Working With Additional Files - Revision history

Vibhin at 11:40, 5 May 2021

2021-05-05T11:40:20Z

Jaehyun: /* Channel definition file conventions and formats */

2018-05-04T11:10:36Z

‎Channel definition file conventions and formats

Jaehyun: /* cot (Head center) file */

2017-07-19T09:25:26Z

‎cot (Head center) file

Jaehyun: /* Channel definition file conventions and formats */

2017-07-19T09:23:31Z

‎Channel definition file conventions and formats

Jaehyun: /* Generic File Format */

2017-07-19T08:48:58Z

‎Generic File Format

Show changes

Jaehyun: /* sfn (surface point name) file */

2017-07-19T07:40:04Z

‎sfn (surface point name) file

Jaehyun: /* pos or pmg (MEG sensor coordinate) file */

2017-07-19T07:37:50Z

‎pos or pmg (MEG sensor coordinate) file

Jaehyun: /* ASCII Multiplexed format (.mul) /

2017-07-19T07:29:52Z

‎ASCII Multiplexed format (*.mul)

Jaehyun: /* ASCII vectorized format (.avr) /

2017-07-19T07:24:37Z

‎ASCII vectorized format (*.avr)

Jaehyun at 09:13, 11 July 2017

2017-07-11T09:13:03Z

@@ Line 2: / Line 2: @@
 |title = Module information
 |module = BESA Research Basic or higher
-|version = 6.1 or higher
+|version = BESA Research 6.1 or higher
 }}

@@ Line 121: / Line 121: @@
 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:
@@ Line 132: / Line 131: @@
 * MEG - MEG sensor
 * REF - reference electrode (this can only occur once, and must be the last item in the file)
 For example:
-Fz&nbsp;&nbsp;&nbsp;('''scalp''' electrode, coordinates assigned by default.ecd)
+Cz   ('''scalp '''electrode, coordinates assigned by default.ecd)
-−
-Cz&nbsp;&nbsp;&nbsp;('''scalp '''electrode, coordinates assigned by default.ecd)
 ......
-VEOG&nbsp;&nbsp;&nbsp;(vertical EOG,''' Polygraphic''' type is assigned by default)
+VEOG   (vertical EOG,''' Polygraphic''' type is assigned by default)
-Exx&nbsp;&nbsp;&nbsp;(xx=01, 02.. electrode number, '''Polygraphic '''type is assigned by default)
+Exx   (xx=01, 02.. electrode number, '''Polygraphic '''type is assigned by default)
 ......
@@ Line 153: / Line 151: @@
 ......
-POL XX&nbsp;&nbsp;(identifier sets '''Polygraphic'''&nbsp;type -- an alternative to the "POL" prefix is "PGR")
+POL XX  (identifier sets '''Polygraphic''' type -- an alternative to the "POL" prefix is "PGR")
 ......
-ICR&nbsp;A01&nbsp;&nbsp;(identifier sets '''Intracranial''' type to electrode A01 - do not use A1!)
+ICR A01  (identifier sets '''Intracranial''' type to electrode A01 - do not use A1!)
-ICR&nbsp;A02&nbsp;&nbsp;(identifier sets''' Intracranial''' type to electrode A02 - do not use A2!)
+ICR A02  (identifier sets''' Intracranial''' type to electrode A02 - do not use A2!)
-ICR&nbsp;A03&nbsp;&nbsp;(identifier sets''' Intracranial''' type to electrode A03)
+ICR A03  (identifier sets''' Intracranial''' type to electrode A03)
 ......
-MEG&nbsp;M01&nbsp;&nbsp;(identifier sets '''MEG '''type to electrode M01 - do not use M1!)
+MEG M01  (identifier sets '''MEG '''type to electrode M01 - do not use M1!)
-MEG&nbsp;M02&nbsp;&nbsp;(identifier sets '''MEG''' type to electrode M02 - do not use M2!)
+MEG M02  (identifier sets '''MEG''' type to electrode M02 - do not use M2!)
 ......
-REF Cz&nbsp;&nbsp;(the label is assigned to the electrode reference, no channel is associated with this entry. This must be the last line of the file!)
+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!)
@@ Line 178: / Line 177: @@
 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;">'''<nowiki>*.ela</nowiki>'''</span>) file.
+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 ==

@@ Line 190: / Line 190: @@
 '''Units:''' must be in meters!
-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.
+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.
-The ''cot ''file has also been extended for reading CTF MEG files. Documentation for these extensions is found in the CTF help file.)
+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.
 == pos or pmg (MEG sensor coordinate) file ==

@@ Line 99: / Line 99: @@
 BESA Research can read 3 types of file to define channels. These are identified by different extensions:
-* channel definition files containing labels and, optionally, channel types (ASCII, 1 label /line): <span style="color:#ff9c00;">'''<nowiki>*.ela</nowiki>'''</span>
+* <span style="color:#ff9c00;">'''<tt>*.ela</tt>'''</span>: channel definition files containing labels and, optionally, channel types (ASCII, 1 label / line)
-* channel definition files containing coordinates and, optionally, channel types and labels (ASCII): <span style="color:#ff9c00;">'''<nowiki>*.elp.</nowiki>'''</span> This is the format of the file written by the ''Channel Configuration Dialog.''
+* <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.''
-* channel definition files stored by older versions of BESA Research (binary format): <span style="color:#ff9c00;">'''<nowiki>*.elb.</nowiki>'''</span> This format can still be read, but is no longer written by BESA Research.
+* <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.
@@ Line 107: / Line 107: @@
 # 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 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>)
@@ Line 118: / Line 118: @@
-'''Channel Label Files (*.ela)'''
+'''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
+* EEG - scalp electrode
-POL -- polygraphic channel
+For example:
 Fz&nbsp;&nbsp;&nbsp;('''scalp''' electrode, coordinates assigned by default.ecd)
@@ Line 178: / Line 174: @@
-'''Channel spherical coordinate files (*.elp)'''
+'''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. Fz' instead of Fz.
+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;">'''<nowiki>*.ela</nowiki>'''</span>) file.
 == cot (Head center) file ==

@@ Line 245: / Line 245: @@
 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.
+The ''sfn'' file need not exist if labels are defined in the ''sfp'' file.
-See chapter “''3D Coordinates for Precise Analysis / Data reading rules for EEG”.''
+See chapter ''[[Electrodes_and_Surface_Locations#Data_reading_rules_for_EEG|Data reading rules for EEG]]''.
-−
 == sfp (surface point coordinate) file ==

@@ Line 204: / Line 204: @@
 == 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;">'''<nowiki>*.pmg</nowiki>'''</span>, and gradiometer information in <span style="color:#ff9c00;">'''<nowiki>*.pos</nowiki>'''</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.
+'''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: label (optional), six coordinates per line (location, orientation)
 e.g. for BTi:
-" Channel 'A1': -0.0019193 0.0304846 0.1081738 0.1188222 0.2394208 0.9636177"
+<source lang="dos">
 Gradiometers: label (optional), nine coordinates per line (location of primary sensor, location of secondary sensor, orientation). The program decides whether gradiometers are planar or axial based on the distance between the primary and secondary sensor locations and the center of the head.
 e.g. for Neuromag:
-" 0.108510 -0.000143 -0.044954 0.108510 0.000463 -0.028766 0.999999 0.001450 0.000000 "
+<source lang="dos">
 Labels in these files are ignored.
-See chapter “''3D Coordinates for Precise Analysis/Data reading rules for MEG''”.
+See chapter ''[[Electrodes_and_Surface_Locations#Data_reading_rules_for_MEG|Data reading rules for MEG]]''.
-−
 == sfn (surface point name) file ==

@@ Line 50: / Line 50: @@
 == ASCII Multiplexed format (*.mul) ==
-Select '''ASCII Multiplexed Format''' to output segments one time point (all channels) per line. &nbsp;
+Select '''ASCII Multiplexed Format''' to output segments one time point (all channels) per line.
 The '''ASCII Multiplexed Format '''is as follows:
 The first of two header lines contains similar information to that of the ASCII vectorized file:
-''TimePoints= 200 Channels= 27 BeginSweep[ms]= -500.00 SamplingInterval[ms]= 5.000 Bins/uV= 1.000 SegmentName=Condition1''
+Note that the item '''<tt>SegmentName</tt>''' is missing if no segment comment is specified when writing a segment to file.
-Note that the item 'SegmentName' is missing if no segment comment is specified when writing a segment to file.
+If an epoch of a continuous EEG is exported in ASCII multiplexed format, the first header line contains the additional item '''<tt>Time</tt>''', which indicates the daytime of the first sample in the exported segment:
-If an epoch of a continuous EEG is exported in ASCII multiplexed format, the first header line contains the additional item 'Time', which indicates the daytime of the first sample in the exported segment:
+<source lang="dos">
 The second line of the header contains labels for each channel, which may be either the original channel names, or the names of the channels of the current montage, e.g.
-''O1 Oz P3 T5 T3 C3 F7 F3 Fp1 Fz Cz Pz Fp2 F4 F8 C4 T4 T6 P4 Fpz O2 M2 M1 F10 F9 T10 T9''
+<source lang="dos">
 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.

@@ Line 23: / Line 23: @@
 The first of two header lines contains the following data descriptors (6 descriptors, the values shown are only examples):
+{|
-''Npts= 200''&nbsp;number of sampled points in each channel
+| width="30%" |''Npts= 200'' || number of sampled points in each channel
+|-
-''TSB= -500''&nbsp;time sweep begin [ms]. Time of first data point relative to zero of epoch
+| ''TSB= -500'' || time sweep begin [ms]. Time of first data point relative to zero of epoch
+|-
-''DI= 5''&nbsp;digitization or sampling interval [ms]
+| ''DI= 5'' || digitization or sampling interval [ms]
+|-
-''SB= 2''&nbsp;scaling bins/microvolt in file = number corresponding to 1 microvolt
+| ''SB= 2'' || scaling bins/microvolt in file = number corresponding to 1 microvolt
+|-
-''SC= 50''&nbsp;scaling calibration, used for setting magnitude of display in BESA
+| ''SC= 50'' || scaling calibration, used for setting magnitude of display in BESA
+|-
-''Nchan= 27''&nbsp;number of channels
+| ''Nchan= 27'' || number of channels
+|-
-''SegmentName= 60dB'' &nbsp;An optional label describing the data.
+| ''SegmentName= 60dB'' || an optional label describing the data
 The second line of the header contains a label for each channel, e.g.
@@ Line 43: / Line 44: @@
-Each of the subsequent ''Nchan'' lines of the file contains values for all ''Npts'' time points in floating point or scientific format. For more details about scalp electrodes, see chapter "''Working With Electrodes and Surface Locations/Electrodes/Electrode Conventions".''
+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 '''Nchan=xx''' information in the first line, and there is no second header line. Labels must be defined elsewhere. See "''Electrodes/Electrode file conventions and formats''" and “''Reading MEG files in ASCII format”''. In the older versions, only scalp channels were exported, and the data were average referenced.
 == ASCII Multiplexed format (*.mul) ==

@@ Line 4: / Line 4: @@
 |version = 6.1 or higher
 }}
-=== Binary format (*.foc, *.fsg) ===
+== 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''' 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.
 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) ===
+== 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:'''
@@ Line 46: / Line 48: @@
-=== ASCII Multiplexed format (*.mul) ===
+== ASCII Multiplexed format (*.mul) ==
 Select '''ASCII Multiplexed Format''' to output segments one time point (all channels) per line. &nbsp;
@@ Line 87: / Line 89: @@
 * The final letter after the hyphen indicates L=left, M=middle, R=right.
-=== Channel definition file conventions and formats ===
+== Channel definition file conventions and formats ==
 BESA Research can read 3 types of file to define channels. These are identified by different extensions:
@@ Line 176: / Line 178: @@
-=== cot (Head center) 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.
@@ Line 193: / Line 195: @@
-=== pos or pmg (MEG sensor coordinate) 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;">'''<nowiki>*.pmg</nowiki>'''</span>, and gradiometer information in <span style="color:#ff9c00;">'''<nowiki>*.pos</nowiki>'''</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.
@@ Line 217: / Line 219: @@
-=== sfn (surface point name) file ===
+== 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.).
@@ Line 235: / Line 237: @@
-=== sfp (surface point coordinate) file ===
+== 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.
@@ Line 261: / Line 263: @@
-=== Generic File Format ===
+== 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.

Working With Additional Files - Revision history

Vibhin at 11:40, 5 May 2021

Jaehyun: /* Channel definition file conventions and formats */

Jaehyun: /* cot (Head center) file */

Jaehyun: /* Channel definition file conventions and formats */

Jaehyun: /* Generic File Format */

Jaehyun: /* sfn (surface point name) file */

Jaehyun: /* pos or pmg (MEG sensor coordinate) file */

Jaehyun: /* ASCII Multiplexed format (*.mul) */

Jaehyun: /* ASCII vectorized format (*.avr) */

Jaehyun at 09:13, 11 July 2017

Jaehyun: /* ASCII Multiplexed format (.mul) /

Jaehyun: /* ASCII vectorized format (.avr) /