BESA® Wiki - User contributions [en]

Wrong characters in BESA software

2021-05-05T11:46:18Z

Vibhin:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = BESA Research 7.0 or higher
}}

= Problem description =
Recently windows 10 introduced multi language support. This can however cause troubles with displaying special characters in any type of software (i.e. µV). Instead you can see something similar to this:

[[File:CharactersProblem.png]]

= Solution =
To solve this you need to change your system "Region & language" preferences.
* Please press windows start button, and press settings button (the cog wheel).
* Select '''Time & Language''' section
* Select '''Region & language'''

A window similar to this will be displayed:

[[File:CharactersProblemReason.png|800px]]

First select '''Administrative language settings''' on right side and select '''Adminitstative''' tab. Then press '''Change system locale...''' button. Check if '''Beta: Use Unicode UTF-8 for worldwide language support''' is checked. If it is please uncheck it:

[[File:Characterproblemsolution2.png|800px]]

You may also need to install the proper language configuration. Press the '''Add a language''' button and select the language pack that is the correct one for you. After installation make sure that the new language pack is at the top of the list. Alternatively you can also select one of the installed languages if there is any. When you click on the selected language the up and down arrow will be shown. Press the up arrow until the selected language is at the top. You should end up with a configuration similar to this one:

[[File:CharactersProblemSolution.png|800px]]

Once this is done you may close all the windows and restart BESA. If the problem still persists try to install another language pack or contact [https://www.besa.de/support/support-page/ BESA support]

[[Category:Troubleshooting]]

Working With Additional Files

2021-05-05T11:40:20Z

Vibhin:

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

== 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):

{|
| width="30%" |''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 ''[[Electrodes_and_Surface_Locations#Electrode_Conventions|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 '''<tt>Nchan=xx</tt>''' information in the first line, and there is no second header line. Labels must be defined elsewhere. See ''[[Working_With_Additional_Files#Channel_definition_file_conventions_and_formats|Channel definition file conventions and formats]]'' and ''[[Electrodes_and_Surface_Locations#Reading_MEG_files_in_ASCII_format|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:

<source lang="dos">
TimePoints= 200 Channels= 27 BeginSweep[ms]= -500.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 SegmentName=Condition1
</source>

Note that the item '''<tt>SegmentName</tt>''' 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 '''<tt>Time</tt>''', which indicates the daytime of the first sample in the exported segment:

<source lang="dos">
TimePoints= 200 Channels= 27 BeginSweep[ms]= 0.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 Time=22:02:53 SegmentName=Segment1
</source>

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.

<source lang="dos">
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
</source>

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:
** TA: temporal-anterior
** TP: temporal-posterior
** TB: temporal-basal
** FL: fronto-lateral
** FP: fronto-polar
** PC: posterior-central
** OL: occipito-lateral
** OC: occipito-central
** CL: centro-lateral
** CC: central


* 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:
* <span style="color:#ff9c00;">'''<tt>*.ela</tt>'''</span>: channel definition files containing labels and, optionally, channel types (ASCII, 1 label / line)
* <span style="color:#ff9c00;">'''<tt>*.elp</tt>'''</span>: channel definition files containing coordinates and, optionally, channel types and labels (ASCII). This is the format of the file written by the ''Channel Configuration Dialog.''
* <span style="color:#ff9c00;">'''<tt>*.elb</tt>'''</span>: channel definition files stored by older versions of BESA Research (binary format). 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 <span style="color:#ff9c00;">'''.eeg'''</span>, <span style="color:#ff9c00;">'''.cnt'''</span> and <span style="color:#ff9c00;">'''.foc'''</span>, check in the additional database file in the data directory with the same basename as the data file and the extension <span style="color:#ff9c00;">'''.fst'''</span>, 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 (<span style="color:#ff9c00;">'''xxxx.elb'''</span>)
# Search for a corresponding channel definition file with the same basename as the data file containing labels in the data folder (<span style="color:#ff9c00;">'''xxxx.ela)'''</span>
# Search for a corresponding channel definition file with the same basename as the data file containing labels and/or coordinates in the data folder (<span style="color:#ff9c00;">'''xxxx.elp'''</span>)
# Search for a file named <span style="color:#ff9c00;">'''default.elb'''</span>, <span style="color:#ff9c00;">'''default.ela'''</span> or <span style="color:#ff9c00;">'''default.elp'''</span> (in this order)) in the data folder
# Search for a file named <span style="color:#ff9c00;">'''default.elb'''</span>, <span style="color:#ff9c00;">'''default.ela'''</span> or <span style="color:#ff9c00;">'''default.elp'''</span> one directory above the data folder (e.g. <span style="color:#ff9c00;">'''..\default.elb'''</span>)
# 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 <span style="color:#ff9c00;">'''<nowiki>*.sfp</nowiki>'''</span>, <span style="color:#ff9c00;">'''<nowiki>*.cot</nowiki>'''</span>, <span style="color:#ff9c00;">'''<nowiki>*.pos</nowiki>'''</span>, <span style="color:#ff9c00;">'''<nowiki>*.pmg</nowiki>'''</span>) 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 (<span style="color:#ff9c00;">*.ela</span>)'''

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 (<span style="color:#ff9c00;">'''.ela'''</span>) 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:

<blockquote style="background-color: lightgrey; border: solid thin grey;">
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 <span style="color:#ff9c00;">'''default.ecd'''</span> or by a surface point (+<span style="color:#ff9c00;">'''.sfp'''</span>) 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!)
</blockquote>

'''Channel spherical coordinate files (<span style="color:#ff9c00;">*.elp</span>)'''

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 <span style="color:#ff9c00;">'''default.ecd'''</span> file. To indicate that the coordinates have been assigned, the label will have a tick, e.g. '''<span style="color:#3366ff;">Fz'</span>''' instead of '''Fz'''.

Channels of other types (polygraphic, intracranial) are defined exactly as in the channel label (<span style="color:#ff9c00;">'''*.ela'''</span>) 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 (<span style="color:#ff9c00;">'''<nowiki>*.sfh</nowiki>'''</span>) 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 <span style="color:#ff9c00;"><tt>*.pmg</tt></span>, and gradiometer information in <span style="color:#ff9c00;"><tt>*.pos</tt></span>. 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''' (<span style="color:#ff9c00;"><tt>*.pmg</tt></span>): label (optional), six coordinates per line (location, orientation)

e.g. for BTi:

<source lang="dos">
Channel 'A1': -0.0019193 0.0304846 0.1081738 0.1188222 0.2394208 0.9636177
</source>

'''Gradiometers''' (<span style="color:#ff9c00;"><tt>*.pos</tt></span>): 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:

<source lang="dos">
0.108510 -0.000143 -0.044954 0.108510 0.000463 -0.028766 0.999999 0.001450 0.000000
</source>

Labels in these files are ignored.

See chapter ''[[Electrodes_and_Surface_Locations#Data_reading_rules_for_MEG|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 ''[[Electrodes_and_Surface_Locations#Data_reading_rules_for_EEG|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.

<span style="color:#ff0000;">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 (</span><span style="color:#ff9c00;"><span style="color:#ff0000;">'''<nowiki>*.ela, *.elp, *.elb</nowiki>'''</span></span><span style="color:#ff0000;">).</span>

'''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 <span style="color:#ff9c00;">'''GenericBesa.dll'''</span> 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 “<span style="color:#ff9c00;">'''.generic'''</span>”, this file will be used.
** '''Generalized:''' if a specific file is not found, the reader will look for the file “<span style="color:#ff9c00;">'''BESA.generic'''</span>” in the same subdirectory.

<span style="color:#ff0000;">'''Important note:'''</span><span style="color:#ff0000;"> We recommend using mechanism A, using a header with the extension "</span><span style="color:#ff9c00;"><span style="color:#ff0000;">'''.generic'''</span></span><span style="color:#ff0000;">". 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.</span>

'''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):

{| class="wikitable"
| width="20%" | '' '''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):

{| class="wikitable"
| width="15%" | '' '''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 (<span style="color ||#ff9c00;">'''<nowiki>*.evt</nowiki>'''</span>) 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 <span style="color:#ff9c00;">'''<nowiki>*.ela </nowiki>'''</span>file (or <span style="color:#ff9c00;">'''<nowiki>*.elp</nowiki>'''</span>, optionally combined with <span style="color:#ff9c00;">'''<nowiki>*.sfp</nowiki>'''</span>) 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:

# latency (units specified by the header, can be µs, ms, s)
# code (defines the type of event: trigger, comment, marker, pattern, average segment, data break segment)
# parameter (depends on the event type, e.g. trigger code)
# 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.

<source lang="dos">
Tmu Code TriNo Comnt
</source>

'''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...'').

<source lang="dos">
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
</source>

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:

<source lang="dos">
BESA Generic Data
nchannels = 64
srate = 100
nsamples = 10000
dataoffset = 2
format = ASCII
file = name.mul
factor = 1
</source>

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}}

Using BESA to correct blink and EKG artifacts in MEG data

2021-05-05T11:29:10Z

Vibhin:

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

Eyeblinks and EKG cause large artifact signals in the magnetometer channels. The artifact correction facilities of BESA can correct these artifacts quite well. The procedure is quite simple for blinks but more complex for EKG. The following text outlines the procedures and current limitations of BESA for artifact correction.

The principles of the artifact correction procedure are described in Berg and Scherg (1994).

In summary, the following steps are required:

* Use pattern search and average to identify the latencies of blink/EKG signals in the raw data. Pattern search works best if you have recorded a vertical EOG and EKG with the MEG data, but it will also work on selected MEG channels, using the appropriate filters.
* A spatial PCA is performed on the average to identify the main topographies/components of the artifact signal. For blinks, only one topography is required. For EKG, two or three topographies may be required.
* The topographies/components are combined into a coefficient file (''*.atf''). Using the '''Artifact''' Menu, the ''atf'' file can be loaded and correction switched on. Contrary to the warning message displayed by the ERP module, averaging can be performed using artifact corrected data.
* When the average is loaded into the Source Analysis module, the artifact coefficients (saved in the average file) need to be activated. They will then be incorporated into source modeling using Adaptive, Surrogate or Ssubspace projection (SSP – see also Uusitalo et al. (1997)). Note that SSP approach is not recommended. Usually, for continuous data, the best effect is achieved using the Adaptive method, for ERP Surrogate.

'''References'''
* Berg, P., and Scherg, M. A multiple source approach to the correction of eye artifacts, Electroenceph. clin. Neurophysiol., 1994, 90: 229-241.
* Uusitalo, M.A., Ilmoniemi, R.J. Signal-space projection method for separating MEG or EEG into components. Med. Biol. Eng. Comput., 1997, 35: 135-140.

== Pattern search for blinks and EKG ==

=== Eyeblinks ===

# Select filters 0.5 – 8 Hz ('''Filters/Edit Filter Settings…'''). Make sure the low cutoff filter type is '''Forward'''! (This is to ensure that no contribution from the blink topography bleeds back into the baseline time interval).
# View Polygraphic signals only (press the '''Pgr''' button at the top right of the BESA window), so that the vertical EOG channel is displayed
# Define the search block from –100 ms to +400 ms ('''Edit/Default Block Epoch…''')
# Select Pattern Search ('''Search/Pattern''')
# Select Search Query ('''Search/Query''')
# Select Buffer 1 for averaging ('''Tags/Pattern 1''')
# Identify a clear blink signal on the vertical EOG channel. Right-click at the '''onset''' of the blink, and select '''Default Block''' in the dropdown menu. The marked block should look something like this: [[File:EKG_artifacts_in_MEG_data__(1).png|75x55px]]
# Click once on the VEOG channel label, so that a rightward arrow is displayed (ignore the correlation window that opens on the right): [[File:EKG_artifacts_in_MEG_data__(2).png|100x55px]]
# Press the '''SAW''' button (Search/Average/Write). BESA will start scanning through the file, and it will stop at each occurrence of a blink. Press “Yes” to accept. “No” to reject, or “Stop asking” to let BESA accept everything automatically. Save the result to a file name of your choice (e.g. ''name_artifact.fsg''), labelling the segment, e.g. “blink”.
Note that instead of '''SAW''' the '''SAV''' can be displayed (Search/Average/View). This interaction has exactly the same meaning as '''SAW''' but does not prompt for saving averaged data but just display it in the average buffer. This behaviour can be switched in '''Search''' Menu by checking '''Search, Average, View''' option

=== EKG ===

# In contrast to blink averaging we use two steps: first, filters are set to enhance the EKG for pattern search. Second, the filters are opened up, and the average is repeated.
# Select filters 5-20 Hz. This should generate a fairly clear signal on the EKG.
# Set the default block epoch so that the R-wave and the T-wave are well inside the epoch. The setting used for blinks may be OK, but you may need to extend the post-cursor interval, e.g. from 400 to 500 ms.
# Proceed as with blinks, but selecting Buffer 2 for averaging ('''Tags/Pattern 2'''). Mark a block around the onset of an R-wave. The marked block should look something like this: [[File:EKG_artifacts_in_MEG_data__(3).png|100x56px]]
# Save the average in the same file as the averaged blinks, labelling the segment, e.g. “EKG”.
# Select filters 1-30 Hz. Select '''Search/Tagged Events''', and press '''SAW'''. This repeats the average using the tags that were identified during the first step. Opening up the filters ensures that the average includes more of the EKG signal.

=== What to do if there is no VEOG or EKG channel ===

The procedure is similar to the above, but you need to identify a MEG channel that displays the blink or EKG waveform clearly. You may need to experiment with filter settings to make the artifact pattern clearer (the filter settings described above are not fixed rules – you may find that other settings work better for pattern search). You may find the “Create Triggers from EMG/EEG” tool helpful for detecting EKG ('''ERP/Create Triggers from EMG/EEG…'''). See the BESA help file (tutorial on creating triggers).

== Spatial PCA and the *.atf file ==

Open the file in which you saved the averages (e.g. ''name_artifact.fsg''). Make sure that prestimulus baseline correction is switched on ('''Filters/Use Prestimulus Baseline''').

=== Blinks ===

# Mark the whole blink epoch: Right-click onto the epoch, and select '''Whole Segment'''.
# Select '''Artifact/Assign/Blink'''. The spatial PCA is computed, and the first spatial component is assigned to describe the blink. You may check if the correction works by selecting '''Artifact/Correct'''.
# The coefficients are saved automatically to a file with the same basename as the average, and the extension ''“.atf''”.

=== EKG ===

EKG coefficients are corrected analogously to blinks. A difference is that the topographic distribution of the EKG over the MEG sensors is more complex than that of blinks. It changes over time. The reasons for this are unclear, and may be due to movement of the heart (and its equivalent dipoles) over time, but also to ballistic effects: movement of the head due to blood flow.

Since topographic distribution changes over time, more than one component is required for correction. We choose the number of components in the Artifact Select Dialog Box empirically: As a rule of thumb, if a component explains more than 5-10% of the variance of the averaged EKG signal, the component is included. Note that the number of components you select can also be changed when the coefficients are applied to the raw data.

== Correcting the raw data ==

* After defining the artifact coefficients, they are automatically loaded and used for data. Note that you can enable and disable artifact correction by pressing '''CTRL-E''' or by menu '''Artifact/Correct''' you can load the defined artifact coefficient to another data set (i.e. subsequent recording from the same subject within the same session) using ('''Artifact/Load…''') and providing the ''*.atf'' file you have created (by default with the same name as initial datafile)
* Optionally, check that the artifact correction channels are visible (Artifact/View).
* The figure below shows the result of correction of channels A75-A148 on a three-second interval containing both EKG and eye activity. The blue label “1” marks the onset of a blink found during pattern search. The red “2” shows the onset of R-waves found during pattern search.
* Note that correction is quite good, but it is not perfect. In particular, there is some residual eye activity, e.g. around channels A91, A113, A131. It is intended behaviour since the most important during artifact correction is to not distort brain data.

{|
! '''uncorrected'''
! '''corrected'''
|-
| [[File:EKG_artifacts_in_MEG_data__(4).png|57x57px]][[File:EKG_artifacts_in_MEG_data__(5).png|272x802px]]
| [[File:EKG_artifacts_in_MEG_data__(6).png|273x801px]]
|}

== Averaging the raw data ==
When you press the Average button, a warning dialog will appear:

[[File:EKG_artifacts_in_MEG_data__(7).png|539x124px]]

You can leave artifact correction on during data averaging but it is not recommended.

==== Option “Yes” – turn off artifact correction ====

The averaged data will include EKG and eye artifacts, but these artifacts will not cause epochs to be rejected. The same number of epochs will be included in the average whether or not “Yes” or “No” is chosen. If you disable artifact correction during averaging you can reapply it using the "Artifact/Load" menu entry or loading artifact topographies later during Source Analysis. this approach assures that source analysis will be not affected by artifact correction and allows for full control of data. (i.e. comparing ERP data with artifact correction on and off, redefining the number of topographies used for artifact correction, and so on)

==== Option “No” – leave artifact correction on ====

The averaged data will be corrected. Since this operation cannot be reverted without recreating the average. Each epoch is corrected before being included in the average.

==== Artifact options: which correction model? ====

The result of the correction on the raw data or the averaged data can be slightly different. The effects of correction will also vary, depending on the settings in '''Artifact/Options'''. These differences can be considered as consequences of variations in the “surrogate” or “adaptive” model of brain activity concurrent with the artifact activity (cf. Berg & Scherg 1994). These differences lead to changes in the estimate of the amounts of artifact activity to be removed by correction. If you intend to use the data waveforms outside BESA, and if you don’t use SSP with the artifact coefficients, then the settings in '''Artifact/Options''' become important. In current versions of BESA, these settings are based on EEG amplitude levels.
[[File:EKG_artifacts_in_MEG_data__(8).png|353x231px]]

== Sending the data to Source Analysis ==

When the average is generated, the correction coefficients are saved in the ''*.fsg'' file. Before you send the data to the Source Module, these coefficients must be '''activated'''.

* If you averaged the corrected data, coefficients are already activated. This should be apparent from the red “corrected” displayed above the channel labels.
* If you averaged the uncorrected data, load the saved ''*.atf'' file ('''Artifact/Load…'''), and switch on correction ('''Artifact/Correct''').

Then mark a time range and send the data to Source Analysis. At the right of the status bar, the text '''ART''' indicates that the artifact components are used in SSP.

[[File:EKG_artifacts_in_MEG_data__(9).png|143x158px]]

'''Alternatively, if you averaged the uncorrected data, load the average to Source Analysis, and then load the artifact coefficients as part of the dipole model (load or append solution, and use the dropdown list in the File Open box to select ''*.atf'' instead of ''*.bsa''). This approach has the advantage that the source waveforms of the spatial components show the contribution of eye and EKG activity to the model.'''

This implicit application of artifact topographies during Source Analysis is mathematically equivalent to the “optimizing” correction method (cf. Berg & Scherg 1994)

== Limitations of the correction method in BESA ==

=== Bad channels ===

The ''*.atf'' file contains a two-line header with a) the number of channels, and b) the channel labels. If these do not match with the current data file, artifact correction is not possible. Bad channels are marked (with an asterisk next to the label), and the corresponding coefficient is set to zero. The irritating, but logical, consequence is that if a channel was excluded (defined as “bad”) when the coefficients were generated, it is not possible to make the channel “good” again.

The solution is to regenerate the ''*.atf'' file, making sure the same bad channels are defined in the averaged artifact file as the to-be-corrected raw or average data file. You do not need to regenerate the artifact averages.

EKG correction is difficult because the topographic distribution of EKG signals is close to some MEG distributions: for instance, we sometimes observe a considerable reduction in alpha amplitudes with EKG correction. For event-related averaging, an EKG correction is often unnecessary, because the EKG is not synchronized with the stimulus.

[[Category:Data Import/Export]] [[Category:Preprocessing]] [[Category:Source Analysis]]

Updating the Matlab Interface after Matlab Upgrade

2021-05-05T11:27:43Z

Vibhin:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = BESA Research 5.2 or higher
}}

Sometimes after installation of new/additional Matlab version on one computer the BESA to Matlab interface stops working. The reason is the registry change/corruption caused by the newly installed version. In order to correct this one has to perform the following steps:
# Make sure that in the ''"Path"'' environment variable only the path to one Matlab version exists.
# Make sure that the correct <span style="color:#ff9c00;">Matlab.dll</span> is installed by starting the tool "<span style="color:#ff9c00;">ConfigureBesaMatlabInterface.exe</span>" and selecting the corresponding Matlab version and architecture.
# In the DOS command prompt execute the following command with administrator rights <source lang="dos">matlab -regserver</source> (registers MATLAB as a Component Object Model (COM) server).
# Sometimes if the Matlab license is connected to a specific user account and the user account does not have administrator rights it could be problematic to execute that command. In that case change the corresponding account to an administrator account and then perform the actions again. After that the account could be made to regular user account again. Alternatively, you can also run the attached [ftp://h1772544.stratoserver.net/public/Matlab/BESA_Utilities/UserRegMATLAB.p UserRegMATLAB.p] function to manually register your MATLAB version as a COM Automation Server. To switch the version of MATLAB that is registered, simply run the ''UserRegMATLAB'' command on the new version so that it becomes the new COM Automation Server. Finally for MATLAB 2020a and above you can just type ''comserver('register')'' in the desired MATLAB command line.
[[Category:Setup]]

The Initialization File: BESA.ini

2021-05-05T11:14:45Z

Vibhin:

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

== Introduction ==

'''BESA.ini File'''

BESA Research uses settings provided in the initialization file <span style="color:#ff9c00;">'''BESA.ini'''</span> 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 (<span style="color:#ff9c00;">'''<nowiki>*.ini</nowiki>'''</span>) of Windows. You may change the settings in <span style="color:#ff9c00;">'''BESA.ini'''</span> using <span style="color:#ff9c00;"><span style="color:#00000a;">Notepad.exe</span></span> from the ACCESSORIES group, or other plain text editors to adapt BESA Research to '''your own everyday needs'''. The default settings provided in <span style="color:#ff9c00;">'''BESA.ini'''</span> 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 <span style="color:#ff9c00;">'''BESA.ini'''</span> before you change the default settings.

'''Location of BESA.ini'''

You can place <span style="color:#ff9c00;">'''BESA.ini'''</span> at three possible locations:

# '''Private''': each user on a PC should have his/her own private settings. This is normally in ''Documents/BESA/Research_7_0''
# '''Public''': all users should use one setting, but they can edit <span style="color:#ff9c00;">'''BESA.ini'''</span> to change the settings. This is normally in ''Public Documents/BESA/Research_7_0''
# '''Administrator''': the PC administrator determines the settings. This is normally in ''C:Program Files(x86)/BESA/Research_7_0''

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

<span style="color:#ff0000;">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.</span>

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

{| class="wikitable"
| [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 <span style="color:#3366ff;">'''Tags'''</span> 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
|-
| [Updates]
| Options for program updates
|-
| [Matlab]
| Settings for the MATLAB interface
|-
| [fMRI]
| Settings for the fMRI arfifact removal
|-
| [Montages]
| A setting for a default source montage
|}

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

== Defaults ==

<br>
'''Default settings provided for section [Defaults]:'''

'''DatabaseAllowLocalFiles=Yes''' (If set to "Yes", BESA Research will write filenames "<span style="color:#ff9c00;">'''datafilename.ftg'''</span>" and "<span style="color:#ff9c00;">'''datafilename.fst"'''</span> 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=200''' scale of MEG/GRA channels in [fT or fT/cm]

'''MagScale=1000''' scale of MAG channels in [fT] (''this feature requires BESA Research 7.1 or higher'')

'''SrcScale=100''' scale of source of source montages

'''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. <span style="color:#ff9c00;">'''C:\Program Files\BESA\Research_x\Montages\AdditionalChannels\EKG.sel'''</span>

'''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.

'''ParallelComputing=On''' defines if parallel computing during extensive computation should be used or not (''this feature requires BESA Research 7.1 or higher'')

'''MapSmoothing=0''' set a non-zero value to specify a default map smoothing parameter (normally specified in ''Options/Mapping/Spline Interpolation Smoothing Constant''). Valid values are within the range between 1e-8 and 1e-4. Values outside this range will be set to within the range.

The following optional parameters are not defined as default and can be set manually in<span style="color:#ff9c00;">''' BESA.ini'''</span>:

'''TextEditor="Notepad.exe"''' defines the path to your preferred text editor. This will be used when you press the <span style="color:#3366ff;">'''Edit'''</span> button in 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 <span style="color:#ff9c00;">'''.ini'''</span> 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. 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 (<span style="color:#ff9c00;">'''Besa.set'''</span>, <span style="color:#ff9c00;">'''Besa.cfg'''</span>, 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 <span style="color:#ff9c00;">'''.ini'''</span> 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 Windows system. 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)

'''DataExport=%privateprog%Export''' The path for data to be exported for BESA Connectivity (not listed by default, but can be adjusted by the user)

'''Placeholders'''

The strings enclosed by percent signs (%) are placeholders for the following folders in English-language versions of Windows. Folder names differ depending on Windows version, and for other language settings. BESA Research will substitute the placeholders by the appropriate folder name for the system and the system language:

'''Windows 7, 8.1, and 10 (English):'''

'''%localapp%''' = "''C:\Users\[user]\Documents\BESA\Research_7_0''", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as "''Desktop\[user]\Documents\BESA\Research_7_0''".

'''%publicprog%''' = "''C:\Users\Public\Public Documents\BESA\Research_7_0''".

'''%privateprog%''' = "''C:\Users\[user]\Documents\BESA\Research_7_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_7_0''".

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program Files (x86)\BESA\Research_7_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 <span style="color:#ff9c00;">'''eog-ecg.mtg'''</span> 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<span style="color:#3366ff;">''' Tags'''</span> menu,
* in the <span style="color:#3366ff;">'''TAG push-button'''</span> 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 <span style="color:#3366ff;">'''function keys'''</span> 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 <span style="color:#3366ff;">'''<shift>'''</span> key while pressing the <span style="color:#3366ff;">'''function key'''</span> will always open the dialog. Hold the<span style="color:#3366ff;">''' <ctrl> '''</span>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 <span style="color:#3366ff;">'''<shift> '''</span>key while pressing the <span style="color:#3366ff;">'''function key'''</span> 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 <span style="color:#3366ff;">'''Options'''</span> 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<span style="color:#3366ff;">''' Process '''</span>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 OpenGL).

'''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.

'''UseDoubleBuffering=On'''

Set this to "Off" to disable double buffering mechanism that prevents the screen from flickering while paging through data and dragging window (''this feature requires BESA Research 7.1 or higher'').

Note: '''MapSmoothing''', the default map smoothing parameter, can be specified in the '''[Defaults]''' section.

== 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 "<span style="color:#ff9c00;">'''UpdateVersions.txt'''</span>" (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

== FMRI ==

''(requires Besa Research 7.0 or higher)''

These settings define the default parameters for the fMRI artifact removal in the BESA Research (see [[BESA_Research_Artifact_Correction#fMRI_artifact_removal|fMRI artifact removal]] chapter for further details). For example:

<syntaxhighlight lang="text">
[FMRI]
FMRIRemovalMode=1
TRDelay=200
TRLength=800
NumberOfAverages=21
fMRImoveThreshold=0.15
FMRITRID=8015
ScansToSkip=0
</syntaxhighlight>

These values indicate:

* '''FMRIRemovalMode''': Removal method (0: Turned off; 1: Allen et al, 2000; 2: Allen et al., 2000 Modified; 3: Moosmann et al.,2003)
* '''TRDelay''': Delay between marker and start of volume acquisition [ms]
* '''NumberOfAverages''': Number of artifact occurrence averages
* '''fMRImoveThreshold''': Movement threshold [mm]
* '''FMRITRID''': fMRI Trigger code
* '''ScansToSkip''': Number of scans to skip

== Montage ==

This section allows to specify a source montage that is set the first time when the source montage button is pressed. For example,

<syntaxhighlight lang="text">
[Montage]
Source=FR_Frontal Region
</syntaxhighlight>

specifies that when the ''Src'' button in the control ribbon is pressed for the first time, the source montage "FR_Frontal Region" will be selected. If <span style="color:#ff9c00;">'''BESA.ini'''</span> does not specify a montage, pressing the ''Src'' button opens the drop-down menu offering all the available source montages for the current file.

== Reader-Specific Settings ==

<br>
=== 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 <span style="color:#ff9c00;">'''BESA.ini'''</span> 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>

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 <span style="color:#ff9c00;">'''.ini'''</span> 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 <span style="color:#3366ff;">'''ctrl-L'''</span> 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}}

Review

2021-05-05T11:07:01Z

Vibhin:

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



== 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

<span style="color:#ff0000;">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.</span>

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:Screen_layout_klein.png]]

''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 <span style="color:#3366ff;">'''Menus'''</span> 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:control_ribbon_shrunk.png]]</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. <span style="color:#3366ff;">'''Scp, Pgr'''</span> 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 <span style="color:#3366ff;">'''Auto'''</span> 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".''

== <span style="color:#00000a;">Using the Mouse</span> ==

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 (<span style="color:#ff9c00;">'''EEG2.eeg'''</span>), 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: '''

*'''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''”.

*'''Left mouse click:''' Remove cursor and maps or images, if displayed.

*'''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.

*'''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.

*'''Right mouse drag:''' Measure peaks and frequency of marked channels segment (cf. figure below).

'''Event bar: '''

*'''Left mouse click:''' Jump to events.

*'''Right mouse click:''' Display information about events.

'''Control buttons: '''

*'''Left mouse click:''' Use button.

*'''Right mouse click:''' Display information on use of button.

[[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|700px]]

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 <span style="color:#3366ff;">'''<Space>'''</span> bar on the keyboard to start paging. Automatic paging may be stopped by clicking the Auto button again, or by pressing the <span style="color:#3366ff;">'''<Space>'''</span> bar or any key on the keyboard. You can speed up or slow down automatic paging using the menu <span style="color:#3366ff;">'''Options / Paging / Timing of Auto-Page Mode'''</span>''. ''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)_01.png|700px]]


These controls are described in more detail in online help chapter "''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 <span style="color:#3366ff;">'''<Space>'''</span> bar (left hand). Stop paging by pressing the <span style="color:#3366ff;">'''<Space>'''</span> bar again and press the <span style="color:#3366ff;">''''B' '''</span>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 <span style="color:#3366ff;">''''B''''</span> key. Move forward by a half page with the <span style="color:#3366ff;">''''N' '''</span>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 '''

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 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.

You can also use the
<span title="Outside the average buffer view, the numeric keys can be used to define tags if a cursor is set: 1-5: Set a tag of type 1-5. 6: Set a comment. 7: Set artifact epoch. 8: Set named epoch. ">'''<u>keyboard shortcuts</u>'''</span>
to set any event.

<div><ul>
<li style="display: inline-block;"> [[File:Review (1).gif|thumb|180px|Popup menu after right click somewhere in the EEG.]] </li>
<li style="display: inline-block;"> [[File:Review (2).gif|thumb|250px|Popup menu after right click when a block is marked]] </li>
</ul></div>

'''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 <span style="color:#3366ff;">'''Goto'''</span> 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 <span style="color:#3366ff;">'''Rec, Vir, Src or Usr'''</span>, which provide a shortcut to the <span style="color:#3366ff;">'''Recorded</span>,''' <span style="color:#3366ff;">'''Virtual, Source '''</span>and <span style="color:#3366ff;">'''User-Defined</span> '''submenus of the <span style="color:#3366ff;">'''Montage'''</span> menu. The push buttons''''' ''<span style="color:#3366ff;">Opt'''</span> and <span style="color:#3366ff;">'''EdM '''</span>allow for setting montage options and editing of user-defined and additional montages.

[[Image:Review (7).png]]

The following standardized montages are provided in BESA Research and can be selected using the <span style="color:#3366ff;">'''Montage'''</span>'' ''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)'''.

'''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 <span style="color:#3366ff;">'''Opt</span>'' '''''push button, which provides a shortcut to the <span style="color:#3366ff;">'''Montage / Options'''</span>'' ''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 <span style="color:#3366ff;">'''Rec, Vir, Src, Usr'''</span> at the top of the main window below the menus. Clicking on the <span style="color:#3366ff;">'''Rec'''</span>'' (''<span style="color:#3366ff;">'''Vir, Src, Usr'''</span>'')'' 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 <span style="color:#3366ff;">'''Montage / User-Defined'''</span> menu. User-defined montage files located elsewhere can be loaded in the Montage Editor. After loading they are available from the <span style="color:#3366ff;">'''Usr '''</span>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''"<span style="color:#ff0000;">.</span>

=== Recorded montages ===

Press the push button''''' ''<span style="color:#3366ff;">Rec'''</span> 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''''' ''<span style="color:#3366ff;">EdM</span>'' '''''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 (<span style="color:#3366ff;">'''Scp</span>'' '''''<nowiki>= scalp EEG, </nowiki><span style="color:#3366ff;">'''Pgr</span>'' '''''<nowiki>= polygraphic, </nowiki><span style="color:#3366ff;">'''Icr</span>'' '''''<nowiki>= intracranial, </nowiki><span style="color:#3366ff;">'''MEG</span>'' '''''<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 ===

Press the push button <span style="color:#3366ff;">'''Vir '''</span>twice or use the menu <span style="color:#3366ff;">'''Montage/Virtual'''</span> 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 <span style="color:#3366ff;">'''EdM'''</span>'' ''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 [[BESA_Research_Montage_Editor#Virtual_Standard_Montages|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 <span style="color:#3366ff;">'''Src'''</span> twice or use the menu <span style="color:#3366ff;">'''Montage/Source '''</span>to select a pre-defined source montage. These source montages are available for EEG or MEG, except for the Evoked Potentials montages (EEG only).

[[Image:Source_montages.png]]

'''25r and 25s''' ''(requires BESA Research 7.1 or higher)''

<div style="margin-left:1.55cm;margin-right:0cm;">The 25r and 25s source montages are based on sources below the standard 25 electrodes of the IFCN (International Federation of Clinical Neurophysiology). The sequence of channels is a reasonable compromise between transversal and longitudinal arrangements while an optimal separation of the major regions, i.e. frontal, central, temporal and parietal-occipital, has been achieved. At the same time, easy hemispheric comparison has been enabled.

Source montage 25s depicts only the 25 inward radial activities of each region except for the temporal regions below F9/F10 and T9/T10, for which the first orientation of each underlying source was chosen to match the inward net orientations of the temporal polar and basal sublobar surfaces, respectively.

Source montage 25r depicts the activity of each regional source after rotating the first dipole to the maximum of activity over the whole 3 displayed source trace.</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 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.</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 brain region bilaterally in the first 6 dipole traces. Head schemes illustrate location and orientation of each virtual electrode. The other 13 regional sources separate 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 brain region bilaterally in the first 6 dipole traces. Head schemes illustrate location and orientation of each virtual electrode. The other 13 regional sources separate 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 brain region bilaterally in the first 6 dipole traces. Head schemes illustrate location and orientation of each virtual electrode. The other 13 regional sources separate 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 lobe bilaterally and largely separates them from the radial activities in the other 11 brain regions. 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. Head schemes illustrate location and orientation of each virtual electrode. The montage TA_Temporal Lobe is equivalent to the montage T-A in previous versions of BESA Research. However, the use of the TR_Temporal Region source montage is more recommended because it provides a better separation of the 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 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.</div>

'''25_regional''' ''(requires BESA Research 7.1 or higher)''

<div style="margin-left:1.55cm;margin-right:0cm;">Source montages located in subfolder 25_regional are the sub selection of the 25r montage where source are limited only to fronto-central areas (25F), parieto-occipital areas (25P) and temporal areas (25T). In addition, the regional sources were converted to single dipoles (so for every regional source in 25r there are 3 corresponding sources – i.e. Fp1r, Fp1v and Fp1h in 25F correspond to Fp1 in 25r montage).</div>

'''Atlas Montages''' ''(requires BESA Research 7.1 or higher)''

<div style="margin-left:1.55cm;margin-right:0cm;">Atlas-based montages are available for any dataset (with number of channels higher than 12).</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>

'''Resting State Montages'''

<div style="margin-left:1.55cm;margin-right:0cm;">Source montages have been provided which cover the relevant brain regions involved during resting state.</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 <span style="color:#3366ff;">'''EdM'''</span>'' ''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 [[BESA_Research_Montage_Editor#Standard_Source_Montages|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.

[[Image:Review (6).gif|600px]]

''Left: Horizontal bipolar montage of the file <span style="color:#ff9c00;">eeg2.eeg</span>; Right: TR_Temporal Lobe source montage of the same data segment.''

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 <span style="color:#3366ff;">'''Usr</span>'' '''''twice or use the menu <span style="color:#3366ff;">'''Montage/User-Defined'''</span>'' ''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<span style="color:#3366ff;">''' Montage/User-Defined '''</span>popup menu. General user montages (stored in <span style="color:#3366ff;">'''Montages\UserMontages'''</span>) 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: <span style="color:#ff9c00;">'''AB_Full Name.mtg'''</span>. 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 ===

Press the push button<span style="color:#3366ff;">''' Add '''</span>at upper right of the review window or use the menu ''Montage/Additional Channels ''to select an additional channel montage.

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

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 drop-down 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 <span style="color:#ff9c00;">'''BESA.ini'''</span> (entry AdditionalChannelFile in the section [Defaults]). The additional channels will be displayed automatically if they are available, if the entry AdditionalChannelStatus in <span style="color:#ff9c00;">'''BESA.ini'''</span> 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<span style="color:#3366ff;">''' Add'''</span> button in the upper right corner of the main window or by a right mouse click on the label of an additional channel.

=== Options ===

Press the push button <span style="color:#3366ff;">'''Opt'''</span> twice or use the menu <span style="color:#3366ff;">'''Montage / Options'''</span> to

* 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

[[Image:Review (8).gif]]

'''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'' ''<span style="color:#3366ff;">'''Montage / Options'''</span>'' ''to set the montage order.

If ''Midline Channels'' is On in <span style="color:#3366ff;">'''Montage / Options'''</span>, 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. Using the slider in the dialog, also longer epochs up to 1 hour are possible (depending on sampling rate).

'''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 (<span style="color:#3366ff;">'''Scp'''</span> = scalp, <span style="color:#3366ff;">'''Icr'''</span><nowiki> = intracranial,</nowiki> <span style="color:#3366ff;">'''Pgr'''</span> = polygraphic, <span style="color:#3366ff;">'''MEG'''</span>). 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, 31/31). 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. The "+" and "-" signs indicate waveforms display polarity that can be changed using the ''View'' setting: ''Show Negativity Up''. Note that by default this setting is enabled and if it is disabled the signs are displayed in red color.
To change, for example, the scaling of the EEG channels to 100 µV, click on the lower button of the '<span style="color:#3366ff;">'''Scp'''</span>' 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 <span style="color:#00000a;">''"Review / Reference / Controls / Timing, Scaling, and Channel Selection".''</span>

== <span style="color:#00000a;">Filtering</span> ==

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 (<span style="color:#ff9c00;">'''BESA.ini'''</span>) 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 <span style="color:#3366ff;">'''LF</span> '''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''' <span style="color:#3366ff;">HF</span> '''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''' <span style="color:#3366ff;">NF '''</span>button. Click the button to choose between 50 Hz or 60 Hz suppression.

'''Edit Filters Button'''

The<span style="color:#3366ff;">''' EdF'''</span> button starts the dialog box to edit the variable filter settings and to select special band pass and notch filter settings.

In the <span style="color:#3366ff;">'''Filter '''</span>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 <span style="color:#00000a;">''"</span><span style="color:#00000a;">Review / Reference / Menus / Filters".''</span>

== 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|350px]]

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 ==

[[Image:Review (14).gif|thumb|left]]

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 <span style="color:#3366ff;">'''Process / Nonlinear Regression'''</span>, the non-linear regression is calculated for the marked block.

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 <span style="color:#3366ff;">'''Edit / Default Block Epoch'''</span>. To compute '''non-linear''' correlation, use the menu <span style="color:#3366ff;">'''Process / Nonlinear Correlation'''</span>. The computation of non-linear regression may be slow if the marked epoch is long. You may type''' any''' '''key''' to stop computing.

Press <span style="color:#3366ff;">'''<Space>'''</span> to remove the block marking or the cursor. Press <span style="color:#3366ff;">'''<Space>'''</span> 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 <span style="color:#3366ff;">'''Search/Options '''</span>(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 <span style="color:#3366ff;">'''Ctrl'''</span>-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 <span style="color:#3366ff;">'''Search '''</span>menu,

* define the '''Buffer''' number either in the <span style="color:#3366ff;">'''Tags'''</span> menu, or more simply by typing the buffer

* set the toggle items in the<span style="color:#3366ff;">''' Search'''</span> menu (query search, artifact rejection), and the range in the data file which is searched

* for '''Pattern Search''' set correlation threshold in <span style="color:#3366ff;">'''Search / Options'''</span> 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 <span style="color:#3366ff;">'''Edit'''</span> menu) to define the length of the average buffer.

The search and/or average starts when a range is selected in the<span style="color:#3366ff;">''' Search'''</span> menu, or

the button<span style="color:#3366ff;">''' SAW'''</span> ('''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 <span style="color:#3366ff;">'''File / Open'''</span>. 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 <span style="color:#3366ff;">'''Shift'''</span> or the <span style="color:#3366ff;">'''Ctrl'''</span> 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 <span style="color:#3366ff;">'''File '''</span>Menu or the <span style="color:#3366ff;">'''F+'''</span> and <span style="color:#3366ff;">'''-F'''</span> 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 <span style="color:#3366ff;">'''File/Recent Files'''</span>...) can be used to open recent files. Note also that the files from the previous session can be opened using <span style="color:#3366ff;">'''File/Recent'''</span><span style="color:#3366ff;"><span style="color:#00000a;"> </span></span><span style="color:#3366ff;">'''Files.../Open All Files'''</span> from Previous Session. A keyboard short-cut for this operation is to hold down the <span style="color:#3366ff;">'''Ctrl'''</span> key and press the <span style="color:#3366ff;">'''-F'''</span> button.

When BESA Research is started, and no data files have been opened, pressing <span style="color:#3366ff;">'''-F'''</span> will open the most recent file. If only one file is open, pressing the button again will open the second most recent file.

<span style="color:#ff0000;">'''Data Readers'''</span>

<span style="color:#ff0000;">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.</span>

== 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 <span style="color:#3366ff;">'''Edit / Channel'''</span>

<span style="color:#3366ff;">'''Configuration / Advanced'''</span>. 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:

* <span style="color:#3366ff;">'''Edit / Channel Configuration '''</span>: 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

* <span style="color:#3366ff;">'''File / Load Channel Configuration'''</span>: Loads a file containing a predefined configuration.

* <span style="color:#3366ff;">'''File / Head Surface Points and Sensors / Load Coordinate Files (CTRL-L)'''</span>: 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 <span style="color:#3366ff;">'''Edit / Channel Configuration'''</span> menu. It is strongly recommended that you read the '''[[Electrodes_and_Surface_Locations#Electrodes|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]]

{{BESAManualNav}}

Analyzing Electrocorticography Data

2021-05-05T10:59:42Z

Vibhin:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = BESA Research 5.2 or higher
}}

There is increasing interest in using ECoG data in a quantitative manner. BESA Research offers a variety of tools for the processing of intracranial channels, which can prove extremely useful when analysing these data.
Intracranial channels are assigned to a specific channel group (either PGR – polygraphic, or ICR – intracranial). It is then possible to perform the following types of analysis (and more).

*'''Pattern search.''' This can be very useful in order to identify similar events that happen either in one or in several channels. Simply select one or several channel labels using the CTRL key and the mouse button, mark a block over a pattern of interest, and press the “SAW” button (or “SAV” button if your are using the BESA Research options for EEG review) to start the pattern search. At the end of the search, you will have all similar events marked by tags, which can be converted to triggers, too, if further event-related processing is to take place.

*'''Trigger generation.''' Another way of finding and tagging similar events is the Schmitt trigger dialog which is reached from “ERP | Create triggers from EMG/EEG”. You are best to mark an event of interest first. Then open the dialog, select the channel of interest from the dropdown, and play around with additional filter settings, viewing the results with the “View Current Settings” button until the channel signal rises over a threshold (you can manually adjust the threshold in the viewing window). Pressing the “Search Selected” button in the dialog will find all events with similar spiking and tag them with a trigger code for further analysis like averaging, or time-frequency analysis.

*'''FFT analysis.''' FFT analysis can be performed on all types of channel data, and ECoG is no exception. It can give you great insights into the frequencies at play in your intracranial recording. Simply mark a block over the interval of interest, and press the “F” button to invoke FFT. Note that frequency bands can be freely adjusted in the FFT result window.
[[File:ScreenShot_ICR_FFT.png|600px|thumb|c|none|FFT analysis of intracranial EEG data]]

*'''Time-frequency analysis.''' This feature requires a source coherence module. It is quite straight forward once you have created some triggers marking your events as mentioned above. You should create a montage that contains just the intracranial channels you are interested in (using the Montage Editor). Then, open the ERP paradigm editor to define trigger values to average over, epochs, and filters, and use the Coherence tab to perform the analysis.
[[File:ScreenShot_ICR_TF2.jpg|600px|thumb|c|none|Time-frequency analysis of intracranial EEG data]]

[[Category:ERP/ERF]]
[[Category:Epilepsy]]

Advanced Top Viewer Features

2021-05-05T10:38:51Z

Vibhin:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = BESA Research 5.2 or higher
}}

=== Introduction ===
The BESA Top Viewer, which is part of the BESA Research Basic package, offers many interesting features to view and analyze your ERP data. Let us just point out some of the lesser known features here:

=== Window background colour ===
Change the background color for using Top Viewer in illustrations by selecting “View | Preferences” from the menu. In the dialog box that appears, use the dropdown list in section “Colors” to select “Background” and then press the “Choose Color” button in that section. You can save the Top Viewer display as bitmap or eps file from the File menu.

[[File:TopView_Preferences.png|none]]

=== Channel overplot ===
Show an overplot of all channels by using the “View → Show Overplot Window” menu entry. You can select which channels will be plotted in “View → Select Overplot Channels”.

[[File:TopView_Overplot.png|750px]]

=== Condition overplot ===
Show an overplot of several conditions by simply clicking on the condition label on the top left and holding down CTRL or SHIFT keys to select several conditions. The last condition clicked (bold print) is the relevant one for amplitude displays and mapping.

[[File:TopView_Overplotcnds.png|750px]]

=== Additional channel plot ===
Show polygraphic, myographic, or virtual channels beside the Top Viewer montage display by using the Additional Channels option (see example screen shot below from a recording with additional FDI channels):
* In “Montage → Additional Channels”, select the set of additional channels from the list that appears.
* Should your channel set not appear, then go back to the Montage Editor and create an Additional Channels montage by pressing the ‘N’ key to create a new ''Edit Montage'', dragging your channels over to the channel list, and saving it as a user montage (select Montage type “Additional Channel montage” in the Save dialog box). Then your channel set will be available in the Top Viewer.

[[File:Top_Viewer.jpg|750px]]

[[Category:ERP/ERF]]

Artifact correction with intracranial channels

2021-02-02T11:54:13Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels

• Create an *.sfp file with hypothetical coordinates for the EEG channels

• Load these files into BESA using the channel and digitized head surface point dialog

• Perform an ICA over a screen that shows the artifact

• Export the file without the ICA artifact components

• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger

• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

[[File:2_vv1.jpg]]

Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

[[File:3_vv.jpg]]

Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

[[File:4_vv.jpg]]

Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

[[File:5_vv.jpg]]

Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

[[File:6_vv.jpg]]

Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

[[File:7_vv.jpg]]

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

[[File:8_vv.jpg]]
[[File:9_vv.jpg]]

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

[[Category:Research Manual]]
[[Category:Methods]]
[[Category:Mathematical]]

{{BESAManualNav}}

File:9 vv.jpg

2021-02-02T11:51:15Z

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File:8 vv.jpg

2021-02-02T11:50:30Z

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File:6 vv.jpg

2021-02-02T11:50:00Z

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File:5 vv.jpg

2021-02-02T11:49:18Z

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File:2 vv1.jpg

2021-02-02T11:48:30Z

Vibhin:

Artifact correction with intracranial channels

2021-02-02T11:41:40Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

[[File:2_vv1.jpg]]

Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

[[File:3_vv.jpg]]

Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

[[File:4_vv.jpg]]

Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

[[File:5_vv.jpg]]

Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

[[File:6_vv.jpg]]

Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

[[File:7_vv.jpg]]

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

[[File:8_vv.jpg]]
[[File:9_vv.jpg]]

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

[[Category:Research Manual]]
[[Category:Methods]]
[[Category:Mathematical]]

{{BESAManualNav}}

File:4 vv.jpg

2021-02-02T11:40:50Z

Vibhin: Vibhin uploaded a new version of "File:4 vv.jpg"

File:4 vv.jpg

2021-02-02T11:36:35Z

Vibhin: Vibhin uploaded a new version of "File:4 vv.jpg"

Artifact correction with intracranial channels

2021-02-02T11:34:16Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

[[File:2_vv1.jpg]]

Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

[[File:3_vv.jpg]]

Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

[[File:4_vv1.jpg]]

Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

[[File:5_vv.jpg]]

Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

[[File:6_vv.jpg]]

Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

[[File:7_vv.jpg]]

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

[[File:8_vv.jpg]]
[[File:9_vv.jpg]]

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

[[Category:Research Manual]]
[[Category:Methods]]
[[Category:Mathematical]]

{{BESAManualNav}}

Artifact correction with intracranial channels

2021-02-02T11:32:03Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

[[File:2_vv.jpg]]

Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

[[File:3_vv.jpg]]

Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

[[File:4_vv1.jpg]]

Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

[[File:5_vv.jpg]]

Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

[[File:6_vv.jpg]]

Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

[[File:7_vv.jpg]]

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

[[File:8_vv.jpg]]
[[File:9_vv.jpg]]

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

[[Category:Research Manual]]
[[Category:Methods]]
[[Category:Mathematical]]

{{BESAManualNav}}

Artifact correction with intracranial channels

2021-02-02T11:22:31Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

[[File:2_vv.jpg]]

Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

[[File:3_vv.jpg]]

Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

[[File:4_vv.jpg]]

Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

[[File:5_vv.jpg]]

Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

[[File:6_vv.jpg]]

Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

[[File:7_vv.jpg]]

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

[[File:8_vv.jpg]]
[[File:9_vv.jpg]]

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

[[Category:Research Manual]]
[[Category:Methods]]
[[Category:Mathematical]]

{{BESAManualNav}}

Artifact correction with intracranial channels

2021-02-02T11:17:34Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

[[File:2.jpg]]

Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

[[File:3.jpg]]

Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

[[File:4.jpg]]

Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

[[File:5.jpg]]

Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

[[File:6.jpg]]

Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

[[File:7.jpg]]

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

[[File:8.jpg]]
[[File:9.jpg]]

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

File:9 vv.jpg

2021-02-02T11:13:33Z

Vibhin:

File:8 vv.jpg

2021-02-02T11:13:12Z

Vibhin:

File:7 vv.jpg

2021-02-02T11:12:56Z

Vibhin:

File:6 vv.jpg

2021-02-02T11:12:38Z

Vibhin:

File:5 vv.jpg

2021-02-02T11:12:21Z

Vibhin:

File:4 vv.jpg

2021-02-02T11:12:06Z

Vibhin:

File:3 vv.jpg

2021-02-02T11:11:52Z

Vibhin:

File:2.jpg

2021-02-02T11:10:13Z

Vibhin:

Artifact correction with intracranial channels

2021-02-02T11:08:53Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

2.1. Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

2.2. Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

2.3. Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

2.4. Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

2.5. Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

2.6. Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

2.7. Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

Artifact correction with intracranial channels

2021-02-02T11:07:38Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

2.1. Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

2.2. Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

[[File:2.jpg]]

2.3. Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

2.4. Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

2.5. Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

2.6. Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

2.7. Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

Artifact correction with intracranial channels

2021-02-02T11:06:24Z

Vibhin:

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

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

2.1. Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.jpg]]

2.2. Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

2.3. Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

2.4. Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

2.5. Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

2.6. Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

2.7. Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

Artifact correction with intracranial channels

2021-02-02T11:04:48Z

Vibhin:

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

2.1. Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:Example.jpg]]

2.2. Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

2.3. Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

2.4. Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

2.5. Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

2.6. Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

2.7. Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

Artifact correction with intracranial channels

2021-02-02T11:00:10Z

Vibhin:

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

2.1. Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

[[File:1.png]]

2.2. Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

2.3. Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

2.4. Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

2.5. Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

2.6. Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

2.7. Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.

File:1.jpg

2021-02-02T10:57:43Z

Vibhin:

Artifact correction with intracranial channels

2021-02-02T10:55:50Z

Vibhin: Created page with " == Introduction to artifacts correction with intracranial channels == Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected..."

== Introduction to artifacts correction with intracranial channels ==

Intracranial channels may contain artifacts, e.g. if a stimulation is applied. These can be corrected using ICA. However, ICA is only available for scalp channels. Thus, for the purpose of artifact correction, it is necessary to re-label these channels as scalp channels.

• Create an *.ela file that lists the channel labels as EEG channels
• Create an *.sfp file with hypothetical coordinates for the EEG channels
• Load these files into BESA using the channel and digitized head surface point dialog
• Perform an ICA over a screen that shows the artifact
• Export the file without the ICA artifact components
• Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
• Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data

Caution: Any operation that requires coordinates (like mapping, source analysis, virtual channel montaging, source montaging, PCA-based artifact correction that models brain activity) is discouraged, as coordinates are wrong, and as the underlying assumption that the channels are on the scalp is invalid!

== Step-by-step explanation ==

2.1. Create an *.ela file that lists the channel labels as EEG channels
Simply list the channel labels that should be used in the analysis in a text file like in the example below.

2.2. Create an *.sfp file with hypothetical coordinates for the EEG channels
For the channels in the *.ela file, provide fictitious coordinates. It is probably best to vary coordinates somewhat.
The first 3 lines need to contain fiducials – then the channels are listed.

2.3. Load these files into BESA using the channel and digitized head surface point dialog
After opening the file, use CTRL-L to specify these files as shown in the example below.

2.4. Perform an ICA over a screen that shows the artifact
The ICA will disentangle the components and show the artifact. Please note that the screen needs to contain one or more artifacts – adjust time scaling and position accordingly.

2.5. Export the file without the ICA artifact components
Mark the ICA components which carry the artifact by clicking on the labels (hold down the CTRL key if more than one), and right-click to select the export option for the whole file as shown below.

2.6. Optional: Use the stimulus component to create tags via pattern search, and export the tags for later use as averaging trigger
This step is optional and makes sense if you want to use the stimulus artifact as a trigger event for averaging or time-frequency analysis. Mark the pattern of interest, select the ICA component where it shows the clearest signal, and press “SAW” to find this pattern in the file, and tag with the “Pattern 1” tag.

Then export the event file that contains this tag with the menu “ERP->Save Events As”.

2.7. Load the exported file, and (optionally) import the tags, average over the tags, and analyse the averaged data
To import the tags, use the menu “ERP->Open Event File”.

To average over the events, select “Tags->Pattern 1”, “Search->Tagged Events”, and press “SAW”. You may want to adjust the default block epoch in “Edit->Default Block Epoch” before starting the average in order to adjust the width of the average buffer. The example below shows an average buffer of 2 seconds before and after the stimulus.

Note that it is also possible to perform time-frequency analysis on these data. To do this, you will need to convert the tags into triggers first using ERP->Edit Triggers. Then use the ERP->Coherence to define the condition and run time-frequency analysis.