Electrodes and Surface Locations - Revision history

Jaehyun: /* Polhemus Digitizer Data */

2021-08-06T14:21:17Z

‎Polhemus Digitizer Data

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Jaehyun: /* 3D Coordinates for Precise Analysis */

2021-08-05T13:09:09Z

‎3D Coordinates for Precise Analysis

Jaehyun: /* Data reading rules for MEG */

2021-08-05T13:05:35Z

‎Data reading rules for MEG

Jaehyun: /* Electrode Conventions */

2021-08-05T09:43:09Z

‎Electrode Conventions

Robert: /* Digitization points with and without Fiducials */

2021-05-05T09:55:52Z

‎Digitization points with and without Fiducials

Robert: /* 3D Coordinates for Precise Analysis */

2021-05-05T09:54:02Z

‎3D Coordinates for Precise Analysis

Robert: /* Recommendations for electrode placement */

2021-05-05T09:43:34Z

‎Recommendations for electrode placement

Robert at 09:41, 5 May 2021

2021-05-05T09:41:44Z

Robert: /* Introduction - Electrodes and Surface Locations */

2021-05-05T09:37:22Z

‎Introduction - Electrodes and Surface Locations

Robert at 09:21, 5 May 2021

2021-05-05T09:21:53Z

@@ Line 299: / Line 299: @@
 Working with digitized electrode coordinates usually requires reading in additional (auxiliary) files. The procedure is described on the page [[Working With Additional Files]].
 === Data reading rules for EEG ===
@@ Line 321: / Line 322: @@
 '''Define head center.''' No coregistration file exists (<span style="color:#ff9c00;">'''<nowiki>*.sfh</nowiki>'''</span>, see above). File <span style="color:#ff9c00;">'''datafile.cot'''</span> exists, or file <span style="color:#ff9c00;">'''default.cot'''</span> exists, or file <span style="color:#ff9c00;">'''..\default.cot'''</span> exists (i.e. file<span style="color:#ff9c00;">''' default.cot</span><span style="color:#ff9c00;"> '''</span>one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"[[Working_With_Additional_Files#cot_.28Head_center.29_file|Working with additional files / cot (Head center) file]]"''.
 === Data reading rules for MEG ===
@@ Line 347: / Line 349: @@
 '''Define head center.''' No coregistration file exists (<span style="color:#ff9c00;">'''<nowiki>*.sfh</nowiki>'''</span>, see above). File <span style="color:#ff9c00;">'''datafile.cot'''</span> exists, or file <span style="color:#ff9c00;">'''default.cot'''</span> exists, or file <span style="color:#ff9c00;">'''..\default.cot'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.cot</span><span style="color:#ff9c00;"> '''</span>one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter [[Working_With_Additional_Files#cot_.28Head_center.29_file | cot (Head center) file]].
 === Reading MEG files in ASCII format ===

@@ Line 324: / Line 324: @@
 === Data reading rules for MEG ===
-Assume file name is <span style="color:#ff9c00;">''''datafile.xxx''''</span>. '''datafile''' is the base name. '''xxx''' is the extension. Replace the text '''datafile''' by the base name of your own file, and the extension '''xxx''' by the extension of your own file.
+Assume file name is <span style="color:#ff9c00;">'''datafile.xxx'''</span>. '''datafile''' is the base name. '''xxx''' is the extension. Replace the text '''datafile''' by the base name of your own file, and the extension '''xxx''' by the extension of your own file.
+Here we consider cases a) MEG alone and b) MEG+EEG.
-Here we consider cases a) MEG alone, b) MEG+EEG.
@@ Line 333: / Line 332: @@
 Labels have names defined in the files <span style="color:#ff9c00;">'''bti.ecd'''</span> or <span style="color:#ff9c00;">'''nmag.ecd'''</span>. Channels are interpreted as MEG. However, sensor locations and head surface point locations must be defined in additional files as described below. Mapping and source analysis are not possible without one or more of the following additional files.
-'''Define channel names and types.''' File <span style="color:#ff9c00;">'''datafile.ela'''</span>, <span style="color:#ff9c00;">'''datafile.elp'''</span>, or <span style="color:#ff9c00;">'''datafile.elb'''</span> exist, or files <span style="color:#ff9c00;">'''default.ela'''</span>, <span style="color:#ff9c00;">'''default.elp'''</span>, or <span style="color:#ff9c00;">'''default.elb'''</span> exist, or files <span style="color:#ff9c00;">'''..\default.ela'''</span>, <span style="color:#ff9c00;">'''..\default.elp'''</span>, or <span style="color:#ff9c00;">'''..\default.elb'''</span> exist (i.e. files with basename'' default'' one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence. The'' ela''&nbsp;file contains just labels and (optionally) channel types. The ''elp'' file contains spherical coordinates and can contain labels and types. The'' elb'' file contains the equivalent information in binary format. See chapter “''Electrode file conventions'' ''and formats.”''
+'''Define channel names and types.''' File <span style="color:#ff9c00;">'''datafile.ela'''</span>, <span style="color:#ff9c00;">'''datafile.elp'''</span>, or <span style="color:#ff9c00;">'''datafile.elb'''</span> exist, or files <span style="color:#ff9c00;">'''default.ela'''</span>, <span style="color:#ff9c00;">'''default.elp'''</span>, or <span style="color:#ff9c00;">'''default.elb'''</span> exist, or files <span style="color:#ff9c00;">'''..\default.ela'''</span>, <span style="color:#ff9c00;">'''..\default.elp'''</span>, or <span style="color:#ff9c00;">'''..\default.elb'''</span> exist (i.e. files with basename'' default'' one folder above the data file): Channel names and types will be replaced by those defined in this file, in order of occurrence.
-'''MEG+EEG.''' Define order in which electrodes were digitized. File <span style="color:#ff9c00;">'''datafile.sfn'''</span> exists, or file <span style="color:#ff9c00;">'''default.sfn '''</span>exists, or file <span style="color:#ff9c00;">'''..\default.sfn'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.sfn'''</span> one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file (or in the location descriptor in the data file: e.g. Neuromag). These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. See chapter “''Working with additional files/ sfn (surface point name) file”.''
+'''MEG+EEG.''' Define order in which electrodes were digitized. File <span style="color:#ff9c00;">'''datafile.sfn'''</span> exists, or file <span style="color:#ff9c00;">'''default.sfn '''</span>exists, or file <span style="color:#ff9c00;">'''..\default.sfn'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.sfn'''</span> one folder above the data file): electrode names are supplied in the order in which coordinates were supplied in the ''sfp'' file (or in the location descriptor in the data file: e.g. Neuromag). These names must match with the names supplied in the data file or defined in the ''ela/elp/elb'' file. BESA Research uses this to sort coordinates into the order of channels in the file. See chapter [[Working_With_Additional_Files#sfn_.28surface_point_name.29_file | sfn (surface point name) file]].
-'''MEG+EEG.''' Define head surface point/electrode coordinates. File <span style="color:#ff9c00;">'''datafile.sfp'''</span>'' ''exists, or file <span style="color:#ff9c00;">'''default.sfp'''</span> exists, or file <span style="color:#ff9c00;">'''..\default.sfp'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.sfp'''</span> one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If <span style="color:#ff9c00;">'''datafile.sfn'''</span> does not exist, labels can also be defined in this file. See chapter “''Working with additional files/ sfp (surface point'' ''coordinate) file''”. The labels of electrode coordinates '''must '''match to those defined for the data channels. BESA Research will use the labels to associate coordinates with the correct channel.
+'''MEG+EEG.''' Define head surface point/electrode coordinates. File <span style="color:#ff9c00;">'''datafile.sfp'''</span>'' ''exists, or file <span style="color:#ff9c00;">'''default.sfp'''</span> exists, or file <span style="color:#ff9c00;">'''..\default.sfp'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.sfp'''</span> one folder above the data file): electrode coordinates will be replaced/defined by the coordinates defined in this file. If <span style="color:#ff9c00;">'''datafile.sfn'''</span> does not exist, labels can also be defined in this file. See chapter [[Working_With_Additional_Files#sfn_.28surface_point_name.29_file | sfn (surface point name) file]]. The labels of electrode coordinates '''must '''match to those defined for the data channels. BESA Research will use the labels to associate coordinates with the correct channel.
-'''Define sensor coordinates'''. File <span style="color:#ff9c00;">'''datafile.pos'''</span> or <span style="color:#ff9c00;">'''datafile.pmg'''</span> exists, or file <span style="color:#ff9c00;">'''default.pos(.pmg)'''</span> exists, or file <span style="color:#ff9c00;">'''..\default.pos(.pmg)'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.pos(.pmg)'''</span> one folder above the data file): coordinates are defined in this file. The convention is that'' pos'' files contain gradiometer coordinates and'' pmg'' files contain magnetometer coordinates. This is not necessary for the program to read in values properly: the program makes its decision about the sensor type on the basis of the number of coordinate values on one line in the file (6 = magnetometers, 9 = gradiometers). See chapter “''Working with additional files/ pos or pmg (MEG sensor coordinate) file”.''
+'''Define sensor coordinates'''. File <span style="color:#ff9c00;">'''datafile.pos'''</span> or <span style="color:#ff9c00;">'''datafile.pmg'''</span> exists, or file <span style="color:#ff9c00;">'''default.pos(.pmg)'''</span> exists, or file <span style="color:#ff9c00;">'''..\default.pos(.pmg)'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.pos(.pmg)'''</span> one folder above the data file): coordinates are defined in this file. The convention is that ''pos'' files contain gradiometer coordinates and'' pmg'' files contain magnetometer coordinates. This is not necessary for the program to read in values properly: the program makes its decision about the sensor type on the basis of the number of coordinate values on one line in the file (6 = magnetometers, 9 = gradiometers). See chapter [[Working_With_Additional_Files#pos_or_pmg_.28MEG_sensor_coordinate.29_file | pos or pmg (MEG sensor coordinate) file]].
 '''Define coregistration information.''' File <span style="color:#ff9c00;">'''datafile.sfh'''</span> exists, or file<span style="color:#ff9c00;">''' default.sfh</span><span style="color:#ff9c00;"> '''</span>exists, or file <span style="color:#ff9c00;">'''..\default.sfh'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.sfh'''</span> one folder above the data file): head center and relative position of the unit sphere with respect to the head coordinate system is determined by the coregistration of the head coordinates with MRI. See (online) help chapter ''"Integration with MRI and fMRI".''
-'''Define head center.''' No coregistration file exists (<span style="color:#ff9c00;">'''<nowiki>*.sfh</nowiki>'''</span>, see above). File <span style="color:#ff9c00;">'''datafile.cot'''</span> exists, or file <span style="color:#ff9c00;">'''default.cot'''</span> exists, or file <span style="color:#ff9c00;">'''..\default.cot'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.cot</span><span style="color:#ff9c00;"> '''</span>one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter ''"Working with additional files / cot (Head center) file".''
+'''Define head center.''' No coregistration file exists (<span style="color:#ff9c00;">'''<nowiki>*.sfh</nowiki>'''</span>, see above). File <span style="color:#ff9c00;">'''datafile.cot'''</span> exists, or file <span style="color:#ff9c00;">'''default.cot'''</span> exists, or file <span style="color:#ff9c00;">'''..\default.cot'''</span> exists (i.e. file <span style="color:#ff9c00;">'''default.cot</span><span style="color:#ff9c00;"> '''</span>one folder above the data file): head center as computed by fitting a sphere to the surface points is replaced by the head center coordinates contained in this file. See chapter [[Working_With_Additional_Files#cot_.28Head_center.29_file | cot (Head center) file]].
-−
 === Reading MEG files in ASCII format ===

@@ Line 155: / Line 155: @@
 [[Image:ST Electrodes (19).gif ]]
 ''Electrode labels in the file <span style="color:#ff9c00;">'''default.ecd '''</span>and their spherical coordinates. 10-20 electrodes are shown in<span style="color:#ff0000;"> red and italic.''</span>
-The spherical coordinates are defined in degrees by the azimuth (from Cz, positive = right, negative = left hemisphere) and the latitude (counterclockwise from T7/T3 for left and from T8/T4 for right hemisphere) of each electrode. Please do not modify the existing labels or coordinates in this file, because this would adversely affect the interpolated (virtual) montages, the maps and the source montages and source images in BESA Research. However, you may add additional labels for scalp electrodes at the end of this file if needed (up to a total of 196). When you edit the electrode configuration or read in electrode files, BESA Research may replace the 10/20 standard labels T3, T4, T5, T6 by their new 10/10 equivalents T7,
+The spherical coordinates are defined in degrees by the azimuth (from Cz, positive = right, negative = left hemisphere) and the latitude (counterclockwise from T7/T3 for left and from T8/T4 for right hemisphere) of each electrode. Please do not modify the existing labels or coordinates in this file, because this would adversely affect the interpolated (virtual) montages, the maps and the source montages and source images in BESA Research. However, you may add additional labels for scalp electrodes at the end of this file if needed (up to a total of 196).
-T8, P7, P8. However, in the initialization file <span style="color:#ff9c00;">'''BESA.ini '''</span>you can reset to the old 10/20 standard by relabeling T7=T3, P7=T5, T8=T4, P8=T6 under the heading [Electrodes]. You may use the same feature to assign appropriate labels to the X1..X8 channels which exist in many systems, e.g. X1=EKG1 etc.
+When you edit the electrode configuration or read in electrode files, BESA Research may replace the 10/20 standard labels T3, T4, T5, T6 by their new 10/10 equivalents T7, T8, P7, P8. However, in the initialization file <span style="color:#ff9c00;">'''BESA.ini '''</span>you can reset to the old 10/20 standard by relabeling T7=T3, P7=T5, T8=T4, P8=T6 under the heading <code>'''[Electrodes]'''</code>. You may use the same feature to assign appropriate labels to the X1...X8 channels which exist in many systems, e.g. X1=EKG1 etc.
 === Recommendations for electrode placement ===

@@ Line 636: / Line 636: @@
 '''Consequences of omitting fiducials'''
-When these files have been read into BESA Research, look at the head surface points in 3D using ''File/Head Surface Points'' ''and Sensors/View'' (or use the shortcut <span style="color:#3366ff;">'''‘V’'''</span>). You will see small differences in fiducial locations between the real and the simulated locations. You can expect very slight influences on the results of source modeling (the spherical head may be rotated slightly, although the head center and radius will be identical), and output of source locations in head coordinates will be different, because these coordinates are based on fiducial locations (see chapter ''“Working with Electrodes and Surface'' ''Locations/ Coordinate systems''”).
+When these files have been read into BESA Research, look at the head surface points in 3D using ''File/Head Surface Points'' ''and Sensors/View'' (or use the shortcut <span style="color:#3366ff;">'''‘V’'''</span>). You will see small differences in fiducial locations between the real and the simulated locations. You can expect very slight influences on the results of source modeling (the spherical head may be rotated slightly, although the head center and radius will be identical), and output of source locations in head coordinates will be different, because these coordinates are based on fiducial locations (see section [[Electrodes_and_Surface_Locations#Coordinate_systems|Coordinate systems]]).
-−
 === ASCII Import ===

@@ Line 299: / Line 299: @@
 === Introduction - Working with Digitized 3D Coordinates ===
-Working with digitized electrode coordinates usually requires reading in additional (auxiliary) files. The procedure is described in the chapter "''Working with auxiliary files''".
+Working with digitized electrode coordinates usually requires reading in additional (auxiliary) files. The procedure is described on the page [[Working With Additional Files]].
 === Data reading rules for EEG ===

@@ Line 170: / Line 170: @@
 # Covering of the lower head with inferior electrodes to record activity from the inferior surfaces of the brain, especially from the basal temporal lobe, from the temporal pole, from orbito-frontal cortex, and from basal occipital and cerebellar areas.
 # Equal spacing of the electrodes over the whole head to cover all brain areas.
 In the following montage EEGxx, the number xx indicates the number of electrodes.

@@ Line 10: / Line 10: @@
 Here you will find out how BESA Research works with electrode and MEG sensor coordinates and labels, and how head surface points can be used to improve source modeling and coregistration of source models with the MRI. In most cases, electrode positions are sufficiently defined by their labels. The section "''Electrode Conventions''" lists the standard position which BESA Research assigns to EEG channels. In some cases, especially for larger electrode arrays or for MEG measurements, additional information is required to add sufficient information for mapping and for source analysis. The additional information is supplied in additional, auxiliary files which are read by BESA Research and associated with the data files. The auxiliary files, and how they are supplied to BESA Research, are described in this chapter.
-Examples for using auxiliary files to define the 3D locations of electrodes are found in the chapter "''Special Topics / Working with Electrodes... / Examples''" in the online help.
+Examples for using auxiliary files to define the 3D locations of electrodes are found in the [[Electrodes_and_Surface_Locations#Examples|Examples]] section .
 Descriptions of file formats that BESA Research uses are given in the online help chapter [[Working_With_Additional_Files|Working With Additional Files]].
@@ Line 386: / Line 386: @@
 Note that all coordinates should be within the same frame of reference, i.e. the same coordinate system. Units must be in meters, centimeters, or millimeters.
-== Example: Defining Channel Labels ==
+=== Defining Channel Labels ===
 The files described in these examples can be found in the ''.\Examples\Xtras\EEG+Channel Labels'' subdirectory.
@@ Line 473: / Line 474: @@
-== Example: Mixed EEG and Polygraphic Data ==
+=== Mixed EEG and Polygraphic Data ===
 The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Polygraphic'' subdirectory.
@@ Line 494: / Line 495: @@
 Note that you can also define channels as EEG by specifying the ''"EEG" ''prefix (e.g. ''"EEG E1". ''This is useful if there are many more channels than are defined in the 10-10 or 10-20 systems, and if the channel coordinates are defined.
-== Example: EEG with Digitized Coordinates ==
+=== EEG with Digitized Coordinates ===
 The files described in this example can be found in the .''\Examples\Xtras\ EEG+Digitization Points ''subdirectory.
@@ Line 527: / Line 528: @@
-== Example: Polhemus Digitizer Data ==
+=== Polhemus Digitizer Data ===
 The files described in this example can be found in the ''.\Examples\Xtras\ EEG+Digitization Points'' subdirectory.
@@ Line 625: / Line 626: @@
-== Example: Digitization points with and without Fiducials ==
+=== Digitization points with and without Fiducials ===
 We recommend that if electrodes are digitized, you should also digitize the three fiduciary points:''' Nasion''', '''and left and right preauricular points'''. We refer to these points as "fiducials". We name them '''"FidNz",''' '''"FidT9",''' and '''"FidT10".'''
@@ Line 639: / Line 640: @@
-== Example: ASCII Import ==
+=== ASCII Import ===
 The files described in this example can be found in the ''.\Examples\Xtras\ASCII Import'' subdirectory.
@@ Line 733: / Line 734: @@
 # If you have digitized coordinates, these can be specified in the Channel and digitized head surface point information dialog box. Since the procedure is the same as when reading data, this is described elsewhere under “''Example: EEG with Digitized Coordinates''”.
-== Example: MEG ASCII ==
+=== MEG ASCII ===
 The files described in this example can be found in the'' \Examples\Xtras\ MEG ASCII'' subdirectory of the BESA Research installation folder.
@@ Line 779: / Line 780: @@
-== Example: Reading combined EEG and MEG from an ASCII file ==
+=== Reading combined EEG and MEG from an ASCII file ===
 The files described in this example can be found in the ''Examples\Xtras\MEG+EEG'' subdirectory of the BESA Research installation folder.

@@ Line 6: / Line 6: @@
 = Working with Electrodes and Surface Locations =
-== Introduction - Electrodes and Surface Locations ==
+== Introduction ==
 Here you will find out how BESA Research works with electrode and MEG sensor coordinates and labels, and how head surface points can be used to improve source modeling and coregistration of source models with the MRI. In most cases, electrode positions are sufficiently defined by their labels. The section "''Electrode Conventions''" lists the standard position which BESA Research assigns to EEG channels. In some cases, especially for larger electrode arrays or for MEG measurements, additional information is required to add sufficient information for mapping and for source analysis. The additional information is supplied in additional, auxiliary files which are read by BESA Research and associated with the data files. The auxiliary files, and how they are supplied to BESA Research, are described in this chapter.
@@ Line 12: / Line 12: @@
 Examples for using auxiliary files to define the 3D locations of electrodes are found in the chapter "''Special Topics / Working with Electrodes... / Examples''" in the online help.
-Descriptions of file formats that BESA Research uses are given in the online help chapter "''Special Topics'' ''/ Working with additional files''".
+Descriptions of file formats that BESA Research uses are given in the online help chapter [[Working_With_Additional_Files|Working With Additional Files]].
 == Working with auxiliary files ==

@@ 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
 }}
 = Working with Electrodes and Surface Locations =