float, double, ASCII''. If the format is ''ASCII'', the parameter''' nSamples''' must be specified as well (see below)

The following parameters are optional (values in square brackets denote optional parameters):

'''''nSamples'' '''<nowiki>= </nowiki>''nnn ''          The number of time samples in the data. If this value is 0, or the line is omitted, then use the file size to estimate the number of samples.

'''''file''''' = ''name   ''   The data file name, without path information. If this is omitted, you can only read the data with mechanism B (see above). This line '''must''' be included if you want to read the data with mechanism A.

'''''DataOffset''''' = ''nnn  ''                   Offset of data in bytes for binary data, in lines for ASCII data (default = 0).

'''''Factor''' ''<nowiki>= </nowiki>''fff  [range]''                Data values are multiplied by this factor to obtain µV values (default = 1). Optional parameters can be appended to define a channel range, e.g. ''1-3''. Thus, this command can be used multiply, to define different scaling factors for different channels. If only one channel is specified, use on number only, e.g. ''5''.

'''''SwapBytes''''' = ''ccc  ''           One of ''off'' or ''on'' (default = off). If the data block originated from Unix or Mac, this will need to be ''on''. (binary data only)

'''''Prestimulus''' ''<nowiki>= </nowiki>''fff   ''                   Prestimulus interval in milliseconds.

'''''Label '''''<nowiki>= </nowiki>''ccc   ''                           Segment label.

'''''Trigger''''' = ''chan….''            Channel number containing triggers. Without further parameters, the values are read directly as digital trigger values. Other parameters are described below, for the case where the trigger channel contains analog signals.

'''''nBlocks '''''<nowiki>= </nowiki>''nnn    ''                  The data are epoched. This specifies the number of equal sized blocks in the data. In BESA Research, each block will be separated by a segment boundary. The number of samples in each epoch is computed from the total number of samples divided by ''nBlocks''.

'''''nEpochs'' '''<nowiki>= </nowiki>''nnn        ''                Same as '''nBlocks'''.

'''''EventFile''''' = ''name      ''              Load events from an event file, using BESA's event file ('''<nowiki>*.evt</nowiki>''') format. See below for a description of how to prepare this file.

'''''Order''''' = ''type   ''                         One of ''multiplexed'', ''vectorized''. The default is multiplexed (i.e. channels fastest). Specify ''vectorized'' if your data are ordered so that all time samples for channel 1 are followed by all time samples from channel 2, etc.

'''''Orientation''' ''<nowiki>= </nowiki>''type ''                   Same as '''Order'''.

'''''Arrangement'' '''<nowiki>= </nowiki>''type''                 Same as '''Order'''.

'''Trigger events'''

This section describes how the reader can be used to encode trigger events when the trigger channel contains analog signals. In this case, a '''Trigger '''command is required for each target code in BESA Research.

Syntax:

'''Trigger''' = ''chan  code  fromLevel  toLevel  timerange''  ''deadtime''

'''''chan''' ''is the channel number on which to find the trigger

'''''code''''' is the trigger number that the reader will assign (must be positive!)

'''''fromLevel'' '''is the value in mV defining the lower range for trigger detection

'''''toLevel'' '''is the value in mV defining the upper range for trigger detection. If this is “-“, then only ''fromLevel ''needs to be exceeded for the trigger to be detected.

'''''timerange '''''is the range in milliseconds to define a trigger. The reader will search for the maximum deviation from baseline within the range to find the level that will define the trigger.

'''''deadtime''' ''defines the time after detecting a trigger during which no further trigger with this code can be detected. This does not affect other codes. Also, if the voltage level stays at a level corresponding to a code, the trigger is only defined at the onset of this voltage level.

Multiple lines are required if different trigger codes and different trigger channels are required, one for each new code.

'''Notes'''

'''Channel labels:''' The data channels are labeled ''E1, E2, E3,…,'' and they are initially classified by BESA Research as polygraphic. As with other BESA Research data files, use a '''<nowiki>*.ela </nowiki>'''file (or '''<nowiki>*.elp</nowiki>''', optionally combined with '''<nowiki>*.sfp</nowiki>''') to redefine labels and channel types.

'''Data formats:'''

* Short 16-bit
* Int 32-bit
* Float 32-bit
* Double 64-bit
* ASCII Decimal numbers separated by spaces or tabs (engineering format also permitted)

'''Prestimulus interval and label:''' If either of these are defined, BESA Research reads the data in to define an averaged data segment. The label is displayed, and a vertical dotted line marks timepoint zero. If no prestimulus interval is defined, a zero prestimulus interval is assumed.

'''Future changes'''

Possible developments:
* Read channel labels

If any of these changes are particularly important to you, please contact [mailto:support@besa.de support@besa.de] and let us know.

'''Event File'''

The event file is a text (ASCII) file containing a header line and subsequent lines, with one event description per line.

Each line contains four parameters:

1. latency (units specified by the header, can be µs, ms, s)

2. code (defines the type of event: trigger, comment, marker, pattern, average segment, data break segment)

3. parameter (depends on the event type, e.g. trigger code)

4. label (label assigned to the event)

'''Header Line:'''

The header line contains four values. The first specifies the time units, e.g. '''Tmu '''specifies microseconds.

''    Tmu    Code    TriNo    Comnt''

'''Tms''' specifies milliseconds. '''Tsec''' specifies seconds.

'''Event Code and Parameter 3 (TriNo):'''

'''Code''' specifies the event type:

1 = trigger -- '''TriNo '''specifies the trigger number

2 = comment

3 = marker

11-15 = patterns 1-5

21 = artifact on

22 = artifact off

31 = epoch on

32 = epoch off

41 = segment onset -- '''TriNo '''is a time string that specifies date and time, in the format ''YYYY-MM-DDTHH:MM:SS'', e.g. ''2010-04-26T15:30:20.31'' (note: seconds are a decimal number).

42 = average segment onset -- '''TriNo '''is a number specifying the prestimulus baseline of the subsequent average in microseconds. '''TriNo '''(parameter) is 0 for markers, comments, artifacts, and epochs.

'''Comment'''

The event label. This is not used for markers, artifacts, and epochs.

'''Example of event file:'''

A simple way to generate example files is to export events from BESA (''ERP/Save Events As...'').

Tmu         Code     TriNo     Comnt

0              42     100000    Ave: 25 avs  

10000000  2       0            Comment at 10s

20000000  41     26-04-2010T15:30:20.000   TestSeg2

21000000  3       0

22000000 1        99          Trigger – 99

This specifies an average segment starting at the beginning of the file, with a prestimulus interval of 100 ms, a comment at 10 s, a new segment specifying date and time at 20 s, a marker at 21 s, and a trigger with code 99 at 22 s.

'''Examples'''

The following reads ASCII multiplexed data that were previously exported from BESA Research:

''BESA Generic Data''

''nchannels = 64''

''srate = 100''

''nsamples = 10000''

''dataoffset = 2''

''format = ASCII''

''file = name.mul''

''factor = 1''

With the sampling rate of 100 Hz and 10000 samples, this represents 100 s of 64-channel data. The first two lines of the data are skipped.

The Initialization File: BESA.ini

2017-04-07T09:23:15Z

Alexa:

== The Initialization File: BESA.ini ==

=== Introduction ===

'''BESA.ini File'''

BESA Research uses settings provided in the initialization file '''BESA.ini''' whenever BESA Research is started or a new file is opened for the first time. The format of this file conforms with standard initialization files ('''<nowiki>*.ini</nowiki>''') of Windows. You may change the settings in '''BESA.ini''' using NOTEPAD.exe from the ACCESSORIES group, or other plain text editors to adapt BESA Research to '''your own everyday needs'''. The default settings provided in '''BESA.ini''' will be used by BESA Research whenever BESA Research or the launch program is started. It is advised that you make a backup copy of '''BESA.ini''' before you change the default settings.

'''Location of BESA.ini'''

You can place '''BESA.ini''' at three possible locations:

'''a) Private''': each user on a PC should have his/her own private settings. This is normally in ''My'' ''Documents/BESA/Research_6_0''

'''b) Public''':  all users should use one setting, but they can edit '''BESA.ini''' to change the settings. This is normally in ''Shared Documents/BESA/Research_6_0''

'''c) Administrator''': the PC administrator determines the settings. This is normally in ''C:Program'' ''Files/BESA/Research_6_0''

The actual folder names depend on the operating system and the system language.

When BESA starts, it first looks for the''' administrator''' version of '''BESA.ini'''. If this is not found, it looks for the '''private''' version. If this is not found, it looks for the '''public''' version. If this is not found, internal default values are used.

'''There are 13 general sections, and several reader-specific sections:'''

[Defaults]                   -- General settings (filters, scaling, and various other settings)

[Folders]                    -- Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)

[Electrodes]               -- Electrode renaming

[Patterns]                   -- Rename patterns in the '''Tags''' menu

[Artifacts]                   -- Settings for artifact correction

[KEYCONTROLS]     -- Function key definitions

[Search]                     -- Default parameters for search

[FFT]                          -- Frequency band definitions

[Printer]                      -- Printer control

[Calibration]              -- Calibration control

[Video]                      -- Digital video control

[Mapping]                  -- Mapping control

[Matlab]                     -- Settings for the Matlab interface

[Updates]                  -- Options for program updates

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

=== Defaults ===

'''Default settings provided for section [Defaults]:'''

'''DatabaseAllowLocalFiles=Yes''' (If set to "Yes", BESA Research will write filenames "'''datafilename.ftg'''" and "'''datafilename.fst"''' to the data folder, saving current file tag and display settings there. If set to "No", these files are only written to the database. If set to "Yes", you can copy these files along with the data to a new folder, and display settings and tags will be preserved.)

'''DataBuffering=Off''' (If set to "On", an internal buffer of length 180 s of data is kept to speed up paging). This can speed up paging, particularly when the data are in a network folder.

'''DisplayedTime=10''' displayed time window [s] on the screen

'''Montage=Org''' montage used when opening a new file

'''ScpScale=50''' scale of scalp channels in [mV]

'''PgrScale=500''' scale of polygraphic channels in [mV]

'''IcrScale=500''' scale of intracranial channels in [mV]

'''MegScale=500''' scale of MEG/marker channels in [fT]

'''BaselineCorrection=On''' baseline correction, do not switch off in AC systems

'''ClippingPercent= '''set from 100 to 200 if you want to clip artifacts in displayed EEG (not used if empty or 0)

'''LowFilter=''' low filter cutoff frequency [Hz] (variable filter)

'''TimeConstant=0.3''' time constant for low filter cutoff frequency [sec] (fixed forward filter, 0.3 sec is equivalent to 0.53 Hz)

'''HighFilter=70''' high filter cutoff frequency [Hz] (variable filter)

'''NotchFilter=50''' notch filter center frequency [Hz]

'''NotchFilterStatus=Off''' notch filter is off, set=On if you want to use as default

'''BandFilter=12''' band pass filter center frequency [Hz]

'''BandFilterStatus=Off''' band pass is off, set=On if you want to use as default

'''AdditionalChannelFile=''' defines the full path and name of an additional channels montage file, e.g. '''C:\Program Files\BESA\Research_x\Montages\AdditionalChannels\EKG.sel'''

'''ColoredWaveforms=On''' scalp waveforms are (not) colored according to region

'''WriteSegmentPath=''' defines default path for saving segments/averages. If blank, the path of the current data file is used.

'''ShowSubjectInfo=Off''' subject info will (not) be displayed.

The following optional parameters are not defined as default and can be set manually in''' BESA.ini''':

'''TextEditor="Notepad.exe"''' defines the path to your preferred text editor. This will be used when you press the '''Edit''' button the ''Load Coordinate Files dialog box''.

'''NeuroScanDataNumberOfBits=32''' defines the format of NeuroScan data files ('16' for 16-bit, '32' for 32-bit). If this variable is not specified, BESA uses a heuristic to (try to) decide which of the two data formats is used. This variable overrides the heuristic. If you want to specify the NeuroScan data format for specific files, create a file, named "16bit" or "32bit", and place it in the data folder.

'''ScaleAmplitudesForNNChannels=25''' Scale waveforms as if a fixed number of channels were displayed in the window (here: 25). A minimum of 10 channels can be used for the scaling. This parameter is superseded if the parameter "''ScaleAmplitudesFixedPixelHeight"'' is specified.

'''ScaleAmplitudesFixedPixelHeight=70''' Set the scale bar for amplitudes to a fixed pixel height (here: 70). If this parameter is set in the '''.ini''' file, it supersedes the parameter "''ScaleAmplitudesForNNChannels''".

'''Notes'''

Check the Menu descriptions for the various definitions of filters, montages etc. For montage preselection, use the labels as visible on the montage push-buttons.

The additional channels file should contain all polygraphic channels (e.g. EKG, EOG, respiratory) that you want to view regularly along with the scalp channels. The entry AdditionalChannelFile must specify the full path pointing to the location of additional channel files (recommended: ''Montages\AdditionalChannels''). If no drive is specified, the installation drive of BESA is used.

If BaselineCorrection is set to 'On', before displaying a screen of data, BESA subtracts for each channel the mean over its displayed time points. This optimizes viewing, because it ensures that the vertical position of each channel is not shifted upward or downward from the channel label at the left of the screen. There are some cases in which you will not want baseline correction, i.e. when the DC level in the data is already correctly defined. This is usually the case, for instance, when reading in files that have been processed by BESA. In this case, BaselineCorrection should be set to 'Off', because otherwise maps and source montage displays may be distorted.

=== Folders ===

'''The [Folders] section defines where BESA Research places its files. In versions 5.1 and earlier, files were located in various subfolders of the program folder. This led to problems if the user did not have administrator rights, e.g. to create or write to a file. For Vista compatibility, many folders are now located by default in locations where normal users can create and write files. If you wish, you can also specify paths in the [Folders] section to use the previous locations. The previous location is given for each variable.'''

These settings allow some flexibility that can be useful if you want to tune BESA Research for use by several users, or on a network. For instance, the Examples and Montages folders might be located on a network disk. For the current defaults, the database, Examples, Montages, and Scripts are set up for use by all users on the PC on which BESA Research is installed. The settings files ('''Besa.set''', '''Besa.cfg''', etc.) are located in private folders so that each user retains his or her own settings.

The '''default''' settings (i.e. settings that BESA Research uses if the entries are omitted in the '''.ini''' file) are shown for each variable definition.

The folder definitions can use '''placeholders''', labels enclosed by a % sign (e.g. %localapp%), to define paths that vary depending on the language version and on the system (XP or Vista). These are defined below.

'''The Variables'''

'''Database=%localapp%''' The path of the BESA Research database folder (used to be ''%progdir%System\DB'' in BESA versions up to 5.1.x). Unless the provided path ends with ''\DB'' or ''\Database'', BESA Research will automatically create a folder named ''Database'' in the provided path.

'''Settings=%privatprog%Settings''' The path of the BESA Research settings folder (used to be ''%progdir%System'' in BESA versions up to 5.1.x)

'''Montages=%publicprog%Montages''' The path of the BESA Research montages folder (used to be ''%progdir%Montages'' in BESA versions up to 5.1.x)

'''Scripts=%publicprog%Scripts''' The path of the BESA Research Scripts folder (used to be ''%progdir%Scripts'' in BESA versions up to 5.1.x)

'''Examples=%publicprog%Examples''' The path of the BESA Research Examples folder (used to be ''%progdir%Examples'' in BESA versions up to 5.1.x)

'''User=%privatprog%Settings''' The path for user defined settings (used to be ''%progdir%System\Userdirs'' in BESA versions up to 5.1.x)

'''Placeholders'''

The strings enclosed by percent signs (%) are placeholders for the following folders in English-language versions of Windows. Folder names are different for Vista and XP/2000 and for other language settings. BESA Research will substitute the placeholders by the appropriate folder name for the system (W2K, XP, Vista, or Win7) and the system language:

* '''Windows 7(English):'''

'''%localapp%''' = "''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Libraries\Documents\Public'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Libraries\Documents\My'' ''Documents\Research_6_0''" or "''Desktop\[User]\My Documents\BESA\Research_6_0''.

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

* '''Windows Vista (English'''):

'''%localapp% '''<nowiki>= "</nowiki>''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Desktop\Public\Public Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''  

* '''Windows XP (English):'''

'''%localapp% '''<nowiki>= "</nowiki>''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0". ''This folder is directly accessible from the Windows Explorer under "''My Computer\Shared'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''My Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%  '''

* '''Windows 2000 (English):'''

'''%localapp%''' = "''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer '''as "'''''My Documents\BESA\Research_6_0'''''". '''

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

=== Electrodes ===

'''This section allows for automatic relabeling of electrodes. For instance, the 10-20 label "T3" can be replaced by the 10-10 convention "T7".'''

'''Default settings provided for section [Electrodes]:'''

T7=T3 replace 10-10 label with old 10-20 convention

T8=T4 replace 10-10 label with old 10-20 convention

P7=T5 replace 10-10 label with old 10-20 convention

P8=T6 replace 10-10 label with old 10-20 convention

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

Other examples, depending on your electrode input box definition, could be:

PG1=LO1 define X3 as lateral orbital eye electrode left

PG2=LO2 bipolar LO1-LO2 defines horizontal EOG (additional channel)

X3=IO1 infraorbital, e.g. use with FP1 as additional channel for VEOG

X9=Rsp define X9 channel to be a respiratory channel

Relabeling of channel names (as stored in the EEG file header) is helpful to predefine your standard sequence of channels and to avoid the need for reading and/or editing a Channel Configuration file for every EEG file.

'''Note 1''': For polygraphic channels, or if your EKG has been recorded differentially, you should edit and define an ''Additional Channels Montage'' according to your recording channel configuration (e.g. Fp1-IO1=vertical EOG). The Additional Channels group permits to display these channels regularly below the scalp montages with individual scales.

'''Note 2''': EOG channels record both eye and scalp activity. In digital EEG systems, EOG electrodes should be labeled according to their position in the 10-10 system (see "''Electrode Conventions''"). This permits use of these electrodes for mapping and suppression of eye artifacts. The standard definitions above give an example of how to relabel extra channels (X1...X10, PG1, PG2) for the use of EOG, EKG and respiratory (Rsp) channels. Use an ''Additional Channels'' file to define horizontal and vertical EOG channels by using the appropriate electrodes in a bipolar montage (an example is provided in '''eog-ecg.mtg''' in ''Montages\AdditionalChannels''). Differentially recorded EKG and respiratory channel can be defined in the same file.

=== Patterns ===

'''Default settings provided for section [Patterns]:'''

These settings define labels for each of the five patterns. The labels are shown* in the''' Tags''' menu,
* in the '''TAG push-button''' popup menu, and
* when displaying tag info clicking with the right mouse on a tag at the bottom of the EEG or on the event bar.

By default, no labels are defined. Define a label, e.g. for Pattern1 and Pattern2, as in the following example:

Pattern1=Spike

Pattern2=Sharp Wave

=== Artifacts ===

'''Artifact default settings:'''

See the chapter "''Artifact Correction / Reference / Artifact settings in the BESA.ini file''" in the online help.

=== Search ===

Default settings for pattern search.

'''Default Settings for the ''Search/Options ''Dialog box:'''

'''CorrelationThreshold''' = '''75%'''

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

'''Default Settings for the ''Search/Average/View'' (SAV) Dialog box:'''

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

'''HighPassSlope = 12 dB/Octave'''

'''HighPassType = 0 (0 = zero phase, 1 = forward, 2 = backward'''

'''LowPassFreq = 35 Hz'''

'''LowPassSlope = 24 dB/Octave'''

'''LowPassType = 0 (0 = zero phase, 1 = forward, 2 = backward)'''

'''CorrelationThresholdNoMarked = 60%'''

Default correlation threshold if no channel labels are marked when the SAV Dialog is opened.

'''CorrelationThresholdOneMarked = 85%'''

Default correlation threshold if one channel label is marked when the SAV Dialog is opened.

'''CorrelationThresholdFourMarked = 65%'''

Default correlation threshold if between two channel labels are marked when the SAV Dialog is opened.

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

If set to "Yes", a File Save dialog will open, to allow to save the search average to a file (as with the SAW function).

'''WriteAfterSearchCheckBox = No'''

If set to "Yes", an additional checkbox "Write after search" is displayed at the bottom of the SAV Dialog, allowing to choose whether or not to write the search average after a search:

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

If set to "No", the SAV Dialog will open with the same boxes checked as the last time the dialog was opened during the current session.

If set to "Yes", the default frequency, buffer width, selected view after search, and default threshold are always checked when the dialog is opened.

=== KeyControls ===

In the [KeyControls] section you can specify functions that can be allocated to '''function keys''' or to the ''Del'' key. Specify using the form:

'''Fn=function''' or

'''Del=function'''

where "''n''" is a number between 2 and 12 (F1 is reserved for Help). For example:

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

'''Pattern''n''''', where ''n''<nowiki>=1-5: Sets the tag number </nowiki>''n'' at the cursor latency.

'''Epochfast:''' sets one boundary of an epoch at the cursor latency, but does not open the epoch text box to define a label.

'''Marker:'''  sets a marker at the cursor latency.

'''Comment:''' sets a comment at the cursor latency and opens the comment box to enter text.

'''Epoch:''' sets one boundary of an epoch at the cursor latency and opens the epoch text box to enter a label.

'''Artifact:''' sets one boundary of an artifact segment at the cursor latency.

'''Delete:'''  deletes a tag at the cursor latency

'''Batches and Montages:'''

'''Batch''n''''', where n=1-12: Runs a predefined batch file corresponding to the number ''n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a batch, pressing it will open a ''File Open Dialog'' to select a batch. The setting you have chosen will be retained across BESA Research sessions. Holding the '''<shift>''' key while pressing the '''function key''' will always open the dialog. Hold the''' <ctrl> '''key with the function key to open the associated batch in the batch edit dialog.</div>

'''Montage''n''''', where n=1-12: Sets a montage corresponding to the number'' n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a montage, pressing it will generate a message asking you to associate a montage as follows: Holding the '''<shift> '''key while pressing the '''function key''' will remove the current association, and substitute it with the current montage.</div>

The default settings after program installation are listed in the online help chapter ''Review / Reference / Controls / Mouse and Keyboard / Keyboard Controls''.

=== FFT ===

'''Default settings provided for section [FFT]:'''

These settings define the setup in the Spectral Analysis section of the BESA Research program (FFT window, see the chapter "''Spectral Analysis / FFT''"). Up to 7 frequency bands may be defined. Five are defined by default.

'''FFTBand1=On''' FFT Bands 1-5 are defined

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

'''FFTBand6=Off''' FFT Bands 6-7 are not defined

'''FFTBand7=Off'''

'''FFTNameBand1=Delta''' Names of the defined bands

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

'''FFTColorBand1=RGB(0,0,0)'''  Default color of each band

'''FFTColorBand2=RGB(0,128,64)'''

'''FFTColorBand3=RGB(128,0,0)'''

'''FFTColorBand4=RGB(255,0,0)'''

'''FFTColorBand5=RGB(255,128,0)'''

'''FFTColorBand6=RGB(255,192,0)'''

'''FFTColorBand7=RGB(255,255,0)'''

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

'''FFTLowBand3=8''' Alpha from 8-14 Hz

'''FFTHighBand3=14'''

'''FFTLowBand4=14''' Beta from 14-30 Hz

'''FFTHighBand4=30'''

'''FFTLowBand5=30''' Gamma from 30-50 Hz

'''FFTHighBand5=50'''

These values are best set from within BESA Research, using the '''Options''' menu in the FFT window (see the chapter "''Spectral Analysis / FFT / FFT Options Menu''"). Current settings are stored after each session and retrieved in the next session.

=== Printer ===

'''Default settings provided for section [Printer]:'''

'''PrinterMarginPercent=100''' controls size of printout

'''PrinterColors=256''' set to 1/2 for black&white, 0/256 for color printers

'''PrinterLineMode=1''' set to 2 for thicker lines and to save printer memory

'''PrinterMapResolution=1''' set to 2, 3, 4 to save printer memory and increase speed

=== Calibration ===

'''Default settings provided for section [Calibration]:'''

'''AutoCalibration=Off''' On: automatic calibration of signals >= 4 cycles

'''MicrovoltCalibration=50''' peak voltage of calibration signal

If calibration is set to'' On'', the menu item ''Calibration ''will appear in the''' Process '''menu. Position your current screen at an epoch containing at least 4 regular cycles of the calibration signal (in all channels!) and select Calibration.

=== Video ===

'''Default settings provided for section [Video]:'''

'''DVCFilePath=C:\DVC\DVPlay.exe''' holds the path to the digital video player

'''DVCCommandLineArguments=/S:3 /M:P /T:M'''  arguments to be passed to the digital video player

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

'''MappingRepetitionRateWithVideoInMS=100'''  gives the number of milliseconds between two maps if the mapping window is open while the video is running. If the graphics board encounters problems during the display, this value should be increased.

=== Mapping ===

'''Default settings provided for section [Mapping]:'''

'''UseBitmapDrawing=Off'''

Set this to "On" if 3D maps show a strange pattern of black triangular shapes (this is frequently observed with modern Intel On-Board graphics controllers, and is a result of inadequate drivers for Open-GL).

'''Use3DVBlending=Auto'''

Set this to "Off" if the 3D view in the Montage Editor or the Source Analysis window does not show up properly (this may happen with some older graphics cards).

Set this to "On" if the 3D view in the Montage Editor or the Source Analysis window shows a ragged surface boundary.

'''MapSmoothing=0 '''

Set a non-zero value to specify a default map smoothing parameter (normally specified in ''Options/Mapping/Spline Interpolation Smoothing Constant'').

=== Matlab ===

'''Default settings for the [Matlab] section:'''

'''Platform=32'''

'''Set Platform=64''' if you want to use the 64-bit version of Matlab

=== Updates ===

This section is not normally required, but the variables here can be altered or defined to determine how BESA Research checks for dongle and program updates.

'''DaysBetweenUpdateChecks=7'''

Sets the number of days between automatic checks for updates. Set the value to 0 to check every time BESA Research is started. Set to -1 to turn off automatic update checks.

'''CheckNetworkDongle=Off'''

For the network administrator: If set to "On", BESA Research will check the dongle on the network for updates. Otherwise the state of the network dongle will be ignored.

'''LocalPath'''

For the network administrator. This can be set to a path on the local network to the BESA update files, so that users can obtain their updates locally. The path is given to the text file "'''UpdateVersions.txt'''" (e.g. ''LocalPath=\\transtec-sak\zarascratch\BESA\Updates\UpdateVersions.txt''), which contains further details for the program to obtain its updates. If you want to use this feature, please contact us at support@besa.de.

The following variables are not required, because BESA Research has the paths hardwired:

'''FTP1 (also FTP2, FTP3)'''

ftp download server

'''Path1 (also Path2, Path3)'''

Path on the server to UpdateVersions.txt.

'''HaspPath1 (also HaspPath2, HaspPath3)'''

Path on the server to HASP (dongle) update files.

'''History'''

Path on the server to general history file

=== Reader-Specific Settings ===

'''BrainLab'''

'''Default settings provided for section [BrainLab]:'''

'''BrainLabFormat=New''' this entry ensures that the newer BrainLab file format can be read by BESA Research.

'''Bio-Logic'''

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:
* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>
* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

'''EDF+/BDF/Trackit'''

'''TriggerScan=On'''

Set '''TriggerScan=Off '''to prevent BESA Research from scanning the file for triggers. This is done separately for EDF+, BDF, and Trackit files in sections '''[EDF+], [BDF],''' and '''[Trackit]''' in the '''BESA.ini''' file.

'''EGI'''

The treatment of DIN events can be modified in the''' [EGI] '''section:

'''CombineDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you want to treat DIN events separately, and not generate combined values.

'''SeparateDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you don’t want to treat DIN events separately.

Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

'''CombineDINeventsPrefix'''<nowiki>=dinComb</nowiki>

<div style="margin-left:0.953cm;margin-right:0cm;">This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

'''Harmonie'''

'''Default settings provided for section [Harmonie] (Stellate Harmonie systems):'''

'''SeizurePreEpoch=60''' length of the epoch preceding a seizure detection in s

'''SeizurePostEpoch=60''' length of the epoch following a seizure detection in s

'''PushButtonPreEpoch=60''' length of the epoch preceding a push button detection

'''PushButtonPostEpoch=60''' length of the epoch following a push button detection

When BESA Research encounters a seizure detection event or a push button detection event in a Stellate Harmonie file, it automatically sets an epoch around the event, which makes it convenient to view just those epochs for analysis. The length of the epochs preceding and following the events can be adjusted in the '''.ini''' file.

'''Neuroscan Keys'''

'''Note that there is a setting "NeuroScanDataNumberOfBits" in the [Defaults] section of BESA.ini that is used for distinguishing the data format of Neuroscan files (16 or 32-bit).'''

'''Default settings provided for section [NeuroScan Keys] (NeuroScan systems):'''

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

'''NKT2100'''

'''Default settings provided for section [NKT2100] (Nihon Kohden EEG 21xx systems):'''

'''TriggerScan=On'''   Set to "Off" to prevent a scan for trigger events.

'''Country=NotKanji''' set to NotKanji for non-Kanji characters else to Kanji

'''KanjiCharSize=16''' Kanji character size

'''KanjiPrinterCharSize=32''' Kanji printer character size

'''EEG_Sensitivity=50''' default sensitivity of Nihon Kohden EEG-2100 system

'''DC_Sensitivity=50''' default sensitivity of Nihon Kohden DAE-2100 system

'''QJ_Sensitivity=100''' default sensitivity of Nihon Kohden QJ-403 system

'''Mark_Sensitivity=100''' default sensitivity of EEG-2100 marker channels

These settings need to be changed only if the manufacturer has specified different gains for your system. Otherwise do not alter these settings.

'''Vangard'''

'''AlwaysOpenFileSelect=Yes'''

If "Yes" is selected, each time a Vangard file is opened, a dialog box will open, asking for a selection of the segment type to display.

If "No" is selected, the selection dialog is opened whenever a Vangard file is opened for the first time, or if the ''Channel and digitized head surface point information dialog box'' is opened (e.g. with '''ctrl-L''' or ''File/Head Surface Points and Sensors/Load Coordinate Files...'' ).

'''XLTEK'''

'''TriggerScan=Off '''Set to "On" to scan the data file for trigger events

'''MontageNo=2''' Set to 1 or 2. If two montages for the data file are defined, this variable determines whether the first or the second alternative should be used.

The Initialization File: BESA.ini

2017-04-07T09:21:29Z

Alexa:

== The Initialization File: BESA.ini ==

=== Introduction ===

'''BESA.ini File'''

BESA Research uses settings provided in the initialization file '''BESA.ini''' whenever BESA Research is started or a new file is opened for the first time. The format of this file conforms with standard initialization files ('''<nowiki>*.ini</nowiki>''') of Windows. You may change the settings in '''BESA.ini''' using NOTEPAD.exe from the ACCESSORIES group, or other plain text editors to adapt BESA Research to '''your own everyday needs'''. The default settings provided in '''BESA.ini''' will be used by BESA Research whenever BESA Research or the launch program is started. It is advised that you make a backup copy of '''BESA.ini''' before you change the default settings.

'''Location of BESA.ini'''

You can place '''BESA.ini''' at three possible locations:

'''a) Private''': each user on a PC should have his/her own private settings. This is normally in ''My'' ''Documents/BESA/Research_6_0''

'''b) Public''':  all users should use one setting, but they can edit '''BESA.ini''' to change the settings. This is normally in ''Shared Documents/BESA/Research_6_0''

'''c) Administrator''': the PC administrator determines the settings. This is normally in ''C:Program'' ''Files/BESA/Research_6_0''

The actual folder names depend on the operating system and the system language.

When BESA starts, it first looks for the''' administrator''' version of '''BESA.ini'''. If this is not found, it looks for the '''private''' version. If this is not found, it looks for the '''public''' version. If this is not found, internal default values are used.

'''There are 13 general sections, and several reader-specific sections:'''

[Defaults]                   -- General settings (filters, scaling, and various other settings)

[Folders]                    -- Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)

[Electrodes]               -- Electrode renaming

[Patterns]                   -- Rename patterns in the '''Tags''' menu

[Artifacts]                   -- Settings for artifact correction

[KEYCONTROLS]     -- Function key definitions

[Search]                     -- Default parameters for search

[FFT]                          -- Frequency band definitions

[Printer]                      -- Printer control

[Calibration]              -- Calibration control

[Video]                      -- Digital video control

[Mapping]                  -- Mapping control

[Matlab]                     -- Settings for the Matlab interface

[Updates]                  -- Options for program updates

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

=== Defaults ===

'''Default settings provided for section [Defaults]:'''

'''DatabaseAllowLocalFiles=Yes''' (If set to "Yes", BESA Research will write filenames "'''datafilename.ftg'''" and "'''datafilename.fst"''' to the data folder, saving current file tag and display settings there. If set to "No", these files are only written to the database. If set to "Yes", you can copy these files along with the data to a new folder, and display settings and tags will be preserved.)

'''DataBuffering=Off''' (If set to "On", an internal buffer of length 180 s of data is kept to speed up paging). This can speed up paging, particularly when the data are in a network folder.

'''DisplayedTime=10''' displayed time window [s] on the screen

'''Montage=Org''' montage used when opening a new file

'''ScpScale=50''' scale of scalp channels in [mV]

'''PgrScale=500''' scale of polygraphic channels in [mV]

'''IcrScale=500''' scale of intracranial channels in [mV]

'''MegScale=500''' scale of MEG/marker channels in [fT]

'''BaselineCorrection=On''' baseline correction, do not switch off in AC systems

'''ClippingPercent= '''set from 100 to 200 if you want to clip artifacts in displayed EEG (not used if empty or 0)

'''LowFilter=''' low filter cutoff frequency [Hz] (variable filter)

'''TimeConstant=0.3''' time constant for low filter cutoff frequency [sec] (fixed forward filter, 0.3 sec is equivalent to 0.53 Hz)

'''HighFilter=70''' high filter cutoff frequency [Hz] (variable filter)

'''NotchFilter=50''' notch filter center frequency [Hz]

'''NotchFilterStatus=Off''' notch filter is off, set=On if you want to use as default

'''BandFilter=12''' band pass filter center frequency [Hz]

'''BandFilterStatus=Off''' band pass is off, set=On if you want to use as default

'''AdditionalChannelFile=''' defines the full path and name of an additional channels montage file, e.g. '''C:\Program Files\BESA\Research_x\Montages\AdditionalChannels\EKG.sel'''

'''ColoredWaveforms=On''' scalp waveforms are (not) colored according to region

'''WriteSegmentPath=''' defines default path for saving segments/averages. If blank, the path of the current data file is used.

'''ShowSubjectInfo=Off''' subject info will (not) be displayed.

The following optional parameters are not defined as default and can be set manually in''' BESA.ini''':

'''TextEditor="Notepad.exe"''' defines the path to your preferred text editor. This will be used when you press the '''Edit''' button the ''Load Coordinate Files dialog box''.

'''NeuroScanDataNumberOfBits=32''' defines the format of NeuroScan data files ('16' for 16-bit, '32' for 32-bit). If this variable is not specified, BESA uses a heuristic to (try to) decide which of the two data formats is used. This variable overrides the heuristic. If you want to specify the NeuroScan data format for specific files, create a file, named "16bit" or "32bit", and place it in the data folder.

'''ScaleAmplitudesForNNChannels=25''' Scale waveforms as if a fixed number of channels were displayed in the window (here: 25). A minimum of 10 channels can be used for the scaling. This parameter is superseded if the parameter "''ScaleAmplitudesFixedPixelHeight"'' is specified.

'''ScaleAmplitudesFixedPixelHeight=70''' Set the scale bar for amplitudes to a fixed pixel height (here: 70). If this parameter is set in the '''.ini''' file, it supersedes the parameter "''ScaleAmplitudesForNNChannels''".

'''Notes'''

Check the Menu descriptions for the various definitions of filters, montages etc. For montage preselection, use the labels as visible on the montage push-buttons.

The additional channels file should contain all polygraphic channels (e.g. EKG, EOG, respiratory) that you want to view regularly along with the scalp channels. The entry AdditionalChannelFile must specify the full path pointing to the location of additional channel files (recommended: ''Montages\AdditionalChannels''). If no drive is specified, the installation drive of BESA is used.

If BaselineCorrection is set to 'On', before displaying a screen of data, BESA subtracts for each channel the mean over its displayed time points. This optimizes viewing, because it ensures that the vertical position of each channel is not shifted upward or downward from the channel label at the left of the screen. There are some cases in which you will not want baseline correction, i.e. when the DC level in the data is already correctly defined. This is usually the case, for instance, when reading in files that have been processed by BESA. In this case, BaselineCorrection should be set to 'Off', because otherwise maps and source montage displays may be distorted.

=== Folders ===

'''The [Folders] section defines where BESA Research places its files. In versions 5.1 and earlier, files were located in various subfolders of the program folder. This led to problems if the user did not have administrator rights, e.g. to create or write to a file. For Vista compatibility, many folders are now located by default in locations where normal users can create and write files. If you wish, you can also specify paths in the [Folders] section to use the previous locations. The previous location is given for each variable.'''

These settings allow some flexibility that can be useful if you want to tune BESA Research for use by several users, or on a network. For instance, the Examples and Montages folders might be located on a network disk. For the current defaults, the database, Examples, Montages, and Scripts are set up for use by all users on the PC on which BESA Research is installed. The settings files ('''Besa.set''', '''Besa.cfg''', etc.) are located in private folders so that each user retains his or her own settings.

The '''default''' settings (i.e. settings that BESA Research uses if the entries are omitted in the '''.ini''' file) are shown for each variable definition.

The folder definitions can use '''placeholders''', labels enclosed by a % sign (e.g. %localapp%), to define paths that vary depending on the language version and on the system (XP or Vista). These are defined below.

'''The Variables'''

'''Database=%localapp%''' The path of the BESA Research database folder (used to be ''%progdir%System\DB'' in BESA versions up to 5.1.x). Unless the provided path ends with ''\DB'' or ''\Database'', BESA Research will automatically create a folder named ''Database'' in the provided path.

'''Settings=%privatprog%Settings''' The path of the BESA Research settings folder (used to be ''%progdir%System'' in BESA versions up to 5.1.x)

'''Montages=%publicprog%Montages''' The path of the BESA Research montages folder (used to be ''%progdir%Montages'' in BESA versions up to 5.1.x)

'''Scripts=%publicprog%Scripts''' The path of the BESA Research Scripts folder (used to be ''%progdir%Scripts'' in BESA versions up to 5.1.x)

'''Examples=%publicprog%Examples''' The path of the BESA Research Examples folder (used to be ''%progdir%Examples'' in BESA versions up to 5.1.x)

'''User=%privatprog%Settings''' The path for user defined settings (used to be ''%progdir%System\Userdirs'' in BESA versions up to 5.1.x)

'''Placeholders'''

The strings enclosed by percent signs (%) are placeholders for the following folders in English-language versions of Windows. Folder names are different for Vista and XP/2000 and for other language settings. BESA Research will substitute the placeholders by the appropriate folder name for the system (W2K, XP, Vista, or Win7) and the system language:

* '''Windows 7(English):'''

'''%localapp%''' = "''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Libraries\Documents\Public'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Libraries\Documents\My'' ''Documents\Research_6_0''" or "''Desktop\[User]\My Documents\BESA\Research_6_0''.

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

* '''Windows Vista (English'''):

'''%localapp% '''<nowiki>= "</nowiki>''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Desktop\Public\Public Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''  

* '''Windows XP (English):'''

'''%localapp% '''<nowiki>= "</nowiki>''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0". ''This folder is directly accessible from the Windows Explorer under "''My Computer\Shared'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''My Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%  '''

* '''Windows 2000 (English):'''

'''%localapp%''' = "''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer '''as "'''''My Documents\BESA\Research_6_0'''''". '''

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

=== Electrodes ===

'''This section allows for automatic relabeling of electrodes. For instance, the 10-20 label "T3" can be replaced by the 10-10 convention "T7".'''

'''Default settings provided for section [Electrodes]:'''

T7=T3 replace 10-10 label with old 10-20 convention

T8=T4 replace 10-10 label with old 10-20 convention

P7=T5 replace 10-10 label with old 10-20 convention

P8=T6 replace 10-10 label with old 10-20 convention

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

Other examples, depending on your electrode input box definition, could be:

PG1=LO1 define X3 as lateral orbital eye electrode left

PG2=LO2 bipolar LO1-LO2 defines horizontal EOG (additional channel)

X3=IO1 infraorbital, e.g. use with FP1 as additional channel for VEOG

X9=Rsp define X9 channel to be a respiratory channel

Relabeling of channel names (as stored in the EEG file header) is helpful to predefine your standard sequence of channels and to avoid the need for reading and/or editing a Channel Configuration file for every EEG file.

'''Note 1''': For polygraphic channels, or if your EKG has been recorded differentially, you should edit and define an ''Additional Channels Montage'' according to your recording channel configuration (e.g. Fp1-IO1=vertical EOG). The Additional Channels group permits to display these channels regularly below the scalp montages with individual scales.

'''Note 2''': EOG channels record both eye and scalp activity. In digital EEG systems, EOG electrodes should be labeled according to their position in the 10-10 system (see "''Electrode Conventions''"). This permits use of these electrodes for mapping and suppression of eye artifacts. The standard definitions above give an example of how to relabel extra channels (X1...X10, PG1, PG2) for the use of EOG, EKG and respiratory (Rsp) channels. Use an ''Additional Channels'' file to define horizontal and vertical EOG channels by using the appropriate electrodes in a bipolar montage (an example is provided in '''eog-ecg.mtg''' in ''Montages\AdditionalChannels''). Differentially recorded EKG and respiratory channel can be defined in the same file.

=== Patterns ===

'''Default settings provided for section [Patterns]:'''

These settings define labels for each of the five patterns. The labels are shown* in the''' Tags''' menu,
* in the '''TAG push-button''' popup menu, and
* when displaying tag info clicking with the right mouse on a tag at the bottom of the EEG or on the event bar.

By default, no labels are defined. Define a label, e.g. for Pattern1 and Pattern2, as in the following example:

Pattern1=Spike

Pattern2=Sharp Wave

=== Artifacts ===

'''Artifact default settings:'''

See the chapter "''Artifact Correction / Reference / Artifact settings in the BESA.ini file''" in the online help.

=== Search ===

Default settings for pattern search.

'''Default Settings for the ''Search/Options ''Dialog box:'''

'''CorrelationThreshold''' = '''75%'''

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

'''Default Settings for the ''Search/Average/View'' (SAV) Dialog box:'''

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

'''HighPassSlope = 12 dB/Octave'''

'''HighPassType = 0 (0 = zero phase, 1 = forward, 2 = backward'''

'''LowPassFreq = 35 Hz'''

'''LowPassSlope = 24 dB/Octave'''

'''LowPassType = 0 (0 = zero phase, 1 = forward, 2 = backward)'''

'''CorrelationThresholdNoMarked = 60%'''

Default correlation threshold if no channel labels are marked when the SAV Dialog is opened.

'''CorrelationThresholdOneMarked = 85%'''

Default correlation threshold if one channel label is marked when the SAV Dialog is opened.

'''CorrelationThresholdFourMarked = 65%'''

Default correlation threshold if between two channel labels are marked when the SAV Dialog is opened.

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

If set to "Yes", a File Save dialog will open, to allow to save the search average to a file (as with the SAW function).

'''WriteAfterSearchCheckBox = No'''

If set to "Yes", an additional checkbox "Write after search" is displayed at the bottom of the SAV Dialog, allowing to choose whether or not to write the search average after a search:

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

If set to "No", the SAV Dialog will open with the same boxes checked as the last time the dialog was opened during the current session.

If set to "Yes", the default frequency, buffer width, selected view after search, and default threshold are always checked when the dialog is opened.

=== KeyControls ===

In the [KeyControls] section you can specify functions that can be allocated to '''function keys''' or to the ''<Del>'' key. Specify using the form:

'''Fn=function''' or

'''Del=function'''

where "''n''" is a number between 2 and 12 (F1 is reserved for Help). For example:

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

'''Pattern''n''''', where ''n''<nowiki>=1-5: Sets the tag number </nowiki>''n'' at the cursor latency.

'''Epochfast:''' sets one boundary of an epoch at the cursor latency, but does not open the epoch text box to define a label.

'''Marker:'''  sets a marker at the cursor latency.

'''Comment:''' sets a comment at the cursor latency and opens the comment box to enter text.

'''Epoch:''' sets one boundary of an epoch at the cursor latency and opens the epoch text box to enter a label.

'''Artifact:''' sets one boundary of an artifact segment at the cursor latency.

'''Delete:'''  deletes a tag at the cursor latency

'''Batches and Montages:'''

'''Batch''n''''', where n=1-12: Runs a predefined batch file corresponding to the number ''n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a batch, pressing it will open a ''File Open Dialog'' to select a batch. The setting you have chosen will be retained across BESA Research sessions. Holding the '''<shift>''' key while pressing the '''function key''' will always open the dialog. Hold the''' <ctrl> '''key with the function key to open the associated batch in the batch edit dialog.</div>

'''Montage''n''''', where n=1-12: Sets a montage corresponding to the number'' n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a montage, pressing it will generate a message asking you to associate a montage as follows: Holding the '''<shift> '''key while pressing the '''function key''' will remove the current association, and substitute it with the current montage.</div>

The default settings after program installation are listed in the online help chapter ''Review / Reference / Controls / Mouse and Keyboard / Keyboard Controls''.

=== FFT ===

'''Default settings provided for section [FFT]:'''

These settings define the setup in the Spectral Analysis section of the BESA Research program (FFT window, see the chapter "''Spectral Analysis / FFT''"). Up to 7 frequency bands may be defined. Five are defined by default.

'''FFTBand1=On''' FFT Bands 1-5 are defined

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

'''FFTBand6=Off''' FFT Bands 6-7 are not defined

'''FFTBand7=Off'''

'''FFTNameBand1=Delta''' Names of the defined bands

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

'''FFTColorBand1=RGB(0,0,0)'''  Default color of each band

'''FFTColorBand2=RGB(0,128,64)'''

'''FFTColorBand3=RGB(128,0,0)'''

'''FFTColorBand4=RGB(255,0,0)'''

'''FFTColorBand5=RGB(255,128,0)'''

'''FFTColorBand6=RGB(255,192,0)'''

'''FFTColorBand7=RGB(255,255,0)'''

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

'''FFTLowBand3=8''' Alpha from 8-14 Hz

'''FFTHighBand3=14'''

'''FFTLowBand4=14''' Beta from 14-30 Hz

'''FFTHighBand4=30'''

'''FFTLowBand5=30''' Gamma from 30-50 Hz

'''FFTHighBand5=50'''

These values are best set from within BESA Research, using the '''Options''' menu in the FFT window (see the chapter "''Spectral Analysis / FFT / FFT Options Menu''"). Current settings are stored after each session and retrieved in the next session.

=== Printer ===

'''Default settings provided for section [Printer]:'''

'''PrinterMarginPercent=100''' controls size of printout

'''PrinterColors=256''' set to 1/2 for black&white, 0/256 for color printers

'''PrinterLineMode=1''' set to 2 for thicker lines and to save printer memory

'''PrinterMapResolution=1''' set to 2, 3, 4 to save printer memory and increase speed

=== Calibration ===

'''Default settings provided for section [Calibration]:'''

'''AutoCalibration=Off''' On: automatic calibration of signals >= 4 cycles

'''MicrovoltCalibration=50''' peak voltage of calibration signal

If calibration is set to'' On'', the menu item ''Calibration ''will appear in the''' Process '''menu. Position your current screen at an epoch containing at least 4 regular cycles of the calibration signal (in all channels!) and select Calibration.

=== Video ===

'''Default settings provided for section [Video]:'''

'''DVCFilePath=C:\DVC\DVPlay.exe''' holds the path to the digital video player

'''DVCCommandLineArguments=/S:3 /M:P /T:M'''  arguments to be passed to the digital video player

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

'''MappingRepetitionRateWithVideoInMS=100'''  gives the number of milliseconds between two maps if the mapping window is open while the video is running. If the graphics board encounters problems during the display, this value should be increased.

=== Mapping ===

'''Default settings provided for section [Mapping]:'''

'''UseBitmapDrawing=Off'''

Set this to "On" if 3D maps show a strange pattern of black triangular shapes (this is frequently observed with modern Intel On-Board graphics controllers, and is a result of inadequate drivers for Open-GL).

'''Use3DVBlending=Auto'''

Set this to "Off" if the 3D view in the Montage Editor or the Source Analysis window does not show up properly (this may happen with some older graphics cards).

Set this to "On" if the 3D view in the Montage Editor or the Source Analysis window shows a ragged surface boundary.

'''MapSmoothing=0 '''

Set a non-zero value to specify a default map smoothing parameter (normally specified in ''Options/Mapping/Spline Interpolation Smoothing Constant'').

=== Matlab ===

'''Default settings for the [Matlab] section:'''

'''Platform=32'''

'''Set Platform=64''' if you want to use the 64-bit version of Matlab

=== Updates ===

This section is not normally required, but the variables here can be altered or defined to determine how BESA Research checks for dongle and program updates.

'''DaysBetweenUpdateChecks=7'''

Sets the number of days between automatic checks for updates. Set the value to 0 to check every time BESA Research is started. Set to -1 to turn off automatic update checks.

'''CheckNetworkDongle=Off'''

For the network administrator: If set to "On", BESA Research will check the dongle on the network for updates. Otherwise the state of the network dongle will be ignored.

'''LocalPath'''

For the network administrator. This can be set to a path on the local network to the BESA update files, so that users can obtain their updates locally. The path is given to the text file "'''UpdateVersions.txt'''" (e.g. ''LocalPath=\\transtec-sak\zarascratch\BESA\Updates\UpdateVersions.txt''), which contains further details for the program to obtain its updates. If you want to use this feature, please contact us at support@besa.de.

The following variables are not required, because BESA Research has the paths hardwired:

'''FTP1 (also FTP2, FTP3)'''

ftp download server

'''Path1 (also Path2, Path3)'''

Path on the server to UpdateVersions.txt.

'''HaspPath1 (also HaspPath2, HaspPath3)'''

Path on the server to HASP (dongle) update files.

'''History'''

Path on the server to general history file

=== Reader-Specific Settings ===

'''BrainLab'''

'''Default settings provided for section [BrainLab]:'''

'''BrainLabFormat=New''' this entry ensures that the newer BrainLab file format can be read by BESA Research.

'''Bio-Logic'''

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:
* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>
* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

'''EDF+/BDF/Trackit'''

'''TriggerScan=On'''

Set '''TriggerScan=Off '''to prevent BESA Research from scanning the file for triggers. This is done separately for EDF+, BDF, and Trackit files in sections '''[EDF+], [BDF],''' and '''[Trackit]''' in the '''BESA.ini''' file.

'''EGI'''

The treatment of DIN events can be modified in the''' [EGI] '''section:

'''CombineDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you want to treat DIN events separately, and not generate combined values.

'''SeparateDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you don’t want to treat DIN events separately.

Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

'''CombineDINeventsPrefix'''<nowiki>=dinComb</nowiki>

<div style="margin-left:0.953cm;margin-right:0cm;">This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

'''Harmonie'''

'''Default settings provided for section [Harmonie] (Stellate Harmonie systems):'''

'''SeizurePreEpoch=60''' length of the epoch preceding a seizure detection in s

'''SeizurePostEpoch=60''' length of the epoch following a seizure detection in s

'''PushButtonPreEpoch=60''' length of the epoch preceding a push button detection

'''PushButtonPostEpoch=60''' length of the epoch following a push button detection

When BESA Research encounters a seizure detection event or a push button detection event in a Stellate Harmonie file, it automatically sets an epoch around the event, which makes it convenient to view just those epochs for analysis. The length of the epochs preceding and following the events can be adjusted in the '''.ini''' file.

'''Neuroscan Keys'''

'''Note that there is a setting "NeuroScanDataNumberOfBits" in the [Defaults] section of BESA.ini that is used for distinguishing the data format of Neuroscan files (16 or 32-bit).'''

'''Default settings provided for section [NeuroScan Keys] (NeuroScan systems):'''

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

'''NKT2100'''

'''Default settings provided for section [NKT2100] (Nihon Kohden EEG 21xx systems):'''

'''TriggerScan=On'''   Set to "Off" to prevent a scan for trigger events.

'''Country=NotKanji''' set to NotKanji for non-Kanji characters else to Kanji

'''KanjiCharSize=16''' Kanji character size

'''KanjiPrinterCharSize=32''' Kanji printer character size

'''EEG_Sensitivity=50''' default sensitivity of Nihon Kohden EEG-2100 system

'''DC_Sensitivity=50''' default sensitivity of Nihon Kohden DAE-2100 system

'''QJ_Sensitivity=100''' default sensitivity of Nihon Kohden QJ-403 system

'''Mark_Sensitivity=100''' default sensitivity of EEG-2100 marker channels

These settings need to be changed only if the manufacturer has specified different gains for your system. Otherwise do not alter these settings.

'''Vangard'''

'''AlwaysOpenFileSelect=Yes'''

If "Yes" is selected, each time a Vangard file is opened, a dialog box will open, asking for a selection of the segment type to display.

If "No" is selected, the selection dialog is opened whenever a Vangard file is opened for the first time, or if the ''Channel and digitized head surface point information dialog box'' is opened (e.g. with '''ctrl-L''' or ''File/Head Surface Points and Sensors/Load Coordinate Files...'' ).

'''XLTEK'''

'''TriggerScan=Off '''Set to "On" to scan the data file for trigger events

'''MontageNo=2''' Set to 1 or 2. If two montages for the data file are defined, this variable determines whether the first or the second alternative should be used.

The Initialization File: BESA.ini

2017-04-07T09:15:46Z

Alexa:

== The Initialization File: BESA.ini ==

=== Introduction ===

'''BESA.ini File'''

BESA Research uses settings provided in the initialization file '''BESA.ini''' whenever BESA Research is started or a new file is opened for the first time. The format of this file conforms with standard initialization files ('''<nowiki>*.ini</nowiki>''') of Windows. You may change the settings in '''BESA.ini''' using NOTEPAD.exe from the ACCESSORIES group, or other plain text editors to adapt BESA Research to '''your own everyday needs'''. The default settings provided in '''BESA.ini''' will be used by BESA Research whenever BESA Research or the launch program is started. It is advised that you make a backup copy of '''BESA.ini''' before you change the default settings.

'''Location of BESA.ini'''

You can place '''BESA.ini''' at three possible locations:

'''a) Private''': each user on a PC should have his/her own private settings. This is normally in ''My'' ''Documents/BESA/Research_6_0''

'''b) Public''':  all users should use one setting, but they can edit '''BESA.ini''' to change the settings. This is normally in ''Shared Documents/BESA/Research_6_0''

'''c) Administrator''': the PC administrator determines the settings. This is normally in ''C:Program'' ''Files/BESA/Research_6_0''

The actual folder names depend on the operating system and the system language.

When BESA starts, it first looks for the''' administrator''' version of '''BESA.ini'''. If this is not found, it looks for the '''private''' version. If this is not found, it looks for the '''public''' version. If this is not found, internal default values are used.

'''There are 13 general sections, and several reader-specific sections:'''

[Defaults]                   -- General settings (filters, scaling, and various other settings)

[Folders]                    -- Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)

[Electrodes]               -- Electrode renaming

[Patterns]                   -- Rename patterns in the '''Tags''' menu

[Artifacts]                   -- Settings for artifact correction

[KEYCONTROLS]     -- Function key definitions

[Search]                     -- Default parameters for search

[FFT]                          -- Frequency band definitions

[Printer]                      -- Printer control

[Calibration]              -- Calibration control

[Video]                      -- Digital video control

[Mapping]                  -- Mapping control

[Matlab]                     -- Settings for the Matlab interface

[Updates]                  -- Options for program updates

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

=== Defaults ===

'''Default settings provided for section [Defaults]:'''

'''DatabaseAllowLocalFiles=Yes''' (If set to "Yes", BESA Research will write filenames "'''datafilename.ftg'''" and "'''datafilename.fst"''' to the data folder, saving current file tag and display settings there. If set to "No", these files are only written to the database. If set to "Yes", you can copy these files along with the data to a new folder, and display settings and tags will be preserved.)

'''DataBuffering=Off''' (If set to "On", an internal buffer of length 180 s of data is kept to speed up paging). This can speed up paging, particularly when the data are in a network folder.

'''DisplayedTime=10''' displayed time window [s] on the screen

'''Montage=Org''' montage used when opening a new file

'''ScpScale=50''' scale of scalp channels in [mV]

'''PgrScale=500''' scale of polygraphic channels in [mV]

'''IcrScale=500''' scale of intracranial channels in [mV]

'''MegScale=500''' scale of MEG/marker channels in [fT]

'''BaselineCorrection=On''' baseline correction, do not switch off in AC systems

'''ClippingPercent= '''set from 100 to 200 if you want to clip artifacts in displayed EEG (not used if empty or 0)

'''LowFilter=''' low filter cutoff frequency [Hz] (variable filter)

'''TimeConstant=0.3''' time constant for low filter cutoff frequency [sec] (fixed forward filter, 0.3 sec is equivalent to 0.53 Hz)

'''HighFilter=70''' high filter cutoff frequency [Hz] (variable filter)

'''NotchFilter=50''' notch filter center frequency [Hz]

'''NotchFilterStatus=Off''' notch filter is off, set=On if you want to use as default

'''BandFilter=12''' band pass filter center frequency [Hz]

'''BandFilterStatus=Off''' band pass is off, set=On if you want to use as default

'''AdditionalChannelFile=''' defines the full path and name of an additional channels montage file, e.g. '''C:\Program Files\BESA\Research_x\Montages\AdditionalChannels\EKG.sel'''

'''ColoredWaveforms=On''' scalp waveforms are (not) colored according to region

'''WriteSegmentPath=''' defines default path for saving segments/averages. If blank, the path of the current data file is used.

'''ShowSubjectInfo=Off''' subject info will (not) be displayed.

The following optional parameters are not defined as default and can be set manually in''' BESA.ini''':

'''TextEditor="Notepad.exe"''' defines the path to your preferred text editor. This will be used when you press the '''Edit''' button the ''Load Coordinate Files dialog box''.

'''NeuroScanDataNumberOfBits=32''' defines the format of NeuroScan data files ('16' for 16-bit, '32' for 32-bit). If this variable is not specified, BESA uses a heuristic to (try to) decide which of the two data formats is used. This variable overrides the heuristic. If you want to specify the NeuroScan data format for specific files, create a file, named "16bit" or "32bit", and place it in the data folder.

'''ScaleAmplitudesForNNChannels=25''' Scale waveforms as if a fixed number of channels were displayed in the window (here: 25). A minimum of 10 channels can be used for the scaling. This parameter is superseded if the parameter "''ScaleAmplitudesFixedPixelHeight"'' is specified.

'''ScaleAmplitudesFixedPixelHeight=70''' Set the scale bar for amplitudes to a fixed pixel height (here: 70). If this parameter is set in the '''.ini''' file, it supersedes the parameter "''ScaleAmplitudesForNNChannels''".

'''Notes'''

Check the Menu descriptions for the various definitions of filters, montages etc. For montage preselection, use the labels as visible on the montage push-buttons.

The additional channels file should contain all polygraphic channels (e.g. EKG, EOG, respiratory) that you want to view regularly along with the scalp channels. The entry AdditionalChannelFile must specify the full path pointing to the location of additional channel files (recommended: ''Montages\AdditionalChannels''). If no drive is specified, the installation drive of BESA is used.

If BaselineCorrection is set to 'On', before displaying a screen of data, BESA subtracts for each channel the mean over its displayed time points. This optimizes viewing, because it ensures that the vertical position of each channel is not shifted upward or downward from the channel label at the left of the screen. There are some cases in which you will not want baseline correction, i.e. when the DC level in the data is already correctly defined. This is usually the case, for instance, when reading in files that have been processed by BESA. In this case, BaselineCorrection should be set to 'Off', because otherwise maps and source montage displays may be distorted.

=== Folders ===

'''The [Folders] section defines where BESA Research places its files. In versions 5.1 and earlier, files were located in various subfolders of the program folder. This led to problems if the user did not have administrator rights, e.g. to create or write to a file. For Vista compatibility, many folders are now located by default in locations where normal users can create and write files. If you wish, you can also specify paths in the [Folders] section to use the previous locations. The previous location is given for each variable.'''

These settings allow some flexibility that can be useful if you want to tune BESA Research for use by several users, or on a network. For instance, the Examples and Montages folders might be located on a network disk. For the current defaults, the database, Examples, Montages, and Scripts are set up for use by all users on the PC on which BESA Research is installed. The settings files ('''Besa.set''', '''Besa.cfg''', etc.) are located in private folders so that each user retains his or her own settings.

The '''default''' settings (i.e. settings that BESA Research uses if the entries are omitted in the '''.ini''' file) are shown for each variable definition.

The folder definitions can use '''placeholders''', labels enclosed by a % sign (e.g. %localapp%), to define paths that vary depending on the language version and on the system (XP or Vista). These are defined below.

'''The Variables'''

'''Database=%localapp%''' The path of the BESA Research database folder (used to be ''%progdir%System\DB'' in BESA versions up to 5.1.x). Unless the provided path ends with ''\DB'' or ''\Database'', BESA Research will automatically create a folder named ''Database'' in the provided path.

'''Settings=%privatprog%Settings''' The path of the BESA Research settings folder (used to be ''%progdir%System'' in BESA versions up to 5.1.x)

'''Montages=%publicprog%Montages''' The path of the BESA Research montages folder (used to be ''%progdir%Montages'' in BESA versions up to 5.1.x)

'''Scripts=%publicprog%Scripts''' The path of the BESA Research Scripts folder (used to be ''%progdir%Scripts'' in BESA versions up to 5.1.x)

'''Examples=%publicprog%Examples''' The path of the BESA Research Examples folder (used to be ''%progdir%Examples'' in BESA versions up to 5.1.x)

'''User=%privatprog%Settings''' The path for user defined settings (used to be ''%progdir%System\Userdirs'' in BESA versions up to 5.1.x)

'''Placeholders'''

The strings enclosed by percent signs (%) are placeholders for the following folders in English-language versions of Windows. Folder names are different for Vista and XP/2000 and for other language settings. BESA Research will substitute the placeholders by the appropriate folder name for the system (W2K, XP, Vista, or Win7) and the system language:

* '''Windows 7(English):'''

'''%localapp%''' = "''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Libraries\Documents\Public'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Libraries\Documents\My'' ''Documents\Research_6_0''" or "''Desktop\[User]\My Documents\BESA\Research_6_0''.

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

* '''Windows Vista (English'''):

'''%localapp% '''<nowiki>= "</nowiki>''C:\Users\[user]\AppData\Local\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\AppData\Local\BESA\Research_6_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_6_0''". This folder is directly accessible from the Windows Explorer under "''Desktop\Public\Public Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''Desktop\[user]\Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''  

* '''Windows XP (English):'''

'''%localapp% '''<nowiki>= "</nowiki>''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0". ''This folder is directly accessible from the Windows Explorer under "''My Computer\Shared'' ''Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "''My Documents\BESA\Research_6_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%  '''

* '''Windows 2000 (English):'''

'''%localapp%''' = "''C:\Documents and Settings\[user]\Local Settings\Application Data\BESA\Research_6_0''", where [user] is the logon name of the current user.

'''%publicprog%''' = "''C:\Documents and Settings\All Users\Documents\BESA\Research_6_0''".

'''%privateprog%''' = "''C:\Documents and Settings\[user]\My Documents\BESA\Research_6_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer '''as "'''''My Documents\BESA\Research_6_0'''''". '''

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program'' ''Files\BESA\\Research_6_0''".

'''%besaroot%''' is the same as '''%progdir%'''

=== Electrodes ===

'''This section allows for automatic relabeling of electrodes. For instance, the 10-20 label "T3" can be replaced by the 10-10 convention "T7".'''

'''Default settings provided for section [Electrodes]:'''

T7=T3 replace 10-10 label with old 10-20 convention

T8=T4 replace 10-10 label with old 10-20 convention

P7=T5 replace 10-10 label with old 10-20 convention

P8=T6 replace 10-10 label with old 10-20 convention

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

Other examples, depending on your electrode input box definition, could be:

PG1=LO1 define X3 as lateral orbital eye electrode left

PG2=LO2 bipolar LO1-LO2 defines horizontal EOG (additional channel)

X3=IO1 infraorbital, e.g. use with FP1 as additional channel for VEOG

X9=Rsp define X9 channel to be a respiratory channel

Relabeling of channel names (as stored in the EEG file header) is helpful to predefine your standard sequence of channels and to avoid the need for reading and/or editing a Channel Configuration file for every EEG file.

'''Note 1''': For polygraphic channels, or if your EKG has been recorded differentially, you should edit and define an ''Additional Channels Montage'' according to your recording channel configuration (e.g. Fp1-IO1=vertical EOG). The Additional Channels group permits to display these channels regularly below the scalp montages with individual scales.

'''Note 2''': EOG channels record both eye and scalp activity. In digital EEG systems, EOG electrodes should be labeled according to their position in the 10-10 system (see "''Electrode Conventions''"). This permits use of these electrodes for mapping and suppression of eye artifacts. The standard definitions above give an example of how to relabel extra channels (X1...X10, PG1, PG2) for the use of EOG, EKG and respiratory (Rsp) channels. Use an ''Additional Channels'' file to define horizontal and vertical EOG channels by using the appropriate electrodes in a bipolar montage (an example is provided in '''eog-ecg.mtg''' in ''Montages\AdditionalChannels''). Differentially recorded EKG and respiratory channel can be defined in the same file.

=== Patterns ===

'''Default settings provided for section [Patterns]:'''

These settings define labels for each of the five patterns. The labels are shown* in the''' Tags''' menu,
* in the '''TAG push-button''' popup menu, and
* when displaying tag info clicking with the right mouse on a tag at the bottom of the EEG or on the event bar.

By default, no labels are defined. Define a label, e.g. for Pattern1 and Pattern2, as in the following example:

Pattern1=Spike

Pattern2=Sharp Wave

=== Artifacts ===

'''Artifact default settings:'''

See the chapter "''Artifact Correction / Reference / Artifact settings in the BESA.ini file''" in the online help.

=== Search ===

Default settings for pattern search.

'''Default Settings for the ''Search/Options ''Dialog box:'''

'''CorrelationThreshold''' = '''75%'''

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

'''Default Settings for the ''Search/Average/View'' (SAV) Dialog box:'''

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

'''HighPassSlope = 12 dB/Octave'''

'''HighPassType = 0 (0 = zero phase, 1 = forward, 2 = backward'''

'''LowPassFreq = 35 Hz'''

'''LowPassSlope = 24 dB/Octave'''

'''LowPassType = 0 (0 = zero phase, 1 = forward, 2 = backward)'''

'''CorrelationThresholdNoMarked = 60%'''

Default correlation threshold if no channel labels are marked when the SAV Dialog is opened.

'''CorrelationThresholdOneMarked = 85%'''

Default correlation threshold if one channel label is marked when the SAV Dialog is opened.

'''CorrelationThresholdFourMarked = 65%'''

Default correlation threshold if between two channel labels are marked when the SAV Dialog is opened.

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

If set to "Yes", a File Save dialog will open, to allow to save the search average to a file (as with the SAW function).

'''WriteAfterSearchCheckBox = No'''

If set to "Yes", an additional checkbox "Write after search" is displayed at the bottom of the SAV Dialog, allowing to choose whether or not to write the search average after a search:

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

If set to "No", the SAV Dialog will open with the same boxes checked as the last time the dialog was opened during the current session.

If set to "Yes", the default frequency, buffer width, selected view after search, and default threshold are always checked when the dialog is opened.

=== KeyControls ===

In the [KeyControls] section you can specify functions that can be allocated to '''function keys''' or to the '''<Del>''' key. Specify using the form:

'''Fn=function''' or

'''Del=function'''

where "''n''" is a number between 2 and 12 (F1 is reserved for Help). For example:

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

'''Pattern''n''''', where ''n''<nowiki>=1-5: Sets the tag number </nowiki>''n'' at the cursor latency.

'''Epochfast:''' sets one boundary of an epoch at the cursor latency, but does not open the epoch text box to define a label.

'''Marker:'''  sets a marker at the cursor latency.

'''Comment:''' sets a comment at the cursor latency and opens the comment box to enter text.

'''Epoch:''' sets one boundary of an epoch at the cursor latency and opens the epoch text box to enter a label.

'''Artifact:''' sets one boundary of an artifact segment at the cursor latency.

'''Delete:'''  deletes a tag at the cursor latency

'''Batches and Montages:'''

'''Batch''n''''', where n=1-12: Runs a predefined batch file corresponding to the number ''n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a batch, pressing it will open a ''File Open Dialog'' to select a batch. The setting you have chosen will be retained across BESA Research sessions. Holding the '''<shift>''' key while pressing the '''function key''' will always open the dialog. Hold the''' <ctrl> '''key with the function key to open the associated batch in the batch edit dialog.</div>

'''Montage''n''''', where n=1-12: Sets a montage corresponding to the number'' n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a montage, pressing it will generate a message asking you to associate a montage as follows: Holding the '''<shift> '''key while pressing the '''function key''' will remove the current association, and substitute it with the current montage.</div>

The default settings after program installation are listed in the online help chapter ''Review / Reference / Controls / Mouse and Keyboard / Keyboard Controls''.

=== FFT ===

'''Default settings provided for section [FFT]:'''

These settings define the setup in the Spectral Analysis section of the BESA Research program (FFT window, see the chapter "''Spectral Analysis / FFT''"). Up to 7 frequency bands may be defined. Five are defined by default.

'''FFTBand1=On''' FFT Bands 1-5 are defined

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

'''FFTBand6=Off''' FFT Bands 6-7 are not defined

'''FFTBand7=Off'''

'''FFTNameBand1=Delta''' Names of the defined bands

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

'''FFTColorBand1=RGB(0,0,0)'''  Default color of each band

'''FFTColorBand2=RGB(0,128,64)'''

'''FFTColorBand3=RGB(128,0,0)'''

'''FFTColorBand4=RGB(255,0,0)'''

'''FFTColorBand5=RGB(255,128,0)'''

'''FFTColorBand6=RGB(255,192,0)'''

'''FFTColorBand7=RGB(255,255,0)'''

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

'''FFTLowBand3=8''' Alpha from 8-14 Hz

'''FFTHighBand3=14'''

'''FFTLowBand4=14''' Beta from 14-30 Hz

'''FFTHighBand4=30'''

'''FFTLowBand5=30''' Gamma from 30-50 Hz

'''FFTHighBand5=50'''

These values are best set from within BESA Research, using the '''Options''' menu in the FFT window (see the chapter "''Spectral Analysis / FFT / FFT Options Menu''"). Current settings are stored after each session and retrieved in the next session.

=== Printer ===

'''Default settings provided for section [Printer]:'''

'''PrinterMarginPercent=100''' controls size of printout

'''PrinterColors=256''' set to 1/2 for black&white, 0/256 for color printers

'''PrinterLineMode=1''' set to 2 for thicker lines and to save printer memory

'''PrinterMapResolution=1''' set to 2, 3, 4 to save printer memory and increase speed

=== Calibration ===

'''Default settings provided for section [Calibration]:'''

'''AutoCalibration=Off''' On: automatic calibration of signals >= 4 cycles

'''MicrovoltCalibration=50''' peak voltage of calibration signal

If calibration is set to'' On'', the menu item ''Calibration ''will appear in the''' Process '''menu. Position your current screen at an epoch containing at least 4 regular cycles of the calibration signal (in all channels!) and select Calibration.

=== Video ===

'''Default settings provided for section [Video]:'''

'''DVCFilePath=C:\DVC\DVPlay.exe''' holds the path to the digital video player

'''DVCCommandLineArguments=/S:3 /M:P /T:M'''  arguments to be passed to the digital video player

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

'''MappingRepetitionRateWithVideoInMS=100'''  gives the number of milliseconds between two maps if the mapping window is open while the video is running. If the graphics board encounters problems during the display, this value should be increased.

=== Mapping ===

'''Default settings provided for section [Mapping]:'''

'''UseBitmapDrawing=Off'''

Set this to "On" if 3D maps show a strange pattern of black triangular shapes (this is frequently observed with modern Intel On-Board graphics controllers, and is a result of inadequate drivers for Open-GL).

'''Use3DVBlending=Auto'''

Set this to "Off" if the 3D view in the Montage Editor or the Source Analysis window does not show up properly (this may happen with some older graphics cards).

Set this to "On" if the 3D view in the Montage Editor or the Source Analysis window shows a ragged surface boundary.

'''MapSmoothing=0 '''

Set a non-zero value to specify a default map smoothing parameter (normally specified in ''Options/Mapping/Spline Interpolation Smoothing Constant'').

=== Matlab ===

'''Default settings for the [Matlab] section:'''

'''Platform=32'''

'''Set Platform=64''' if you want to use the 64-bit version of Matlab

=== Updates ===

This section is not normally required, but the variables here can be altered or defined to determine how BESA Research checks for dongle and program updates.

'''DaysBetweenUpdateChecks=7'''

Sets the number of days between automatic checks for updates. Set the value to 0 to check every time BESA Research is started. Set to -1 to turn off automatic update checks.

'''CheckNetworkDongle=Off'''

For the network administrator: If set to "On", BESA Research will check the dongle on the network for updates. Otherwise the state of the network dongle will be ignored.

'''LocalPath'''

For the network administrator. This can be set to a path on the local network to the BESA update files, so that users can obtain their updates locally. The path is given to the text file "'''UpdateVersions.txt'''" (e.g. ''LocalPath=\\transtec-sak\zarascratch\BESA\Updates\UpdateVersions.txt''), which contains further details for the program to obtain its updates. If you want to use this feature, please contact us at support@besa.de.

The following variables are not required, because BESA Research has the paths hardwired:

'''FTP1 (also FTP2, FTP3)'''

ftp download server

'''Path1 (also Path2, Path3)'''

Path on the server to UpdateVersions.txt.

'''HaspPath1 (also HaspPath2, HaspPath3)'''

Path on the server to HASP (dongle) update files.

'''History'''

Path on the server to general history file

=== Reader-Specific Settings ===

'''BrainLab'''

'''Default settings provided for section [BrainLab]:'''

'''BrainLabFormat=New''' this entry ensures that the newer BrainLab file format can be read by BESA Research.

'''Bio-Logic'''

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:
* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>
* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

'''EDF+/BDF/Trackit'''

'''TriggerScan=On'''

Set '''TriggerScan=Off '''to prevent BESA Research from scanning the file for triggers. This is done separately for EDF+, BDF, and Trackit files in sections '''[EDF+], [BDF],''' and '''[Trackit]''' in the '''BESA.ini''' file.

'''EGI'''

The treatment of DIN events can be modified in the''' [EGI] '''section:

'''CombineDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you want to treat DIN events separately, and not generate combined values.

'''SeparateDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you don’t want to treat DIN events separately.

Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

'''CombineDINeventsPrefix'''<nowiki>=dinComb</nowiki>

<div style="margin-left:0.953cm;margin-right:0cm;">This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

'''Harmonie'''

'''Default settings provided for section [Harmonie] (Stellate Harmonie systems):'''

'''SeizurePreEpoch=60''' length of the epoch preceding a seizure detection in s

'''SeizurePostEpoch=60''' length of the epoch following a seizure detection in s

'''PushButtonPreEpoch=60''' length of the epoch preceding a push button detection

'''PushButtonPostEpoch=60''' length of the epoch following a push button detection

When BESA Research encounters a seizure detection event or a push button detection event in a Stellate Harmonie file, it automatically sets an epoch around the event, which makes it convenient to view just those epochs for analysis. The length of the epochs preceding and following the events can be adjusted in the '''.ini''' file.

'''Neuroscan Keys'''

'''Note that there is a setting "NeuroScanDataNumberOfBits" in the [Defaults] section of BESA.ini that is used for distinguishing the data format of Neuroscan files (16 or 32-bit).'''

'''Default settings provided for section [NeuroScan Keys] (NeuroScan systems):'''

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

'''NKT2100'''

'''Default settings provided for section [NKT2100] (Nihon Kohden EEG 21xx systems):'''

'''TriggerScan=On'''   Set to "Off" to prevent a scan for trigger events.

'''Country=NotKanji''' set to NotKanji for non-Kanji characters else to Kanji

'''KanjiCharSize=16''' Kanji character size

'''KanjiPrinterCharSize=32''' Kanji printer character size

'''EEG_Sensitivity=50''' default sensitivity of Nihon Kohden EEG-2100 system

'''DC_Sensitivity=50''' default sensitivity of Nihon Kohden DAE-2100 system

'''QJ_Sensitivity=100''' default sensitivity of Nihon Kohden QJ-403 system

'''Mark_Sensitivity=100''' default sensitivity of EEG-2100 marker channels

These settings need to be changed only if the manufacturer has specified different gains for your system. Otherwise do not alter these settings.

'''Vangard'''

'''AlwaysOpenFileSelect=Yes'''

If "Yes" is selected, each time a Vangard file is opened, a dialog box will open, asking for a selection of the segment type to display.

If "No" is selected, the selection dialog is opened whenever a Vangard file is opened for the first time, or if the ''Channel and digitized head surface point information dialog box'' is opened (e.g. with '''ctrl-L''' or ''File/Head Surface Points and Sensors/Load Coordinate Files...'' ).

'''XLTEK'''

'''TriggerScan=Off '''Set to "On" to scan the data file for trigger events

'''MontageNo=2''' Set to 1 or 2. If two montages for the data file are defined, this variable determines whether the first or the second alternative should be used.

Electrodes and Surface Locations

2017-04-07T08:52:41Z

Alexa:

= Working with Electrodes and Surface Locations =

== Introduction - Electrodes and Surface Locations ==

Here you will find out how BESA Research works with electrode and MEG sensor coordinates and labels, and how head surface points can be used to improve source modeling and coregistration of source models with the MRI. In most cases, electrode positions are sufficiently defined by their labels. The section "''Electrode Conventions''" lists the standard position which BESA Research assigns to EEG channels. In some cases, especially for larger electrode arrays or for MEG measurements, additional information is required to add sufficient information for mapping and for source analysis. The additional information is supplied in additional, auxiliary files which are read by BESA Research and associated with the data files. The auxiliary files, and how they are supplied to BESA Research, are described in this chapter.

Examples for using auxiliary files to define the 3D locations of electrodes are found in the chapter "''Special Topics / Working with Electrodes... / Examples''" in the online help.

Descriptions of file formats that BESA Research uses are given in the online help chapter "''Special Topics'' ''/ Working with additional files''".

== Working with auxiliary files ==

Data files come with varying amounts of prior information about electrode/sensor locations, depending on the recording system. BESA Research allows you to read auxiliary files that define additional information, such as channel labels, and coordinates of the electrodes, sensors, and other head surface points. The information is required for mapping and for source montages.
* '''Mapping.''' BESA Research uses spherical spline mapping. For this, electrode/sensor locations are projected onto a sphere. The minimum requirement is 10-10 or 10-20 labels: if only channel labels are available without additional information, BESA Research uses default spherical coordinates.
* '''Source modeling'''. Spherical coordinates of electrode locations are sufficient, but digitized locations are better. Digitized locations can be defined in the data file or in auxiliary files. BESA Research will use digitized head surface points (electrodes + additional points) to fit a sphere for the spherical model. Points anterior to the left and right preauricular points and below the plane formed by these points and the nasion are excluded when fitting the sphere.

Files can also be written, for instance for
* '''Source modelling with MRI coregistration'''. BESA Research allows for the export of surface points in a special format ('''sfh''' file) which can be read by the BESA MRI (or BrainVoyager) program. These are fitted to the head surface defined by BESA MRI (or BrainVoyager) in order to define rotation, translation, and deformation parameters required to coregister the coordinate systems (see "''Integration with MRI and fMRi''").
* '''Export of coordinates.''' Electrode, other surface point locations, and MEG sensor coordinates and other surface point locations can be written to ASCII files so that they can be reread when reading other files into BESA Research (e.g. ASCII files), or used by other programs.

Feedback and control over how these files are read is provided by
* '''the Channel and digitized head surface point information dialog box.''' This dialog is usually opened when you open a file for the first time. It allows you to specify the names of auxiliary files, and it makes initial checks on the files to see whether they are consistent with each other and with the data file. If the check is OK, you will see a green tick at the top right hand corner of the dialog box. If there are inconsistencies, the tick is replaced by a red exclamation mark. In this case, you will usually need to edit the auxiliary files or specify other files. The dialog box is not opened if the file is recognized to contain all the necessary information (files with the '''foc''', '''fsg''' extensions), or if the program only finds a channel definition file (with extensions '''ela, elp,''' or '''elb'''). The dialog box is not opened if the data file has been opened before. You can always open the dialog box manually by specifying ''" File / Head Surface Points and Sensors/Load Coordinate'' ''Files.''
* '''The log file''' ('''<nowiki>*_LoadFile.log</nowiki>''')'''.''' Coordinating the information between the data file and its auxiliary files can be a complex procedure. To help you check whether the coordination is being done properly, if you select the menu entry ''" Options / File / Generate Log "'' during File Open, BESA Research writes a log file with the same base name as the data file, appending "'''_LoadFile.log'''" to the base name, recording which files have been read, and some of the parameters that have been found. This file is created every time auxiliary files are read (e.g. on file open, when reading in channel configuration files, head surface point files, MEG sensor locations), or changed ("''Edit /'' ''Channel Configuration''").
* '''The log window. '''If there are inconsistencies during the processing of auxiliary files and 3D coordinates, a logging window is opened showing the information that would be written to the log file. You can read what has been done to help diagnose the problems. Select '''OK''' to continue in spite of the problems, or''' Reset''' to reject. Typing '''Reset''' also deletes the database files associated with the current data file, thus allowing you to start reading this file from scratch.

'''BESA Research remembers which auxiliary files are associated with the current file'''. When a data file is first opened, and BESA Research finds auxiliary files with the same base name as the data file, you will be asked if you want this file to be read. The decision you make will be recorded in the database for this data file. Next time the file is opened, the files will or will not be read, according to your previous decision. Similarly, when an auxiliary file is read using the menu, this is recorded in the database, and the file will be opened automatically next time the data file is opened. To override previous decisions, you must delete the database files (see the''' log window '''above) or change the entries in the Channel and digitized head surface point information dialog box (see the chapter ''"Electrode Conventions / Channel and digitized head surface point information dialog box''").

== Coordinate systems ==

We need to deal with four different coordinate systems. These differ in how the x, y, and z axes are defined, and in the units of measurement (e.g. mm, cm, m). The first three are illustrated in the following figure:

[[Image:ST Electrodes (1).gif ]]

'''Device coordinates.''' These are the coordinates used by the recording system. The axes may be anywhere in relation to the head. For instance, in the Polhemus digitizer, the axes go through the magnetic field transmitter which is located somewhere outside the head. The units of measurement may be millimeters, centimeters, or meters.

'''Head coordinates'''. This coordinate system is defined by reference points on the head known as ''fiducials''. The reference points are normally the nasion (Nz, NAS), the left preauricular point (T9, LPA), and the right preauricular point (T10, RPA). The x axis is defined by the line joining T9 and T10, positive towards T10. The y axis is defined by the line through Nz that is perpendicular to the x axis (positive towards Nz). The z axis is perpendicular to the x and y axes, and goes up out of the head in the vicinity of Cz. The units of measurement may be millimeters, centimeters, or meters. In BESA Research these are labelled with the prefix 'Fid', e.g. 'FidT9', 'FidNz'.

'''BESA Research coordinates.''' For dipole analyses the head model consists of a sphere. In the default situation where no digitized sensor information is available, the center of the sphere is defined by the crossing point between the lines joining T7 (=T3) and T8 (=T4) and Fpz and Oz.. The x axis is the T8-T7 line, positive at T8. The y axis is the Oz-Fpz line, positive at Fpz. The z-axis goes up out of the head through Cz. If digitized information is available, the axes are defined by the best fit between the idealized electrode locations and the real locations. The diameter of the sphere is also defined by the best fit. Units given in the display are in millimeters.

The '''center of the spherical model''' is on average about 4 cm above the origin of the Head Coordinates. If digitized surface points are available, the sphere is fitted to these points. Using a cot file, it is possible to override the fit and define your own head center. In conjunction with BrainVoyager, you can use the MRI to seed the location of the head center (e.g. a fixed distance anterior to the posterior commissure) and save it as a cot file. Using MRI coregistration (see "''Integration with MRI and'' ''fMRi''"), the center is placed between the anterior (AC) and posterior (PC) commissures, at the half-way point between the anterior and posterior points (AP and PP). Without coregistration, the center corresponds to a point 17.5 mm behind AC in the standard MRI head.

'''MRI coordinates.''' These are the coordinates used by BrainVoyager. These are defined by the MRI slices. Measurement units are millimeters.

== The Channel and Digitized Head Surface Point Information Dialog Box ==

Many data formats read by BESA Research require additional information about data channel, which are specified by additional, auxiliary files. This dialog box allows you to specify which auxiliary files are read in to supplement the information in the data file.

The dialog box is opened automatically the first time a data file is opened, if
* auxiliary files other than a channel definition file ('''<nowiki>*.ela</nowiki>''', '''<nowiki>*.elp</nowiki>''', '''<nowiki>*.elb</nowiki>''') are found
* no auxiliary files are found, and the data file was not written in compressed binary format ('''<nowiki>*.foc</nowiki>''', '''<nowiki>*.fsg</nowiki>''') by BESA Research

When a data file is closed, the information about which auxiliary files have been read is stored in the database. When the file is opened for a second time the dialog box is not opened automatically, because the information is assumed to be correct – the files are read automatically.

The dialog box can be opened manually by selecting "''File / Head Surface Points and Sensors/Load'' ''Coordinate Files''", or using the shortcut '''ctrl-L'''

[[Image:ST Electrodes (2).gif ]]

The dialog box is divided into several sections:

* '''Internal data file information.''' Here you can see the file name, the originating system (file format), the name of the database file, if any, and the channel information as specified by the data file alone.

[[Image:ST Electrodes (4).gif ]]

* '''Suggestions.''' This box makes suggestions about what needs to be filled in, e.g. "Please enter electrode thickness"

[[Image:ST Electrodes (5).gif ]]

* '''Main feedback (top right hand corner).''' A green tick indicates that the currently selected data files are consistent among themselves and with the data file. A red exclamation mark indicates an inconsistency. Check the feedback texts in the subsequent sections for more information:

[[Image:ST Electrodes (8).gif ]][[Image:ST Electrodes (7).gif ]]

* '''Channel configuration file specification.''' If the channel labels and types defined in the data file ("Internal data file information") need to be changed, enter a file name here ('''<nowiki>*.ela</nowiki>''', '''<nowiki>*.elp</nowiki>''', '''<nowiki>*.elb</nowiki>'''). If a channel definition file exists with the same basename as the data file, or if a channel definition file has been specified previously (database entry exists), it will be selected automatically. To the right of the file name, feedback is provided about the number of channels and channel types found. If the labels are consistent with the data file, to the right the text "Good" is shown. If they are inconsistent, e.g. the file contains the wrong number of channel definitions, the text "Bad" is shown.

[[Image:ST Electrodes (9).gif ]]

* '''Digitized head surface point specification.''' Here you may specify a file containing digitized electrode and other head surface points. Optionally, the information can be split into two files, containing the coordinates ('''<nowiki>*.sfp, .eps</nowiki>''') and the coordinate names ('''.sfn'''). Alternatively, both labels and names can be contained in the coordinate file. If the files specify electrode coordinates, there '''must''' be a coordinate name for each electrode. The sequence may be different. BESA Research will use the names to assign each coordinate to the electrodes. Additional head surface points can have any other names. It is recommended that the first three digitized coordinates are the fiducials (fiduciary points), labelled "FidT9", "FidT10", "FidNz". If your electrode labels not follow the 10-10- or 10-20 standard (e.g. in high-density electrode recordings), it is recommended to tick the box "Electrode labels non -conforming to 10-10 standard". This will prevent BESA Research from using electrodes for an optimal rotation of the coordinate system which should not be used (e.g. A1, A2 which have known locations in 10-10, but are sometimes used in a nomenclature outside of 10-10). The example below shows the sphere adaption for an example data set with and without taking this into account. The right picture shows that when discarding the non-conforming electrodes, the fiducials are correctly placed along the x any y axes.

[[Image:ST Electrodes (10).gif ]] [[Image:ST Electrodes (11).gif ]]

(In the special case of Neuromag files with electrode channels, the data file contains head surface points with the wrong labels. Here you may provide a label file ('''<nowiki>*.sfn</nowiki>''') without a corresponding digitized coordinate file.)

[[Image:ST Electrodes (12).gif ]]

* '''Coregistration file.''' Here you may specify a file containing the coordinates of the head center ('''<nowiki>*.cot</nowiki>''') or an ''MRI Coregistration File ''('''<nowiki>*.sfh</nowiki>'''). Head center redefinition is only necessary if you want to provide an external definition, e.g. from the MRI. The ''MRI Coregistration File ''is used if the data are to be coregistered with individual MRI. (see "''Integration with MRI and fMRi'' "). '''Note''' that if a head center file (cot file) with the same base name as the data file exists, it will be read automatically if the head center coordinates deviate by more than 1 mm from the internally calculated values. Changes are ignored if the radio button is set to "No". This automated function allows you to change the head center during a session, using BrainVoyager's view of the MRI and the Source Module.

[[Image:ST Electrodes (14).gif ]]

* '''MEG sensor specification'''. If the file contains MEG channels, you may enter the name of a sensor coordinate file ('''<nowiki>*.pmg</nowiki>''', '''<nowiki>*.pos</nowiki>'''). This field is grayed if there are no MEG channels.

[[Image:ST Electrodes (15).gif ]]

* '''Artifact coefficients file.''' If the data are to be artifact corrected, your pre-prepared coefficient file may be defined here. See the chapter "''Artifact Correction''". Selecting the file here is equivalent to loading the file using the menu entry "''Artifact / Load''".

[[Image:ST Electrodes (17).gif ]]

For each of the selected files, make sure the radio button "'''Yes"''' is selected on the left-hand side of the dialog box. If files have been selected automatically, and you do not wish them to be read, select the "'''No'''" radio button.

If some of the settings are incorrect or the text "Bad" is shown, you may edit the auxiliary files (the file is opened with the NotePad program) or browse for another file by pressing the '''Edit''' or '''Browse''' buttons.

After you have entered the required information, and the green tick at the top right indicates consistency, press '''OK''' to continue. Press '''Cancel''' to ignore the current settings. Press '''Clear DB''' to delete the database files. Press '''Clear Events''' to delete the tag files (the part of the database that records events). Both '''Clear''' buttons close the currently-opened data file.

== General Reading Rules for Data Files and Auxiliary Files ==

Auxiliary files can complement the information in the data file. Here we specify what happens when a data file is opened:

'''1.''' If the data file has been read previously, the database entry specifies which auxiliary files should be read. The file and the specified auxiliary files are opened and the data are displayed.

'''2'''. If a) there is a channel definition file '''(*.el'''''?'') with the same basename as the data file, and

b) this file includes spherical coordinates for the EEG channels (including labels with entries in the '''default.ecd''' file), and

c) there are no other auxiliary files with the same base name, the file will be opened and the data displayed. If files with the same basename are not found, BESA Research will look for files with the basename “default” (e.g. '''default.ela''') in the data folder. If such files are not found, BESA Research will look for files with the basename “default” one folder above (e.g.''' ..\default.ela''').

'''3'''. If the data file has been written in binary format ('''<nowiki>*.foc</nowiki>''', '''<nowiki>*.fsg</nowiki>''') by BESA Research (after Jan.2000), the file will be read, and all information is assumed to be complete. The file is opened and the data are displayed.

'''4.''' In all other cases, the ''Channel and digitized head surface point information dialog box'' will be opened for you to specify and check auxiliary files. Auxiliary files with the same base name as the data file will be specified in the text boxes for file names. If files with the same basename are not found, BESA Research will look for files with the basename “default” (e.g. '''default.ela''') in the data directory. If such files are not found, BESA Research will look for files with the basename “default” one directory above (e.g. '''..\default.ela'''). Otherwise the text boxes will be left blank.

'''5.''' Auxiliary files can be specified at a later time by selecting ''File/Head Surface Points'' and ''Sensors/Load'' ''Coordinate Files''. The ''Channel and digitized head surface point information dialog box'' will be opened.

== Electrodes ==

=== Electrode Conventions ===

BESA Research adheres to the 10/20 and to the new 10/10 standard of the IEF (international EEG Federation). BESA Research will recognize the labels defined by these standards. The labels are stored in most EEG file headers. Otherwise, or in the case of erroneous labeling or sequencing of the recording channels, you may edit the channel labels and/or coordinates, or you may read an electrode file stored previously on disk. In addition to the 10/20 and 10/10 standard labels BESA Research recognizes the following labels: M1, M2 (left, right mastoids), SP1, SP2 (sphenoidal), CB1, CB2 (cerebellar), Chin, Neck, LO1, LO2 (lateral ocular), SO1, SO2 (supra-ocular), IO1, IO2 (infra-ocular). BESA Research will translate all the labels into spherical coordinates for spherical spline interpolation, mapping and source imaging. The following assignments are stored in the file '''default.ecd''' in the BESA folder:

[[Image:ST Electrodes (19).gif ]]

''Electrode labels in the file '''default.ecd '''and their spherical coordinates. 10-20 electrodes are shown in red and italic.''

The spherical coordinates are defined in degrees by the azimuth (from Cz, positive = right, negative = left hemisphere) and the latitude (counterclockwise from T7/T3 for left and from T8/T4 for right hemisphere) of each electrode. Please do not modify the existing labels or coordinates in this file, because this would adversely affect the interpolated (virtual) montages, the maps and the source montages and source images in BESA Research. However, you may add additional labels for scalp electrodes at the end of this file if needed (up to a total of 196). When you edit the electrode configuration or read in electrode files, BESA Research may replace the 10/20 standard labels T3, T4, T5, T6 by their new 10/10 equivalents T7,

T8, P7, P8. However, in the initialization file '''BESA.ini '''you can reset to the old 10/20 standard by relabeling T7=T3, P7=T5, T8=T4, P8=T6 under the heading [Electrodes]. You may use the same feature to assign appropriate labels to the X1..X8 channels which exist in many systems, e.g. X1=EKG1 etc.

=== Recommendations for electrode placement ===

For source montages and source analysis two principles are important:

# Covering of the lower head with inferior electrodes to record activity from the inferior surfaces of the brain, especially from the basal temporal lobe, from the temporal pole, from orbito-frontal cortex, and from basal occipital and cerebellar areas.
# Equal spacing of the electrodes over the whole head to cover all brain areas.

In the following montage EEGxx the number xx indicates the number of electrodes.

'''EEG25 - Minimum 10-20 configuration including inferior electrodes'''

This covers the 19 standard 10-20 electrodes:

Fp1, Fp2, F7, F3, Fz, F4, F8 ....

plus 6 inferior electrodes on both sides:

F11, A1, P11, F12, A2, P12

with a recommended continuation of the 20% distances, i.e. use F11 instead of F9, P11 instead of P9, A1 instead of T9 to have a wider coverage of the inferior head. A1 / A2 may be replaced by T9 / T10 (or FT9 / FT10) for convenience and comfort.

[[Image:ST Electrodes (21).gif ]]

''Left: recommended configuration for 25 electrodes. Right: left temporal basal activity mapped with 25 electrodes.''

'''EEG33 - Additional 10-10 electrodes within the major squares'''

To the above electrodes add the following 8 intermediate electrodes:

FC5, FC1, FC2, FC6,   CP5, CP1, CP2, CP6

[[Image:ST Electrodes (23).gif]]

''Left: recommended configuration for 33 electrodes. Right: left temporal basal activity mapped with 33 electrodes.''

'''EEG35 - Additional supraorbital electrodes for better EOG separation'''

SO1, SO2

'''EEG37 - Wider inferior coverage at interlaced 20% distances'''

Continue 20% down from F7, FC5, CP5, P7 etc. and use the following 8 inferior electrodes instead of 6:

F11, FT9, TP9, P11,    F12, FT10, TP10, P12

'''EEG41 – Improved frontal and occipital coverage'''

Additional electrodes halfway between Fz and Fp1 / FP2 and Pz and O1 / O2:

AF1, AF2,   PO1, PO2

'''EEG43 – Inferior chain with 5 electrodes including A1 / A2'''

F11, FT9, A1, TP9, P11,    F12, FT10, A2, TP10, P12

EEG43 represents the widest coverage with relatively even spacing.

[[Image:ST Electrodes (25).gif]]

''Left: recommended configuration for 43 electrodes. Right: left temporal polar activity mapped with 43 electrodes.''

'''EEG64-256'''

With 64 or more channel caps, it is similarly recommended to use a sufficient number of inferior electrodes all around the head. At least 4 inferior temporal electrodes on each side and additional electrodes above or below the eyes (outside of the cap) are suggested.

=== Editing the channel configuration ===

Only use the channel configuration editing facility if the electrodes or the common reference have not been correctly defined by your digital EEG system, or if you want to define specific spherical coordinates for your scalp electrodes. It is your responsibility to check and provide the correct sequence of electrode labels in correspondence with the sequence of channels in the EEG data file. If these sequences do not match exactly, errors will occur in the computation of maps, source images and interpolated montages.

We will use the example EEG file '''eeg2.eeg''' in the subdirectory ''Examples/EEG-Focus'' of the BESA Research directory to explain the editing of electrode labels and coordinates:

1. Select ''File'', then click on ''Open'', or click on '''eeg2.eeg '''if this file is contained in the list of currently selected EEG files.

2. Select ''Edit'', then click ''Channel Configuration''. The dialog box shown below will appear.

[[Image:ST Electrodes (27).gif]]

At the upper left of the figure you see the dropdown menu after selecting the '''File '''menu in the dialog box. This menu allows to edit a new ('''''New''''') or an existing ('''''Open''''') electrode file and to save the changes to the same ('''''Save''''') or a different ('''''Save As''''') file. Normally, it will not be necessary to use this menu. The control fields on the right will be sufficient. If you type ''''''Ok'''''', you will be given the option of saving the changes to a file.

3. Click on '''Reload org. Labels''' to reread the original labels as stored in the file header of '''eeg2.eeg'''. BESA Research quits editing and redisplays the EEG. Repeat step 2 and select "''Edit / Channel'' ''Configuration''" again. Note: The button '''Reload org. Labels''' is not available if there are no labels in the file header.

4. Click on the empty space of the scroll bar below the '''scroll '''button and on the '''down arrow''' of the '''scroll bar''' to display the remaining electrodes in the file.

5. Click on electrode '''R''' (line 32), then on the button '''Delete Electrode''' to remove the associated channel, which does not contain any signal. Note that you may not omit intermediate channels, even if they do not exhibit signals, because the correct correspondence between the series of electrodes and the EEG channels will not be maintained. Use the '''"Edit / Bad Channels"''' menu to disable artifactual or empty channels.

6. Click on''' EOG''' (line 30) and change the entry to '''EOG1'''. Do not type '''<Enter>,''' but click on the next or a different electrode box to accept the changes.

7. '''Double click''' on '''EOG '''(line 31). This will highlight the entry. Simply type the new name '''EOG2''', and note that the old label is replaced when highlighted. Electrodes '''30 '''and '''31 '''are now defined as distinct electrodes. Next, we want to replace the label '''T10 '''by '''A2'''.

8. Click on the label '''T10''' (line 24). Then click on the '''drop down''' arrow right of the highlighted label to obtain the list of default scalp electrodes (read from '''default.ecd''' and sorted alphabetically). Type '''A''' to jump to the electrodes beginning with letter A (see below). Type '''2''' or '''click''' on '''A2''' in the list. Click on the '''type '''box (Scalp channel) to close the list and display the new entry in line 24. Note that this is the most convenient way to edit an electrode label.

[[Image:ST Electrodes (28).gif]]

9. Exercise: repeat step 8 to replace '''T9''' by '''A1'''. Restore labels '''T10''' and '''T9''' in lines 24 and 21.

10. Replace SO1 and SO2 (supra-orbital) by '''PSO1 '''and '''PSO2 '''and note that these electrodes are changed to the''' 'Polygraphy'''' type, because no coordinates are associated with these labels.

11. After you click ''''OK'''', the box '''Write Channel Configuration File''' will appear and display a name for the current electrode file. By default, the BESA electrode file path and current file name will be used and supplemented by the extension ''''.elb''''. The electrode file path may be set in the '''BESA.ini''' file [Defaults] section under ElectrodeFilePath. If no electrode file path is specified in the '''BESA.ini''' file, the default electrode file path ''Montages\Channels ''is used. Simply click ''''OK'''' or type '''<Enter> '''to save the changes to this file, or select a new file name and/or path, if you do not want to store the electrode file in the BESA Research electrode file directory.

Note that by using the default 10/10 labels (see chapter "''Electrode conventions''") you specify that the associated electrode is a scalp electrode. Hence, different labels must be used for polygraphic, intracranial or MEG channels. After you have entered a new non-scalp label, you may select the type of the electrode/channel amongst the different groups ('''Polygraphy, Intracranial, MEG Channel''') from the drop down list in the ''''''Type'''''' box. This will allow for using separate selection and scaling facilities of the channel group control push-buttons at the right of the screen ('''All, Scp, Pgr, Icr, MEG'''). If you have entered a new non-scalp label and select the type '''Scalp Channel''', or if you click on the ''''Advanced>>'''' field, boxes will appear to enter the spherical coordinates (azimuth and latitude) of this electrode (cf. Fig. 6.5). These features may be used to specify non-standard scalp electrodes. Please check the earlier sections of this chapter for electrode conventions. You may view the locations of the scalp electrodes on the head schemes in the mapping window. Select '''Show Electrodes in Maps''' in the "'''View / Options'''" menu.

[[Image:ST Electrodes (29).gif]]

'''Hint:''' If you want to specify the spherical coordinates of an electrode which is close to a standard electrode, click on the ''''Advanced >>'''' field, enter the label of the standard electrode and append a single quotation mark. This will specify that the electrode is close to the labeled location but has different coordinates. The ''Scalp Channel'' type will not be replaced by '''Polygraphy.''' Then edit '''Azimuth''' and '''Latitude'''. This convention is used by BESA Research when reading electrode coordinate files '''(*.elp'''), e.g. from the BESA program. The coordinates are read and compared with the default coordinates to assign the closest label. Then a single quotation mark is appended to the label, and the coordinates are assigned as specified in the '''.elp''' file. For example, open '''segm1.eeg''' in the ''Examples\EEG-Focus'' subdirectory.

Note that the file '''segm1.elp '''is searched for automatically in the directory of the data file when opening the data file.

'''Edit Common Scalp Reference'''

There is a separate line at the bottom in the ''Channel Configuration dialog box'' to enter the label and coordinates of the '''Common Scalp Reference electrode'''. If this is specified and enabled (click on field '''Enabled'''), the information provided by the fact that all scalp electrodes were recorded against a common recording reference will be used for mapping, source imaging and virtual montages. This information will be lost if the common reference has not been specified or if a combination of electrodes has been used as reference during recording. Specify the '''Common Scalp Reference electrode''' only if all electrodes have been referenced to the same single electrode and if a standard 10/10 location has been used for the common recording reference.

'''Note that BESA Research cannot process digital EEG data correctly if there is no common recording reference''', and if different recording references were used for the various scalp electrodes. For intracranial and polygraphic channels different references may be used. It is preferable to use the common reference also for electrode channels near the eyes, because these electrodes provide valuable information for mapping, source imaging and interpolated montages. The traditional bipolar channels (e.g. horizontal and vertical '''EOG''') may be '''reconstructed digitally''' using the ''Selected Channels'' group or user-defined montages.

== 3D Coordinates for Precise Analysis ==

=== Introduction - Working with Digitized 3D Coordinates ===

Working with digitized electrode coordinates usually requires reading in additional (auxiliary) files. The procedure is described in the chapter "''Working with auxiliary files''".

=== Data reading rules for EEG ===

This section explains which additional files are read, or which files have to be read in order to provide the necessary information for mapping and source montages.

Assume file name is '''datafile.xxx'''. datafile is the base name, '''.xxx''' is the extension. Replace the text ''datafile'' by the base name of your own file, and the extension'' xxx'' by the extension of your own file.

'''Channel definitions for EEG:'''

Labels have 10-10 names: default locations will be used.

Labels do not have 10-10 names: Channels are interpreted as '''polygraphic'''. Mapping is not possible without one or more of the following additional files.

'''Define channel names and types.''' File '''datafile.ela''', '''datafile.elp''', or '''datafile.elb''' exist, or files '''default.ela''', '''default.elp''', or '''default.elb''' exist, or files '''..\default.ela''', '''..\default.elp''', or '''..\default.elb''' exist (i.e. files with basename d''efault ''one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The ''ela'' file contains just labels and, optionally, types. The ''elp'' file contains spherical coordinates and can contain labels and types. The ''elb'' file contains the same information in binary format. See chapter "''Working with additional files / Channel Definition File Conventions''".

'''Define order in which electrodes were digitized.''' File '''datafile.sfn '''exists, or file '''default.sfn''' exists, or file '''..\default.sfn''' exists (i.e. file '''default.sfn''' one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file. These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. If fiducials exist, they should be defined on the first three lines. If they do not exist, BESA Research will simulate them (so that it can define the head coordinate system). See chapter ''"Working with additional files / sfn (surface point name) file''".

'''Define electrode coordinates.''' File '''datafile.sfp''' exists, or file '''default.sfp''' exists, or file '''..\default.sfp''' exists (i.e. file default.sfp one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If '''datafile.sfn''' does not exist, labels can also be defined in this file. If fiducials exist, they should be defined on the first three lines. If they do not exist, BESA Research will simulate them. See chapter "''Working with additional files / sfp (surface point coordinate) file''".

'''Define coregistration information.''' File '''datafile.sfh''' exists, or file '''default.sfh''' exists, or file '''..\default.sfh''' exists (i.e. file''' default.sfh '''one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration between EEG and MRI. See online help chapter "''Integration with MRI and fMRI".''

'''Define head center.''' No coregistration file exists ('''<nowiki>*.sfh</nowiki>''', see above). File '''datafile.cot''' exists, or file '''default.cot''' exists, or file '''..\default.cot''' exists (i.e. file''' default.cot '''one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''

=== Data reading rules for MEG ===

Assume file name is ''''datafile.xxx''''. '''datafile''' is the base name. '''xxx''' is the extension. Replace the text '''datafile''' by the base name of your own file, and the extension '''xxx''' by the extension of your own file.

Here we consider cases a) MEG alone, b) MEG+EEG.

'''Automatic procedure:'''

Labels have names defined in the files '''bti.ecd''' or '''nmag.ecd'''. Channels are interpreted as MEG. However, sensor locations and head surface point locations must be defined in additional files as described below. Mapping and source analysis are not possible without one or more of the following additional files.

'''Define channel names and types.''' File '''datafile.ela''', '''datafile.elp''', or '''datafile.elb''' exist, or files '''default.ela''', '''default.elp''', or '''default.elb''' exist, or files '''..\default.ela''', '''..\default.elp''', or '''..\default.elb''' exist (i.e. files with basename'' default'' one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The'' ela'' file contains just labels and (optionally) channel types. The ''elp'' file contains spherical coordinates and can contain labels and types. The'' elb'' file contains the equivalent information in binary format. See chapter “''Electrode file conventions'' ''and formats.”''

'''MEG+EEG.''' Define order in which electrodes were digitized. File '''datafile.sfn''' exists, or file '''default.sfn '''exists, or file '''..\default.sfn''' exists (i.e. file '''default.sfn''' one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file (or in the location descriptor in the data file: e.g. Neuromag). These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. See chapter “''Working with additional files/ sfn (surface point name) file”.''

'''MEG+EEG.''' Define head surface point/electrode coordinates. File '''datafile.sfp''''' ''exists, or file '''default.sfp''' exists, or file '''..\default.sfp''' exists (i.e. file '''default.sfp''' one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If '''datafile.sfn''' does not exist, labels can also be defined in this file. See chapter “''Working with additional files/ sfp (surface point'' ''coordinate) file''”. The labels of electrode coordinates '''must '''match to those defined for the data channels. BESA Research will use the labels to associate coordinates with the correct channel.

'''Define sensor coordinates'''. File '''datafile.pos''' or '''datafile.pmg''' exists, or file '''default.pos(.pmg)''' exists, or file '''..\default.pos(.pmg)''' exists (i.e. file '''default.pos(.pmg)''' one folder above the data file): coordinates are defined in this file. The convention is that'' pos'' files contain gradiometer coordinates and'' pmg'' files contain magnetometer coordinates. This is not necessary for the program to read in values properly: the program makes its decision about the sensor type on the basis of the number of coordinate values on one line in the file (6 = magnetometers, 9 = gradiometers). See chapter “''Working with additional files/ pos or pmg (MEG sensor coordinate) file”.''

'''Define coregistration information.''' File '''datafile.sfh''' exists, or file''' default.sfh '''exists, or file '''..\default.sfh''' exists (i.e. file '''default.sfh''' one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration of the head coordinates with MRI. See (online) help chapter ''"Integration with MRI and fMRI".''

'''Define head center.''' No coregistration file exists ('''<nowiki>*.sfh</nowiki>''', see above). File '''datafile.cot''' exists, or file '''default.cot''' exists, or file '''..\default.cot''' exists (i.e. file '''default.cot '''one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''

=== Reading MEG files in ASCII format ===

'''BESA Research uses labeling or channel type definitions to decide whether channels are EEG or MEG. '''Based on the labels defined for the channels, or the type specified by the channel definition file, the program will try to find auxiliary files that define electrode coordinates or MEG sensors.

BESA Research uses four files to make its decision:
* '''.ela/.elp''' The channel type defined here overrides definitions in '''<nowiki>*.ecd</nowiki>''' (below).
* '''default.ecd''' defines electrode labels and default spherical coordinates based on the 10-20 and 10-10 naming system
* '''bti.ecd''' defines labels and default spherical coordinates for the BTi whole-head system
* '''nmag.ecd''' defines labels and default spherical coordinates for the Neuromag whole-head system

If the program finds a label in '''default.ecd''', the channel will automatically be defined as EEG. If not, if it finds a label in one of the other files, the channel will be defined as MEG. If it doesn't find the label anywhere, the channel will be defined as Polygraphic.

The spherical coordinates defined in these files are sufficient for mapping the data. Auxiliary files defining the real sensor coordinates are required for source analysis.

'''Defining default label and coordinate file for a new MEG system'''

When preparing an MEG from a system other than BTi-WHS or Neuromag for import to BESA Research, you should edit either '''bti.ecd''' or '''nmag.ecd '''to conform with your system. If sensor files ('''<nowiki>*.pos/*.pmg</nowiki>''') are always available for your files, the coordinates in the ''ecd ''files are irrelevant: all you need do is define the labels for your own MEG system or use the labels as already defined.

'''Files to prepare for reading in each data file'''

Each auxiliary file should have the same base name as your data file.

'''Define channel labels.''' There are several possibilities:
* Generate your data file according to the BESA'' avr'' ''format or the ASCII multiplexed format.'' Labels are listed in the second line of the file.
* Generate a ''label file'' (extension '''.ela''') with one MEG channel label per line (matching with your ''ecd ''file as defined above) or with the type "MEG" and a label for each line.

Label definitions are also possible using ''elp'' or ''elb'' files, but the above two solutions are recommended because they are the simplest.

'''Define sensor coordinates.''' Generate a ''pos'' or ''pmg'' file. Make sure that the number of sensors matches with the number of MEG channel definitions in your data file.

'''Define fiducials and other head surface points.''' Generate an ''sfp'' file. The first three lines define the fiducials. Subsequent lines define additional surface points.

'''Define coordinates of the center of the head.''' Generate a ''cot'' file. If this file is absent, BESA Research generates the coordinates by fitting a sphere to the head surface points.

Note that all coordinates should be within the same frame of reference, i.e. the same coordinate system. Units must be in meters, centimeters, or millimeters.

== Example: Defining Channel Labels ==

The files described in these examples can be found in the ''.\Examples\Xtras\EEG+Channel Labels'' subdirectory.

The simplest way to define electrode coordinates is to use BESA Research’s default settings (defined in the file, '''default.ecd'''). In this case, you only need to provide a list of channel labels. If a channel label is defined in '''default.ecd''' (i.e. if the labels belong to the 10-20 or 10-10 system), BESA Research will recognize the channel as EEG, and will allocate 3D coordinates.

Labels are not always supplied correctly in the data file. You can override the internal labels in several ways:
* Read the data file, and then use "''Edit / Channel Configuration''" to redefine the channels. The configuration is stored in a file with the name '''basename.elb''' (for binary data) or '''basename.elp''' (for ASCII data), where basename is the base name (name without the extension) of your data file.
* Prepare a label file (with the extension ''ela'') containing a list of labels. This can also specify channel types (e.g. EEG, Polygraphic, Intracranial, MEG).
* Prepare a file (with the extension ''elp'') containing spherical coordinates of the channels. This is the method used with the previous version of BESA Research. If the file doesn’t contain labels, labels are allocated based on their proximity to the 10-20 or 10-10 definitions in '''default.ecd'''.

The following examples illustrate the above three methods. The input files are all in ''BESA avr format, ''although these examples apply to all EEG data formats in which only EEG channels exist.

If the data file contains polygraphic or other types of non-EEG channel, the types need to be defined. See the ''EEG+Polygraphic channels example.'' MEG is a special case, because the sensor coordinates need to be defined. See the ''MEG ASCII and the MEG+EEG'' ''examples''.

'''Example 1. EEG file containing wrong labels – use ''Edit/Channel Configuration ''to redefine labels'''
* The'' avr'' file, '''EEGwithLabels.avr''', contains the EEG labels. Channels 4 and 14 have been mislabeled – the labels need to be swapped.
* Open the file with '''''File/Open''''' (Select file type ''BESA avr''. Find the correct directory ''Xtras\EEG+Channel Labels'').
* The file should open correctly, displaying 32 channels of EEG.
* The channel coordinates can be viewed by typing the '''‘V’ '''key (make sure the cursor is off). There will be a 3D display of the electrodes. Clicking on an electrode will display the label and the coordinates.
* In this file, channels 4 and 14 have been mislabeled as P3 and F3. In fact, the labels should be the other way around. We will now correct this:
* Select '''''Edit / Channel Configuration'''''.
* Type ‘F3’ into the label for channel 4, and ‘P3’ into the label for channel 14. Then type ‘'''OK'''’. The new channel configuration will be saved in '''EEGwithLabels.elp'''.
* In the data display, the labels of channels 4 and 14 will now be displayed correctly.
* Close the file ('''''File/Close''''') and open it again. Note that the labels are still correct. This is because the new channel configuration file, '''EEGwithLabels.elp''', is read automatically.

'''Example 2. EEG file with no labels – channel labels in auxiliary file'''
* The ''avr'' file, '''EEGwithoutLabels.avr''', has no labels.
* EEG labels are defined in '''EEGwithoutLabels.ela'''. This is read automatically when the file is opened.
* In this example, labels are correct. Each label in the ''ela'' file is on one line:

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F7''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F3''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fz''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''...''</div>

'''Example 3. EEG file with no labels – channel labels derived from spherical coordinates'''
* The ''avr'' file, '''EEGwithSphericalCoords.avr''', has no labels.
* Spherical coordinates are defined in the ''elp'' file, '''EEGwithSphericalCoords.elp'''. This contains spherical coordinates (theta and phi) and no labels:

<div style="margin-left:1.3cm;margin-right:0cm;">''-93 -72''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''92 74''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''-97 -40''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''-61 -49''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''-46 -88''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''62 51''</div>

* When the data file is opened, the ''elp'' file is read automatically, and BESA Research uses the tables in '''default.ecd''' to assign channel labels. To indicate that it has assigned user defined coordinates and matched with the closest standard electrode, BESA appends an apostrophe (‘) to each label:

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp1’''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp2’''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F7’''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F3’''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fz’''</div>

* We advise to assign specific labels as well as spherical coordinates if you want to use your own spherical coordinate system, e.g.:

<div style="margin-left:1.3cm;margin-right:0cm;">''FP1u -90 -72''</div>

'''Example 4. EEG file with no labels – channel labels not in basename.el?'''
* The ''avr ''file, '''EEGnoLabelsNoElaFile.avr''', has no corresponding ''ela, elp'', or ''elb'' file, i.e. no file with the same base name and the ''el?'' extension.
* When you open the file, BESA Research will ask for a channel configuration file. The ''File Open'' ''dialog ''will select the ''directory .\Montages\Channels''. The idea is that standard (= frequently used) electrode configurations should be kept in this directory.
* Select the file '''XtrasExample.ela'''.
* Close the data file and reopen it. The file will open with the correct labels. In the BESA window title you will see that the file '''EEGnoLabelsNoElaFile.elp''' has been read automatically. This file was created when '''XtrasExample.ela''' was read.

== Example: Mixed EEG and Polygraphic Data ==

The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Polygraphic'' subdirectory.

The data are in '''EEG+Polygraphic.avr'''.

The third channel is defined as polygraphic in the '''EEG+Polygraphic.ela '''file:

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''POLY Test''</div>

<div style="margin-left:1.3cm;margin-right:0cm;">''F3''</div>

The prefix "''POLY''" specifies that the channel is polygraphic. Most other channels are interpreted as EEG because the labels are known in the 10-20 system.

Similarly, channel 31 is defined as intercranial, using the prefix "''ICR''".

Note that you can also define channels as EEG by specifying the ''"EEG" ''prefix (e.g. ''"EEG E1". ''This is useful if there are many more channels than are defined in the 10-10 or 10-20 systems, and if the channel coordinates are defined.

== Example: EEG with Digitized Coordinates ==

The files described in this example can be found in the .''\Examples\Xtras\ EEG+Digitization Points ''subdirectory.

In the previous examples, we have illustrated how to assign labels to channels using channel definition files. In those examples, only spherical coordinates were defined. Here we will show how to read digitized surface points into BESA Research, using the surface point (''sfp'') coordinate file and the surface point name (''sfn'') file.

The principles of defining digitization coordinate files are:
* The labels in the ''sfp/sfn'' file combination are used to assign coordinates to electrodes. Thus, if a coordinate has the name ‘''Fz''’ it will be assigned to the channel with the label ‘''Fz''’.
* In consequence, digitization of surface points can be in a different order to the sequence of channels in the data file. Matching to channels is done by comparing the labels.
* We recommend that the fiducial points, '''nasion, left preauricular point, right preauricular point''' be digitized. If you do not digitize them, BESA Research will simulate these locations (see ''“Example: Digitization points with and without Fiducials”''). Fiducial points, labeled '''FidNz, FidT9, FidT10''' should be the first three coordinates in the ''sfp'' file.
* As with the channel definition files, it is easiest for BESA Research if you name the ''sfp/sfn'' files using the base name of the data file, e.g. if the data file is named '''doodah.avr''', name the'' sfp'' file '''doodah.sfp''' and the ''sfn'' file '''doodah.sfn'''.
* You specify the files to be read in the ''Channel and digitized head surface point information dialog box.''

See ''“Example: Polhemus Digitizer Data” ''for a discussion of how to format the files originating from Polhemus and other digitizers.

'''Example 1. EEG file containing labels, ''sfp'' file containing coordinates, ''sfn ''file containing coordinate names'''
* The ''avr'' file, '''EEGdigitized1.avr''', contains the channel labels. Therefore, we don’t need a channel definition file.
* The ''sfp'' file, '''EEGdigitized1.avr''', contains digitized coordinates of electrodes and of additional surface points. The labels in the file do not correspond to the electrode labels in the ''avr ''file.
* The ''sfn'' file contains the corrected labels (1 line for each corresponding line in the'' sfp'' file). Now it is possible to match up electrode labels with the labels in the ''avr ''file.
* Open the data file, '''EEGdigitized1.avr'''. The ''Channel and digitized head surface point information dialog box'' will open automatically.
* Note the green tick mark at the top right of the dialog box. This is feedback to say that coordinates of all 32 electrodes have been found.
* Look at the entry ‘''Digitized head surface points’''. Here you will see that the ''sfp'' and the ''sfn ''files have been read automatically (because of the common base name). There are 51 locations. Note that the digitizer file can contain many more locations than the electrodes. BESA Research uses the locations for fitting the sphere of the spherical head model in source analysis. BESA Research can export these locations for coregistration with the MRI.
* Define the electrode thickness as 6 mm (at the right of the ‘''Digitized head surface points’'' box. This is the distance of the digitized point on the electrode to the surface of the head.
* Press '''‘OK’''' in the dialog box and view the coordinates by pressing the '''‘V’''' key.

'''Example 2. EEG file without labels, channel labels in ''ela'' file, surface point coordinates and names in ''sfp'' file'''
* The ''avr'' file, '''EEGdigitized2.avr''', has no channel label. Therefore, a label file is required. Here, the label file is '''EEGdigitized2.ela'''.
* The ''sfp'' file, '''EEGdigitized2.sfp''', contains digitized coordinates of electrodes and of additional surface points. The labels are defined correctly in the ''sfp ''file, i.e. for every EEG channel label there is a corresponding coordinate. Therefore, no ''sfn'' file is required.
* When you open the file, don’t forget to define the electrode thickness as 6 mm in the ''Channel and digitized head surface point information dialog box.''

== Example: Polhemus Digitizer Data ==

The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Digitization Points'' subdirectory.

Data from the Polhemus (other digitizers too) may often not fit the format BESA Research requires for the surface point file. Note that Polhemus data can be exported directly into BESA-compatible ''sfp''-files using the LOCATOR software.

BESA Research requires either
* just the cartesian coordinates (x, y, z) values -- one set of coordinates per line. In this case, labels must be defined in a parallel surface point name file, e.g.

<div style="margin-left:1.27cm;margin-right:0cm;">''0.5  3.75  12.68''</div>

<div style="margin-left:0cm;margin-right:0cm;">or</div>

* the cartesian coordinates plus a label. The label can be in front of or behind the coordinates on the line, e.g.

<div style="margin-left:1.27cm;margin-right:0cm;">''0.5    3.75  12.68  Fz''</div>

<div style="margin-left:2.54cm;margin-right:0cm;">or</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''Fz  0.5  3.75  12.68'' </div>

Here is an example of a few lines of a (''sfp'') file that are not read correctly by BESA Research:

<div style="margin-left:1.27cm;margin-right:0cm;">''Nz  0  87.721  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''T9  -79.131  0  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''T10  67.253  0  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''1  -34.192  103.374  31.868''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''2  23.642  103.048  30.351''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''3  -81.179  62.913  27.596''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''4  -60.701  79.631  78.273''</div>

What is wrong?

* First, some of the points are just numbered. These numbers don't tell BESA Research which electrode channel to which the coordinates should be assigned – assignments should be via channel labels and not numbers.
* Second, Nz, T9, T10 define the fiducials. Instead, the labels FidNz, FidT9, FidT10 are required (prefix "Fid").

What should be done? Probably the best way is

 a) keep only the coordinates in the '''<nowiki>*.sfp </nowiki>'''file:

<div style="margin-left:1.27cm;margin-right:0cm;">''0  87.721  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''-79.131  0  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''67.253  0  0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''-34.192  103.374  31.868''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''23.642  103.048  30.351''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''-81.179  62.913  27.596''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''-60.701  79.631  78.273''</div>

b) prepare a surface point name file ('''<nowiki>*.sfn</nowiki>''') containing the corresponding labels:

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidNz''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidT9''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidT10''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''Fp1''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''Fp2''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''F7''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''F3''</div>

Keeping labels and coordinates separate means that the label file needs generating only once. The coordinate file is different for each subject.

Alternatively, if your digitizer program attaches the labels correctly to the coordinates, then you can prepare the ''sfp'' file like this:

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidNz    0       87.721   0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''FidT9  -79.131    0       0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''FidT10  67.253    0       0''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''Fp1    -34.192  103.374  31.868''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''Fp2     23.642  103.048  30.351''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''F7     -81.179   62.913  27.596''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''F3     -60.701   79.631  78.273''</div>

== Example: Digitization points with and without Fiducials ==

We recommend that if electrodes are digitized, you should also digitize the three fiduciary points:''' Nasion''', '''and left and right preauricular points'''. We refer to these points as "fiducials". We name them '''"FidNz",''' '''"FidT9",''' and '''"FidT10".'''

If you do not digitize these points, BESA Research will simulate them, i.e. it will generate the points where it expects them to be, based on the fit of a sphere to the existing points, and on the names of surface points of known locations. "Known locations" means: the surface point name must be a 10-20 or 10-10 electrode name (e.g. "Cz" -- arbitrary labels, such as "E10" is not a known location). Therefore, BESA Research requires that at least 3 surface points with known labels are defined.

In a file containing digitization points ('''<nowiki>*.sfp</nowiki>'''), the fiducials should be the first three sets of coordinates, i.e. the first three lines of the file. The remaining coordinates in the file can be electrode (or other surface point) coordinates, in any order. The assignment of electrode coordinates to data channels is achieved by matching the coordinate labels to data channel labels.

'''Consequences of omitting fiducials'''

When these files have been read into BESA Research, look at the head surface points in 3D using ''File/Head Surface Points'' ''and Sensors/View'' (or use the shortcut '''‘V’'''). You will see small differences in fiducial locations between the real and the simulated locations. You can expect very slight influences on the results of source modeling (the spherical head may be rotated slightly, although the head center and radius will be identical), and output of source locations in head coordinates will be different, because these coordinates are based on fiducial locations (see chapter ''“Working with Electrodes and Surface'' ''Locations/ Coordinate systems''”).

== Example: ASCII Import ==

The files described in this example can be found in the ''.\Examples\Xtras\ASCII Import'' subdirectory.

When should the Import ASCII function be used? If you have data in BESA Research average referenced or multiplexed format, use the Open File function to read in a file directly. If you have data in a different ASCII format, BESA Research offers a flexible import function to import data from an array of numbers in an ASCII file.

The array can be '''vectorized '''(one channel, all time points, per line) or '''multiplexed''' (one time point, all channels, per line). These alternatives are illustrated in the two example files '''vectorized.asc''' and '''multiplexed.asc''', and in the tables below:

'''Vectorized array:'''

{| style="border-spacing:0;width:12.993cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 1 ''
|| ''channel 1, time 2''
|| ''channel 1, time 3''
|| ''channel 1, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 2, time 1''
|| ''channel 2, time 2''
|| ''channel 2, time 3''
|| ''channel 2, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 3, time 1''
|| ''channel 3, time 2''
|| ''channel 3, time 3''
|| ''channel 3, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 4, time 1''
|| ''channel 4, time 2''
|| ''channel 4, time 3''
|| ''channel 4, time 4''
|-
|}

'''Multiplexed array:'''

{| style="border-spacing:0;width:12.993cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 1 ''
|| ''channel 2, time 1''
|| ''channel 3, time 1''
|| ''channel 4, time 1''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 2''
|| ''channel 2, time 2''
|| ''channel 3, time 2''
|| ''channel 4, time 2''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 3''
|| ''channel 2, time 3''
|| ''channel 3, time 3''
|| ''channel 4, time 3''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 4''
|| ''channel 2, time 4''
|| ''channel 3, time 4''
|| ''channel 4, time 4''
|-
|}

BESA Research needs channel labels. If the labels are in the 10-20 or 10-10 system, BESA Research will assign the channels default coordinates. This is the minimum requirement to be able to map EEG.

If you have 3D digitized coordinates, these can also be specified in ASCII files. This is described under the chapter “''Example: EEG with Digitized Coordinates''”.

'''Example 1. Vectorized data'''
* The file '''vectorized.asc''' contains the data. The file should be imported via ''File/Import ASCII File''.
* First you will be asked for a name for the binary target file. The name '''vectorized.fsg''' is suggested. You may accept this name by pressing '''‘OK’''' or choose an alternative name. Note that if the file already exists, the imported data will be appended to the file.
* Next, the ''ASCII File Properties dialog box'' will open. First select ''‘Vectorized’'', and make sure the subsequent entries are correct:

<div style="margin-left:1.27cm;margin-right:0cm;">Header Lines = 0 (i.e. in this example the numbers start on the first line)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Bins/Microvolt = 1.0 (i.e. a value 1 in the data represents 1 µV)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Sampling Rate = 320 Hz (When the dialog box is opened, BESA Research always chooses the setting it used previously)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Number of channels = 32 (the number of rows in the matrix)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Number of Samples = 640 (the number of columns in the matrix)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Prestimulus Time = 1000 ms (defines the zero time point 1 s after the beginning)</div>

* Press '''‘OK’''' to accept the settings.
* Next, the ''Channel and digitized head surface point information dialog box'' will open. In the ''‘Channel configuration’'' box, the label file, '''vectorized.ela''', will be detected automatically. Automatic detection occurs when the label file has the same base name as the data file (in this case, vectorized). To the right of the file name is a summary of channel types: 32 channels found, 30 are EEG, 1 is intercranial, 1 is polygraphic.

Note the green tick at the top left of the dialog box. This indicates that BESA Research thinks that it has sufficient information to read the file, and map and do source analysis on the data.

* To see how channel types are specified in '''vectorized.ela''', click on the '''Edit '''button to view the file with the Notepad program. Here you will see that most channels have 10-20 electrode names. Channel 3 has the prefix ‘''POLY''’, specifying that this channel is polygraphic. Channel 31 has the prefix ‘''ICR''’, specifying that this channel is intercranial. Close Notepad, and click ‘'''OK'''’ in the dialog box.
* A final dialog box asks for a Segment Comment. This is a label that will be displayed in the resulting file. The label is particularly useful if you import several ASCII files into one target file. Each segment is then easily identified by its own label.

'''Example 2. Multiplexed data'''
* This example is similar to Example 1. In this case, import the file '''multiplexed.asc''', and select ‘Multiplexed’ in the ''ASCII File Properties dialog box''. Other settings in the dialog box stay as they were.

'''Notes'''
# The numbers in the source files can be split into several lines per channel or per time point. Then you will have to enter the correct number of time points and channels in the dialog box. In the present examples, the lines are not split (the vectorized file has all 640 time points in each line, and the multiplexed file has all 32 channels in each line). In this case, BESA Research selects the correct numbers of time points and channels automatically.
# If you have digitized coordinates, these can be specified in the Channel and digitized head surface point information dialog box. Since the procedure is the same as when reading data, this is described elsewhere under “''Example: EEG with Digitized Coordinates''”.

== Example: MEG ASCII ==

The files described in this example can be found in the'' \Examples\Xtras\ MEG ASCII'' subdirectory of the BESA Research installation folder.

'''Multiplexed MEG ASCII file with labels in the header (''med.mul'')'''

For reading MEG data, BESA Research expects
* Correct channel definitions, i.e. channels should be defined as MEG.
* Head surface points.
* Sensor coordinates, in '''the same coordinate system''' as the head surface points.
* Optionally, you can define the coordinates of the center of the head. This will be important if too few head surface points are available to specify where to place the spherical head used by BESA Research for source modeling, or if you want to use some external definition, e.g. from the MRI.

As with digitized EEG coordinates, we use the ''Channel and digitized head surface point information'' ''dialog box'' to specify the files which need to be read.

'''Example 1. File Open'''
* The file, '''MEGASCII.mul''', contains MEG data in the ASCII multiplexed format. This format contains channel labels. The labels used are recognized by BESA Research as originating from the Neuromag system. They are therefore identified as MEG and do not need further identification.
* The ''sfp'' file, '''MEGASCII.sfp''', defines fiducials and head surface points. Coordinate labels are included in the file, so no'' sfn'' file is required.
* The cot file, '''MEGASCII.cot''', defines the coordinates of the head center. If this were missing, BESA Research would compute the head center based on the sphere that best fits the head surface points.
* The ''pos'' file, '''MEGASCII.pos''', defines the coordinates of the 122 sensors. For the Neuromag system there are 9 values per line, defining primary coil location, secondary coil location, and orientation cosines. The sequence of coordinates in the ''pos'' file '''must''' match the sequence of MEG channels! The file format and locations of the primary and secondary coils allow BESA Research to identify the sensor type as planar gradiometers. If the file had only six values per line, BESA Research would classify the sensors as magnetometers (one primary coil and the orientation cosines).
* Open the file, selecting current file type as ''‘*,m''??’. The ''Channel and digitized head surface point'' ''information dialog box'' will open, displaying the different auxiliary file names. The green tick indicates that BESA Research finds everything to be OK.
* Press the '''‘OK’''' button and then the''' ‘V’ '''key to view the coordinates.

'''Example 2. File Import'''
* The file, '''MEGASCIIimport.asc''', contains MEG data in a multiplexed array, without a header. This needs to be imported using ''File/Import ASCII'' (see ''“Example: ASCII Import”).''
* On import you have to specify the file as ‘Multiplexed’, the number of time points (285), the number of channels (132), the bins/µV (or bins/fT) (=1), the time at which the stimulus occurred (50 ms), and the sampling rate (949.667 Hz).
* This format contains no channel labels. The labels in '''MEGASCIIimport.ela''' are recognized by BESA Research as originating from the Neuromag system. They are therefore identified as MEG and do not need further identification.
* Since it recognizes the channels as MEG, the ''Channel and digitized head surface point information dialog box'' will open, displaying the different auxiliary file names as before. Since all necessary files with the same base name as the data file are supplied, they are read automatically.
* Press the ‘'''OK’''' button, enter a segment name, and then the '''‘V’''' key to view the coordinates.

'''Example 3. File Open -- MEG information recorded elsewhere'''

This example illustrates the case where the auxiliary files have a different base name from the data file: you must select the file name in the ''Channel and digitized head surface point information dialog box''.

* Open the file, '''MEGASCIIelsewhere.mul'''. It is read as an MEG magnetometer file.
* In the ''Channel and digitized head surface point information dialog box'', specify
<div style="margin-left:1.27cm;margin-right:0cm;">'''MEGASCII.sfp''' for the head surface points, and</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''MEGASCII.pos''' for the MEG sensors</div>
* MEG coordinates will be correct. The sensor definition file specifies the sensors as planar gradiometers.
* Where the auxiliary files came from will be recorded in the database. If you open the file again, the auxiliary files will be found automatically, without asking any questions.

== Example: Reading combined EEG and MEG from an ASCII file ==

The files described in this example can be found in the ''Examples\Xtras\MEG+EEG'' subdirectory of the BESA Research installation folder.

Here are two examples containing mixed MEG, EEG, and polygraphic channels:
* Open a file using the ''File/Open'' command
* Import a file using ''File/Import ASCII'' command

In both cases

* The '''<nowiki>*.ela</nowiki>''' file defines the channel labels. Based on the labels, BESA Research knows which channels are EEG and MEG. The remainder are classified as polygraphic channels.
* The '''<nowiki>*.pos</nowiki>''' file defines the MEG sensor coordinates. The number of values on a line of this file (=9) defines the MEG as gradiometers. The relative locations of primary and secondary coils identify the gradiometers as planar.

'''1. Example with ''File/Open'''''
* Open the file '''MEG+EEG.mul'''. The ''Channel and digitized head surface point information dialog box'' will open automatically (unless the file has already been read once and the information is in the database).
* You will see under ''‘internal data file information’'' that BESA Research finds 122 MEG sensors, and 162 channels in all.
* Under ‘''Channel configuration’'', you will see that as a result of reading the file '''MEG+EEG.ela''', 32 channels are defined as EEG, and 8 channels as polygraphic.
* Under ‘''Digitized head surface points’'' is the feedback that out of the 51 locations in the file '''MEG+EEG.sfp''', all electrode locations have been defined.
* Under ‘''MEG sensors’'', the sensors have been identified as gradiometers.
* The green tick at the top right of the window indicates that BESA Research classifies everything as OK.

'''2. Example with ''File/Import ASCII'''''
* Import the file '''MEG+EEGimport.asc'''. Select '''MEG+EEGimport.fsg '''as the target file (see ''“Example: ASCII Import”'').
* Select 320 Hz sampling rate, and 500 ms pre-stimulus time. Other selections in the dialog box should be ‘Multiplexed’, 1 bin/microvolt (this is interpreted as 1 bin/fT for MEG), 162 channels and 320 samples.
* The ''Channel and digitized head surface point information dialog box'' will open as above.

Electrodes and Surface Locations

2017-04-07T08:48:44Z

Alexa:

Electrodes and Surface Locations

2017-04-07T08:31:46Z

Alexa:

= Working with Electrodes and Surface Locations =

== Introduction - Electrodes and Surface Locations ==

Here you will find out how BESA Research works with electrode and MEG sensor coordinates and labels, and how head surface points can be used to improve source modeling and coregistration of source models with the MRI. In most cases, electrode positions are sufficiently defined by their labels. The section "''Electrode Conventions''" lists the standard position which BESA Research assigns to EEG channels. In some cases, especially for larger electrode arrays or for MEG measurements, additional information is required to add sufficient information for mapping and for source analysis. The additional information is supplied in additional, auxiliary files which are read by BESA Research and associated with the data files. The auxiliary files, and how they are supplied to BESA Research, are described in this chapter.

Examples for using auxiliary files to define the 3D locations of electrodes are found in the chapter "''Special Topics / Working with Electrodes... / Examples''" in the online help.

Descriptions of file formats that BESA Research uses are given in the online help chapter "''Special Topics'' ''/ Working with additional files''".

== Working with auxiliary files ==

Data files come with varying amounts of prior information about electrode/sensor locations, depending on the recording system. BESA Research allows you to read auxiliary files that define additional information, such as channel labels, and coordinates of the electrodes, sensors, and other head surface points. The information is required for mapping and for source montages.
* '''Mapping.''' BESA Research uses spherical spline mapping. For this, electrode/sensor locations are projected onto a sphere. The minimum requirement is 10-10 or 10-20 labels: if only channel labels are available without additional information, BESA Research uses default spherical coordinates.
* '''Source modeling'''. Spherical coordinates of electrode locations are sufficient, but digitized locations are better. Digitized locations can be defined in the data file or in auxiliary files. BESA Research will use digitized head surface points (electrodes + additional points) to fit a sphere for the spherical model. Points anterior to the left and right preauricular points and below the plane formed by these points and the nasion are excluded when fitting the sphere.

Files can also be written, for instance for
* '''Source modelling with MRI coregistration'''. BESA Research allows for the export of surface points in a special format ('''sfh''' file) which can be read by the BESA MRI (or BrainVoyager) program. These are fitted to the head surface defined by BESA MRI (or BrainVoyager) in order to define rotation, translation, and deformation parameters required to coregister the coordinate systems (see "''Integration with MRI and fMRi''").
* '''Export of coordinates.''' Electrode, other surface point locations, and MEG sensor coordinates and other surface point locations can be written to ASCII files so that they can be reread when reading other files into BESA Research (e.g. ASCII files), or used by other programs.

Feedback and control over how these files are read is provided by
* '''the Channel and digitized head surface point information dialog box.''' This dialog is usually opened when you open a file for the first time. It allows you to specify the names of auxiliary files, and it makes initial checks on the files to see whether they are consistent with each other and with the data file. If the check is OK, you will see a green tick at the top right hand corner of the dialog box. If there are inconsistencies, the tick is replaced by a red exclamation mark. In this case, you will usually need to edit the auxiliary files or specify other files. The dialog box is not opened if the file is recognized to contain all the necessary information (files with the '''foc''', '''fsg''' extensions), or if the program only finds a channel definition file (with extensions '''ela, elp,''' or '''elb'''). The dialog box is not opened if the data file has been opened before. You can always open the dialog box manually by specifying ''" File / Head Surface Points and Sensors/Load Coordinate'' ''Files.''
* '''The log file''' ('''<nowiki>*_LoadFile.log</nowiki>''')'''.''' Coordinating the information between the data file and its auxiliary files can be a complex procedure. To help you check whether the coordination is being done properly, if you select the menu entry ''" Options / File / Generate Log "'' during File Open, BESA Research writes a log file with the same base name as the data file, appending "'''_LoadFile.log'''" to the base name, recording which files have been read, and some of the parameters that have been found. This file is created every time auxiliary files are read (e.g. on file open, when reading in channel configuration files, head surface point files, MEG sensor locations), or changed ("''Edit /'' ''Channel Configuration''").
* '''The log window. '''If there are inconsistencies during the processing of auxiliary files and 3D coordinates, a logging window is opened showing the information that would be written to the log file. You can read what has been done to help diagnose the problems. Select '''OK''' to continue in spite of the problems, or''' Reset''' to reject. Typing '''Reset''' also deletes the database files associated with the current data file, thus allowing you to start reading this file from scratch.

'''BESA Research remembers which auxiliary files are associated with the current file'''. When a data file is first opened, and BESA Research finds auxiliary files with the same base name as the data file, you will be asked if you want this file to be read. The decision you make will be recorded in the database for this data file. Next time the file is opened, the files will or will not be read, according to your previous decision. Similarly, when an auxiliary file is read using the menu, this is recorded in the database, and the file will be opened automatically next time the data file is opened. To override previous decisions, you must delete the database files (see the''' log window '''above) or change the entries in the Channel and digitized head surface point information dialog box (see the chapter ''"Electrode Conventions / Channel and digitized head surface point information dialog box''").

== Coordinate systems ==

We need to deal with four different coordinate systems. These differ in how the x, y, and z axes are defined, and in the units of measurement (e.g. mm, cm, m). The first three are illustrated in the following figure:

[[Image:ST Electrodes (1).gif ]]

'''Device coordinates.''' These are the coordinates used by the recording system. The axes may be anywhere in relation to the head. For instance, in the Polhemus digitizer, the axes go through the magnetic field transmitter which is located somewhere outside the head. The units of measurement may be millimeters, centimeters, or meters.

'''Head coordinates'''. This coordinate system is defined by reference points on the head known as ''fiducials''. The reference points are normally the nasion (Nz, NAS), the left preauricular point (T9, LPA), and the right preauricular point (T10, RPA). The x axis is defined by the line joining T9 and T10, positive towards T10. The y axis is defined by the line through Nz that is perpendicular to the x axis (positive towards Nz). The z axis is perpendicular to the x and y axes, and goes up out of the head in the vicinity of Cz. The units of measurement may be millimeters, centimeters, or meters. In BESA Research these are labelled with the prefix 'Fid', e.g. 'FidT9', 'FidNz'.

'''BESA Research coordinates.''' For dipole analyses the head model consists of a sphere. In the default situation where no digitized sensor information is available, the center of the sphere is defined by the crossing point between the lines joining T7 (=T3) and T8 (=T4) and Fpz and Oz.. The x axis is the T8-T7 line, positive at T8. The y axis is the Oz-Fpz line, positive at Fpz. The z-axis goes up out of the head through Cz. If digitized information is available, the axes are defined by the best fit between the idealized electrode locations and the real locations. The diameter of the sphere is also defined by the best fit. Units given in the display are in millimeters.

The '''center of the spherical model''' is on average about 4 cm above the origin of the Head Coordinates. If digitized surface points are available, the sphere is fitted to these points. Using a cot file, it is possible to override the fit and define your own head center. In conjunction with BrainVoyager, you can use the MRI to seed the location of the head center (e.g. a fixed distance anterior to the posterior commissure) and save it as a cot file. Using MRI coregistration (see "''Integration with MRI and'' ''fMRi''"), the center is placed between the anterior (AC) and posterior (PC) commissures, at the half-way point between the anterior and posterior points (AP and PP). Without coregistration, the center corresponds to a point 17.5 mm behind AC in the standard MRI head.

'''MRI coordinates.''' These are the coordinates used by BrainVoyager. These are defined by the MRI slices. Measurement units are millimeters.

== The Channel and Digitized Head Surface Point Information Dialog Box ==

Many data formats read by BESA Research require additional information about data channel, which are specified by additional, auxiliary files. This dialog box allows you to specify which auxiliary files are read in to supplement the information in the data file.

The dialog box is opened automatically the first time a data file is opened, if
* auxiliary files other than a channel definition file ('''<nowiki>*.ela</nowiki>''', '''<nowiki>*.elp</nowiki>''', '''<nowiki>*.elb</nowiki>''') are found
* no auxiliary files are found, and the data file was not written in compressed binary format ('''<nowiki>*.foc</nowiki>''', '''<nowiki>*.fsg</nowiki>''') by BESA Research

When a data file is closed, the information about which auxiliary files have been read is stored in the database. When the file is opened for a second time the dialog box is not opened automatically, because the information is assumed to be correct – the files are read automatically.

The dialog box can be opened manually by selecting "''File / Head Surface Points and Sensors/Load'' ''Coordinate Files''", or using the shortcut '''ctrl-L'''

[[Image:ST Electrodes (2).gif ]]

The dialog box is divided into several sections:

* '''Internal data file information.''' Here you can see the file name, the originating system (file format), the name of the database file, if any, and the channel information as specified by the data file alone.

[[Image:ST Electrodes (4).gif ]]

* '''Suggestions.''' This box makes suggestions about what needs to be filled in, e.g. "Please enter electrode thickness"

[[Image:ST Electrodes (5).gif ]]

* '''Main feedback (top right hand corner).''' A green tick indicates that the currently selected data files are consistent among themselves and with the data file. A red exclamation mark indicates an inconsistency. Check the feedback texts in the subsequent sections for more information:

[[Image:ST Electrodes (8).gif ]][[Image:ST Electrodes (7).gif ]]

* '''Channel configuration file specification.''' If the channel labels and types defined in the data file ("Internal data file information") need to be changed, enter a file name here ('''<nowiki>*.ela</nowiki>''', '''<nowiki>*.elp</nowiki>''', '''<nowiki>*.elb</nowiki>'''). If a channel definition file exists with the same basename as the data file, or if a channel definition file has been specified previously (database entry exists), it will be selected automatically. To the right of the file name, feedback is provided about the number of channels and channel types found. If the labels are consistent with the data file, to the right the text "Good" is shown. If they are inconsistent, e.g. the file contains the wrong number of channel definitions, the text "Bad" is shown.

[[Image:ST Electrodes (9).gif ]]

* '''Digitized head surface point specification.''' Here you may specify a file containing digitized electrode and other head surface points. Optionally, the information can be split into two files, containing the coordinates ('''<nowiki>*.sfp, .eps</nowiki>''') and the coordinate names ('''.sfn'''). Alternatively, both labels and names can be contained in the coordinate file. If the files specify electrode coordinates, there '''must''' be a coordinate name for each electrode. The sequence may be different. BESA Research will use the names to assign each coordinate to the electrodes. Additional head surface points can have any other names. It is recommended that the first three digitized coordinates are the fiducials (fiduciary points), labelled "FidT9", "FidT10", "FidNz". If your electrode labels not follow the 10-10- or 10-20 standard (e.g. in high-density electrode recordings), it is recommended to tick the box "Electrode labels non -conforming to 10-10 standard". This will prevent BESA Research from using electrodes for an optimal rotation of the coordinate system which should not be used (e.g. A1, A2 which have known locations in 10-10, but are sometimes used in a nomenclature outside of 10-10). The example below shows the sphere adaption for an example data set with and without taking this into account. The right picture shows that when discarding the non-conforming electrodes, the fiducials are correctly placed along the x any y axes.

[[Image:ST Electrodes (10).gif ]] [[Image:ST Electrodes (11).gif ]]

(In the special case of Neuromag files with electrode channels, the data file contains head surface points with the wrong labels. Here you may provide a label file ('''<nowiki>*.sfn</nowiki>''') without a corresponding digitized coordinate file.)

[[Image:ST Electrodes (12).gif ]]

* '''Coregistration file.''' Here you may specify a file containing the coordinates of the head center ('''<nowiki>*.cot</nowiki>''') or an ''MRI Coregistration File ''('''<nowiki>*.sfh</nowiki>'''). Head center redefinition is only necessary if you

<div style="margin-left:1.27cm;margin-right:0cm;">want to provide an external definition, e.g. from the MRI. The ''MRI Coregistration File ''is used if the data are to be coregistered with individual MRI. (see "''Integration with MRI and fMRi'' "). '''Note''' that if a head center file (cot file) with the same base name as the data file exists, it will be read automatically if the head center coordinates deviate by more than 1 mm from the internally calculated values. Changes are ignored if the radio button is set to "No". This automated function allows you to change the head center during a session, using BrainVoyager's view of the MRI and the Source Module.</div>

[[Image:ST Electrodes (14).gif ]]

* '''MEG sensor specification'''. If the file contains MEG channels, you may enter the name of a sensor coordinate file ('''<nowiki>*.pmg</nowiki>''', '''<nowiki>*.pos</nowiki>'''). This field is grayed if there are no MEG channels.

[[Image:ST Electrodes (15).gif ]]

* '''Artifact coefficients file.''' If the data are to be artifact corrected, your pre-prepared coefficient file may be defined here. See the chapter "''Artifact Correction''". Selecting the file here is equivalent to loading the file using the menu entry "''Artifact / Load''".

[[Image:ST Electrodes (17).gif ]]

For each of the selected files, make sure the radio button "'''Yes"''' is selected on the left-hand side of the dialog box. If files have been selected automatically, and you do not wish them to be read, select the "'''No'''" radio button.

If some of the settings are incorrect or the text "Bad" is shown, you may edit the auxiliary files (the file is opened with the NotePad program) or browse for another file by pressing the '''Edit''' or '''Browse''' buttons.

After you have entered the required information, and the green tick at the top right indicates consistency, press '''OK''' to continue. Press '''Cancel''' to ignore the current settings. Press '''Clear DB''' to delete the database files. Press '''Clear Events''' to delete the tag files (the part of the database that records events). Both '''Clear''' buttons close the currently-opened data file.

== General Reading Rules for Data Files and Auxiliary Files ==

Auxiliary files can complement the information in the data file. Here we specify what happens when a data file is opened:

'''1.''' If the data file has been read previously, the database entry specifies which auxiliary files should be read. The file and the specified auxiliary files are opened and the data are displayed.

'''2'''. If a) there is a channel definition file '''(*.el'''''?'') with the same basename as the data file, and

b) this file includes spherical coordinates for the EEG channels (including labels with entries in the '''default.ecd''' file), and

c) there are no other auxiliary files with the same base name, the file will be opened and the data displayed. If files with the same basename are not found, BESA Research will look for files with the basename “default” (e.g. '''default.ela''') in the data folder. If such files are not found, BESA Research will look for files with the basename “default” one folder above (e.g.''' ..\default.ela''').

'''3'''. If the data file has been written in binary format ('''<nowiki>*.foc</nowiki>''', '''<nowiki>*.fsg</nowiki>''') by BESA Research (after Jan.2000), the file will be read, and all information is assumed to be complete. The file is opened and the data are displayed.

'''4.''' In all other cases, the ''Channel and digitized head surface point information dialog box'' will be opened for you to specify and check auxiliary files. Auxiliary files with the same base name as the data file will be specified in the text boxes for file names. If files with the same basename are not found, BESA Research will look for files with the basename “default” (e.g. '''default.ela''') in the data directory. If such files are not found, BESA Research will look for files with the basename “default” one directory above (e.g. '''..\default.ela'''). Otherwise the text boxes will be left blank.

'''5.''' Auxiliary files can be specified at a later time by selecting ''File/Head Surface Points'' and ''Sensors/Load'' ''Coordinate Files''. The ''Channel and digitized head surface point information dialog box'' will be opened.

== Electrodes ==

=== Electrode Conventions ===

BESA Research adheres to the 10/20 and to the new 10/10 standard of the IEF (international EEG Federation). BESA Research will recognize the labels defined by these standards. The labels are stored in most EEG file headers. Otherwise, or in the case of erroneous labeling or sequencing of the recording channels, you may edit the channel labels and/or coordinates, or you may read an electrode file stored previously on disk. In addition to the 10/20 and 10/10 standard labels BESA Research recognizes the following labels: M1, M2 (left, right mastoids), SP1, SP2 (sphenoidal), CB1, CB2 (cerebellar), Chin, Neck, LO1, LO2 (lateral ocular), SO1, SO2 (supra-ocular), IO1, IO2 (infra-ocular). BESA Research will translate all the labels into spherical coordinates for spherical spline interpolation, mapping and source imaging. The following assignments are stored in the file '''default.ecd''' in the BESA folder:

[[Image:ST Electrodes (19).gif ]]

 

''Electrode labels in the file '''default.ecd '''and their spherical coordinates. 10-20 electrodes are shown in red and italic.''

The spherical coordinates are defined in degrees by the azimuth (from Cz, positive = right, negative = left hemisphere) and the latitude (counterclockwise from T7/T3 for left and from T8/T4 for right hemisphere) of each electrode. Please do not modify the existing labels or coordinates in this file, because this would adversely affect the interpolated (virtual) montages, the maps and the source montages and source images in BESA Research. However, you may add additional labels for scalp electrodes at the end of this file if needed (up to a total of 196). When you edit the electrode configuration or read in electrode files, BESA Research may replace the 10/20 standard labels T3, T4, T5, T6 by their new 10/10 equivalents T7,

T8, P7, P8. However, in the initialization file '''BESA.ini '''you can reset to the old 10/20 standard by relabeling T7=T3, P7=T5, T8=T4, P8=T6 under the heading [Electrodes]. You may use the same feature to assign appropriate labels to the X1..X8 channels which exist in many systems, e.g. X1=EKG1 etc.

=== Recommendations for electrode placement ===

For source montages and source analysis two principles are important:

# Covering of the lower head with inferior electrodes to record activity from the inferior surfaces of the brain, especially from the basal temporal lobe, from the temporal pole, from orbito-frontal cortex, and from basal occipital and cerebellar areas.
# Equal spacing of the electrodes over the whole head to cover all brain areas.

In the following montage EEGxx the number xx indicates the number of electrodes.

'''EEG25 - Minimum 10-20 configuration including inferior electrodes'''

This covers the 19 standard 10-20 electrodes:

Fp1, Fp2, F7, F3, Fz, F4, F8 ....

plus 6 inferior electrodes on both sides:

F11, A1, P11, F12, A2, P12

with a recommended continuation of the 20% distances, i.e. use F11 instead of F9, P11 instead of P9, A1 instead of T9 to have a wider coverage of the inferior head. A1 / A2 may be replaced by T9 / T10 (or FT9 / FT10) for convenience and comfort.

[[Image:ST Electrodes (21).gif ]]

''Left: recommended configuration for 25 electrodes. Right: left temporal basal activity mapped with 25 electrodes.''

'''EEG33 - Additional 10-10 electrodes within the major squares'''

To the above electrodes add the following 8 intermediate electrodes:

FC5, FC1, FC2, FC6,   CP5, CP1, CP2, CP6

[[Image:ST Electrodes (23).gif]]

''Left: recommended configuration for 33 electrodes. Right: left temporal basal activity mapped with 33 electrodes.''

'''EEG35 - Additional supraorbital electrodes for better EOG separation'''

SO1, SO2

'''EEG37 - Wider inferior coverage at interlaced 20% distances'''

Continue 20% down from F7, FC5, CP5, P7 etc. and use the following 8 inferior electrodes instead of 6:

F11, FT9, TP9, P11,    F12, FT10, TP10, P12

'''EEG41 – Improved frontal and occipital coverage'''

Additional electrodes halfway between Fz and Fp1 / FP2 and Pz and O1 / O2:

AF1, AF2,   PO1, PO2

'''EEG43 – Inferior chain with 5 electrodes including A1 / A2'''

F11, FT9, A1, TP9, P11,    F12, FT10, A2, TP10, P12

EEG43 represents the widest coverage with relatively even spacing.

[[Image:ST Electrodes (25).gif]]

''Left: recommended configuration for 43 electrodes. Right: left temporal polar activity mapped with 43 electrodes.''

'''EEG64-256'''

With 64 or more channel caps, it is similarly recommended to use a sufficient number of inferior electrodes all around the head. At least 4 inferior temporal electrodes on each side and additional electrodes above or below the eyes (outside of the cap) are suggested.

=== Editing the channel configuration ===

Only use the channel configuration editing facility if the electrodes or the common reference have not been correctly defined by your digital EEG system, or if you want to define specific spherical coordinates for your scalp electrodes. It is your responsibility to check and provide the correct sequence of electrode labels in correspondence with the sequence of channels in the EEG data file. If these sequences do not match exactly, errors will occur in the computation of maps, source images and interpolated montages.

We will use the example EEG file '''eeg2.eeg''' in the subdirectory ''Examples/EEG-Focus'' of the BESA Research directory to explain the editing of electrode labels and coordinates:

1. Select ''File'', then click on ''Open'', or click on '''eeg2.eeg '''if this file is contained in the list of currently selected EEG files.
2. Select ''Edit'', then click ''Channel Configuration''. The dialog box shown below will appear.

[[Image:ST Electrodes (27).gif]]

At the upper left of the figure you see the dropdown menu after selecting the '''File '''menu in the dialog box. This menu allows to edit a new ('''''New''''') or an existing ('''''Open''''') electrode file and to save the changes to the same ('''''Save''''') or a different ('''''Save As''''') file. Normally, it will not be necessary to use this menu. The control fields on the right will be sufficient. If you type ''''''Ok'''''', you will be given the option of saving the changes to a file.

3. Click on '''Reload org. Labels''' to reread the original labels as stored in the file header of '''eeg2.eeg'''. BESA Research quits editing and redisplays the EEG. Repeat step 2 and select "''Edit / Channel'' ''Configuration''" again. Note: The button '''Reload org. Labels''' is not available if there are no labels in the file header.
4. Click on the empty space of the scroll bar below the '''scroll '''button and on the '''down arrow''' of the '''scroll bar''' to display the remaining electrodes in the file.
5. Click on electrode '''R''' (line 32), then on the button '''Delete Electrode''' to remove the associated channel, which does not contain any signal. Note that you may not omit intermediate channels, even if they do not exhibit signals, because the correct correspondence between the series of electrodes and the EEG channels will not be maintained. Use the '''"Edit / Bad Channels"''' menu to disable artifactual or empty channels.
6. Click on''' EOG''' (line 30) and change the entry to '''EOG1'''. Do not type '''<Enter>,''' but click on the next or a different electrode box to accept the changes.
7. '''Double click''' on '''EOG '''(line 31). This will highlight the entry. Simply type the new name '''EOG2''', and note that the old label is replaced when highlighted. Electrodes '''30 '''and '''31 '''are now defined as distinct electrodes. Next, we want to replace the label '''T10 '''by '''A2'''.
8. Click on the label '''T10''' (line 24). Then click on the '''drop down''' arrow right of the highlighted label to obtain the list of default scalp electrodes (read from '''default.ecd''' and sorted alphabetically). Type '''A''' to jump to the electrodes beginning with letter A (see below). Type '''2''' or '''click''' on '''A2''' in the list. Click on the '''type '''box (Scalp channel) to close the list and display the new entry in line 24. Note that this is the most convenient way to edit an electrode label.

[[Image:ST Electrodes (28).gif]]

9. Exercise: repeat step 8 to replace '''T9''' by '''A1'''. Restore labels '''T10''' and '''T9''' in lines 24 and 21.
10. Replace SO1 and SO2 (supra-orbital) by '''PSO1 '''and '''PSO2 '''and note that these electrodes are changed to the''' 'Polygraphy'''' type, because no coordinates are associated with these labels.
11. After you click ''''OK'''', the box '''Write Channel Configuration File''' will appear and display a name for the current electrode file. By default, the BESA electrode file path and current file name will be used and supplemented by the extension ''''.elb''''. The electrode file path may be set in the '''BESA.ini''' file [Defaults] section under ElectrodeFilePath. If no electrode file path is specified in the '''BESA.ini''' file, the default electrode file path ''Montages\Channels ''is used. Simply click ''''OK'''' or type '''<Enter> '''to save the changes to this file, or select a new file name and/or path, if you do not want to store the electrode file in the BESA Research electrode file directory.

Note that by using the default 10/10 labels (see chapter "''Electrode conventions''") you specify that the associated electrode is a scalp electrode. Hence, different labels must be used for polygraphic, intracranial or MEG channels. After you have entered a new non-scalp label, you may select the type of the electrode/channel amongst the different groups ('''Polygraphy, Intracranial, MEG Channel''') from the drop down list in the ''''''Type'''''' box. This will allow for using separate selection and scaling facilities of the channel group control push-buttons at the right of the screen ('''All, Scp, Pgr, Icr, MEG'''). If you have entered a new non-scalp label and select the type '''Scalp Channel''', or if you click on the ''''Advanced>>'''' field, boxes will appear to enter the spherical coordinates (azimuth and latitude) of this electrode (cf. Fig. 6.5). These features may be used to specify non-standard scalp electrodes. Please check the earlier sections of this chapter for electrode conventions. You may view the locations of the scalp electrodes on the head schemes in the mapping window. Select '''Show Electrodes in Maps''' in the "'''View / Options'''" menu.

[[Image:ST Electrodes (29).gif]]

'''Hint:''' If you want to specify the spherical coordinates of an electrode which is close to a standard electrode, click on the ''''Advanced >>'''' field, enter the label of the standard electrode and append a single quotation mark. This will specify that the electrode is close to the labeled location but has different coordinates. The ''Scalp Channel'' type will not be replaced by '''Polygraphy.''' Then edit '''Azimuth''' and '''Latitude'''. This convention is used by BESA Research when reading electrode coordinate files '''(*.elp'''), e.g. from the BESA program. The coordinates are read and compared with the default coordinates to assign the closest label. Then a single quotation mark is appended to the label, and the coordinates are assigned as specified in the '''.elp''' file. For example, open '''segm1.eeg''' in the ''Examples\EEG-Focus'' subdirectory.

Note that the file '''segm1.elp '''is searched for automatically in the directory of the data file when opening the data file.

'''Edit Common Scalp Reference'''

There is a separate line at the bottom in the ''Channel Configuration dialog box'' to enter the label and coordinates of the '''Common Scalp Reference electrode'''. If this is specified and enabled (click on field '''Enabled'''), the information provided by the fact that all scalp electrodes were recorded against a common recording reference will be used for mapping, source imaging and virtual montages. This information will be lost if the common reference has not been specified or if a combination of electrodes has been used as reference during recording. Specify the '''Common Scalp Reference electrode''' only if all electrodes have been referenced to the same single electrode and if a standard 10/10 location has been used for the common recording reference.

''Note that BESA Research cannot process digital EEG data correctly if there is no common recording reference'', and if different recording references were used for the various scalp electrodes. For intracranial and polygraphic channels different references may be used. It is preferable to use the common reference also for electrode channels near the eyes, because these electrodes provide valuable information for mapping, source imaging and interpolated montages. The traditional bipolar channels (e.g. horizontal and vertical ''EOG'') may be ''reconstructed digitally'' using the '''Selected Channels''' group or user-defined montages.

== 3D Coordinates for Precise Analysis ==

=== Introduction - Working with Digitized 3D Coordinates ===

Working with digitized electrode coordinates usually requires reading in additional (auxiliary) files. The procedure is described in the chapter "''Working with auxiliary files''".

=== Data reading rules for EEG ===

This section explains which additional files are read, or which files have to be read in order to provide the necessary information for mapping and source montages.

Assume file name is '''datafile.xxx'''. datafile is the base name, '''.xxx''' is the extension. Replace the text ''datafile'' by the base name of your own file, and the extension'' xxx'' by the extension of your own file.

'''Channel definitions for EEG:'''

Labels have 10-10 names: default locations will be used.

Labels do not have 10-10 names: Channels are interpreted as '''polygraphic'''. Mapping is not possible without one or more of the following additional files.

'''Define channel names and types.''' File '''datafile.ela''', '''datafile.elp''', or '''datafile.elb''' exist, or files '''default.ela''', '''default.elp''', or '''default.elb''' exist, or files '''..\default.ela''', '''..\default.elp''', or '''..\default.elb''' exist (i.e. files with basename d''efault ''one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The ''ela'' file contains just labels and, optionally, types. The ''elp'' file contains spherical coordinates and can contain labels and types. The ''elb'' file contains the same information in binary format. See chapter "''Working with additional files / Channel Definition File Conventions''".

'''Define order in which electrodes were digitized.''' File '''datafile.sfn '''exists, or file '''default.sfn''' exists, or file '''..\default.sfn''' exists (i.e. file '''default.sfn''' one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file. These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. If fiducials exist, they should be defined on the first three lines. If they do not exist, BESA Research will simulate them (so that it can define the head coordinate system). See chapter ''"Working with additional files / sfn (surface point name) file''".

'''Define electrode coordinates.''' File '''datafile.sfp''' exists, or file '''default.sfp''' exists, or file '''..\default.sfp''' exists (i.e. file default.sfp one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If '''datafile.sfn''' does not exist, labels can also be defined in this file. If fiducials exist, they should be defined on the first three lines. If they do not exist, BESA Research will simulate them. See chapter "''Working with additional files / sfp (surface point coordinate) file''".

'''Define coregistration information.''' File '''datafile.sfh''' exists, or file '''default.sfh''' exists, or file '''..\default.sfh''' exists (i.e. file''' default.sfh '''one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration between EEG and MRI. See online help chapter "''Integration with MRI and fMRI".''

'''Define head center.''' No coregistration file exists ('''<nowiki>*.sfh</nowiki>''', see above). File '''datafile.cot''' exists, or file '''default.cot''' exists, or file '''..\default.cot''' exists (i.e. file''' default.cot '''one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''

=== Data reading rules for MEG ===

Assume file name is ''''datafile.xxx''''. '''datafile''' is the base name. '''xxx''' is the extension. Replace the text '''datafile''' by the base name of your own file, and the extension '''xxx''' by the extension of your own file.

Here we consider cases a) MEG alone, b) MEG+EEG.

'''Automatic procedure:'''

Labels have names defined in the files '''bti.ecd''' or '''nmag.ecd'''. Channels are interpreted as MEG. However, sensor locations and head surface point locations must be defined in additional files as described below. Mapping and source analysis are not possible without one or more of the following additional files.

'''Define channel names and types.''' File '''datafile.ela''', '''datafile.elp''', or '''datafile.elb''' exist, or files '''default.ela''', '''default.elp''', or '''default.elb''' exist, or files '''..\default.ela''', '''..\default.elp''', or '''..\default.elb''' exist (i.e. files with basename'' default'' one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The'' ela'' file contains just labels and (optionally) channel types. The ''elp'' file contains spherical coordinates and can contain labels and types. The'' elb'' file contains the equivalent information in binary format. See chapter “''Electrode file conventions'' ''and formats.”''

'''MEG+EEG.''' Define order in which electrodes were digitized. File '''datafile.sfn''' exists, or file '''default.sfn '''exists, or file '''..\default.sfn''' exists (i.e. file '''default.sfn''' one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file (or in the location descriptor in the data file: e.g. Neuromag). These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. See chapter “''Working with additional files/ sfn (surface point name) file”.''

'''MEG+EEG.''' Define head surface point/electrode coordinates. File '''datafile.sfp''''' ''exists, or file '''default.sfp''' exists, or file '''..\default.sfp''' exists (i.e. file '''default.sfp''' one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If '''datafile.sfn''' does not exist, labels can also be defined in this file. See chapter “''Working with additional files/ sfp (surface point'' ''coordinate) file''”. The labels of electrode coordinates '''must '''match to those defined for the data channels. BESA Research will use the labels to associate coordinates with the correct channel.

'''Define sensor coordinates'''. File '''datafile.pos''' or '''datafile.pmg''' exists, or file '''default.pos(.pmg)''' exists, or file '''..\default.pos(.pmg)''' exists (i.e. file '''default.pos(.pmg)''' one folder above the data file): coordinates are defined in this file. The convention is that'' pos'' files contain gradiometer coordinates and'' pmg'' files contain magnetometer coordinates. This is not necessary for the program to read in values properly: the program makes its decision about the sensor type on the basis of the number of coordinate values on one line in the file (6 = magnetometers, 9 = gradiometers). See chapter “''Working with additional files/ pos or pmg (MEG sensor coordinate) file”.''

'''Define coregistration information.''' File '''datafile.sfh''' exists, or file''' default.sfh '''exists, or file '''..\default.sfh''' exists (i.e. file '''default.sfh''' one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration of the head coordinates with MRI. See (online) help chapter ''"Integration with MRI and fMRI".''

'''Define head center.''' No coregistration file exists ('''<nowiki>*.sfh</nowiki>''', see above). File '''datafile.cot''' exists, or file '''default.cot''' exists, or file '''..\default.cot''' exists (i.e. file '''default.cot '''one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''

=== Reading MEG files in ASCII format ===

'''BESA Research uses labeling or channel type definitions to decide whether channels are EEG or MEG. '''Based on the labels defined for the channels, or the type specified by the channel definition file, the program will try to find auxiliary files that define electrode coordinates or MEG sensors.

BESA Research uses four files to make its decision:
* '''.ela/.elp''' The channel type defined here overrides definitions in '''<nowiki>*.ecd</nowiki>''' (below).
* '''default.ecd''' defines electrode labels and default spherical coordinates based on the 10-20 and 10-10 naming system
* '''bti.ecd''' defines labels and default spherical coordinates for the BTi whole-head system
* '''nmag.ecd''' defines labels and default spherical coordinates for the Neuromag whole-head system

If the program finds a label in '''default.ecd''', the channel will automatically be defined as EEG. If not, if it finds a label in one of the other files, the channel will be defined as MEG. If it doesn't find the label anywhere, the channel will be defined as Polygraphic.

The spherical coordinates defined in these files are sufficient for mapping the data. Auxiliary files defining the real sensor coordinates are required for source analysis.

'''Defining default label and coordinate file for a new MEG system'''

When preparing an MEG from a system other than BTi-WHS or Neuromag for import to BESA Research, you should edit either '''bti.ecd''' or '''nmag.ecd '''to conform with your system. If sensor files ('''<nowiki>*.pos/*.pmg</nowiki>''') are always available for your files, the coordinates in the ''ecd ''files are irrelevant: all you need do is define the labels for your own MEG system or use the labels as already defined.

'''Files to prepare for reading in each data file'''

Each auxiliary file should have the same base name as your data file.

'''Define channel labels.''' There are several possibilities:
* Generate your data file according to the BESA'' avr'' ''format or the ASCII multiplexed format.'' Labels are listed in the second line of the file.
* Generate a ''label file'' (extension '''.ela''') with one MEG channel label per line (matching with your ''ecd ''file as defined above) or with the type "MEG" and a label for each line.

Label definitions are also possible using ''elp'' or ''elb'' files, but the above two solutions are recommended because they are the simplest.

'''Define sensor coordinates.''' Generate a ''pos'' or ''pmg'' file. Make sure that the number of sensors matches with the number of MEG channel definitions in your data file.

'''Define fiducials and other head surface points.''' Generate an ''sfp'' file. The first three lines define the fiducials. Subsequent lines define additional surface points.

'''Define coordinates of the center of the head.''' Generate a ''cot'' file. If this file is absent, BESA Research generates the coordinates by fitting a sphere to the head surface points.

Note that all coordinates should be within the same frame of reference, i.e. the same coordinate system. Units must be in meters, centimeters, or millimeters.

== Example: Defining Channel Labels ==

The files described in these examples can be found in the ''.\Examples\Xtras\EEG+Channel Labels'' subdirectory.

The simplest way to define electrode coordinates is to use BESA Research’s default settings (defined in the file, '''default.ecd'''). In this case, you only need to provide a list of channel labels. If a channel label is defined in '''default.ecd''' (i.e. if the labels belong to the 10-20 or 10-10 system), BESA Research will recognize the channel as EEG, and will allocate 3D coordinates.

Labels are not always supplied correctly in the data file. You can override the internal labels in several ways:
* Read the data file, and then use "''Edit / Channel Configuration''" to redefine the channels. The configuration is stored in a file with the name '''basename.elb''' (for binary data) or '''basename.elp''' (for ASCII data), where basename is the base name (name without the extension) of your data file.
* Prepare a label file (with the extension ''ela'') containing a list of labels. This can also specify channel types (e.g. EEG, Polygraphic, Intracranial, MEG).
* Prepare a file (with the extension ''elp'') containing spherical coordinates of the channels. This is the method used with the previous version of BESA Research. If the file doesn’t contain labels, labels are allocated based on their proximity to the 10-20 or 10-10 definitions in '''default.ecd'''.

The following examples illustrate the above three methods. The input files are all in ''BESA avr format, ''although these examples apply to all EEG data formats in which only EEG channels exist.

If the data file contains polygraphic or other types of non-EEG channel, the types need to be defined. See the ''EEG+Polygraphic channels example.'' MEG is a special case, because the sensor coordinates need to be defined. See the ''MEG ASCII and the MEG+EEG'' ''examples''.

'''Example 1. EEG file containing wrong labels – use ''Edit/Channel Configuration ''to redefine labels'''
* The'' avr'' file, '''EEGwithLabels.avr''', contains the EEG labels. Channels 4 and 14 have been mislabeled – the labels need to be swapped.
* Open the file with '''''File/Open''''' (Select file type ''BESA avr''. Find the correct directory ''Xtras\EEG+Channel Labels'').
* The file should open correctly, displaying 32 channels of EEG.
* The channel coordinates can be viewed by typing the '''‘V’ '''key (make sure the cursor is off). There will be a 3D display of the electrodes. Clicking on an electrode will display the label and the coordinates.
* In this file, channels 4 and 14 have been mislabeled as P3 and F3. In fact, the labels should be the other way around. We will now correct this:
* Select '''''Edit / Channel Configuration'''''.
* Type ‘F3’ into the label for channel 4, and ‘P3’ into the label for channel 14. Then type ‘'''OK'''’. The new channel configuration will be saved in '''EEGwithLabels.elp'''.
* In the data display, the labels of channels 4 and 14 will now be displayed correctly.
* Close the file ('''''File/Close''''') and open it again. Note that the labels are still correct. This is because the new channel configuration file, '''EEGwithLabels.elp''', is read automatically.

'''Example 2. EEG file with no labels – channel labels in auxiliary file'''
* The ''avr'' file, '''EEGwithoutLabels.avr''', has no labels.
* EEG labels are defined in '''EEGwithoutLabels.ela'''. This is read automatically when the file is opened.
* In this example, labels are correct. Each label in the ''ela'' file is on one line:

<div style="margin-left:0cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F7''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fz''</div>

<div style="margin-left:0cm;margin-right:0cm;">''...''</div>

'''Example 3. EEG file with no labels – channel labels derived from spherical coordinates'''
* The ''avr'' file, '''EEGwithSphericalCoords.avr''', has no labels.
* Spherical coordinates are defined in the ''elp'' file, '''EEGwithSphericalCoords.elp'''. This contains spherical coordinates (theta and phi) and no labels:

<div style="margin-left:0cm;margin-right:0cm;">''-93 -72''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''92 74''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-97 -40''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-61 -49''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-46 -88''</div>

<div style="margin-left:0cm;margin-right:0cm;">''62 51''</div>

* When the data file is opened, the ''elp'' file is read automatically, and BESA Research uses the tables in '''default.ecd''' to assign channel labels. To indicate that it has assigned user defined coordinates and matched with the closest standard electrode, BESA appends an apostrophe (‘) to each label:

<div style="margin-left:0cm;margin-right:0cm;">''Fp1’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F7’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fz’''</div>

* We advise to assign specific labels as well as spherical coordinates if you want to use your own spherical coordinate system, e.g.:

<div style="margin-left:0cm;margin-right:0cm;">''FP1u -90 -72''</div>

'''Example 4. EEG file with no labels – channel labels not in basename.el?'''
* The ''avr ''file, '''EEGnoLabelsNoElaFile.avr''', has no corresponding ''ela, elp'', or ''elb'' file, i.e. no file with the same base name and the ''el?'' extension.
* When you open the file, BESA Research will ask for a channel configuration file. The ''File Open'' ''dialog ''will select the ''directory .\Montages\Channels''. The idea is that standard (= frequently used) electrode configurations should be kept in this directory.
* Select the file '''XtrasExample.ela'''.
* Close the data file and reopen it. The file will open with the correct labels. In the BESA window title you will see that the file '''EEGnoLabelsNoElaFile.elp''' has been read automatically. This file was created when '''XtrasExample.ela''' was read.

== Example: Mixed EEG and Polygraphic Data ==

The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Polygraphic'' subdirectory.

The data are in '''EEG+Polygraphic.avr'''.

The third channel is defined as polygraphic in the '''EEG+Polygraphic.ela '''file:

<div style="margin-left:0cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:0cm;margin-right:0cm;">''POLY Test''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3''</div>

The prefix "''POLY''" specifies that the channel is polygraphic. Most other channels are interpreted as EEG because the labels are known in the 10-20 system.

Similarly, channel 31 is defined as intercranial, using the prefix "''ICR''".

Note that you can also define channels as EEG by specifying the ''"EEG" ''prefix (e.g. ''"EEG E1". ''This is useful if there are many more channels than are defined in the 10-10 or 10-20 systems, and if the channel coordinates are defined.

== Example: EEG with Digitized Coordinates ==

The files described in this example can be found in the .''\Examples\Xtras\ EEG+Digitization Points ''subdirectory.

In the previous examples, we have illustrated how to assign labels to channels using channel definition files. In those examples, only spherical coordinates were defined. Here we will show how to read digitized surface points into BESA Research, using the surface point (''sfp'') coordinate file and the surface point name (''sfn'') file.

The principles of defining digitization coordinate files are:
* The labels in the ''sfp/sfn'' file combination are used to assign coordinates to electrodes. Thus, if a coordinate has the name ‘''Fz''’ it will be assigned to the channel with the label ‘''Fz''’.
* In consequence, digitization of surface points can be in a different order to the sequence of channels in the data file. Matching to channels is done by comparing the labels.
* We recommend that the fiducial points, '''nasion, left preauricular point, right preauricular point''' be digitized. If you do not digitize them, BESA Research will simulate these locations (see ''“Example: Digitization points with and without Fiducials”''). Fiducial points, labeled '''FidNz, FidT9, FidT10''' should be the first three coordinates in the ''sfp'' file.
* As with the channel definition files, it is easiest for BESA Research if you name the ''sfp/sfn'' files using the base name of the data file, e.g. if the data file is named '''doodah.avr''', name the'' sfp'' file '''doodah.sfp''' and the ''sfn'' file '''doodah.sfn'''.
* You specify the files to be read in the ''Channel and digitized head surface point information dialog box.''

See ''“Example: Polhemus Digitizer Data” ''for a discussion of how to format the files originating from Polhemus and other digitizers.

'''Example 1. EEG file containing labels, ''sfp'' file containing coordinates, ''sfn ''file containing coordinate names'''
* The ''avr'' file, '''EEGdigitized1.avr''', contains the channel labels. Therefore, we don’t need a channel definition file.
* The ''sfp'' file, '''EEGdigitized1.avr''', contains digitized coordinates of electrodes and of additional surface points. The labels in the file do not correspond to the electrode labels in the ''avr ''file.
* The ''sfn'' file contains the corrected labels (1 line for each corresponding line in the'' sfp'' file). Now it is possible to match up electrode labels with the labels in the ''avr ''file.
* Open the data file, '''EEGdigitized1.avr'''. The ''Channel and digitized head surface point information dialog box'' will open automatically.
* Note the green tick mark at the top right of the dialog box. This is feedback to say that coordinates of all 32 electrodes have been found.
* Look at the entry ‘''Digitized head surface points’''. Here you will see that the ''sfp'' and the ''sfn ''files have been read automatically (because of the common base name). There are 51 locations. Note that the digitizer file can contain many more locations than the electrodes. BESA Research uses the locations for fitting the sphere of the spherical head model in source analysis. BESA Research can export these locations for coregistration with the MRI.
* Define the electrode thickness as 6 mm (at the right of the ‘''Digitized head surface points’'' box. This is the distance of the digitized point on the electrode to the surface of the head.
* Press '''‘OK’''' in the dialog box and view the coordinates by pressing the '''‘V’''' key.

'''Example 2. EEG file without labels, channel labels in ''ela'' file, surface point coordinates and names in ''sfp'' file'''
* The ''avr'' file, '''EEGdigitized2.avr''', has no channel label. Therefore, a label file is required. Here, the label file is '''EEGdigitized2.ela'''.
* The ''sfp'' file, '''EEGdigitized2.sfp''', contains digitized coordinates of electrodes and of additional surface points. The labels are defined correctly in the ''sfp ''file, i.e. for every EEG channel label there is a corresponding coordinate. Therefore, no ''sfn'' file is required.
* When you open the file, don’t forget to define the electrode thickness as 6 mm in the ''Channel and digitized head surface point information dialog box.''

== Example: Polhemus Digitizer Data ==

The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Digitization Points'' subdirectory.

Data from the Polhemus (other digitizers too) may often not fit the format BESA Research requires for the surface point file. Note that Polhemus data can be exported directly into BESA-compatible ''sfp''-files using the LOCATOR software.

BESA Research requires either
* just the cartesian coordinates (x, y, z) values -- one set of coordinates per line. In this case, labels must be defined in a parallel surface point name file, e.g.

<div style="margin-left:1.27cm;margin-right:0cm;">''0.5  3.75  12.68''</div>

<div style="margin-left:0cm;margin-right:0cm;">or</div>

* the cartesian coordinates plus a label. The label can be in front of or behind the coordinates on the line, e.g.

<div style="margin-left:1.27cm;margin-right:0cm;">''0.5    3.75  12.68  Fz''</div>

<div style="margin-left:2.54cm;margin-right:0cm;">or</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''Fz  0.5  3.75  12.68'' </div>

Here is an example of a few lines of a (''sfp'') file that are not read correctly by BESA Research:

<div style="margin-left:0cm;margin-right:0cm;">''Nz  0  87.721  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''T9  -79.131  0  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''T10  67.253  0  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''1  -34.192  103.374  31.868''</div>

<div style="margin-left:0cm;margin-right:0cm;">''2  23.642  103.048  30.351''</div>

<div style="margin-left:0cm;margin-right:0cm;">''3  -81.179  62.913  27.596''</div>

<div style="margin-left:0cm;margin-right:0cm;">''4  -60.701  79.631  78.273''</div>

What is wrong?

* First, some of the points are just numbered. These numbers don't tell BESA Research which electrode channel to which the coordinates should be assigned – assignments should be via channel labels and not numbers.
* Second, Nz, T9, T10 define the fiducials. Instead, the labels FidNz, FidT9, FidT10 are required (prefix "Fid").

What should be done? Probably the best way is

 a) keep only the coordinates in the '''<nowiki>*.sfp </nowiki>'''file:

<div style="margin-left:0cm;margin-right:0cm;">''0  87.721  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-79.131  0  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''67.253  0  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-34.192  103.374  31.868''</div>

<div style="margin-left:0cm;margin-right:0cm;">''23.642  103.048  30.351''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-81.179  62.913  27.596''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-60.701  79.631  78.273''</div>

b) prepare a surface point name file ('''<nowiki>*.sfn</nowiki>''') containing the corresponding labels:

<div style="margin-left:0cm;margin-right:0cm;">''FidNz''</div>

<div style="margin-left:0cm;margin-right:0cm;">''FidT9''</div>

<div style="margin-left:0cm;margin-right:0cm;">''FidT10''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F7''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3''</div>

Keeping labels and coordinates separate means that the label file needs generating only once. The coordinate file is different for each subject.

Alternatively, if your digitizer program attaches the labels correctly to the coordinates, then you can prepare the ''sfp'' file like this:

<div style="margin-left:0cm;margin-right:0cm;">''FidNz    0       87.721   0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''FidT9  -79.131    0       0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''FidT10  67.253    0       0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp1    -34.192  103.374  31.868''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2     23.642  103.048  30.351''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F7     -81.179   62.913  27.596''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3     -60.701   79.631  78.273''</div>

== Example: Digitization points with and without Fiducials ==

We recommend that if electrodes are digitized, you should also digitize the three fiduciary points:''' Nasion''', '''and left and right preauricular points'''. We refer to these points as "fiducials". We name them '''"FidNz",''' '''"FidT9",''' and '''"FidT10".'''

If you do not digitize these points, BESA Research will simulate them, i.e. it will generate the points where it expects them to be, based on the fit of a sphere to the existing points, and on the names of surface points of known locations. "Known locations" means: the surface point name must be a 10-20 or 10-10 electrode name (e.g. "Cz" -- arbitrary labels, such as "E10" is not a known location). Therefore, BESA Research requires that at least 3 surface points with known labels are defined.

In a file containing digitization points ('''<nowiki>*.sfp</nowiki>'''), the fiducials should be the first three sets of coordinates, i.e. the first three lines of the file. The remaining coordinates in the file can be electrode (or other surface point) coordinates, in any order. The assignment of electrode coordinates to data channels is achieved by matching the coordinate labels to data channel labels.

'''Consequences of omitting fiducials'''

When these files have been read into BESA Research, look at the head surface points in 3D using ''File/Head Surface Points'' ''and Sensors/View'' (or use the shortcut '''‘V’'''). You will see small differences in fiducial locations between the real and the simulated locations. You can expect very slight influences on the results of source modeling (the spherical head may be rotated slightly, although the head center and radius will be identical), and output of source locations in head coordinates will be different, because these coordinates are based on fiducial locations (see chapter ''“Working with Electrodes and Surface'' ''Locations/ Coordinate systems''”).

== Example: ASCII Import ==

The files described in this example can be found in the ''.\Examples\Xtras\ASCII Import'' subdirectory.

When should the Import ASCII function be used? If you have data in BESA Research average referenced or multiplexed format, use the Open File function to read in a file directly. If you have data in a different ASCII format, BESA Research offers a flexible import function to import data from an array of numbers in an ASCII file.

The array can be '''vectorized '''(one channel, all time points, per line) or '''multiplexed''' (one time point, all channels, per line). These alternatives are illustrated in the two example files '''vectorized.asc''' and '''multiplexed.asc''', and in the tables below:

'''Vectorized array:'''

{| style="border-spacing:0;width:12.993cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 1 ''
|| ''channel 1, time 2''
|| ''channel 1, time 3''
|| ''channel 1, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 2, time 1''
|| ''channel 2, time 2''
|| ''channel 2, time 3''
|| ''channel 2, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 3, time 1''
|| ''channel 3, time 2''
|| ''channel 3, time 3''
|| ''channel 3, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 4, time 1''
|| ''channel 4, time 2''
|| ''channel 4, time 3''
|| ''channel 4, time 4''
|-
|}

'''Multiplexed array:'''

{| style="border-spacing:0;width:12.993cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 1 ''
|| ''channel 2, time 1''
|| ''channel 3, time 1''
|| ''channel 4, time 1''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 2''
|| ''channel 2, time 2''
|| ''channel 3, time 2''
|| ''channel 4, time 2''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 3''
|| ''channel 2, time 3''
|| ''channel 3, time 3''
|| ''channel 4, time 3''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 4''
|| ''channel 2, time 4''
|| ''channel 3, time 4''
|| ''channel 4, time 4''
|-
|}

BESA Research needs channel labels. If the labels are in the 10-20 or 10-10 system, BESA Research will assign the channels default coordinates. This is the minimum requirement to be able to map EEG.

If you have 3D digitized coordinates, these can also be specified in ASCII files. This is described under the chapter “''Example: EEG with Digitized Coordinates''”.

'''Example 1. Vectorized data'''
* The file '''vectorized.asc''' contains the data. The file should be imported via ''File/Import ASCII File''.
* First you will be asked for a name for the binary target file. The name '''vectorized.fsg''' is suggested. You may accept this name by pressing '''‘OK’''' or choose an alternative name. Note that if the file already exists, the imported data will be appended to the file.
* Next, the ''ASCII File Properties dialog box'' will open. First select ''‘Vectorized’'', and make sure the subsequent entries are correct:

<div style="margin-left:1.27cm;margin-right:0cm;">Header Lines = 0 (i.e. in this example the numbers start on the first line)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Bins/Microvolt = 1.0 (i.e. a value 1 in the data represents 1 µV)</div>

<div style="margin-left:2.54cm;margin-right:0cm;">Sampling Rate = 320 Hz (When the dialog box is opened, BESA Research always chooses the setting it used previously)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Number of channels = 32 (the number of rows in the matrix)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Number of Samples = 640 (the number of columns in the matrix)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Prestimulus Time = 1000 ms (defines the zero time point 1 s after the beginning)</div>

<div style="margin-left:0cm;margin-right:0cm;">Press '''‘OK’''' to accept the settings.</div>

* Next, the ''Channel and digitized head surface point information dialog box'' will open. In the ''‘Channel configuration’'' box, the label file, '''vectorized.ela''', will be detected automatically. Automatic detection occurs when the label file has the same base name as the data file (in this case, vectorized). To the right of the file name is a summary of channel types: 32 channels found, 30 are EEG, 1 is intercranial, 1 is polygraphic.

Note the green tick at the top left of the dialog box. This indicates that BESA Research thinks that it has sufficient information to read the file, and map and do source analysis on the data.

* To see how channel types are specified in '''vectorized.ela''', click on the '''Edit '''button to view the file with the Notepad program. Here you will see that most channels have 10-20 electrode names. Channel 3 has the prefix ‘''POLY''’, specifying that this channel is polygraphic. Channel 31 has the prefix ‘''ICR''’, specifying that this channel is intercranial. Close Notepad, and click ‘'''OK'''’ in the dialog box.
* A final dialog box asks for a Segment Comment. This is a label that will be displayed in the resulting file. The label is particularly useful if you import several ASCII files into one target file. Each segment is then easily identified by its own label.

'''Example 2. Multiplexed data'''
* This example is similar to Example 1. In this case, import the file '''multiplexed.asc''', and select ‘Multiplexed’ in the ''ASCII File Properties dialog box''. Other settings in the dialog box stay as they were.

'''Notes'''
# The numbers in the source files can be split into several lines per channel or per time point. Then you will have to enter the correct number of time points and channels in the dialog box. In the present examples, the lines are not split (the vectorized file has all 640 time points in each line, and the multiplexed file has all 32 channels in each line). In this case, BESA Research selects the correct numbers of time points and channels automatically.
# If you have digitized coordinates, these can be specified in the Channel and digitized head surface point information dialog box. Since the procedure is the same as when reading data, this is described elsewhere under “''Example: EEG with Digitized Coordinates''”.

== Example: MEG ASCII ==

The files described in this example can be found in the'' \Examples\Xtras\ MEG ASCII'' subdirectory of the BESA Research installation folder.

'''Multiplexed MEG ASCII file with labels in the header (''med.mul'')'''

For reading MEG data, BESA Research expects
* Correct channel definitions, i.e. channels should be defined as MEG.
* Head surface points.
* Sensor coordinates, in '''the same coordinate system''' as the head surface points.
* Optionally, you can define the coordinates of the center of the head. This will be important if too few head surface points are available to specify where to place the spherical head used by BESA Research for source modeling, or if you want to use some external definition, e.g. from the MRI.

As with digitized EEG coordinates, we use the ''Channel and digitized head surface point information'' ''dialog box'' to specify the files which need to be read.

'''Example 1. File Open'''
* The file, '''MEGASCII.mul''', contains MEG data in the ASCII multiplexed format. This format contains channel labels. The labels used are recognized by BESA Research as originating from the Neuromag system. They are therefore identified as MEG and do not need further identification.
* The ''sfp'' file, '''MEGASCII.sfp''', defines fiducials and head surface points. Coordinate labels are included in the file, so no'' sfn'' file is required.
* The cot file, '''MEGASCII.cot''', defines the coordinates of the head center. If this were missing, BESA Research would compute the head center based on the sphere that best fits the head surface points.
* The ''pos'' file, '''MEGASCII.pos''', defines the coordinates of the 122 sensors. For the Neuromag system there are 9 values per line, defining primary coil location, secondary coil location, and orientation cosines. The sequence of coordinates in the ''pos'' file '''must''' match the sequence of MEG channels! The file format and locations of the primary and secondary coils allow BESA Research to identify the sensor type as planar gradiometers. If the file had only six values per line, BESA Research would classify the sensors as magnetometers (one primary coil and the orientation cosines).
* Open the file, selecting current file type as ''‘*,m''??’. The ''Channel and digitized head surface point'' ''information dialog box'' will open, displaying the different auxiliary file names. The green tick indicates that BESA Research finds everything to be OK.
* Press the '''‘OK’''' button and then the''' ‘V’ '''key to view the coordinates.

'''Example 2. File Import'''
* The file, '''MEGASCIIimport.asc''', contains MEG data in a multiplexed array, without a header. This needs to be imported using ''File/Import ASCII'' (see ''“Example: ASCII Import”).''
* On import you have to specify the file as ‘Multiplexed’, the number of time points (285), the number of channels (132), the bins/µV (or bins/fT) (=1), the time at which the stimulus occurred (50 ms), and the sampling rate (949.667 Hz).
* This format contains no channel labels. The labels in '''MEGASCIIimport.ela''' are recognized by BESA Research as originating from the Neuromag system. They are therefore identified as MEG and do not need further identification.
* Since it recognizes the channels as MEG, the ''Channel and digitized head surface point information dialog box'' will open, displaying the different auxiliary file names as before. Since all necessary files with the same base name as the data file are supplied, they are read automatically.
* Press the ‘'''OK’''' button, enter a segment name, and then the '''‘V’''' key to view the coordinates.

'''Example 3. File Open -- MEG information recorded elsewhere'''

This example illustrates the case where the auxiliary files have a different base name from the data file: you must select the file name in the ''Channel and digitized head surface point information dialog box''.

* Open the file, '''MEGASCIIelsewhere.mul'''. It is read as an MEG magnetometer file.
* In the ''Channel and digitized head surface point information dialog box'', specify
<div style="margin-left:1.27cm;margin-right:0cm;">'''MEGASCII.sfp''' for the head surface points, and</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''MEGASCII.pos''' for the MEG sensors</div>
* MEG coordinates will be correct. The sensor definition file specifies the sensors as planar gradiometers.
* Where the auxiliary files came from will be recorded in the database. If you open the file again, the auxiliary files will be found automatically, without asking any questions.

== Example: Reading combined EEG and MEG from an ASCII file ==

The files described in this example can be found in the ''Examples\Xtras\MEG+EEG'' subdirectory of the BESA Research installation folder.

Here are two examples containing mixed MEG, EEG, and polygraphic channels:
* Open a file using the ''File/Open'' command
* Import a file using ''File/Import ASCII'' command

In both cases

* The '''<nowiki>*.ela</nowiki>''' file defines the channel labels. Based on the labels, BESA Research knows which channels are EEG and MEG. The remainder are classified as polygraphic channels.
* The '''<nowiki>*.pos</nowiki>''' file defines the MEG sensor coordinates. The number of values on a line of this file (=9) defines the MEG as gradiometers. The relative locations of primary and secondary coils identify the gradiometers as planar.

'''1. Example with ''File/Open'''''
* Open the file '''MEG+EEG.mul'''. The ''Channel and digitized head surface point information dialog box'' will open automatically (unless the file has already been read once and the information is in the database).
* You will see under ''‘internal data file information’'' that BESA Research finds 122 MEG sensors, and 162 channels in all.
* Under ‘''Channel configuration’'', you will see that as a result of reading the file '''MEG+EEG.ela''', 32 channels are defined as EEG, and 8 channels as polygraphic.
* Under ‘''Digitized head surface points’'' is the feedback that out of the 51 locations in the file '''MEG+EEG.sfp''', all electrode locations have been defined.
* Under ‘''MEG sensors’'', the sensors have been identified as gradiometers.
* The green tick at the top right of the window indicates that BESA Research classifies everything as OK.

'''2. Example with ''File/Import ASCII'''''
* Import the file '''MEG+EEGimport.asc'''. Select '''MEG+EEGimport.fsg '''as the target file (see ''“Example: ASCII Import”'').
* Select 320 Hz sampling rate, and 500 ms pre-stimulus time. Other selections in the dialog box should be ‘Multiplexed’, 1 bin/microvolt (this is interpreted as 1 bin/fT for MEG), 162 channels and 320 samples.
* The ''Channel and digitized head surface point information dialog box'' will open as above.

Electrodes and Surface Locations

2017-04-07T07:39:33Z

Alexa:

= Working with Electrodes and Surface Locations =

== Introduction - Electrodes and Surface Locations ==

Here you will find out how BESA Research works with electrode and MEG sensor coordinates and labels, and how head surface points can be used to improve source modeling and coregistration of source models with the MRI. In most cases, electrode positions are sufficiently defined by their labels. The section "''Electrode Conventions''" lists the standard position which BESA Research assigns to EEG channels. In some cases, especially for larger electrode arrays or for MEG measurements, additional information is required to add sufficient information for mapping and for source analysis. The additional information is supplied in additional, auxiliary files which are read by BESA Research and associated with the data files. The auxiliary files, and how they are supplied to BESA Research, are described in this chapter.

Examples for using auxiliary files to define the 3D locations of electrodes are found in the chapter "''Special Topics / Working with Electrodes... / Examples''" in the online help.

Descriptions of file formats that BESA Research uses are given in the online help chapter "''Special Topics'' ''/ Working with additional files''".

== Working with auxiliary files ==

Data files come with varying amounts of prior information about electrode/sensor locations, depending on the recording system. BESA Research allows you to read auxiliary files that define additional information, such as channel labels, and coordinates of the electrodes, sensors, and other head surface points. The information is required for mapping and for source montages.
* '''Mapping.''' BESA Research uses spherical spline mapping. For this, electrode/sensor locations are projected onto a sphere. The minimum requirement is 10-10 or 10-20 labels: if only channel labels are available without additional information, BESA Research uses default spherical coordinates.
* '''Source modeling'''. Spherical coordinates of electrode locations are sufficient, but digitized locations are better. Digitized locations can be defined in the data file or in auxiliary files. BESA Research will use digitized head surface points (electrodes + additional points) to fit a sphere for the spherical model. Points anterior to the left and right preauricular points and below the plane formed by these points and the nasion are excluded when fitting the sphere.

Files can also be written, for instance for
* '''Source modelling with MRI coregistration'''. BESA Research allows for the export of surface points in a special format ('''sfh''' file) which can be read by the BESA MRI (or BrainVoyager) program. These are fitted to the head surface defined by BESA MRI (or BrainVoyager) in order to define rotation, translation, and deformation parameters required to coregister the coordinate systems (see "''Integration with MRI and fMRi''").
* '''Export of coordinates.''' Electrode, other surface point locations, and MEG sensor coordinates and other surface point locations can be written to ASCII files so that they can be reread when reading other files into BESA Research (e.g. ASCII files), or used by other programs.

Feedback and control over how these files are read is provided by
* '''the Channel and digitized head surface point information dialog box.''' This dialog is usually opened when you open a file for the first time. It allows you to specify the names of auxiliary files, and it makes initial checks on the files to see whether they are consistent with each other and with the data file. If the check is OK, you will see a green tick at the top right hand corner of the dialog box. If there are inconsistencies, the tick is replaced by a red exclamation mark. In this case, you will usually need to edit the auxiliary files or specify other files. The dialog box is not opened if the file is recognized to contain all the necessary information (files with the '''foc''', '''fsg''' extensions), or if the program only finds a channel definition file (with extensions '''ela, elp,''' or '''elb'''). The dialog box is not opened if the data file has been opened before. You can always open the dialog box manually by specifying ''" File / Head Surface Points and Sensors/Load Coordinate'' ''Files.''
* '''The log file''' ('''<nowiki>*_LoadFile.log</nowiki>''')'''.''' Coordinating the information between the data file and its auxiliary files can be a complex procedure. To help you check whether the coordination is being done properly, if you select the menu entry ''" Options / File / Generate Log "'' during File Open, BESA Research writes a log file with the same base name as the data file, appending "'''_LoadFile.log'''" to the base name, recording which files have been read, and some of the parameters that have been found. This file is created every time auxiliary files are read (e.g. on file open, when reading in channel configuration files, head surface point files, MEG sensor locations), or changed ("''Edit /'' ''Channel Configuration''").
* '''The log window. '''If there are inconsistencies during the processing of auxiliary files and 3D coordinates, a logging window is opened showing the information that would be written to the log file. You can read what has been done to help diagnose the problems. Select '''OK''' to continue in spite of the problems, or''' Reset''' to reject. Typing '''Reset''' also deletes the database files associated with the current data file, thus allowing you to start reading this file from scratch.

'''BESA Research remembers which auxiliary files are associated with the current file'''. When a data file is first opened, and BESA Research finds auxiliary files with the same base name as the data file, you will be asked if you want this file to be read. The decision you make will be recorded in the database for this data file. Next time the file is opened, the files will or will not be read, according to your previous decision. Similarly, when an auxiliary file is read using the menu, this is recorded in the database, and the file will be opened automatically next time the data file is opened. To override previous decisions, you must delete the database files (see the''' log window '''above) or change the entries in the Channel and digitized head surface point information dialog box (see the chapter ''"Electrode Conventions / Channel and digitized head surface point information dialog box''").

== Coordinate systems ==

We need to deal with four different coordinate systems. These differ in how the x, y, and z axes are defined, and in the units of measurement (e.g. mm, cm, m). The first three are illustrated in the following figure:

[[Image:ST Electrodes (1).gif ]]

'''Device coordinates.''' These are the coordinates used by the recording system. The axes may be anywhere in relation to the head. For instance, in the Polhemus digitizer, the axes go through the magnetic field transmitter which is located somewhere outside the head. The units of measurement may be millimeters, centimeters, or meters.

'''Head coordinates'''. This coordinate system is defined by reference points on the head known as ''fiducials''. The reference points are normally the nasion (Nz, NAS), the left preauricular point (T9, LPA), and the right preauricular point (T10, RPA). The x axis is defined by the line joining T9 and T10, positive towards T10. The y axis is defined by the line through Nz that is perpendicular to the x axis (positive towards Nz). The z axis is perpendicular to the x and y axes, and goes up out of the head in the vicinity of Cz. The units of measurement may be millimeters, centimeters, or meters. In BESA Research these are labelled with the prefix 'Fid', e.g. 'FidT9', 'FidNz'.

'''BESA Research coordinates.''' For dipole analyses the head model consists of a sphere. In the default situation where no digitized sensor information is available, the center of the sphere is defined by the crossing point between the lines joining T7 (=T3) and T8 (=T4) and Fpz and Oz.. The x axis is the T8-T7 line, positive at T8. The y axis is the Oz-Fpz line, positive at Fpz. The z-axis goes up out of the head through Cz. If digitized information is available, the axes are defined by the best fit between the idealized electrode locations and the real locations. The diameter of the sphere is also defined by the best fit. Units given in the display are in millimeters.

The '''center of the spherical model''' is on average about 4 cm above the origin of the Head Coordinates. If digitized surface points are available, the sphere is fitted to these points. Using a cot file, it is possible to override the fit and define your own head center. In conjunction with BrainVoyager, you can use the MRI to seed the location of the head center (e.g. a fixed distance anterior to the posterior commissure) and save it as a cot file. Using MRI coregistration (see "''Integration with MRI and'' ''fMRi''"), the center is placed between the anterior (AC) and posterior (PC) commissures, at the half-way point between the anterior and posterior points (AP and PP). Without coregistration, the center corresponds to a point 17.5 mm behind AC in the standard MRI head.

'''MRI coordinates.''' These are the coordinates used by BrainVoyager. These are defined by the MRI slices. Measurement units are millimeters.

== The Channel and Digitized Head Surface Point Information Dialog Box ==

Many data formats read by BESA Research require additional information about data channel, which are specified by additional, auxiliary files. This dialog box allows you to specify which auxiliary files are read in to supplement the information in the data file.

The dialog box is opened automatically the first time a data file is opened, if
* auxiliary files other than a channel definition file ('''<nowiki>*.ela</nowiki>''', '''<nowiki>*.elp</nowiki>''', '''<nowiki>*.elb</nowiki>''') are found
* no auxiliary files are found, and the data file was not written in compressed binary format ('''<nowiki>*.foc</nowiki>''', '''<nowiki>*.fsg</nowiki>''') by BESA Research

When a data file is closed, the information about which auxiliary files have been read is stored in the database. When the file is opened for a second time the dialog box is not opened automatically, because the information is assumed to be correct – the files are read automatically.

The dialog box can be opened manually by selecting "''File / Head Surface Points and Sensors/Load'' ''Coordinate Files''", or using the shortcut '''ctrl-L'''

[[Image:ST Electrodes (2).gif ]]

The dialog box is divided into several sections:

* '''Internal data file information.''' Here you can see the file name, the originating system (file format), the name of the database file, if any, and the channel information as specified by the data file alone.

[[Image:ST Electrodes (4).gif ]]

* '''Suggestions.''' This box makes suggestions about what needs to be filled in, e.g. "Please enter electrode thickness"

[[Image:ST Electrodes (5).gif ]]

* '''Main feedback (top right hand corner).''' A green tick indicates that the currently selected data files are consistent among themselves and with the data file. A red exclamation mark indicates an inconsistency. Check the feedback texts in the subsequent sections for more information:

[[Image:ST Electrodes (8).gif ]][[Image:ST Electrodes (7).gif ]]

* '''Channel configuration file specification.''' If the channel labels and types defined in the data file ("Internal data file information") need to be changed, enter a file name here ('''<nowiki>*.ela</nowiki>''', '''<nowiki>*.elp</nowiki>''', '''<nowiki>*.elb</nowiki>'''). If a channel definition file exists with the same basename as the data file, or if a channel definition file has been specified previously (database entry exists), it will be selected automatically. To the right of the file name, feedback is provided about the number of channels and channel types found. If the labels are consistent with the data file, to the right the text "Good" is shown. If they are inconsistent, e.g. the file contains the wrong number of channel definitions, the text "Bad" is shown.

[[Image:ST Electrodes (9).gif ]]

* '''Digitized head surface point specification.''' Here you may specify a file containing digitized electrode and other head surface points. Optionally, the information can be split into two files, containing the coordinates ('''<nowiki>*.sfp, .eps</nowiki>''') and the coordinate names ('''.sfn'''). Alternatively, both labels and names can be contained in the coordinate file. If the files specify electrode coordinates, there '''must''' be a coordinate name for each electrode. The sequence may be different. BESA Research will use the names to assign each coordinate to the electrodes. Additional head surface points can have any other names. It is recommended that the first three digitized coordinates are the fiducials (fiduciary points), labelled "FidT9", "FidT10", "FidNz". If your electrode labels not follow the 10-10- or 10-20 standard (e.g. in high-density electrode recordings), it is recommended to tick the box "Electrode labels non -conforming to 10-10 standard". This will prevent BESA Research from using electrodes for an optimal rotation of the coordinate system which should not be used (e.g. A1, A2 which have known locations in 10-10, but are sometimes used in a nomenclature outside of 10-10). The example below shows the sphere adaption for an example data set with and without taking this into account. The right picture shows that when discarding the non-conforming electrodes, the fiducials are correctly placed along the x any y axes.

[[Image:ST Electrodes (10).gif ]] [[Image:ST Electrodes (11).gif ]]

(In the special case of Neuromag files with electrode channels, the data file contains head surface points with the wrong labels. Here you may provide a label file ('''<nowiki>*.sfn</nowiki>''') without a corresponding digitized coordinate file.)

[[Image:ST Electrodes (12).gif ]]

* '''Coregistration file.''' Here you may specify a file containing the coordinates of the head center ('''<nowiki>*.cot</nowiki>''') or an ''MRI Coregistration File ''('''<nowiki>*.sfh</nowiki>'''). Head center redefinition is only necessary if you

<div style="margin-left:1.27cm;margin-right:0cm;">want to provide an external definition, e.g. from the MRI. The ''MRI Coregistration File ''is used if the data are to be coregistered with individual MRI. (see "''Integration with MRI and fMRi'' "). '''Note''' that if a head center file (cot file) with the same base name as the data file exists, it will be read automatically if the head center coordinates deviate by more than 1 mm from the internally calculated values. Changes are ignored if the radio button is set to "No". This automated function allows you to change the head center during a session, using BrainVoyager's view of the MRI and the Source Module.</div>

[[Image:ST Electrodes (14).gif ]]

* '''MEG sensor specification'''. If the file contains MEG channels, you may enter the name of a sensor coordinate file ('''<nowiki>*.pmg</nowiki>''', '''<nowiki>*.pos</nowiki>'''). This field is grayed if there are no MEG channels.

[[Image:ST Electrodes (15).gif ]]

* '''Artifact coefficients file.''' If the data are to be artifact corrected, your pre-prepared coefficient file may be defined here. See the chapter "''Artifact Correction''". Selecting the file here is equivalent to loading the file using the menu entry "''Artifact / Load''".

[[Image:ST Electrodes (17).gif ]]

For each of the selected files, make sure the radio button "'''Yes"''' is selected on the left-hand side of the dialog box. If files have been selected automatically, and you do not wish them to be read, select the "'''No'''" radio button.

If some of the settings are incorrect or the text "Bad" is shown, you may edit the auxiliary files (the file is opened with the NotePad program) or browse for another file by pressing the '''Edit''' or '''Browse''' buttons.

After you have entered the required information, and the green tick at the top right indicates consistency, press '''OK''' to continue. Press '''Cancel''' to ignore the current settings. Press '''Clear DB''' to delete the database files. Press '''Clear Events''' to delete the tag files (the part of the database that records events). Both '''Clear''' buttons close the currently-opened data file.

== General Reading Rules for Data Files and Auxiliary Files ==

Auxiliary files can complement the information in the data file. Here we specify what happens when a data file is opened:

'''1.''' If the data file has been read previously, the database entry specifies which auxiliary files should be read. The file and the specified auxiliary files are opened and the data are displayed.

'''2'''. If a) there is a channel definition file '''(*.el'''''?'') with the same basename as the data file, and

b) this file includes spherical coordinates for the EEG channels (including labels with entries in the '''default.ecd''' file), and

c) there are no other auxiliary files with the same base name, the file will be opened and the data displayed. If files with the same basename are not found, BESA Research will look for files with the basename “default” (e.g. '''default.ela''') in the data folder. If such files are not found, BESA Research will look for files with the basename “default” one folder above (e.g.''' ..\default.ela''').

'''3'''. If the data file has been written in binary format ('''<nowiki>*.foc</nowiki>''', '''<nowiki>*.fsg</nowiki>''') by BESA Research (after Jan.2000), the file will be read, and all information is assumed to be complete. The file is opened and the data are displayed.

'''4.''' In all other cases, the ''Channel and digitized head surface point information dialog box'' will be opened for you to specify and check auxiliary files. Auxiliary files with the same base name as the data file will be specified in the text boxes for file names. If files with the same basename are not found, BESA Research will look for files with the basename “default” (e.g. '''default.ela''') in the data directory. If such files are not found, BESA Research will look for files with the basename “default” one directory above (e.g. '''..\default.ela'''). Otherwise the text boxes will be left blank.

'''5.''' Auxiliary files can be specified at a later time by selecting ''File/Head Surface Points'' and ''Sensors/Load'' ''Coordinate Files''. The ''Channel and digitized head surface point information dialog box'' will be opened.

== Electrodes ==

=== Electrode Conventions ===

BESA Research adheres to the 10/20 and to the new 10/10 standard of the IEF (international EEG Federation). BESA Research will recognize the labels defined by these standards. The labels are stored in most EEG file headers. Otherwise, or in the case of erroneous labeling or sequencing of the recording channels, you may edit the channel labels and/or coordinates, or you may read an electrode file stored previously on disk. In addition to the 10/20 and 10/10 standard labels BESA Research recognizes the following labels: M1, M2 (left, right mastoids), SP1, SP2 (sphenoidal), CB1, CB2 (cerebellar), Chin, Neck, LO1, LO2 (lateral ocular), SO1, SO2 (supra-ocular), IO1, IO2 (infra-ocular). BESA Research will translate all the labels into spherical coordinates for spherical spline interpolation, mapping and source imaging. The following assignments are stored in the file '''default.ecd''' in the BESA folder:

[[Image:ST Electrodes (19).gif ]]

 

''Electrode labels in the file '''default.ecd '''and their spherical coordinates. 10-20 electrodes are shown in red and italic.''

The spherical coordinates are defined in degrees by the azimuth (from Cz, positive = right, negative = left hemisphere) and the latitude (counterclockwise from T7/T3 for left and from T8/T4 for right hemisphere) of each electrode. Please do not modify the existing labels or coordinates in this file, because this would adversely affect the interpolated (virtual) montages, the maps and the source montages and source images in BESA Research. However, you may add additional labels for scalp electrodes at the end of this file if needed (up to a total of 196). When you edit the electrode configuration or read in electrode files, BESA Research may replace the 10/20 standard labels T3, T4, T5, T6 by their new 10/10 equivalents T7,

T8, P7, P8. However, in the initialization file '''BESA.ini '''you can reset to the old 10/20 standard by relabeling T7=T3, P7=T5, T8=T4, P8=T6 under the heading [Electrodes]. You may use the same feature to assign appropriate labels to the X1..X8 channels which exist in many systems, e.g. X1=EKG1 etc.

=== Recommendations for electrode placement ===

For source montages and source analysis two principles are important:

# Covering of the lower head with inferior electrodes to record activity from the inferior surfaces of the brain, especially from the basal temporal lobe, from the temporal pole, from orbito-frontal cortex, and from basal occipital and cerebellar areas.
# Equal spacing of the electrodes over the whole head to cover all brain areas.

In the following montage EEGxx the number xx indicates the number of electrodes.

'''EEG25 - Minimum 10-20 configuration including inferior electrodes'''

This covers the 19 standard 10-20 electrodes:

Fp1, Fp2, F7, F3, Fz, F4, F8 ....

plus 6 inferior electrodes on both sides:

F11, A1, P11, F12, A2, P12

with a recommended continuation of the 20% distances, i.e. use F11 instead of F9, P11 instead of P9, A1 instead of T9 to have a wider coverage of the inferior head. A1 / A2 may be replaced by T9 / T10 (or FT9 / FT10) for convenience and comfort.

[[Image:ST Electrodes (21).gif ]]

''Left: recommended configuration for 25 electrodes. Right: left temporal basal activity mapped with 25 electrodes.''

'''EEG33 - Additional 10-10 electrodes within the major squares'''

To the above electrodes add the following 8 intermediate electrodes:

FC5, FC1, FC2, FC6,   CP5, CP1, CP2, CP6

[[Image:ST Electrodes (23).gif]]

''Left: recommended configuration for 33 electrodes. Right: left temporal basal activity mapped with 33 electrodes.''

'''EEG35 - Additional supraorbital electrodes for better EOG separation'''

SO1, SO2

'''EEG37 - Wider inferior coverage at interlaced 20% distances'''

Continue 20% down from F7, FC5, CP5, P7 etc. and use the following 8 inferior electrodes instead of 6:

F11, FT9, TP9, P11,    F12, FT10, TP10, P12

'''EEG41 – Improved frontal and occipital coverage'''

Additional electrodes halfway between Fz and Fp1 / FP2 and Pz and O1 / O2:

AF1, AF2,   PO1, PO2

'''EEG43 – Inferior chain with 5 electrodes including A1 / A2'''

F11, FT9, A1, TP9, P11,    F12, FT10, A2, TP10, P12

EEG43 represents the widest coverage with relatively even spacing.

[[Image:ST Electrodes (25).gif]]

''Left: recommended configuration for 43 electrodes. Right: left temporal polar activity mapped with 43 electrodes.''

'''EEG64-256'''

With 64 or more channel caps, it is similarly recommended to use a sufficient number of inferior electrodes all around the head. At least 4 inferior temporal electrodes on each side and additional electrodes above or below the eyes (outside of the cap) are suggested.

=== Editing the channel configuration ===

Only use the channel configuration editing facility if the electrodes or the common reference have not been correctly defined by your digital EEG system, or if you want to define specific spherical coordinates for your scalp electrodes. It is your responsibility to check and provide the correct sequence of electrode labels in correspondence with the sequence of channels in the EEG data file. If these sequences do not match exactly, errors will occur in the computation of maps, source images and interpolated montages.

We will use the example EEG file '''eeg2.eeg''' in the subdirectory ''Examples/EEG-Focus''

of the BESA Research directory to explain the editing of electrode labels and coordinates:

# Select ''File'', then click on ''Open'', or click on '''eeg2.eeg '''if this file is contained in the list of currently selected EEG files.
# Select ''Edit'', then click ''Channel Configuration''. The dialog box shown below will appear.

[[Image:ST Electrodes (27).gif]]

At the upper left of the figure you see the dropdown menu after selecting the '''File '''menu in the dialog box. This menu allows to edit a new ('''''New''''') or an existing ('''''Open''''') electrode file and to save the changes to the same ('''''Save''''') or a different ('''''Save As''''') file. Normally, it will not be necessary to use this menu. The control fields on the right will be sufficient. If you type ''''''Ok'''''', you will be given the option of saving the changes to a file.

# Click on '''Reload org. Labels''' to reread the original labels as stored in the file header of '''eeg2.eeg'''. BESA Research quits editing and redisplays the EEG. Repeat step 2 and select "''Edit / Channel'' ''Configuration''" again. Note: The button '''Reload org. Labels''' is not available if there are no labels in the file header.
# Click on the empty space of the scroll bar below the '''scroll '''button and on the '''down arrow''' of the '''scroll bar''' to display the remaining electrodes in the file.
# Click on electrode '''R''' (line 32), then on the button '''Delete Electrode''' to remove the associated channel, which does not contain any signal. Note that you may not omit intermediate channels, even if they do not exhibit signals, because the correct correspondence between the series of electrodes and the EEG channels will not be maintained. Use the '''"Edit / Bad Channels"''' menu to disable artifactual or empty channels.
# Click on''' EOG''' (line 30) and change the entry to '''EOG1'''. Do not type '''<Enter>,''' but click on the next or a different electrode box to accept the changes.
# <div style="margin-left:1.259cm;margin-right:0cm;">'''Double click''' on '''EOG '''(line 31). This will highlight the entry. Simply type the new name '''EOG2''', and note that the old label is replaced when highlighted. Electrodes '''30 '''and '''31 '''are now defined as distinct electrodes. Next, we want to replace the label '''T10 '''by '''A2'''.</div>

# <div style="margin-left:1.259cm;margin-right:0cm;">Click on the label '''T10''' (line 24). Then click on the '''drop down''' arrow right of the highlighted label to obtain the list of default scalp electrodes (read from '''default.ecd''' and sorted alphabetically). Type '''A''' to jump to the electrodes beginning with letter A (see below). Type '''2''' or '''click''' on '''A2''' in the list. Click on the '''type '''box (Scalp channel) to close the list and display the new entry in line 24. Note that this is the most convenient way to edit an electrode label.</div>

[[Image:ST Electrodes (28).gif]]

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

<div style="margin-left:1.27cm;margin-right:0cm;"></div>

# Exercise: repeat step 8 to replace '''T9''' by '''A1'''. Restore labels '''T10''' and '''T9''' in lines 24 and 21.
# Replace SO1 and SO2 (supra-orbital) by '''PSO1 '''and '''PSO2 '''and note that these electrodes are changed to the''' 'Polygraphy'''' type, because no coordinates are associated with these labels.
# After you click ''''OK'''', the box '''Write Channel Configuration File''' will appear and display a name for the current electrode file. By default, the BESA electrode file path and current file name will be used and supplemented by the extension ''''.elb''''. The electrode file path may be set in the '''BESA.ini''' file [Defaults] section under ElectrodeFilePath. If no electrode file path is specified in the '''BESA.ini''' file, the default electrode file path ''Montages\Channels ''is used. Simply click ''''OK'''' or type '''<Enter> '''to save the changes to this file, or select a new file name and/or path, if you do not want to store the electrode file in the BESA Research electrode file directory.

Note that by using the default 10/10 labels (see chapter "''Electrode conventions''") you specify that the associated electrode is a scalp electrode. Hence, different labels must be used for polygraphic, intracranial or MEG channels. After you have entered a new non-scalp label, you may select the type of the electrode/channel amongst the different groups ('''Polygraphy, Intracranial, MEG Channel''') from the drop down list in the ''''''Type'''''' box. This will allow for using separate selection and scaling facilities of the channel group control push-buttons at the right of the screen ('''All, Scp, Pgr, Icr, MEG'''). If you have entered a new non-scalp label and select the type '''Scalp Channel''', or if you click on the ''''Advanced>>'''' field, boxes will appear to enter the spherical coordinates (azimuth and latitude) of this electrode (cf. Fig. 6.5). These features may be used to specify non-standard scalp electrodes. Please check the earlier sections of this chapter for electrode conventions. You may view the locations of the scalp electrodes on the head schemes in the mapping window. Select '''Show Electrodes in Maps''' in the "'''View / Options'''" menu.

[[Image:ST Electrodes (29).gif]]

'''Hint:''' If you want to specify the spherical coordinates of an electrode which is close to a standard electrode, click on the ''''Advanced >>'''' field, enter the label of the standard electrode and append a single quotation mark. This will specify that the electrode is close to the labeled location but has different coordinates. The ''Scalp Channel'' type will not be replaced by '''Polygraphy.''' Then edit '''Azimuth''' and '''Latitude'''. This convention is used by BESA Research when reading electrode coordinate files '''(*.elp'''), e.g. from the BESA program. The coordinates are read and compared with the default coordinates to assign the closest label. Then a single quotation mark is appended to the label, and the coordinates are assigned as specified in the '''.elp''' file. For example, open '''segm1.eeg''' in the ''Examples\EEG-Focus'' subdirectory.

Note that the file '''segm1.elp '''is searched for automatically in the directory of the data file when opening the data file.

'''Edit Common Scalp Reference'''

There is a separate line at the bottom in the ''Channel Configuration dialog box'' to enter the label and coordinates of the '''Common Scalp Reference electrode'''. If this is specified and enabled (click on field '''Enabled'''), the information provided by the fact that all scalp electrodes were recorded against a common recording reference will be used for mapping, source imaging and virtual montages. This information will be lost if the common reference has not been specified or if a combination of electrodes has been used as reference during recording. Specify the '''Common Scalp Reference electrode''' only if all electrodes have been referenced to the same single electrode and if a standard 10/10 location has been used for the common recording reference.

'''Note that BESA Research cannot process digital EEG data correctly if there is no common recording reference''', and if different recording references were used for the various scalp electrodes. For intracranial and polygraphic channels different references may be used. It is preferable to use the common reference also for electrode channels near the eyes, because these electrodes provide valuable information for mapping, source imaging and interpolated montages. The traditional bipolar channels (e.g. horizontal and vertical '''EOG''') may be '''reconstructed digitally''' using ''the 'Selected Channels''' group or user-defined montages.

== 3D Coordinates for Precise Analysis ==

=== Introduction - Working with Digitized 3D Coordinates ===

Working with digitized electrode coordinates usually requires reading in additional (auxiliary) files. The procedure is described in the chapter "''Working with auxiliary files''".

=== Data reading rules for EEG ===

This section explains which additional files are read, or which files have to be read in order to provide the necessary information for mapping and source montages.

Assume file name is '''datafile.xxx'''. datafile is the base name, '''.xxx''' is the extension. Replace the text ''datafile'' by the base name of your own file, and the extension'' xxx'' by the extension of your own file.

'''Channel definitions for EEG:'''

Labels have 10-10 names: default locations will be used.

Labels do not have 10-10 names: Channels are interpreted as '''polygraphic'''. Mapping is not possible without one or more of the following additional files.

'''Define channel names and types.''' File '''datafile.ela''', '''datafile.elp''', or '''datafile.elb''' exist, or files '''default.ela''', '''default.elp''', or '''default.elb''' exist, or files '''..\default.ela''', '''..\default.elp''', or '''..\default.elb''' exist (i.e. files with basename d''efault ''one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The ''ela'' file contains just labels and, optionally, types. The ''elp'' file contains spherical coordinates and can contain labels and types. The ''elb'' file contains the same information in binary format. See chapter "''Working with additional files / Channel Definition File Conventions''".

'''Define order in which electrodes were digitized.''' File '''datafile.sfn '''exists, or file '''default.sfn''' exists, or file '''..\default.sfn''' exists (i.e. file '''default.sfn''' one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file. These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. If fiducials exist, they should be defined on the first three lines. If they do not exist, BESA Research will simulate them (so that it can define the head coordinate system). See chapter ''"Working with additional files / sfn (surface point name) file''".

'''Define electrode coordinates.''' File '''datafile.sfp''' exists, or file '''default.sfp''' exists, or file '''..\default.sfp''' exists (i.e. file default.sfp one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If '''datafile.sfn''' does not exist, labels can also be defined in this file. If fiducials exist, they should be defined on the first three lines. If they do not exist, BESA Research will simulate them. See chapter "''Working with additional files / sfp (surface point coordinate) file''".

'''Define coregistration information.''' File '''datafile.sfh''' exists, or file '''default.sfh''' exists, or file '''..\default.sfh''' exists (i.e. file''' default.sfh '''one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration between EEG and MRI. See online help chapter "''Integration with MRI and fMRI".''

'''Define head center.''' No coregistration file exists ('''<nowiki>*.sfh</nowiki>''', see above). File '''datafile.cot''' exists, or file '''default.cot''' exists, or file '''..\default.cot''' exists (i.e. file''' default.cot '''one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''

=== Data reading rules for MEG ===

Assume file name is ''''datafile.xxx''''. '''datafile''' is the base name. '''xxx''' is the extension. Replace the text '''datafile''' by the base name of your own file, and the extension '''xxx''' by the extension of your own file.

Here we consider cases a) MEG alone, b) MEG+EEG.

'''Automatic procedure:'''

Labels have names defined in the files '''bti.ecd''' or '''nmag.ecd'''. Channels are interpreted as MEG. However, sensor locations and head surface point locations must be defined in additional files as described below. Mapping and source analysis are not possible without one or more of the following additional files.

'''Define channel names and types.''' File '''datafile.ela''', '''datafile.elp''', or '''datafile.elb''' exist, or files '''default.ela''', '''default.elp''', or '''default.elb''' exist, or files '''..\default.ela''', '''..\default.elp''', or '''..\default.elb''' exist (i.e. files with basename'' default'' one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The'' ela'' file contains just labels and (optionally) channel types. The ''elp'' file contains spherical coordinates and can contain labels and types. The'' elb'' file contains the equivalent information in binary format. See chapter “''Electrode file conventions'' ''and formats.”''

'''MEG+EEG.''' Define order in which electrodes were digitized. File '''datafile.sfn''' exists, or file '''default.sfn '''exists, or file '''..\default.sfn''' exists (i.e. file '''default.sfn''' one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file (or in the location descriptor in the data file: e.g. Neuromag). These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. See chapter “''Working with additional files/ sfn (surface point name) file”.''

'''MEG+EEG.''' Define head surface point/electrode coordinates. File '''datafile.sfp''''' ''exists, or file '''default.sfp''' exists, or file '''..\default.sfp''' exists (i.e. file '''default.sfp''' one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If '''datafile.sfn''' does not exist, labels can also be defined in this file. See chapter “''Working with additional files/ sfp (surface point'' ''coordinate) file''”. The labels of electrode coordinates '''must '''match to those defined for the data channels. BESA Research will use the labels to associate coordinates with the correct channel.

'''Define sensor coordinates'''. File '''datafile.pos''' or '''datafile.pmg''' exists, or file '''default.pos(.pmg)''' exists, or file '''..\default.pos(.pmg)''' exists (i.e. file '''default.pos(.pmg)''' one folder above the data file): coordinates are defined in this file. The convention is that'' pos'' files contain gradiometer coordinates and'' pmg'' files contain magnetometer coordinates. This is not necessary for the program to read in values properly: the program makes its decision about the sensor type on the basis of the number of coordinate values

on one line in the file (6 = magnetometers, 9 = gradiometers). See chapter “''Working with additional files/ pos or pmg (MEG sensor coordinate) file”.''

'''Define coregistration information.''' File '''datafile.sfh''' exists, or file''' default.sfh '''exists, or file '''..\default.sfh''' exists (i.e. file '''default.sfh''' one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration of the head coordinates with MRI. See (online) help chapter ''"Integration with MRI and fMRI".''

'''Define head center.''' No coregistration file exists ('''<nowiki>*.sfh</nowiki>''', see above). File '''datafile.cot''' exists, or file '''default.cot''' exists, or file '''..\default.cot''' exists (i.e. file '''default.cot '''one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''

=== Reading MEG files in ASCII format ===

'''BESA Research uses labeling or channel type definitions to decide whether channels are EEG or MEG. '''Based on the labels defined for the channels, or the type specified by the channel definition file, the program will try to find auxiliary files that define electrode coordinates or MEG sensors.

BESA Research uses four files to make its decision:* <div style="margin-left:1.259cm;margin-right:0cm;">'''.ela/.elp''' The channel type defined here overrides definitions in '''<nowiki>*.ecd</nowiki>''' (below).</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">'''default.ecd''' defines electrode labels and default spherical coordinates based on the 10-20 and 10-10 naming system</div>
* <div style="margin-left:1.259cm;margin-right:0cm;">'''bti.ecd''' defines labels and default spherical coordinates for the BTi whole-head system</div>
* '''nmag.ecd''' defines labels and default spherical coordinates for the Neuromag whole-head system

If the program finds a label in '''default.ecd''', the channel will automatically be defined as EEG. If not, if it finds a label in one of the other files, the channel will be defined as MEG. If it doesn't find the label anywhere, the channel will be defined as Polygraphic.

The spherical coordinates defined in these files are sufficient for mapping the data. Auxiliary files defining the real sensor coordinates are required for source analysis.

'''Defining default label and coordinate file for a new MEG system'''

When preparing an MEG from a system other than BTi-WHS or Neuromag for import to BESA Research, you should edit either '''bti.ecd''' or '''nmag.ecd '''to conform with your system. If sensor files ('''<nowiki>*.pos/*.pmg</nowiki>''') are always available for your files, the coordinates in the ''ecd ''files are irrelevant: all you need do is define the labels for your own MEG system or use the labels as already defined.

'''Files to prepare for reading in each data file'''

Each auxiliary file should have the same base name as your data file.

'''Define channel labels.''' There are several possibilities:* <div style="margin-left:1.259cm;margin-right:0cm;">Generate your data file according to the BESA'' avr'' ''format or the ASCII multiplexed format.'' Labels are listed in the second line of the file.</div>
* Generate a ''label file'' (extension '''.ela''') with one MEG channel label per line (matching with your ''ecd ''file as defined above) or with the type "MEG" and a label for each line.

Label definitions are also possible using ''elp'' or ''elb'' files, but the above two solutions are recommended because they are the simplest.

'''Define sensor coordinates.''' Generate a ''pos'' or ''pmg'' file. Make sure that the number of sensors matches with the number of MEG channel definitions in your data file.

'''Define fiducials and other head surface points.''' Generate an ''sfp'' file. The first three lines define the fiducials. Subsequent lines define additional surface points.

'''Define coordinates of the center of the head.''' Generate a ''cot'' file. If this file is absent, BESA Research generates the coordinates by fitting a sphere to the head surface points.

Note that all coordinates should be within the same frame of reference, i.e. the same coordinate system. Units must be in meters, centimeters, or millimeters.

== Example: Defining Channel Labels ==

The files described in these examples can be found in the ''.\Examples\Xtras\EEG+Channel''

''Labels'' subdirectory.

The simplest way to define electrode coordinates is to use BESA Research’s default settings (defined in the file, '''default.ecd'''). In this case, you only need to provide a list of channel labels. If a channel label is defined in '''default.ecd''' (i.e. if the labels belong to the 10-20 or 10-10 system), BESA Research will recognize the channel as EEG, and will allocate 3D coordinates.

Labels are not always supplied correctly in the data file. You can override the internal labels in several ways:* Read the data file, and then use "''Edit / Channel Configuration''" to redefine the channels. The configuration is stored in a file with the name '''basename.elb''' (for binary data) or '''basename.elp''' (for ASCII data), where basename is the base name (name without the extension) of your data file.
* Prepare a label file (with the extension ''ela'') containing a list of labels. This can also specify channel types (e.g. EEG, Polygraphic, Intracranial, MEG).
* Prepare a file (with the extension ''elp'') containing spherical coordinates of the channels. This is the method used with the previous version of BESA Research. If the file doesn’t contain labels, labels are allocated based on their proximity to the 10-20 or 10-10 definitions in '''default.ecd'''.

The following examples illustrate the above three methods. The input files are all in ''BESA avr format, ''although these examples apply to all EEG data formats in which only EEG channels exist.

If the data file contains polygraphic or other types of non-EEG channel, the types need to be defined. See the ''EEG+Polygraphic channels example.'' MEG is a special case, because the sensor coordinates need to be defined. See the ''MEG ASCII and the MEG+EEG'' ''examples''.

'''Example 1. EEG file containing wrong labels – use ''Edit/Channel Configuration ''to redefine labels'''* The'' avr'' file, '''EEGwithLabels.avr''', contains the EEG labels. Channels 4 and 14 have been mislabeled – the labels need to be swapped.
* Open the file with '''''File/Open''''' (Select file type ''BESA avr''. Find the correct directory ''Xtras\EEG+Channel Labels'').
* The file should open correctly, displaying 32 channels of EEG.
* The channel coordinates can be viewed by typing the '''‘V’ '''key (make sure the cursor is off). There will be a 3D display of the electrodes. Clicking on an electrode will display the label and the coordinates.
* In this file, channels 4 and 14 have been mislabeled as P3 and F3. In fact, the labels should be the other way around. We will now correct this:
* Select '''''Edit / Channel Configuration'''''.
* Type ‘F3’ into the label for channel 4, and ‘P3’ into the label for channel 14. Then type ‘'''OK'''’. The new channel configuration will be saved in '''EEGwithLabels.elp'''.
* In the data display, the labels of channels 4 and 14 will now be displayed correctly.
* Close the file ('''''File/Close''''') and open it again. Note that the labels are still correct. This is because the new channel configuration file, '''EEGwithLabels.elp''', is read automatically.

'''Example 2. EEG file with no labels – channel labels in auxiliary file'''* The ''avr'' file, '''EEGwithoutLabels.avr''', has no labels.
* EEG labels are defined in '''EEGwithoutLabels.ela'''. This is read automatically when the file is opened.
* In this example, labels are correct. Each label in the ''ela'' file is on one line:

<div style="margin-left:0cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F7''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fz''</div>

<div style="margin-left:0cm;margin-right:0cm;">''...''</div>

'''Example 3. EEG file with no labels – channel labels derived from spherical coordinates'''* The ''avr'' file, '''EEGwithSphericalCoords.avr''', has no labels.
* Spherical coordinates are defined in the ''elp'' file, '''EEGwithSphericalCoords.elp'''. This contains spherical coordinates (theta and phi) and no labels:

<div style="margin-left:0cm;margin-right:0cm;">''-93 -72''</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''92 74''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-97 -40''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-61 -49''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-46 -88''</div>

<div style="margin-left:0cm;margin-right:0cm;">''62 51''</div>

<div style="margin-left:0cm;margin-right:0cm;">''…''</div>* When the data file is opened, the ''elp'' file is read automatically, and BESA Research uses the tables in '''default.ecd''' to assign channel labels. To indicate that it has assigned user defined coordinates and matched with the closest standard electrode, BESA appends an apostrophe (‘) to each label:

<div style="margin-left:0cm;margin-right:0cm;">''Fp1’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F7’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fz’''</div>

<div style="margin-left:0cm;margin-right:0cm;">''...''</div>* We advise to assign specific labels as well as spherical coordinates if you want to use your own spherical coordinate system, e.g.:

<div style="margin-left:0cm;margin-right:0cm;">''FP1u -90 -72''</div>

'''Example 4. EEG file with no labels – channel labels not in basename.el?'''* <div style="margin-left:1.259cm;margin-right:0cm;">The ''avr ''file, '''EEGnoLabelsNoElaFile.avr''', has no corresponding ''ela, elp'', or ''elb'' file, i.e. no file with the same base name and the ''el?'' extension.</div>
* When you open the file, BESA Research will ask for a channel configuration file. The ''File Open'' ''dialog ''will select the ''directory .\Montages\Channels''. The idea is that standard (= frequently used) electrode configurations should be kept in this directory.
* Select the file '''XtrasExample.ela'''.
* Close the data file and reopen it. The file will open with the correct labels. In the BESA window title you will see that the file '''EEGnoLabelsNoElaFile.elp''' has been read automatically. This file was created when '''XtrasExample.ela''' was read.

== Example: Mixed EEG and Polygraphic Data ==

The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Polygraphic'' subdirectory.

The data are in '''EEG+Polygraphic.avr'''.

The third channel is defined as polygraphic in the '''EEG+Polygraphic.ela '''file:

<div style="margin-left:0cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:0cm;margin-right:0cm;">''POLY Test''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3''</div>

The prefix "''POLY''" specifies that the channel is polygraphic. Most other channels are interpreted as EEG because the labels are known in the 10-20 system.

Similarly, channel 31 is defined as intercranial, using the prefix "''ICR''".

Note that you can also define channels as EEG by specifying the ''"EEG" ''prefix (e.g. ''"EEG E1". ''This is useful if there are many more channels than are defined in the 10-10 or 10-20 systems, and if the channel coordinates are defined.

== Example: EEG with Digitized Coordinates ==

The files described in this example can be found in the .''\Examples\Xtras\ EEG+Digitization Points ''subdirectory.

In the previous examples, we have illustrated how to assign labels to channels using channel definition files. In those examples, only spherical coordinates were defined. Here we will show how to read digitized surface points into BESA Research, using the surface point (''sfp'') coordinate file and the surface point name (''sfn'') file.

The principles of defining digitization coordinate files are:* The labels in the ''sfp/sfn'' file combination are used to assign coordinates to electrodes. Thus, if a coordinate has the name ‘''Fz''’ it will be assigned to the channel with the label ‘''Fz''’.
* In consequence, digitization of surface points can be in a different order to the sequence of channels in the data file. Matching to channels is done by comparing the labels.
* We recommend that the fiducial points, '''nasion, left preauricular point, right preauricular point''' be digitized. If you do not digitize them, BESA Research will simulate these locations (see ''“Example: Digitization points with and without Fiducials”''). Fiducial points, labeled '''FidNz, FidT9, FidT10''' should be the first three coordinates in the ''sfp'' file.
* As with the channel definition files, it is easiest for BESA Research if you name the ''sfp/sfn'' files using the base name of the data file, e.g. if the data file is named '''doodah.avr''', name the'' sfp'' file '''doodah.sfp''' and the ''sfn'' file '''doodah.sfn'''.
* You specify the files to be read in the ''Channel and digitized head surface point information dialog box.''

See ''“Example: Polhemus Digitizer Data” ''for a discussion of how to format the files originating from Polhemus and other digitizers.

'''Example 1. EEG file containing labels, ''sfp'' file containing coordinates, ''sfn ''file containing coordinate names'''* The ''avr'' file, '''EEGdigitized1.avr''', contains the channel labels. Therefore, we don’t need a channel definition file.
* The ''sfp'' file, '''EEGdigitized1.avr''', contains digitized coordinates of electrodes and of additional surface points. The labels in the file do not correspond to the electrode labels in the ''avr ''file.
* The ''sfn'' file contains the corrected labels (1 line for each corresponding line in the'' sfp'' file). Now it is possible to match up electrode labels with the labels in the ''avr ''file.
* Open the data file, '''EEGdigitized1.avr'''. The ''Channel and digitized head surface point information dialog box'' will open automatically.
* Note the green tick mark at the top right of the dialog box. This is feedback to say that coordinates of all 32 electrodes have been found.
* Look at the entry ‘''Digitized head surface points’''. Here you will see that the ''sfp'' and the ''sfn ''files have been read automatically (because of the common base name). There are 51 locations. Note that the digitizer file can contain many more locations than the electrodes. BESA Research uses the locations for fitting the sphere of the spherical head model in source analysis. BESA Research can export these locations for coregistration with the MRI.
* Define the electrode thickness as 6 mm (at the right of the ‘''Digitized head surface points’'' box. This is the distance of the digitized point on the electrode to the surface of the head.
* Press '''‘OK’''' in the dialog box and view the coordinates by pressing the '''‘V’''' key.

'''Example 2. EEG file without labels, channel labels in ''ela'' file, surface point coordinates and names in ''sfp'' file'''

* The ''avr'' file, '''EEGdigitized2.avr''', has no channel label. Therefore, a label file is required. Here, the label file is '''EEGdigitized2.ela'''.
* The ''sfp'' file, '''EEGdigitized2.sfp''', contains digitized coordinates of electrodes and of additional surface points. The labels are defined correctly in the ''sfp ''file, i.e. for every EEG channel label there is a corresponding coordinate. Therefore, no ''sfn'' file is required.
* When you open the file, don’t forget to define the electrode thickness as 6 mm in the ''Channel and digitized head surface point information dialog box.''

== Example: Polhemus Digitizer Data ==

The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Digitization Points'' subdirectory.

Data from the Polhemus (other digitizers too) may often not fit the format BESA Research requires for the surface point file. Note that Polhemus data can be exported directly into BESA-compatible ''sfp''-files using the LOCATOR software.

BESA Research requires either* just the cartesian coordinates (x, y, z) values -- one set of coordinates per line. In this case, labels must be defined in a parallel surface point name file, e.g.

<div style="margin-left:1.27cm;margin-right:0cm;">''0.5  3.75  12.68''</div>

<div style="margin-left:0cm;margin-right:0cm;">or</div>

* the cartesian coordinates plus a label. The label can be in front of or behind the coordinates on the line, e.g.

<div style="margin-left:1.27cm;margin-right:0cm;">''0.5    3.75  12.68  Fz''</div>

<div style="margin-left:2.54cm;margin-right:0cm;">or</div>

<div style="margin-left:1.27cm;margin-right:0cm;">''Fz  0.5  3.75  12.68'' </div>

Here is an example of a few lines of a (''sfp'') file that are not read correctly by BESA Research:

<div style="margin-left:0cm;margin-right:0cm;">''Nz  0  87.721  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''T9  -79.131  0  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''T10  67.253  0  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''1  -34.192  103.374  31.868''</div>

<div style="margin-left:0cm;margin-right:0cm;">''2  23.642  103.048  30.351''</div>

<div style="margin-left:0cm;margin-right:0cm;">''3  -81.179  62.913  27.596''</div>

<div style="margin-left:0cm;margin-right:0cm;">''4  -60.701  79.631  78.273''</div>

What is wrong?

* First, some of the points are just numbered. These numbers don't tell BESA Research which electrode channel to which the coordinates should be assigned – assignments should be via channel labels and not numbers.
* Second, Nz, T9, T10 define the fiducials. Instead, the labels FidNz, FidT9, FidT10 are required (prefix "Fid").

What should be done? Probably the best way is

 a) keep only the coordinates in the '''<nowiki>*.sfp </nowiki>'''file:

<div style="margin-left:0cm;margin-right:0cm;">''0  87.721  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-79.131  0  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''67.253  0  0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-34.192  103.374  31.868''</div>

<div style="margin-left:0cm;margin-right:0cm;">''23.642  103.048  30.351''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-81.179  62.913  27.596''</div>

<div style="margin-left:0cm;margin-right:0cm;">''-60.701  79.631  78.273''</div>

b) prepare a surface point name file ('''<nowiki>*.sfn</nowiki>''') containing the corresponding labels:

<div style="margin-left:0cm;margin-right:0cm;">''FidNz''</div>

<div style="margin-left:0cm;margin-right:0cm;">''FidT9''</div>

<div style="margin-left:0cm;margin-right:0cm;">''FidT10''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp1''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F7''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3''</div>

Keeping labels and coordinates separate means that the label file needs generating only once. The coordinate file is different for each subject.

Alternatively, if your digitizer program attaches the labels correctly to the coordinates, then you can prepare the ''sfp'' file like this:

<div style="margin-left:0cm;margin-right:0cm;">''FidNz    0       87.721   0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''FidT9  -79.131    0       0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''FidT10  67.253    0       0''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp1    -34.192  103.374  31.868''</div>

<div style="margin-left:0cm;margin-right:0cm;">''Fp2     23.642  103.048  30.351''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F7     -81.179   62.913  27.596''</div>

<div style="margin-left:0cm;margin-right:0cm;">''F3     -60.701   79.631  78.273''</div>

== Example: Digitization points with and without Fiducials ==

We recommend that if electrodes are digitized, you should also digitize the three fiduciary points:''' Nasion''', '''and left and right preauricular points'''. We refer to these points as "fiducials". We name them '''"FidNz",''' '''"FidT9",''' and '''"FidT10".'''

If you do not digitize these points, BESA Research will simulate them, i.e. it will generate the points where it expects them to be, based on the fit of a sphere to the existing points, and on the names of surface points of known locations. "Known locations" means: the surface point name must be a 10-20 or 10-10 electrode name (e.g. "Cz" -- arbitrary labels, such as "E10" is not a known location). Therefore, BESA Research requires that at least 3 surface points with known labels are defined.

In a file containing digitization points ('''<nowiki>*.sfp</nowiki>'''), the fiducials should be the first three sets of coordinates, i.e. the first three lines of the file. The remaining coordinates in the file can be electrode (or other surface point) coordinates, in any order. The assignment of electrode coordinates to data channels is achieved by matching the coordinate labels to data channel labels.

'''Consequences of omitting fiducials'''

When these files have been read into BESA Research, look at the head surface points in 3D using ''File/Head Surface Points'' ''and Sensors/View'' (or use the shortcut '''‘V’'''). You will see small differences in fiducial locations between the real and the simulated locations. You can expect very slight influences on the results of source modeling (the spherical head may be rotated slightly, although the head center and

radius will be identical), and output of source locations in head coordinates will be different, because these coordinates are based on fiducial locations (see chapter ''“Working with Electrodes and Surface'' ''Locations/ Coordinate systems''”).

== Example: ASCII Import ==

The files described in this example can be found in the ''.\Examples\Xtras\ASCII Import'' subdirectory.

When should the Import ASCII function be used? If you have data in BESA Research average referenced or multiplexed format, use the Open File function to read in a file directly. If you have data in a different ASCII format, BESA Research offers a flexible import function to import data from an array of numbers in an ASCII file.

The array can be '''vectorized '''(one channel, all time points, per line) or '''multiplexed''' (one time point, all channels, per line). These alternatives are illustrated in the two example files '''vectorized.asc''' and '''multiplexed.asc''', and in the tables below:

'''Vectorized array:'''

{| style="border-spacing:0;width:12.993cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 1 ''
|| ''channel 1, time 2''
|| ''channel 1, time 3''
|| ''channel 1, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 2, time 1''
|| ''channel 2, time 2''
|| ''channel 2, time 3''
|| ''channel 2, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 3, time 1''
|| ''channel 3, time 2''
|| ''channel 3, time 3''
|| ''channel 3, time 4''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 4, time 1''
|| ''channel 4, time 2''
|| ''channel 4, time 3''
|| ''channel 4, time 4''
|-
|}

'''Multiplexed array:'''

{| style="border-spacing:0;width:12.993cm;"
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 1 ''
|| ''channel 2, time 1''
|| ''channel 3, time 1''
|| ''channel 4, time 1''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 2''
|| ''channel 2, time 2''
|| ''channel 3, time 2''
|| ''channel 4, time 2''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 3''
|| ''channel 2, time 3''
|| ''channel 3, time 3''
|| ''channel 4, time 3''
|- style="border:0.5pt solid #00000a;padding-top:0cm;padding-bottom:0cm;padding-left:0.199cm;padding-right:0.191cm;"
|| ''channel 1, time 4''
|| ''channel 2, time 4''
|| ''channel 3, time 4''
|| ''channel 4, time 4''
|-
|}

BESA Research needs channel labels. If the labels are in the 10-20 or 10-10 system, BESA Research will assign the channels default coordinates. This is the minimum requirement to be able to map EEG.

If you have 3D digitized coordinates, these can also be specified in ASCII files. This is described under the chapter “''Example: EEG with Digitized Coordinates''”.

'''Example 1. Vectorized data'''* The file '''vectorized.asc''' contains the data. The file should be imported via ''File/Import ASCII File''.
* First you will be asked for a name for the binary target file. The name '''vectorized.fsg''' is suggested. You may accept this name by pressing '''‘OK’''' or choose an alternative name. Note that if the file already exists, the imported data will be appended to the file.
* Next, the ''ASCII File Properties dialog box'' will open. First select ''‘Vectorized’'', and make sure the subsequent entries are correct:

<div style="margin-left:1.27cm;margin-right:0cm;">Header Lines = 0 (i.e. in this example the numbers start on the first line)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Bins/Microvolt = 1.0 (i.e. a value 1 in the data represents 1 µV)</div>

<div style="margin-left:2.54cm;margin-right:0cm;">Sampling Rate = 320 Hz (When the dialog box is opened, BESA Research always chooses the setting it used previously)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Number of channels = 32 (the number of rows in the matrix)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Number of Samples = 640 (the number of columns in the matrix)</div>

<div style="margin-left:1.27cm;margin-right:0cm;">Prestimulus Time = 1000 ms (defines the zero time point 1 s after the beginning)</div>

<div style="margin-left:0cm;margin-right:0cm;">Press '''‘OK’''' to accept the settings.</div>

* Next, the ''Channel and digitized head surface point information dialog box'' will open. In the ''‘Channel configuration’'' box, the label file, '''vectorized.ela''', will be detected automatically. Automatic detection occurs when the label file has the same base name as the data file (in this case, vectorized). To the right of the file name is a summary of channel types: 32 channels found, 30 are EEG, 1 is intercranial, 1 is polygraphic.

Note the green tick at the top left of the dialog box. This indicates that BESA Research thinks that it has sufficient information to read the file, and map and do source analysis on the data.

* To see how channel types are specified in '''vectorized.ela''', click on the '''Edit '''button to view the file with the Notepad program. Here you will see that most channels have 10-20 electrode names. Channel 3 has the prefix ‘''POLY''’, specifying that this channel is polygraphic. Channel 31 has the prefix ‘''ICR''’, specifying that this channel is intercranial. Close Notepad, and click ‘'''OK'''’ in the dialog box.
* A final dialog box asks for a Segment Comment. This is a label that will be displayed in the resulting file. The label is particularly useful if you import several ASCII files into one target file. Each segment is then easily identified by its own label.

'''Example 2. Multiplexed data'''* This example is similar to Example 1. In this case, import the file '''multiplexed.asc''', and select ‘Multiplexed’ in the ''ASCII File Properties dialog box''. Other settings in the dialog box stay as they were.

'''Notes'''# The numbers in the source files can be split into several lines per channel or per time point. Then you will have to enter the correct number of time points and channels in the dialog box. In the present examples, the lines are not split (the vectorized file has all 640 time points in each line, and the multiplexed file has all 32 channels in each line). In this case, BESA Research selects the correct numbers of time points and channels automatically.
# If you have digitized coordinates, these can be specified in the Channel and digitized head surface point information dialog box. Since the procedure is the same as when reading data, this is described elsewhere under “''Example: EEG with Digitized Coordinates''”.

== Example: MEG ASCII ==

The files described in this example can be found in the'' \Examples\Xtras\ MEG ASCII'' subdirectory of the BESA Research installation folder.

'''Multiplexed MEG ASCII file with labels in the header (''med.mul'')'''

For reading MEG data, BESA Research expects* Correct channel definitions, i.e. channels should be defined as MEG.
* Head surface points.
* Sensor coordinates, in '''the same coordinate system''' as the head surface points.
* Optionally, you can define the coordinates of the center of the head. This will be important if too few head surface points are available to specify where to place the spherical head used by BESA Research for source modeling, or if you want to use some external definition, e.g. from the MRI.

As with digitized EEG coordinates, we use the ''Channel and digitized head surface point information'' ''dialog box'' to specify the files which need to be read.

'''Example 1. File Open'''

* The file, '''MEGASCII.mul''', contains MEG data in the ASCII multiplexed format. This format contains channel labels. The labels used are recognized by BESA Research as originating from the Neuromag system. They are therefore identified as MEG and do not need further identification.
* The ''sfp'' file, '''MEGASCII.sfp''', defines fiducials and head surface points. Coordinate labels are included in the file, so no'' sfn'' file is required.
* The cot file, '''MEGASCII.cot''', defines the coordinates of the head center. If this were missing, BESA Research would compute the head center based on the sphere that best fits the head surface points.
* The ''pos'' file, '''MEGASCII.pos''', defines the coordinates of the 122 sensors. For the Neuromag system there are 9 values per line, defining primary coil location, secondary coil location, and orientation cosines. The sequence of coordinates in the ''pos'' file '''must''' match the sequence of MEG channels! The file format and locations of the primary and secondary coils allow BESA Research to identify the sensor type as planar gradiometers. If the file had only six values per line, BESA Research would classify the sensors as magnetometers (one primary coil and the orientation cosines).
* Open the file, selecting current file type as ''‘*,m''??’. The ''Channel and digitized head surface point'' ''information dialog box'' will open, displaying the different auxiliary file names. The green tick indicates that BESA Research finds everything to be OK.
* Press the '''‘OK’''' button and then the''' ‘V’ '''key to view the coordinates.

'''Example 2. File Import'''

* The file, '''MEGASCIIimport.asc''', contains MEG data in a multiplexed array, without a header. This needs to be imported using ''File/Import ASCII'' (see ''“Example: ASCII Import”).''
* On import you have to specify the file as ‘Multiplexed’, the number of time points (285), the number of channels (132), the bins/µV (or bins/fT) (=1), the time at which the stimulus occurred (50 ms), and the sampling rate (949.667 Hz).
* This format contains no channel labels. The labels in '''MEGASCIIimport.ela''' are recognized by BESA Research as originating from the Neuromag system. They are therefore identified as MEG and do not need further identification.
* Since it recognizes the channels as MEG, the ''Channel and digitized head surface point information dialog box'' will open, displaying the different auxiliary file names as before. Since all necessary files with the same base name as the data file are supplied, they are read automatically.
* Press the ‘'''OK’''' button, enter a segment name, and then the '''‘V’''' key to view the coordinates.

'''Example 3. File Open -- MEG information recorded elsewhere'''

This example illustrates the case where the auxiliary files have a different base name from the data file: you must select the file name in the ''Channel and digitized head surface point information dialog box''.* Open the file, '''MEGASCIIelsewhere.mul'''. It is read as an MEG magnetometer file.
* In the ''Channel and digitized head surface point information dialog box'', specify

<div style="margin-left:1.27cm;margin-right:0cm;">'''MEGASCII.sfp''' for the head surface points, and</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''MEGASCII.pos''' for the MEG sensors</div>* MEG coordinates will be correct. The sensor definition file specifies the sensors as planar gradiometers.
* Where the auxiliary files came from will be recorded in the database. If you open the file again, the auxiliary files will be found automatically, without asking any questions.

== Example: Reading combined EEG and MEG from an ASCII file ==

The files described in this example can be found in the ''Examples\Xtras\MEG+EEG'' subdirectory of the BESA Research installation folder.

Here are two examples containing mixed MEG, EEG, and polygraphic channels:* Open a file using the ''File/Open'' command
* Import a file using ''File/Import ASCII'' command

In both cases

* The '''<nowiki>*.ela</nowiki>''' file defines the channel labels. Based on the labels, BESA Research knows which channels are EEG and MEG. The remainder are classified as polygraphic channels.
* The '''<nowiki>*.pos</nowiki>''' file defines the MEG sensor coordinates. The number of values on a line of this file (=9) defines the MEG as gradiometers. The relative locations of primary and secondary coils identify the gradiometers as planar.

'''1. Example with ''File/Open'''''

* Open the file '''MEG+EEG.mul'''. The ''Channel and digitized head surface point information dialog box'' will open automatically (unless the file has already been read once and the information is in the database).
* You will see under ''‘internal data file information’'' that BESA Research finds 122 MEG sensors, and 162 channels in all.
* Under ‘''Channel configuration’'', you will see that as a result of reading the file '''MEG+EEG.ela''', 32 channels are defined as EEG, and 8 channels as polygraphic.
* Under ‘''Digitized head surface points’'' is the feedback that out of the 51 locations in the file '''MEG+EEG.sfp''', all electrode locations have been defined.
* Under ‘''MEG sensors’'', the sensors have been identified as gradiometers.
* The green tick at the top right of the window indicates that BESA Research classifies everything as OK.

'''2. Example with ''File/Import ASCII'''''

* Import the file '''MEG+EEGimport.asc'''. Select '''MEG+EEGimport.fsg '''as the target file (see ''“Example: ASCII Import”'').
* Select 320 Hz sampling rate, and 500 ms pre-stimulus time. Other selections in the dialog box should be ‘Multiplexed’, 1 bin/microvolt (this is interpreted as 1 bin/fT for MEG), 162 channels and 320 samples.
* The ''Channel and digitized head surface point information dialog box'' will open as above.

Working With Additional Files

2017-04-07T07:33:40Z

Alexa:

== Working with Additional Files ==

=== Binary format (*.foc, *.fsg) ===

Select '''Binary High Resolution''' or '''Binary Compressed Format''' to output segments in binary BESA format. If the file already exists, the segment will be appended. Thus, it is possible to create a file combining several segments of interest in a compact form. BESA Research will only allow you to append segments if the number of channels and the sampling interval in source and target files are the same. In

Binary Format all channels (scalp, intracranial, polygraphic, MEG) and file events in the selected time range are exported. '''Note:''' The channels are filtered according to the current filter settings.

Select '''Binary High Resolution''' to retain the resolution of the processed data. This is the preferred binary format for small amplitude signals such as averages. Select '''Binary Compressed Format''' to store raw data using the original resolution or to obtain the space savings of compression (see ''File/Export and Append Data/Convert..'' above). This is the preferred binary format for raw data.

=== ASCII vectorized format (*.avr) ===

Select '''ASCII vectorized Format''' to output segments in BESA ASCII format, one channel (all time points) per line.

'''The Format is as follows:'''

The first of two header lines contains the following data descriptors (6 descriptors, the values shown are only examples):

''Npts= 200'' number of sampled points in each channel

''TSB= -500'' time sweep begin [ms]. Time of first data point relative to zero of epoch

''DI= 5'' digitization or sampling interval [ms]

''SB= 2'' scaling bins/microvolt in file = number corresponding to 1 microvolt

''SC= 50'' scaling calibration, used for setting magnitude of display in BESA

''Nchan= 27'' number of channels

''SegmentName= 60dB''  An optional label describing the data.

The second line of the header contains a label for each channel, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each of the subsequent ''Nchan'' lines of the file contains values for all ''Npts'' time points in floating point or scientific format. For more details about scalp electrodes, see chapter "''Working With Electrodes and Surface Locations/Electrodes/Electrode Conventions".''

A second (older) version of the format (written by BESA versions 1, 2 and 3) omits the '''Nchan=xx''' information in the first line, and there is no second header line. Labels must be defined elsewhere. See "''Electrodes/Electrode file conventions and formats''" and “''Reading MEG files in ASCII format”''. In the older versions, only scalp channels were exported, and the data were average referenced.

=== ASCII Multiplexed format (*.mul) ===

Select '''ASCII Multiplexed Format''' to output segments one time point (all channels) per line.  

The '''ASCII Multiplexed Format '''is as follows:

The first of two header lines contains similar information to that of the ASCII vectorized file:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= -500.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 SegmentName=Condition1''

Note that the item 'SegmentName' is missing if no segment comment is specified when writing a segment to file.

If an epoch of a continuous EEG is exported in ASCII multiplexed format, the first header line contains the additional item 'Time', which indicates the daytime of the first sample in the exported segment:

''TimePoints= 200 Channels= 27 BeginSweep[ms]= 0.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 Time=22:02:53 SegmentName=Segment1''

The second line of the header contains labels for each channel, which may be either the original channel names, or the names of the channels of the current montage, e.g.

''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''

Each subsequent line contains values for all 'Channels' at one time point, in floating point or scientific format. Values are given for the current or the original montage, selected as described above.

Labels for '''source montages''' have the following form: '''TAr-L'''.* The first two letters indicate the head region:

[[Image:ST addfiles (1).gif]]

* The small letter indicates in part the orientation: r=radial, t=tangential, and in part the relative location of the basal temporal source: l=lateral, m=mesial.
* The final letter after the hyphen indicates L=left, M=middle, R=right.

=== Channel definition file conventions and formats ===

BESA Research can read 3 types of file to define channels. These are identified by different extensions:

* channel definition files containing labels and, optionally, channel types (ASCII, 1 label /line): '''<nowiki>*.ela</nowiki>'''
* channel definition files containing coordinates and, optionally, channel types and labels (ASCII): '''<nowiki>*.elp.</nowiki>''' This is the format of the file written by the ''Channel Configuration Dialog.''
* channel definition files stored by older versions of BESA Research (binary format): '''<nowiki>*.elb.</nowiki>''' This format can still be read, but is no longer written by BESA Research.

BESA Research stores and retrieves the channel configuration after editing in binary files. If you open a data file, BESA Research will search for the related channel information in the following sequence:

# For all data files with the extension '''.eeg''', '''.cnt''' and '''.foc''', check in the additional database file in the data directory with the same basename as the data file and the extension '''.fst''', whether a channel file has been associated previously
# Check in the '''''db''''' subdirectory whether a channel file has been associated previously
# Check if labels are defined in the header of the data file
# Search for a corresponding binary channel definition file with the same basename as the data file in the data folder ('''xxxx.elb''')
# Search for a corresponding channel definition file with the same basename as the data file containing labels in the data folder ('''xxxx.ela)'''
# <div style="margin-left:1.259cm;margin-right:0cm;">Search for a corresponding channel definition file with the same basename as the data file containing labels and/or coordinates in the data folder ('''xxxx.elp''')</div>
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' (in this order)) in the data folder
# Search for a file named '''default.elb''', '''default.ela''' or '''default.elp''' one directory above the data folder (e.g. '''..\default.elb''')
# Check if the new data file is of the same type and has the same number of channels as the preceding data file in the list. If this is the case, the electrode configuration of the previous file will be assumed. This will avoid having to load or edit the electrode configuration more than once, if you load several data segments of the same subject from separate files.
# If no channel definition file is found, or digitization points (in files '''<nowiki>*.sfp</nowiki>''', '''<nowiki>*.cot</nowiki>''', '''<nowiki>*.pos</nowiki>''', '''<nowiki>*.pmg</nowiki>''') are found in files with the same basename as the data file, the ''"Channel and digitized surface point'' ''information"'' dialog box is opened, allowing you to specify file names.

'''Channel Label Files (*.ela)'''

Files containing a list of channel labels are an alternative to editing electrode configurations. They can be edited using a standard text editor. Electrode label files ('''.ela''') require a sequence of lines corresponding to the sequence of channels in the data. Each line contains one label and an optional identifier. The format is ' [Identifier] {Label} ', ('Identifier' can be omitted if the electrode label defines the type of signal)

'''Identifiers''' can be one of:

EEG -- scalp electrode

SCP -- scalp electrode

POL -- polygraphic channel

PGR -- polygraphic channel

ICR -- intracranial electrode

MEG -- MEG sensor

REF -- reference electrode (this can only occur once, and must be the last item in the file)

For example:

Fz   ('''scalp''' electrode, coordinates assigned by default.ecd)

Cz   ('''scalp '''electrode, coordinates assigned by default.ecd)

......

VEOG   (vertical EOG,''' Polygraphic''' type is assigned by default)

Exx   (xx=01, 02.. electrode number, '''Polygraphic '''type is assigned by default)

......

EEG xx ('''scalp''' electrode, coordinates must be assigned either by '''default.ecd''' or by a surface point (+'''.sfp''') file. An alternative to the "EEG" prefix is "SCP".

......

POL XX  (identifier sets '''Polygraphic''' type -- an alternative to the "POL" prefix is "PGR")

......

ICR A01  (identifier sets '''Intracranial''' type to electrode A01 - do not use A1!)

ICR A02  (identifier sets''' Intracranial''' type to electrode A02 - do not use A2!)

ICR A03  (identifier sets''' Intracranial''' type to electrode A03)

......

MEG M01  (identifier sets '''MEG '''type to electrode M01 - do not use M1!)

MEG M02  (identifier sets '''MEG''' type to electrode M02 - do not use M2!)

......

REF Cz  (the label is assigned to the electrode reference, no channel is associated with this entry. This must be the last line of the file!)

'''Channel spherical coordinate files (*.elp)'''

These files follow the same rules as the channel label files, with the addition of spherical coordinates (theta, phi) that follow the labels of EEG and MEG channels. Labels can also be omitted. In this case, BESA Research will assign labels according to the nearest coordinate defined in the '''default.ecd''' file. To indicate that the coordinates have been assigned, the label will have a tick, e.g. Fz' instead of Fz.

Channels of other types (polygraphic, intracranial) are defined exactly as in the channel label ('''<nowiki>*.ela</nowiki>''') file.

=== cot (Head center) file ===

'''Function''': to redefine the center of the head for the sphere used in dipole models. If the cot file has the same base name as the data file, it is read automatically by BESA Research. If the coordinates deviate by more than 1 mm from the previously defined head center, a window is opened, asking if the new values should be adopted. This mechanism is turned off if the data have been coregistered to MRI (see online help chapter ''"MRI Coregistration''"), and an MRI Coregistration File ('''<nowiki>*.sfh</nowiki>''') has been associated with the data.

BESA Research uses any head surface points (e.g. electrode locations), excluding those on the lower part of the face, to compute the sphere center automatically. The cot file is used if you want to override the automatic calculation. A mechanism is provided which allows to pass a location from the MRI (viewed by BrainVoyager) to the Source Module and save the resulting location as a ''cot ''file.

'''Format''': one set of coordinates (x y z). These are followed by either "'''DC'''" or "'''HC'''", which specify whether these coordinates are in '''D'''evice or '''H'''ead '''C'''oordinates.

'''Units:''' must be in meters!

(Note: In special cases, a fifth value, the '''head radius''', may follow. This is used when reading simulated MEG data from the DipoleSimulator program. When this value is set, BESA Research uses the specified head radius and head center and does not fit a sphere to the head surface points. and does not create an ellipsoid transformation).

Force BESA Research to use a completely spherical model without creating an ellipsoid: Write "'''DipoleSimulator"''' or "'''Phantom'''" on the second line of the file. Under these circumstances, 100% correspondence between DipoleSimulator and BESA Research is achieved. This is also required for dipole fitting on MEG phantom recordings.

The ''cot ''file has also been extended for reading CTF MEG files. Documentation for these extensions is found in the CTF help file.)

=== pos or pmg (MEG sensor coordinate) file ===

'''Function:''' to define coordinates of MEG sensors. Our convention is to save magnetometer information in '''<nowiki>*.pmg</nowiki>''', and gradiometer information in '''<nowiki>*.pos</nowiki>'''. In practice, BESA Research doesn’t mind which extension is used -- the distinction between gradiometers and magnetometers is based on the number of values on each line in the file.

'''Format:''' one sensor per line.

Magnetometers: label (optional), six coordinates per line (location, orientation)

e.g. for BTi:

" Channel 'A1': -0.0019193 0.0304846 0.1081738 0.1188222 0.2394208 0.9636177"

Gradiometers: label (optional), nine coordinates per line (location of primary sensor, location of secondary sensor, orientation). The program decides whether gradiometers are planar or axial based on the distance between the primary and secondary sensor locations and the center of the head.

e.g. for Neuromag:

" 0.108510 -0.000143 -0.044954 0.108510 0.000463 -0.028766 0.999999 0.001450 0.000000 "

Labels in these files are ignored.

See chapter “''3D Coordinates for Precise Analysis/Data reading rules for MEG''”.

=== sfn (surface point name) file ===

'''Function:''' to match up digitized coordinates with channels that are defined as EEG electrodes and to define labels for additional digitized head surface points (e.g. MEG coils, etc.).

'''Format:''' one label per line.

Contains labels of surface points in the order of digitization. If fiducials are defined, these should be on the first three lines, with the labels 'FidT9', 'FidT10', 'FidNz' or 'FidLPA', 'FidRPA', 'FidNAS'.

If electrodes are defined in the data file, the labels of each electrode as defined in the data file (or in its associated ''ela'', ''elp'', or ''elb ''file) must be present!

The case of labels is not important (e.g. 'Fp1' will match with 'fp1').

The ''sfn'' file need not exist if labels are defined in the ''sfp ''file.

See chapter “''3D Coordinates for Precise Analysis / Data reading rules for EEG”.''

=== sfp (surface point coordinate) file ===

'''Function''': to define coordinates of digitized points on the head surface. The order of points must match with the order in the ''sfn ''file, or if no ''sfn'' file is present, labels must be included in the ''sfp'' file.

Note: If the digitized points include electrodes, the channel labels must correspond to the labels of the digitized points. The sequence of labels in channels and surface point coordinate file need not be the same – the allocation is performed by label matching. Channel labels may be defined in the data file, or they may be assigned using channel definition files ('''<nowiki>*.ela, *.elp, *.elb</nowiki>''').

'''Format:''' one set of coordinates (x, y, z) per line. Coordinate units must be either meter, centimeter or millimeter (BESA Research will perform a plausibility check automatically to determine which units are used). If a label is present this can precede or come after the three coordinate values.

If fiducials are defined, these should be on the first three lines. BESA Research will simulate fiducials if none are defined, but it is preferable to record these locations along with the other head surface points.

If there are MEG sensors, the same coordinate systems must be used in the ''sfp'' file and the ''pos/pmg ''file!

If labels are defined in the ''sfp'' file rather than in an ''sfn'' file, labeling rules apply as for the ''sfn'' file.

Example for the ''sfp'' file format:

[[Image:ST addfiles (2).gif ‎]]

BESA Research will check the coordinates for plausibility. If coordinates are more than 30° away from the expected location on the sphere there will be an error message. Such errors are usually due either to incorrect labeling or to a digitization error.

See chapter “''3D Coordinates for Precise Analysis /'' ''Data reading rules for EEG”.''

=== Generic File Format ===

This reader, incorporated into the '''GenericBesa.dll''' file, allows to read simple multiplexed or vectorized data formats, if you know the structure of the data format.

'''What you have to do'''* With a text editor, write information about the data file you want to read into BESA Research into a text file, the ''Generic Header''.
* Save the edited text in the same subdirectory as the data file.
* '''Mechanism A:''' The generic header contains the data file name. With BESA Research, navigate to the file you just edited, and open it. The data should then be read into BESA Research.
* '''Mechanism B:''' Alternatively, navigate to the data file. The reader will check if there is a generic header in the same subdirectory, and use that to try to open the file. You have two options:

* '''Specific:''' if the file has the same basename as the data file, and the extension “'''.generic'''”, this file will be used.
* '''Generalized:''' if a specific file is not found, the reader will look for the file “'''BESA.generic'''” in the same subdirectory.

'''Important note:''' We recommend using mechanism A, using a header with the extension "'''.generic'''". When opening the data file in BESA, select the generic header. Mechanism B sometimes fails when opening the data file in BESA Research, because one of the other readers in BESA may erroneously interpret the file as their "own" data format, sometimes leading to a crash.

'''Format of the Generic Header'''

The first line '''must '''consist of the text: “''BESA Generic Data''” (without the inverted commas).

Subsequent lines '''must''' contain the following parameters, in any order (note that the parameters are case insensitive):

'''''nChannels''' ''<nowiki>= </nowiki>''nnn''                 The number of channels

'''''sRate''''' = ''fff    ''                           The sampling rate (samples/sec)

<div style="margin-left:3.401cm;margin-right:0cm;">'''''format''''' = ''type''        One of ''short'', ''int, float, double, ASCII''. If the format is ''ASCII'', the </div>

<div style="margin-left:3.401cm;margin-right:0cm;">parameter''' nSamples''' must be specified as well (see below)</div>

The following parameters are optional (values in square brackets denote optional parameters):

<div style="margin-left:5.101cm;margin-right:0cm;">'''''nSamples'' '''<nowiki>= </nowiki>''nnn ''          The number of time samples in the data. If this value is 0, or the line is omitted, then use the file size to estimate the number of samples.</div>

<div style="margin-left:5.101cm;margin-right:0cm;">'''''file''''' = ''name   ''   The data file name, without path information. If this is omitted, you can only read the data with mechanism B (see above). This line '''must''' be included if you want to read the data with mechanism A.</div>

<div style="margin-left:5.101cm;margin-right:0cm;">'''''DataOffset''''' = ''nnn  ''                   Offset of data in bytes for binary data, in lines for ASCII data (default = 0).</div>

<div style="margin-left:5.101cm;margin-right:0cm;">'''''Factor''' ''<nowiki>= </nowiki>''fff  [range]''                Data values are multiplied by this factor to obtain µV values (default = 1). Optional parameters can be appended to define a channel range, e.g. ''1-3''. Thus, this command can be used multiply, to define different scaling factors for different channels. If only one channel is specified, use on number only, e.g. ''5''.</div>

<div style="margin-left:5.101cm;margin-right:0cm;">'''''SwapBytes''''' = ''ccc  ''           One of ''off'' or ''on'' (default = off). If the data block originated from Unix or Mac, this will need to be ''on''. (binary data only)</div>

'''''Prestimulus''' ''<nowiki>= </nowiki>''fff   ''                   Prestimulus interval in milliseconds.

'''''Label '''''<nowiki>= </nowiki>''ccc   ''                           Segment label.

'''''Trigger''''' = ''chan….''            Channel number containing triggers. Without further parameters, the

<div style="margin-left:5.101cm;margin-right:0cm;">values are read directly as digital trigger values. Other parameters are described below, for the case where the trigger channel contains analog signals.</div>

<div style="margin-left:5.101cm;margin-right:0cm;">'''''nBlocks '''''<nowiki>= </nowiki>''nnn    ''                  The data are epoched. This specifies the number of equal sized blocks in the data. In BESA Research, each block will be separated by a segment boundary. The number of samples in each epoch is computed from the total number of samples divided by ''nBlocks''.</div>

'''''nEpochs'' '''<nowiki>= </nowiki>''nnn        ''                Same as '''nBlocks'''.

<div style="margin-left:5.101cm;margin-right:0cm;">'''''EventFile''''' = ''name      ''              Load events from an event file, using BESA's event file ('''<nowiki>*.evt</nowiki>''') format. See below for a description of how to prepare this file.</div>

'''''Order''''' = ''type   ''                         One of ''multiplexed'', ''vectorized''. The default is multiplexed (i.e. channels

<div style="margin-left:5.101cm;margin-right:0cm;">fastest). Specify ''vectorized'' if your data are ordered so that all time samples for channel 1 are followed by all time samples from channel 2, etc.</div>

'''''Orientation''' ''<nowiki>= </nowiki>''type ''                   Same as '''Order'''.

'''''Arrangement'' '''<nowiki>= </nowiki>''type''                 Same as '''Order'''.

'''Trigger events'''

This section describes how the reader can be used to encode trigger events when the trigger channel contains analog signals. In this case, a '''Trigger '''command is required for each target code in BESA Research.

Syntax:

'''Trigger''' = ''chan  code  fromLevel  toLevel  timerange''  ''deadtime''

'''''chan''' ''is the channel number on which to find the trigger

'''''code''''' is the trigger number that the reader will assign (must be positive!)

'''''fromLevel'' '''is the value in mV defining the lower range for trigger detection

'''''toLevel'' '''is the value in mV defining the upper range for trigger detection. If this is “-“, then only ''fromLevel ''needs to be exceeded for the trigger to be detected.

'''''timerange '''''is the range in milliseconds to define a trigger. The reader will search for the maximum deviation from baseline within the range to find the level that will define the trigger.

'''''deadtime''' ''defines the time after detecting a trigger during which no further trigger with this code can be detected. This does not affect other codes. Also, if the voltage level stays at a level corresponding to a code, the trigger is only defined at the onset of this voltage level.

Multiple lines are required if different trigger codes and different trigger channels are required, one for each new code.

'''Notes'''

'''Channel labels:''' The data channels are labeled ''E1, E2, E3,…,'' and they are initially classified by BESA Research as polygraphic. As with other BESA Research data files, use a '''<nowiki>*.ela </nowiki>'''file (or '''<nowiki>*.elp</nowiki>''', optionally combined with '''<nowiki>*.sfp</nowiki>''') to redefine labels and channel types.

'''Data formats:'''

* Short 16-bit
* Int 32-bit
* Float 32-bit
* Double 64-bit
* ASCII Decimal numbers separated by spaces or tabs (engineering format also permitted)

'''Prestimulus interval and label:''' If either of these are defined, BESA Research reads the data in to define an averaged data segment. The label is displayed, and a vertical dotted line marks timepoint zero. If no prestimulus interval is defined, a zero prestimulus interval is assumed.

'''Future changes'''

Possible developments:* Read channel labels

If any of these changes are particularly important to you, please contact [mailto:support@besa.de support@besa.de] and let us know.

'''Event File'''

The event file is a text (ASCII) file containing a header line and subsequent lines, with one event description per line.

Each line contains four parameters:

<div style="margin-left:0cm;margin-right:0cm;">1. latency (units specified by the header, can be µs, ms, s)</div>

<div style="margin-left:1.7cm;margin-right:0cm;">2. code (defines the type of event: trigger, comment, marker, pattern, average segment, data break segment)</div>

<div style="margin-left:0cm;margin-right:0cm;">3. parameter (depends on the event type, e.g. trigger code)</div>

<div style="margin-left:0cm;margin-right:0cm;">4. label (label assigned to the event)</div>

'''Header Line:'''

The header line contains four values. The first specifies the time units, e.g. '''Tmu '''specifies microseconds.

''    Tmu    Code    TriNo    Comnt''

'''Tms''' specifies milliseconds. '''Tsec''' specifies seconds.

'''Event Code and Parameter 3 (TriNo):'''

'''Code''' specifies the event type:

1 = trigger -- '''TriNo '''specifies the trigger number

2 = comment

3 = marker

11-15 = patterns 1-5

21 = artifact on

22 = artifact off

31 = epoch on

32 = epoch off

41 = segment onset -- '''TriNo '''is a time string that specifies date and time, in the format ''YYYY-MM-DDTHH:MM:SS'', e.g. ''2010-04-26T15:30:20.31'' (note: seconds are a decimal number).

42 = average segment onset -- '''TriNo '''is a number specifying the prestimulus baseline of the subsequent average in microseconds. '''TriNo '''(parameter) is 0 for markers, comments, artifacts, and epochs.

'''Comment'''

The event label. This is not used for markers, artifacts, and epochs.

'''Example of event file:'''

A simple way to generate example files is to export events from BESA (''ERP/Save Events As...'').

Tmu         Code     TriNo     Comnt

0              42     100000    Ave: 25 avs  

10000000  2       0            Comment at 10s

20000000  41     26-04-2010T15:30:20.000   TestSeg2

21000000  3       0

22000000 1        99          Trigger – 99

This specifies an average segment starting at the beginning of the file, with a prestimulus interval of 100 ms, a comment at 10 s, a new segment specifying date and time at 20 s, a marker at 21 s, and a trigger with code 99 at 22 s.

'''Examples'''

The following reads ASCII multiplexed data that were previously exported from BESA Research:

''BESA Generic Data''

''nchannels = 64''

''srate = 100''

''nsamples = 10000''

''dataoffset = 2''

''format = ASCII''

''file = name.mul''

''factor = 1''

With the sampling rate of 100 Hz and 10000 samples, this represents 100 s of 64-channel data. The first two lines of the data are skipped.