BESA® Wiki - User contributions [en]

Main Page

2016-05-12T14:38:07Z

Andre: new link

=Welcome to the BESA Wiki!=

This wiki is designed to help users with typical questions around using BESA to achieve their goals.
Topics are available for the following categories:

== FAQ ==

=== Licensing ===

[[Licensing]]

=== File Formats ===

[[Channel Definition File Formats]]

[[Event File Format]]

[[MEG Sensor Coordinate Files]]

[[Supported Data Formats]]

[[Paradigm File Format in BESA]]

[[Importing Electrode Locations in Combined EEG/MEG Measurements with the Neuromag System]]

=== Data Review and Analysis ===

[[Importing Digitized Coordinates]]

[[Verify Electrode Coordinates]]

[[Export Single Trial Data]]

[[How to Average EEG channels]]

[[Averaging Across EEG Datasets from Different Recording Systems]]

[[Time Frequency Resolution In BESA]]

[[Change Waveform Colours]]

[[Best Strategy to Define a Multiple Source Model]]

[[Export Dipole Moments of Fitted Sources]]

[[Recommended Electrode Configurations]]

[[Exporting Artifact-Corrected Data]]

[[Create Triggers for Artifact-Rejected Epochs]]

[[Inserting Triggers Relative to Existing Events]]

[[Change or Exclude Erroneous Head Surface Point Locations]]

[[Exporting Top Viewer Waveforms into other Graphics Software for Further Processing]]

=== Matlab interface ===

[[How Do I Configure the Matlab Interface?]]

[[Updating the Matlab Interface after Matlab Upgrade]]

=== BESA Statistics ===

[[Cluster Alpha vs. Neighbor Distance]]

[[Importing BESA Statistics Results into Excel]]

=== Trouble shooting ===

[[MF Error 211]]

[[3D Graphics Display Issue Handling]]

== BESA recipes ==

[[Control of BESA Research by external programs]]

[[Correcting Volume Conductor Segmentations]]

[[Random Averaging]]

[[Statistical Analysis for More than Two Levels]]

[[Exporting Data from Matlab to BESA Statistics]]

== Did you know...? ==

[[Moving Dipole Fit]]

[[BESA Anonymizer]]

[[Batch Processing]]

[[Analyzing Electrocorticography Data]]

== Coming soon ==
* a collection of useful batches
* and further content we will be publishing on this wiki

Contributions to the Wiki from the community are very welcome! Please create an account with a valid email to edit the BESA Wiki's content.

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Importing Electrode Locations in Combined EEG/MEG Measurements with the Neuromag System

2016-05-12T14:36:56Z

Andre: added box

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

The Neuromag system does not store the electrode names with the coordinates. Thus, it is extremely important that you keep track of the digitization protocol, and provide a file which provides the names of fiducials, electrodes, and additional head surface points in the order of digitization (see BESA help: Working with Electrodes and Surface Locations).

[[Category:ERP/ERF]]

Exporting Top Viewer Waveforms into other Graphics Software for Further Processing

2016-05-12T14:36:22Z

Andre: box added

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

Top Viewer waveforms can be exported into encapsulated post script files using the command ‘File | Print to File’ in the Top Viewer window. Printed files can then be imported into a graphics software (e.g. Corel Draw, Adobe Photoshop). In vector-oriented graphics programs, the scalability of the eps format remains available if you select ‘Post Script Interpreted’ when importing.

[[Category:ERP/ERF]]

Exporting Top Viewer Waveforms into other Graphics Software for Further Processing

2016-05-12T14:34:28Z

Andre: Copied from BESA FAQ page.

Top Viewer waveforms can be exported into encapsulated post script files using the command ‘File | Print to File’ in the Top Viewer window. Printed files can then be imported into a graphics software (e.g. Corel Draw, Adobe Photoshop). In vector-oriented graphics programs, the scalability of the eps format remains available if you select ‘Post Script Interpreted’ when importing.

[[Category:ERP/ERF]]

Main Page

2016-05-12T14:31:09Z

Andre: new link

=Welcome to the BESA Wiki!=

This wiki is designed to help users with typical questions around using BESA to achieve their goals.
Topics are available for the following categories:

== FAQ ==

=== Licensing ===

[[Licensing]]

=== File Formats ===

[[Channel Definition File Formats]]

[[Event File Format]]

[[MEG Sensor Coordinate Files]]

[[Supported Data Formats]]

[[Paradigm File Format in BESA]]

[[Importing Electrode Locations in Combined EEG/MEG Measurements with the Neuromag System]]

=== Data Review and Analysis ===

[[Importing Digitized Coordinates]]

[[Verify Electrode Coordinates]]

[[Export Single Trial Data]]

[[How to Average EEG channels]]

[[Averaging Across EEG Datasets from Different Recording Systems]]

[[Time Frequency Resolution In BESA]]

[[Change Waveform Colours]]

[[Best Strategy to Define a Multiple Source Model]]

[[Export Dipole Moments of Fitted Sources]]

[[Recommended Electrode Configurations]]

[[Exporting Artifact-Corrected Data]]

[[Create Triggers for Artifact-Rejected Epochs]]

[[Inserting Triggers Relative to Existing Events]]

[[Change or Exclude Erroneous Head Surface Point Locations]]

=== Matlab interface ===

[[How Do I Configure the Matlab Interface?]]

[[Updating the Matlab Interface after Matlab Upgrade]]

=== BESA Statistics ===

[[Cluster Alpha vs. Neighbor Distance]]

[[Importing BESA Statistics Results into Excel]]

=== Trouble shooting ===

[[MF Error 211]]

[[3D Graphics Display Issue Handling]]

== BESA recipes ==

[[Control of BESA Research by external programs]]

[[Correcting Volume Conductor Segmentations]]

[[Random Averaging]]

[[Statistical Analysis for More than Two Levels]]

[[Exporting Data from Matlab to BESA Statistics]]

== Did you know...? ==

[[Moving Dipole Fit]]

[[BESA Anonymizer]]

[[Batch Processing]]

[[Analyzing Electrocorticography Data]]

== Coming soon ==
* a collection of useful batches
* and further content we will be publishing on this wiki

Contributions to the Wiki from the community are very welcome! Please create an account with a valid email to edit the BESA Wiki's content.

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Importing Electrode Locations in Combined EEG/MEG Measurements with the Neuromag System

2016-05-12T14:29:47Z

Andre: Copied from BESA FAQ Website.

The Neuromag system does not store the electrode names with the coordinates. Thus, it is extremely important that you keep track of the digitization protocol, and provide a file which provides the names of fiducials, electrodes, and additional head surface points in the order of digitization (see BESA help: Working with Electrodes and Surface Locations).

[[Category:ERP/ERF]]

Main Page

2016-05-12T14:16:50Z

Andre: added entry

=Welcome to the BESA Wiki!=

This wiki is designed to help users with typical questions around using BESA to achieve their goals.
Topics are available for the following categories:

== FAQ ==

=== Licensing ===

[[Licensing]]

=== File Formats ===

[[Channel Definition File Formats]]

[[Event File Format]]

[[MEG Sensor Coordinate Files]]

[[Supported Data Formats]]

[[Paradigm File Format in BESA]]

=== Data Review and Analysis ===

[[Importing Digitized Coordinates]]

[[Verify Electrode Coordinates]]

[[Export Single Trial Data]]

[[How to Average EEG channels]]

[[Averaging Across EEG Datasets from Different Recording Systems]]

[[Time Frequency Resolution In BESA]]

[[Change Waveform Colours]]

[[Best Strategy to Define a Multiple Source Model]]

[[3D Graphics Display Issue Handling]]

[[Export Dipole Moments of Fitted Sources]]

[[Recommended Electrode Configurations]]

[[Exporting Artifact-Corrected Data]]

[[Create Triggers for Artifact-Rejected Epochs]]

[[Inserting Triggers Relative to Existing Events]]

=== Matlab interface ===

[[How Do I Configure the Matlab Interface?]]

[[Updating the Matlab Interface after Matlab Upgrade]]

=== BESA Statistics ===

[[Cluster Alpha vs. Neighbor Distance]]

[[Importing BESA Statistics Results into Excel]]

=== Trouble shooting in BESA MRI and BESA Statistics ===

[[MF Error 211]]

== BESA recipes ==

[[Control of BESA Research by external programs]]

[[Correcting Volume Conductor Segmentations]]

[[Random Averaging]]

[[Statistical Analysis for More than Two Levels]]

[[Exporting Data from Matlab to BESA Statistics]]

== Did you know...? ==

[[Moving Dipole Fit]]

[[BESA Anonymizer]]

[[Batch Processing]]

[[Analyzing Electrocorticography Data]]

== Coming soon ==
* a collection of useful batches
* and further content we will be publishing on this wiki

Contributions to the Wiki from the community are very welcome! Please create an account with a valid email to edit the BESA Wiki's content.

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Inserting Triggers Relative to Existing Events

2016-05-12T14:15:06Z

Andre: line break fixed.

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

Say you are interested in studying neural activity that precedes an existing trigger. This can be addressed in the following ways:

# You are interested in a certain epoch that precedes the trigger event that is already coded. So, instead of entering a new trigger code, you could just add a new condition that works on the existing trigger code, and merely changes the epoch of interest. Presumably you have defined a condition where you are looking at the activity around the trigger event: some baseline before and then the activity that follows the trigger. Now, you can use the ERP-> Edit Paradigm to insert a new condition (CURRENT.code IS ... ). Then click on the “Epoch” tab and modify the epoch of this new condition – e.g. -1000 ms...-200 ms, also change the baseline epoch accordingly, then highlight the new condition in the list, and assign the epoch to the new condition. This condition will now average over the defined epoch that precedes the trigger.
#If you really need a new trigger code, you can export the trigger codes as event file, using the menu ERP->Save Events As... This will save events as a text file. Then open this “*.evt” file in a text editor or e.g. in Excel. The file lists the elapsed time in microseconds, and the event type. Now, for all event types that you want to replace, subtract 1000000 from the number in the first column. Change the code of the trigger to a new value, e.g. 511. Get rid of the events that you don’t want to change. Save this file under a different name in text format, and open it again in BESA using ERP->Open Event File... (For example, you can use Excel in the following way: Open the file. Select all columns, and sort by the “Comnt” column. Delete all rows that contain trigger events that you don’t want to change. In cell E2, type the formula “=A2-1000000” and apply to all rows. Then copy this and paste values back into the A column. Delete column E. Change column C values (TriNo). Then save as text file, and re-load in BESA.)

[[Category:ERP/ERF]]

Inserting Triggers Relative to Existing Events

2016-05-12T14:14:33Z

Andre: Slight alteration of text copied from support email by HB " inserting triggers relative to existing events " .

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

Say you are interested in studying neural activity that precedes an existing trigger. This can be addressed in the following ways:

# You are interested in a certain epoch that precedes the trigger event that is already coded. So, instead of entering a new trigger code, you could just add a new condition that works on the existing trigger code, and merely changes the epoch of interest. Presumably you have defined a condition where you are looking at the activity around the trigger event: some baseline before and then the activity that follows the trigger. Now, you can use the ERP-> Edit Paradigm to insert a new condition (CURRENT.code IS ... ). Then click on the “Epoch” tab and modify the epoch of this new condition – e.g. -1000 ms...-200 ms, also change the baseline epoch accordingly, then highlight the new condition in the list, and assign the epoch to the new condition. This condition will now average over the defined epoch that precedes the trigger.
#If you really need a new trigger code, you can export the trigger codes as event file, using the menu ERP->Save Events As... This will save events as a text file. Then open this “*.evt” file in a text editor or e.g. in Excel. The file lists the elapsed time in microseconds, and the event type. Now, for all event types that you want to replace, subtract 1000000 from the number in the first column. Change the code of the trigger to a new value, e.g. 511. Get rid of the events that you don’t want to change. Save this file under a different name in text format, and open it again in BESA using ERP->Open Event File...
(For example, you can use Excel in the following way: Open the file. Select all columns, and sort by the “Comnt” column. Delete all rows that contain trigger events that you don’t want to change. In cell E2, type the formula “=A2-1000000” and apply to all rows. Then copy this and paste values back into the A column. Delete column E. Change column C values (TriNo). Then save as text file, and re-load in BESA.)

[[Category:ERP/ERF]]

Create Triggers for Artifact-Rejected Epochs

2016-05-12T14:09:17Z

Andre: Andre moved page Create triggers for artifact-rejected epochs to Create Triggers for Artifact-Rejected Epochs: Spelling on the title.

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

=== Overview ===
Here we demonstrate how to track what epochs were rejected by the artifact rejection. There might be experiments were one is interested in actually analyzing the rejected epochs. This information is available in the respective paradigm file but has to be extracted by the user. The idea is to create a new trigger for the rejected epochs that can later be read back into BESA Research.

=== Identifying Rejected Epochs ===
In this example we use the subject 2 of the Auditory Intensity experiment located in the BESA Research examples folder (../Examples/AuditoryIntensity/S2.cnt).
# Open the raw file S2.cnt and create a new paradigm for it. In the conditions tab create only conditions that directly correspond to each of the respective triggers (in my case I have 5 triggers, thus I have 5 conditions, one for each "current" trigger).
# Define the Epochs and Filters as you like.
# Run the artifact rejection.
# Close everything and find the respective paradigm file in the folder of raw file S2.cnt (typically %basename%.pdg, in my case S2.pdg, see [[File:S2.PDG|thumb]]).
# Open the paradigm file in a text editor (e.g. Notepad, please do not use word as it might change the format of the text).
# Find the section starting with [ArtifactScan], ignore the following 4 lines (see the [[Paradigm File Format in BESA|PDG file format description]] for details if you are curious!) and copy everything thereafter to a new txt file.
# Import the newly created file in Excel by specifying that spaces and tabs are the delimiters for the columns. Save the file in excel format and leave it open. Be sure to have the decimal separator set to " . " and the thousands separator set to none.
# Open the attached excel file [[File:ArtifactRejection.xlsx]]. In the first sheet you should be able to see a blue painted area. Please copy the contents of the table you created in there. Be sure to copy the values only (not e.g. the format). The table will basically check if a particular epoch was rejected or not. In case it will substitute the value for the trigger on the left most side of the table with a new trigger (12 in this case, marked in orange in the table). The table was made to support up to 257 channels, in case you have more please just adjust the formulas in Exceeds max Amp etc…
Please also set the right artifact rejection values (cells are marked with green in the table) as in the paradigm window.
Please also make the tables length match the length of your data by copy pasting the 4 row x 10 columns block accordingly (marked in orange for easier identification!).
# Ok, now you should be almost done. The 5 leftmost columns on your table should have all the necessary information to create a new event file. Please copy the 4 columns starting from the cell immediately below the label "Tmu" (A13 if nobody changed the table in the meantime) to the end of the table. Insert them in a new sheet (NewEventFile) from A2 onward. Please be careful to paste values only! (Do paste special->values only in excel).
# Almost there! Please select all the data in the new sheet and press Sort & Filter, select Custom sort, and choose sort by Column A, Sort On Values and choose A->Z as order. This should effectively remove the empty rows.

=== Creating a new evt File ===
# Please select all the relevant rows for the 5 columns in the new sheet and just copy them to a new file in Notepad. Please save the file with the evt extension. You can see the evt file obtained from the example described here [[File:S2_ArtRej_EventFile.evt]].
# Go back to BESA, remove all the existing triggers in ERP->Edit Triggers->Delete. Once this is done please load the file evt file you created by doing ERP->Open Event File.
# Trigger 12 should now appear in your data and represents those triggers that will be removed during artifact rejection.
# Using the paradigm window you should now be able to run your analysis using the new trigger 12 you created.

[[Category:ERP/ERF]]

Create triggers for artifact-rejected epochs

2016-05-12T14:09:17Z

Andre: Andre moved page Create triggers for artifact-rejected epochs to Create Triggers for Artifact-Rejected Epochs: Spelling on the title.

#REDIRECT [[Create Triggers for Artifact-Rejected Epochs]]

Exporting Artifact-Corrected Data

2016-05-12T13:44:43Z

Andre: First draft.

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = 6.0 or higher
}}

== Overview ==
Artifact corrected data can be exported for further analysis in third party software. It is essential to keep in mind that this data will always suffer from some level of distortion. For that reason some earlier versions of BESA would even block some modalities of file export.

== Choosing the Artifact-Correction Method ==
BESA 6.0 onwards provides four different artifact correction possibilities: ICA, adaptive, surrogate and SSP (see the BESA manual or the BESA Research tutorial for more details [ftp://h1772544.stratoserver.net/public/Research/Tutorials/ latest BESA tutorial]).

The adaptive method, also known as PCA-correction, is computed separately for each screen. This is the best correction method when looking through your data. However it might present discontinuities at the end or beginning of each page. The other methods instead correct the whole data set at once. Therefore it is recommended that you use one of these when exporting your artifact-corrected data. Furthermore we strongly recommend you use the ICA or surrogate method rather than the SSP method, as the latter typically causes the largest distortions.

== Exporting the Artifact-Corrected Data ==

After having applied the artifact correction:
# Go to File->Export.
# To enable the artifact correction you should select the option "Current filters and current baseline for segments settings".
# Choose the "Target data formats". Say BESA binary.
# Press Ok to start the export.

Please note that the exported binary will have the usual "corrected" text on the upper right hand corner of the traces screen. It will however be marked red. The artifact correction can no longer be reversed at this stage. Furthermore BESA will not allow a further artifact correction to be attempted on this already corrected file.

Although this is not recommended, you can trick BESA into forgetting that artifact correction was done by for example exporting it to other formats such to ASCII multiplexed.

[[Category:ERP/ERF]]

Create Triggers for Artifact-Rejected Epochs

2016-05-12T11:49:59Z

Andre: Added some extra gizmos.

Event File Format

2016-05-12T11:48:28Z

Andre: Changed level of "Overview" to a level 3 header.

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

=== Overview ===
Event files (extension *.evt) contain triggers and events and can be loaded as an additional file to provide more information about the whole course of an EEG/MEG recording.
An event file can be edited by opening it in any text editor, e.g. Notepad. It is also possible to create new event files from scratch which can be imported into the data file later.
Note the following conventions for event files:
* Event descriptions are given in the columns of the event file
* Each file must contain a header line and data lines

=== File Header ===
The header is comprised of abbreviated descriptions for each column. Each entry in the data line must be specified in the header line at the correct column position. The order of the data elements and their description in the header line can be chosen arbitrarily and the entries can be separated by commas, tabs and/or spaces. The last n data elements can be omitted, if they are neither Code nor one of ''Tms'', ''Tmu'' or ''Tsec''. The following codes are recognized by the ERP module:
* ''Code'' - event code (integer, see section [[#Event Codes|Event Codes]])
* ''Tms'' - event time in milliseconds relative to the start of the data file or ''Tmu'' [in microseconds] or ''Tsec'' [in sec] (floating point value)
* ''TriNo'' - trigger number (integer) (identifies the trigger in the event bar of the main module)
* ''RCode'' - reaction code (integer)
* ''RTms'' - reaction time in milliseconds or ''RTmu'' or ''RTsec'' (floating point value)
* ''Comnt'' - comment to describe event (string of up to 39 characters), will be truncated if longer than 39 characters.
You can also define columns which should not be recognized by the ERP module. Simply specify these columns in the header with any unknown code. Therefore you might be able to use previously generated files without major changes.

=== Event Codes ===
The event code Code must be one of the following integers:

{| class="wikitable"
! style="text-align: center; font-weight: bold;" | Code
! style="text-align: center; font-weight: bold;" | Event/Trigger Type
|-
| 1
| Trigger
|-
| 2
| Comment
|-
| 3
| Marker
|-
| 11
| Pattern1
|-
| 12
| Pattern2
|-
| 13
| Pattern3
|-
| 14
| Pattern4
|-
| 15
| Pattern5
|-
| 21
| Artifact on
|-
| 22
| Artifact off
|-
| 31
| Epoch on
|-
| 32
| Epoch off
|-
| 41
| New segment
|-
| 42
| Average segment
|}

=== Additional Event Information ===
The event reaction time, event reaction code and event comment are represented by the comment in the main module as "''Comment (Rx,T____)''", where ''Comment'' is the event comment, ''x'' describes the reaction code and the underscored line will be filled with the reaction time. Reaction time and reaction code are only read if the event code specifies it as a trigger.
A "New Segment" event can include time information that defines the starting time of the segment. This is defined in the ''TriNo'' column of the event file. The format is YYYY-MM-DDTHH:MM:SS, e.g. 2010-04-26T15:30:20.31 (note: seconds are a decimal number). If no time is defined, use a hyphen ('-'). See [[#Examples|below]]) for an example.
An "Average Segment" includes the prestimulus baseline interval in microseconds. This is defined in the ''TriNo'' column of the event file.

=== Requirements ===
The file is valid if the header line contains at least the entries Code and one of ''Tms'', ''Tmu'' and ''Tsec''. The header specifications are case insensitive.
The file is invalid, if
• there are ambiguities in the header
• there is a data type mismatch in the data line
• an event time specifies an event which happened later than the end of the acquisition
Each omitted data entry is set to 0 or empty string by default.
A line with an invalid or unknown event code ''Code'' is skipped.

=== Examples ===
Here are a couple of typical examples: 
'''1.) Simple trigger file'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| Comnt
|-
| 100.234
| 1
| 3
| Trigger: 3
|-
| 2300.456
| 1
| 1
| Trigger:1
|-
| 4500.21
| 1
| 1
| Trigger:1
|-
| 9800.47
| 1
| 7
| Trigger:7
|-
| 12500.78
| 1
| 2
| Trigger:2
|-
| 21237
| 1
| 1
| Trigger:1
|}

This example event file can be downloaded here: [[Media:EventFileExample1.evt|Example 1]]

'''2.) Trigger file with reaction code and reaction time'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| RTsec
| RCode
|-
| 100.234
| 1
| 3
| 0.23
| 1
|-
| 2300.456
| 1
| 1
| 1.11
| 2
|-
| 4500.21
| 1
| 1
| 0.15
| 1
|-
| 9800.47
| 1
| 7
| 0.87
| 0
|-
| 12500.78
| 1
| 2
| 2.1
| 2
|-
| 21237
| 1
| 1
| 3
| 1
|}

This example event file can be downloaded here: [[Media:EventFileExample2.evt|Example 2]]

'''3.) Event file without triggers'''
{| style="border-spacing: 2px; border: 0px white;"
| Tmu
| Code
| Comnt
|-
| 10000.234
| 3
| Marker
|-
| 230000.456
| 12
|
|-
| 450000.21
| 14
|
|-
| 980000.47
| 12
|
|-
| 1250000.78
| 3
| Marker
|-
| 2123700
| 2
| Comment
|-
| 2534100.567
| 15
|
|}

This example event file can be downloaded here: [[Media:EventFileExample3.evt|Example 3]]

'''4.) File including triggers and events'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| RTsec
| RCode
| Comnt
|-
| 100.234
| 2
| 0
| 0
| 0
| CommentSet
|-
| 2300.456
| 1
| 2
|
|
|
|-
| 4500.21
| 1
| 1
| 0.15
| 1
|
|-
| 9800.47
| 11
|
|
|
|
|-
| 12500.78
| 3
|
|
|
|
|-
| 21237
| 2
| 0
| 3
| 1
| Comment
|-
| 25341.567
| 15
|
|
|
|
|}

This example event file can be downloaded here: [[Media:EventFileExample4.evt|Example 4]]

'''5.) New Segments'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| Comnt
|-
| 0
| 41
| 2010-04-26T15:30:20.31
| Start recording
|-
| 21000
| 41
| 2010-04-27T09:17:00.0
| Next day
|}

The new segment at the time 0 overrides the start time in the file.
A second segment at 21 s starts a new data block one day later at 9:17.

This example event file can be downloaded here: [[Media:EventFileExample5.evt|Example 5]]

'''6.) Average Segments'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| Comnt
|-
| 0
| 42
| 100000
| Cond 1: 25 avs
|-
| 1100
| 42
| 200000
| Cond 2: 201 avs
|}

The file contains two average segments. The first, with a prestimulus interval of 100 ms, has a duration of 1100 ms. The second, with a prestimulus interval of 200 ms, has a length up to the end of the data file.
1
This example event file can be downloaded here: [[Media:EventFileExample6.evt|Example 6]]

[[Category:ERP/ERF]]

Event File Format

2016-05-12T11:44:22Z

Andre: Added extra level 2 header to push the contents box to the top of the page.

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

== Overview ==
Event files (extension *.evt) contain triggers and events and can be loaded as an additional file to provide more information about the whole course of an EEG/MEG recording.
An event file can be edited by opening it in any text editor, e.g. Notepad. It is also possible to create new event files from scratch which can be imported into the data file later.
Note the following conventions for event files:
* Event descriptions are given in the columns of the event file
* Each file must contain a header line and data lines

=== File Header ===
The header is comprised of abbreviated descriptions for each column. Each entry in the data line must be specified in the header line at the correct column position. The order of the data elements and their description in the header line can be chosen arbitrarily and the entries can be separated by commas, tabs and/or spaces. The last n data elements can be omitted, if they are neither Code nor one of ''Tms'', ''Tmu'' or ''Tsec''. The following codes are recognized by the ERP module:
* ''Code'' - event code (integer, see section [[#Event Codes|Event Codes]])
* ''Tms'' - event time in milliseconds relative to the start of the data file or ''Tmu'' [in microseconds] or ''Tsec'' [in sec] (floating point value)
* ''TriNo'' - trigger number (integer) (identifies the trigger in the event bar of the main module)
* ''RCode'' - reaction code (integer)
* ''RTms'' - reaction time in milliseconds or ''RTmu'' or ''RTsec'' (floating point value)
* ''Comnt'' - comment to describe event (string of up to 39 characters), will be truncated if longer than 39 characters.
You can also define columns which should not be recognized by the ERP module. Simply specify these columns in the header with any unknown code. Therefore you might be able to use previously generated files without major changes.

=== Event Codes ===
The event code Code must be one of the following integers:

{| class="wikitable"
! style="text-align: center; font-weight: bold;" | Code
! style="text-align: center; font-weight: bold;" | Event/Trigger Type
|-
| 1
| Trigger
|-
| 2
| Comment
|-
| 3
| Marker
|-
| 11
| Pattern1
|-
| 12
| Pattern2
|-
| 13
| Pattern3
|-
| 14
| Pattern4
|-
| 15
| Pattern5
|-
| 21
| Artifact on
|-
| 22
| Artifact off
|-
| 31
| Epoch on
|-
| 32
| Epoch off
|-
| 41
| New segment
|-
| 42
| Average segment
|}

=== Additional Event Information ===
The event reaction time, event reaction code and event comment are represented by the comment in the main module as "''Comment (Rx,T____)''", where ''Comment'' is the event comment, ''x'' describes the reaction code and the underscored line will be filled with the reaction time. Reaction time and reaction code are only read if the event code specifies it as a trigger.
A "New Segment" event can include time information that defines the starting time of the segment. This is defined in the ''TriNo'' column of the event file. The format is YYYY-MM-DDTHH:MM:SS, e.g. 2010-04-26T15:30:20.31 (note: seconds are a decimal number). If no time is defined, use a hyphen ('-'). See [[#Examples|below]]) for an example.
An "Average Segment" includes the prestimulus baseline interval in microseconds. This is defined in the ''TriNo'' column of the event file.

=== Requirements ===
The file is valid if the header line contains at least the entries Code and one of ''Tms'', ''Tmu'' and ''Tsec''. The header specifications are case insensitive.
The file is invalid, if
• there are ambiguities in the header
• there is a data type mismatch in the data line
• an event time specifies an event which happened later than the end of the acquisition
Each omitted data entry is set to 0 or empty string by default.
A line with an invalid or unknown event code ''Code'' is skipped.

=== Examples ===
Here are a couple of typical examples: 
'''1.) Simple trigger file'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| Comnt
|-
| 100.234
| 1
| 3
| Trigger: 3
|-
| 2300.456
| 1
| 1
| Trigger:1
|-
| 4500.21
| 1
| 1
| Trigger:1
|-
| 9800.47
| 1
| 7
| Trigger:7
|-
| 12500.78
| 1
| 2
| Trigger:2
|-
| 21237
| 1
| 1
| Trigger:1
|}

This example event file can be downloaded here: [[Media:EventFileExample1.evt|Example 1]]

'''2.) Trigger file with reaction code and reaction time'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| RTsec
| RCode
|-
| 100.234
| 1
| 3
| 0.23
| 1
|-
| 2300.456
| 1
| 1
| 1.11
| 2
|-
| 4500.21
| 1
| 1
| 0.15
| 1
|-
| 9800.47
| 1
| 7
| 0.87
| 0
|-
| 12500.78
| 1
| 2
| 2.1
| 2
|-
| 21237
| 1
| 1
| 3
| 1
|}

This example event file can be downloaded here: [[Media:EventFileExample2.evt|Example 2]]

'''3.) Event file without triggers'''
{| style="border-spacing: 2px; border: 0px white;"
| Tmu
| Code
| Comnt
|-
| 10000.234
| 3
| Marker
|-
| 230000.456
| 12
|
|-
| 450000.21
| 14
|
|-
| 980000.47
| 12
|
|-
| 1250000.78
| 3
| Marker
|-
| 2123700
| 2
| Comment
|-
| 2534100.567
| 15
|
|}

This example event file can be downloaded here: [[Media:EventFileExample3.evt|Example 3]]

'''4.) File including triggers and events'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| RTsec
| RCode
| Comnt
|-
| 100.234
| 2
| 0
| 0
| 0
| CommentSet
|-
| 2300.456
| 1
| 2
|
|
|
|-
| 4500.21
| 1
| 1
| 0.15
| 1
|
|-
| 9800.47
| 11
|
|
|
|
|-
| 12500.78
| 3
|
|
|
|
|-
| 21237
| 2
| 0
| 3
| 1
| Comment
|-
| 25341.567
| 15
|
|
|
|
|}

This example event file can be downloaded here: [[Media:EventFileExample4.evt|Example 4]]

'''5.) New Segments'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| Comnt
|-
| 0
| 41
| 2010-04-26T15:30:20.31
| Start recording
|-
| 21000
| 41
| 2010-04-27T09:17:00.0
| Next day
|}

The new segment at the time 0 overrides the start time in the file.
A second segment at 21 s starts a new data block one day later at 9:17.

This example event file can be downloaded here: [[Media:EventFileExample5.evt|Example 5]]

'''6.) Average Segments'''
{| style="border-spacing: 2px; border: 0px white;"
| Tms
| Code
| TriNo
| Comnt
|-
| 0
| 42
| 100000
| Cond 1: 25 avs
|-
| 1100
| 42
| 200000
| Cond 2: 201 avs
|}

The file contains two average segments. The first, with a prestimulus interval of 100 ms, has a duration of 1100 ms. The second, with a prestimulus interval of 200 ms, has a length up to the end of the data file.
1
This example event file can be downloaded here: [[Media:EventFileExample6.evt|Example 6]]

[[Category:ERP/ERF]]

File:S2 ArtRej EventFile.evt

2016-05-12T11:35:46Z

Andre: Event file that includes a trigger identifying the epochs that are rejected by an artifact scan.

Event file that includes a trigger identifying the epochs that are rejected by an artifact scan.

File:ArtifactRejection.xlsx

2016-05-12T11:33:11Z

Andre: Excel table for computing the artifact rejection and assisting in generating a evt file with a trigger for the rejected artifacts.

Excel table for computing the artifact rejection and assisting in generating a evt file with a trigger for the rejected artifacts.

Create Triggers for Artifact-Rejected Epochs

2016-05-12T11:24:31Z

Andre: Fixed pdg page link.

Here we demonstrate how to track what epochs were rejected by the artifact rejection. There might be experiments were one is interested in actually analyzing the rejected epochs. This information is available in the respective paradigm file but has to be extracted by the user. The idea is to create a new trigger for the rejected epochs that can later be read back into BESA Research.

In this example we use the subject 2 of the Auditory Intensity experiment located in the BESA Research examples folder (../Examples/AuditoryIntensity/S2.cnt).
# Open the raw file S2.cnt and create a new paradigm for it. In the conditions tab create only conditions that directly correspond to each of the respective triggers (in my case I have 5 triggers, thus I have 5 conditions, one for each "current" trigger).
# Define the Epochs and Filters as you like.
# Run the artifact rejection.
# Close everything and find the respective paradigm file in the folder of raw file S2.cnt (typically %basename%.pdg, in my case S2.pdg, see [[File:S2.PDG|thumb]]).
# Open the paradigm file in a text editor (e.g. Notepad, please do not use word as it might change the format of the text).
# Find the section starting with [ArtifactScan], ignore the following 4 lines (see the [[Paradigm File Format in BESA|PDG file format description]] for details if you are curious!) and copy everything thereafter to a new txt file.
# Import the newly created file in Excel by specifying that spaces and tabs are the delimiters for the columns. Save the file in excel format and leave it open. Be sure to have the decimal separator set to " . " and the thousands separator set to none.
# Open the attached excel file [[File:ArtifactRejection.xlsx]]. In the first sheet you should be able to see a blue painted area. Please copy the contents of the table you created in there. Be sure to copy the values only (not e.g. the format). The table will basically check if a particular epoch was rejected or not. In case it will substitute the value for the trigger on the left most side of the table with a new trigger (12 in this case, marked in orange in the table). The table was made to support up to 257 channels, in case you have more please just adjust the formulas in Exceeds max Amp etc…
Please also set the right artifact rejection values (cells are marked with green in the table) as in the paradigm window.
Please also make the tables length match the length of your data by copy pasting the 4 row x 10 columns block accordingly (marked in orange for easier identification!).
# Ok, now you should be almost done. The 5 leftmost columns on your table should have all the necessary information to create a new event file. Please copy the 4 columns starting from the cell immediately below the label "Tmu" (A13 if nobody changed the table in the meantime) to the end of the table. Insert them in a new sheet (NewEventFile) from A2 onward. Please be careful to paste values only! (Do paste special->values only in excel).
# Almost there! Please select all the data in the new sheet and press Sort & Filter, select Custom sort, and choose sort by Column A, Sort On Values and choose A->Z as order. This should effectively remove the empty rows.
# Please select all the relevant rows for the 5 columns in the new sheet and just copy them to a new file in Notepad. Please save the file with the evt extension. You can see the evt file obtained from the example described here [[File:S2_ArtRej_EventFile.evt]].
# Go back to BESA, remove all the existing triggers in ERP->Edit Triggers->Delete. Once this is done please load the file evt file you created by doing ERP->Open Event File.
# Trigger 12 should now appear in your data and represents those triggers that will be removed during artifact rejection.
# Using the paradigm window you should now be able to run your analysis using the new trigger 12 you created.

Create Triggers for Artifact-Rejected Epochs

2016-05-12T11:23:04Z

Andre: Added links to the excel table, generated event file and pdg file after artifact rejection.

Here we demonstrate how to track what epochs were rejected by the artifact rejection. There might be experiments were one is interested in actually analyzing the rejected epochs. This information is available in the respective paradigm file but has to be extracted by the user. The idea is to create a new trigger for the rejected epochs that can later be read back into BESA Research.

In this example we use the subject 2 of the Auditory Intensity experiment located in the BESA Research examples folder (../Examples/AuditoryIntensity/S2.cnt).
# Open the raw file S2.cnt and create a new paradigm for it. In the conditions tab create only conditions that directly correspond to each of the respective triggers (in my case I have 5 triggers, thus I have 5 conditions, one for each "current" trigger).
# Define the Epochs and Filters as you like.
# Run the artifact rejection.
# Close everything and find the respective paradigm file in the folder of raw file S2.cnt (typically %basename%.pdg, in my case S2.pdg, see [[File:S2.PDG|thumb]]).
# Open the paradigm file in a text editor (e.g. Notepad, please do not use word as it might change the format of the text).
# Find the section starting with [ArtifactScan], ignore the following 4 lines (see the [[page name for the pdg format|PDG file format description]] for details if you are curious!) and copy everything thereafter to a new txt file.
# Import the newly created file in Excel by specifying that spaces and tabs are the delimiters for the columns. Save the file in excel format and leave it open. Be sure to have the decimal separator set to " . " and the thousands separator set to none.
# Open the attached excel file [[File:ArtifactRejection.xlsx]]. In the first sheet you should be able to see a blue painted area. Please copy the contents of the table you created in there. Be sure to copy the values only (not e.g. the format). The table will basically check if a particular epoch was rejected or not. In case it will substitute the value for the trigger on the left most side of the table with a new trigger (12 in this case, marked in orange in the table). The table was made to support up to 257 channels, in case you have more please just adjust the formulas in Exceeds max Amp etc…
Please also set the right artifact rejection values (cells are marked with green in the table) as in the paradigm window.
Please also make the tables length match the length of your data by copy pasting the 4 row x 10 columns block accordingly (marked in orange for easier identification!).
# Ok, now you should be almost done. The 5 leftmost columns on your table should have all the necessary information to create a new event file. Please copy the 4 columns starting from the cell immediately below the label "Tmu" (A13 if nobody changed the table in the meantime) to the end of the table. Insert them in a new sheet (NewEventFile) from A2 onward. Please be careful to paste values only! (Do paste special->values only in excel).
# Almost there! Please select all the data in the new sheet and press Sort & Filter, select Custom sort, and choose sort by Column A, Sort On Values and choose A->Z as order. This should effectively remove the empty rows.
# Please select all the relevant rows for the 5 columns in the new sheet and just copy them to a new file in Notepad. Please save the file with the evt extension. You can see the evt file obtained from the example described here [[File:S2_ArtRej_EventFile.evt]].
# Go back to BESA, remove all the existing triggers in ERP->Edit Triggers->Delete. Once this is done please load the file evt file you created by doing ERP->Open Event File.
# Trigger 12 should now appear in your data and represents those triggers that will be removed during artifact rejection.
# Using the paradigm window you should now be able to run your analysis using the new trigger 12 you created.

Create Triggers for Artifact-Rejected Epochs

2016-05-12T09:24:50Z

Andre: link to file

Here we demonstrate how to track what epochs were rejected by the artifact rejection. There might be experiments were one is interested in actually analyzing the rejected epochs. This information is available in the respective paradigm file but has to be extracted by the user. The idea is to create a new trigger for the rejected epochs that can later be read back into BESA Research.

In this example we use the subject 2 of the Auditory Intensity experiment located in the BESA Research examples folder (../Examples/AuditoryIntensity/S2.cnt).
# Open the raw file S2.cnt and create a new paradigm for it. In the conditions tab create only conditions that directly correspond to each of the respective triggers (in my case I have 5 triggers, thus I have 5 conditions, one for each "current" trigger).
# Define the Epochs and Filters as you like.
# Run the artifact rejection.
# Close everything and find the respective paradigm file in the folder of raw file S2.cnt (typically %basename%.pdg, in my case S2.pdg, see [[Media:S2.pdg]]).
# Open the paradigm file in a text editor (e.g. Notepad, please do not use word as it might change the format of the text).
# Find the section starting with [ArtifactScan], ignore the following 4 lines (see the [[page name for the pdg format|PDG file format description]] for details if you are curious!) and copy everything thereafter to a new txt file.
# Import the newly created file in Excel by specifying that spaces and tabs are the delimiters for the columns. Save the file in excel format and leave it open.
# Open the attached excel file. In the first sheet you should be able to see a blue painted area. Please copy the contents of the table you created in there. Be sure to copy the values only (not e.g. the format). The table will basically check if a particular epoch was rejected or not. In case it will substitute the value for the trigger on the left most side of the table with a new trigger (12 in this case, marked in orange in the table). The table was made to support up to 256 channels, in case you have more please just adjust the formulas in Exceeds max Amp etc…
Please also set the right artifact rejection values (cells are marked with green in the table) as in the paradigm window.
Please also make the tables length match the length of your data by copy pasting the 4 row x 10 columns block accordingly.
# Ok, now you should be almost done. The 5 leftmost columns on your table should have all the necessary information to create a new event file. Please copy the 4 columns starting from the cell immediately below the label "Tmu" (A13 if nobody changed the table in the meantime) to the end of the table. Insert them in a new sheet (NewEventFile) from A2 onward. Please be careful to paste values only! (Do paste special->values only in excel).
# Almost there! Please select all the data in the new sheet and press Sort & Filter, select Custom sort, and choose sort by Column A, Sort On Values and choose A->Z as order. This should effectively remove the empty rows.
# Please select all the relevant rows for the 5 columns in the new sheet and just copy them to a new file in Notepad. Please save the file with the evt extension. Attached you can see the evt file I got from the example above.
# Go back to BESA, remove all the existing triggers in ERP->Edit Triggers->Delete. Once this is done please load the file evt file you created by doing ERP->Open Event File.
# Trigger 12 should now appear in your data and represents those triggers that will be removed during artifact rejection.
# Using the paradigm window you should now be able to run your analysis using the new trigger 12 you created.

File:S2.PDG

2016-05-12T09:23:04Z

Andre: Example for evaluating the artifact rejection results that are stored in the pdg file.

Example for evaluating the artifact rejection results that are stored in the pdg file.

Create Triggers for Artifact-Rejected Epochs

2016-05-12T09:18:31Z

Andre: Small changes.

Here we demonstrate how to track what epochs were rejected by the artifact rejection. There might be experiments were one is interested in actually analyzing the rejected epochs. This information is available in the respective paradigm file but has to be extracted by the user. The idea is to create a new trigger for the rejected epochs that can later be read back into BESA Research.

In this example we use the subject 2 of the Auditory Intensity experiment located in the BESA Research examples folder (../Examples/AuditoryIntensity/S2.cnt).
# Open the raw file S2.cnt and create a new paradigm for it. In the conditions tab create only conditions that directly correspond to each of the respective triggers (in my case I have 5 triggers, thus I have 5 conditions, one for each "current" trigger).
# Define the Epochs and Filters as you like.
# Run the artifact rejection.
# Close everything and find the respective paradigm file in the folder of raw file S2.cnt (typically %basename%.pdg, in my case S2.pdg).
# Open the paradigm file in a text editor (e.g. Notepad, please do not use word as it might change the format of the text).
# Find the section starting with [ArtifactScan], ignore the following 4 lines (see the [[page name for the pdg format|PDG file format description]] for details if you are curious!) and copy everything thereafter to a new txt file.
# Import the newly created file in Excel by specifying that spaces and tabs are the delimiters for the columns. Save the file in excel format and leave it open.
# Open the attached excel file. In the first sheet you should be able to see a blue painted area. Please copy the contents of the table you created in there. Be sure to copy the values only (not e.g. the format). The table will basically check if a particular epoch was rejected or not. In case it will substitute the value for the trigger on the left most side of the table with a new trigger (12 in this case, marked in orange in the table). The table was made to support up to 256 channels, in case you have more please just adjust the formulas in Exceeds max Amp etc…
Please also set the right artifact rejection values (cells are marked with green in the table) as in the paradigm window.
Please also make the tables length match the length of your data by copy pasting the 4 row x 10 columns block accordingly.
# Ok, now you should be almost done. The 5 leftmost columns on your table should have all the necessary information to create a new event file. Please copy the 4 columns starting from the cell immediately below the label "Tmu" (A13 if nobody changed the table in the meantime) to the end of the table. Insert them in a new sheet (NewEventFile) from A2 onward. Please be careful to paste values only! (Do paste special->values only in excel).
# Almost there! Please select all the data in the new sheet and press Sort & Filter, select Custom sort, and choose sort by Column A, Sort On Values and choose A->Z as order. This should effectively remove the empty rows.
# Please select all the relevant rows for the 5 columns in the new sheet and just copy them to a new file in Notepad. Please save the file with the evt extension. Attached you can see the evt file I got from the example above.
# Go back to BESA, remove all the existing triggers in ERP->Edit Triggers->Delete. Once this is done please load the file evt file you created by doing ERP->Open Event File.
# Trigger 12 should now appear in your data and represents those triggers that will be removed during artifact rejection.
# Using the paradigm window you should now be able to run your analysis using the new trigger 12 you created.

Create Triggers for Artifact-Rejected Epochs

2016-04-08T15:27:33Z

Andre: minor text changes and reference fixes

Here we demonstrate how to track what epochs were rejected by the artifact rejection. There might be experiments were one is interested in actually analyzing the rejected epochs. This information is available in the respective paradigm file but has to be extracted by the user. The idea is to create a new trigger for the rejected epochs that can later be read back in into BESA Research.

In this example we use the subject 2 of the Auditory Intensity experiment located in the BESA Research examples folder (../Examples/AuditoryIntensity/S2.cnt).
# Open the raw file S2.cnt and create a new paradigm for it. In the conditions tab create only conditions that directly correspond to each of the respective triggers (in my case I have 5 triggers, thus I have 5 conditions, one for each "current" trigger).
# Define the Epochs and Filters as you like.
# Run the artifact rejection.
# Close everything and find the respective paradigm file in the folder of raw file S2.cnt (typically baseame.pdg, in my case S2.pdg).
# Open the paradigm file in a text editor (e.g. Notepad, please do not use word as it might change the format of the text).
# Find the section starting with [ArtifactScan], ignore the following 4 lines (see the [[page name for the pdg format|PDG file format description]] for details) and copy everything thereafter to a new txt file.
# Open the newly created file in Excel by specifying that spaces and tabs are the delimiters for the columns. Save the file in excel format and leave it open.
# Open the attached excel file. In the first sheet you should be able to see a blue painted area. Please copy the contents of the table you created in there. Be sure to copy the values only (not e.g. the format). The table will basically check if a particular epoch was rejected or not. In case it will substitute the value for the trigger on the left most side of the table with a new trigger (12 in this case, marked in orange in the table). The table was made to support up to 256 channels, in case you have more please just adjust the formulas in Exceeds max Amp etc…
Please also set the right artifact rejection values (cells are marked with green in the table) as in the paradigm window.
Please also make the tables length match the length of your data by copy pasting the 4 row x 10 columns block accordingly.
# Ok, now you should be almost done. The 5 leftmost columns on your table should have all the necessary information to create a new event file. Please copy the 4 columns starting from the cell immediately below the label "Tmu" (A13 if nobody changed the table in the meantime) to the end of the table. Insert them in a new sheet (NewEventFile, also in the table I sent you) from A2 onwards. Please be careful to paste values only! (Do paste special->values only in excel).
# Almost there! Please select all the data in the new sheet and press Sort & Filter, select Custom sort, and choose sort by Column A, Sort On Values and choose A->Z as order. This should effectively remove the empty rows.
# Please select all the relevant rows for the 5 columns in the new sheet and just copy them to a new file in Notepad. Please save the file with the evt extension. Attached you can see the evt file I got from the example above.
# Go back to BESA, remove all the existing triggers in ERP->Edit Triggers->Delete. Once this is done please load the file evt file you created by doing ERP->Open Event File.
# Trigger 12 should now appear in your data and represents those triggers that will be removed during artefact rejection.
# Using the paradigm window you should now be able to run your analysis.

Create Triggers for Artifact-Rejected Epochs

2016-04-08T15:07:48Z

Andre: minor text changes

Here we demonstrate how to track what epochs were rejected by the artifact rejection. There might be experiments were one is interested in actually analyzing the rejected epochs. This information is available in the respective paradigm file but has to be extracted by the user. The idea is to create a new trigger for the rejected epochs that can later be read back in into BESA Research.

In this example we use the subject 2 of the Auditory Intensity experiment located in the BESA Research examples folder (../Examples/AuditoryIntensity/S2.cnt).
# Open the raw file S2.cnt and create a new paradigm for it. In the conditions tab create only conditions that directly correspond to each of the respective triggers (in my case I have 5 triggers, thus I have 5 conditions, one for each "current" trigger).
# Define the Epochs and Filters as you like.
# Run the artifact rejection.
# Close everything and find the respective paradigm file in the folder of raw file S2.cnt (typically baseame.pdg, in my case S2.pdg).
# Open the paradigm file in a text editor (e.g. Notepad, please do not use word as it might change the format of the text).
# Find the section starting with [ArtifactScan], ignore the following 4 lines (see the [[page name for the pdg format|PDG file format description]] for details) and copy everything thereafter to a new txt file.
# Open the newly created file in Excel by specifying that spaces and tabs are the delimiters for the columns. Save the file in excel format and leave it open.
# Open the attached excel file. In the first sheet you should be able to see a blue painted area. Please copy the contents of the table you created in there. Basically this will check if a particular epoch was rejected or not. In case it will substitute the value for the trigger on the left most side of the table with a new trigger (12 in this case, marked in orange in the table). I made the table to support up to 140 channels, in case you have more please just adjust the formulas in Exceeds max Amp etc…
Please also set the right artefact rejection values (cells are marked with green in the table) as in the paradigm window.
Please also make the tables length match the length of your data by copy pasting the 4 row x 10 lines block accordingly.
# Ok, now you should be almost done. The 5 leftmost columns on your table should have all the necessary information to create a new event file. Please copy the 4 columns starting from A13 to the end of the table. Insert them in a new sheet (NewEventFile, also in the table I sent you) from A2 onwards. Please be careful to paste value only! (Do paste special->values only in excel).
# Almost there! Please select all the data in the new sheet and press Sort & Filter, select Custom sort, and choose sort by Column A, Sort On Values and choose A->Z as order. This should effectively remove the empty rows.
# Please select all the relevant rows for the 5 columns in the new sheet and just copy them to a new file in Notepad. Please save the file with the evt extension.
# Go back to BESA, remove all the existing triggers in ERP->Edit Triggers->Delete. Once this is done please load the file created in 10 by doing ERP->Open Event File.
# Trigger 12 should now appear in your data and represents those triggers that will be removed during artefact rejection.
# Using the paradigm window you should now be able to run your analysis.

Create Triggers for Artifact-Rejected Epochs

2016-04-08T15:05:09Z

Andre: added some text, still quite a lot to do.

Here we demonstrate how to track what epochs were rejected by the artifact rejection. There might be experiments were one is interested in actually analyzing the rejected epochs. This information is available in the respective paradigm file but has to be extracted by the user. The idea is to create a new trigger for the rejected epochs that can later be read back in into BESA Research.

In this example we use the subject 2 of the Auditory Intensity experiment located in the BESA Research examples folder (../Examples/AuditoryIntensity/S2.cnt).
# Open the raw file S2.cnt and create a new paradigm for it. In the conditions tab create only conditions that directly correspond to each of the respective triggers (in my case I have 5 triggers, thus I have 5 conditions, one for each "current" trigger).
# Define the Epochs and Filters as you like.
# Run the artifact rejection.
# Close everything and find the respective paradigm file in the folder of raw file S2.cnt (typically baseame.pdg, in my case S2.pdg).
# Open the paradigm file in a text editor (e.g. Notepad, please do not use word as it might change the format of the text).
# Find the section starting with [ArtifactScan], ignore the following 4 lines (see the [[page name for the pdg format|PDG file format description]] for details) and copy everything thereafter to a new txt file.
# Open the newly created file in Excel by specifying that spaces are the delimiters for the columns. Save the file in excel format and leave it open.
# Open the attached excel file. In the first sheet you should be able to see a blue painted area. Please copy the contents of the table you created in there. Basically this will check if a particular epoch was rejected or not. In case it will substitute the value for the trigger on the left most side of the table with a new trigger (12 in this case, marked in orange in the table). I made the table to support up to 140 channels, in case you have more please just adjust the formulas in Exceeds max Amp etc…
Please also set the right artefact rejection values (cells are marked with green in the table) as in the paradigm window.
Please also make the tables length match the length of your data by copy pasting the 4 row x 10 lines block accordingly.
# Ok, now you should be almost done. The 5 leftmost columns on your table should have all the necessary information to create a new event file. Please copy the 4 columns starting from A13 to the end of the table. Insert them in a new sheet (NewEventFile, also in the table I sent you) from A2 onwards. Please be careful to paste value only! (Do paste special->values only in excel).
# Almost there! Please select all the data in the new sheet and press Sort & Filter, select Custom sort, and choose sort by Column A, Sort On Values and choose A->Z as order. This should effectively remove the empty rows.
# Please select all the relevant rows for the 5 columns in the new sheet and just copy them to a new file in Notepad. Please save the file with the evt extension.
# Go back to BESA, remove all the existing triggers in ERP->Edit Triggers->Delete. Once this is done please load the file created in 10 by doing ERP->Open Event File.
# Trigger 12 should now appear in your data and represents those triggers that will be removed during artefact rejection.
# Using the paradigm window you should now be able to run your analysis.

Create Triggers for Artifact-Rejected Epochs

2016-04-08T12:26:40Z

Andre: migrated available text to wiki

=To Do!=

Main Page

2016-04-08T11:31:21Z

Andre: /* BESA recipes */ fixed new name of Control of BESA Research by external programs

=Welcome to the BESA Wiki!=

We just started working on this wiki!

This wiki is designed to help users with typical questions around using BESA to achieve their goals.
Topics are available for the following categories:

== FAQ ==

=== Licensing ===
[[Licensing]]

=== Data Review and Analysis ===

[[Export Single Trial Data]]

[[How to Average EEG channels]]

[[Averaging Across EEG Datasets from Different Recording Systems]]

[[Time Frequency Resolution In BESA]]

[[Change Waveform Colours]]

[[Supported Data Formats]]

=== Matlab interface ===

[[How Do I Configure the Matlab Interface?]]

[[Updating the Matlab Interface after Matlab Upgrade]]

=== BESA Statistics ===

[[Cluster Alpha vs. Neighbor Distance]]

=== Trouble shooting in BESA MRI and BESA Statistics ===

[[MF Error 211]]

== BESA recipes ==

[[Control of BESA Research by external programs]]

[[Correcting Volume Conductor Segmentations]]

[[Random Averaging]]

[[Statistical Analysis for More than Two Levels]]

== Coming soon ==
* a collection of useful batches
* and further content we will be publishing on this wiki

Contributions to the Wiki from the community are very welcome! Please create an account with a valid email to edit the BESA Wiki's content.

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Control of BESA Research by external programs

2016-04-08T11:30:30Z

Andre: Andre moved page Control BESA Research by external programs to Control of BESA Research by external programs without leaving a redirect: bad english?

=Control of BESA Research by external programs (valid for BESA Research versions 5.2.2 and higher)=

==Purpose and Procedure==
This document describes how to start BESA Research from an external program (a patient database management program or an EEG review program) with a list of one or more files to be opened in BESA Research. It is recommended to create an icon BESA or BESA Research in the external program and to start BESA Research using this icon.
* To start BESA Research from the external program to review EEG data, this program must first write the foc_link.sub file to disk. It must contain the data file(s) to be opened (see [[#Format of foc_link.sub|Format of foc_link.sub]]). Then BESA Research needs to be started as described below in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]].
* If BESA Research is already running, first the file foc_link.sub has to be updated or created.
* If the foc_link.sub file is written to the BESA Research installation folder, BESA Research can either be accessed by executing a WM_COMMAND (see [[#Open EEG data while BESA Research is running|Open EEG data while BESA Research is running]]) or using the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]].
* If the foc_link.sub file is written to another folder, only the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]] can be used.
We recommend using the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]], since this will work in all cases, and the foc_link.sub file can be located in any arbitrary folder.

==Start BESA Research to open EEG data==
Use the following command to start BESA Research with the command line parameter:
<foc_link.sub file path>\foc_link.sub
The foc_link.sub file contains a list of the datasets to be loaded at program start. The file format is described below in [[#Format of foc_link.sub|Format of foc_link.sub]].
For example, to load EEGs in BESA 5.2.2 or higher (e.g. BESA Research 5.3) at program start (assumed to be installed in C:\BESA52 and file foc_link.sub file located in the BESA Research installation folder), apply the following command:

C:\BESA52\BESA.exe C:\BESA52\foc_link.sub
==Open EEG data while BESA Research is running==
If you want to load a different EEG data file while BESA Research is running, simply execute the same command as upon start of BESA Research after updating the file list in foc_link.sub, e.g.
C:\BESA52\BESA.exe C:\BESA52\foc_link.sub
BESA.exe interprets this call from a database or review program. It checks whether BesaMain.exe is already running. If yes, it keeps BesaMain.exe running, closes the old files, and opens the new file(s) listed in foc_link.sub. If not yet running, BESA.exe starts BesaMain.exe with the new file(s) listed in foc_link.sub. Thus, the procedure for changing an EEG file in BESA Research is the same as described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]] for starting BESA Research with the first file(s).

( In older BESA versions (up to version 5.2) a different procedure was required that is still working but not required anymore:
When BESA receives a WM_COMMAND message with Id 3000 (Id = (int)(LOWORD(wParam)), file foc_link.sub in the BESA installation folder was reread. While this feature is still working, it is not recommended anymore because the automatic handling by BESA.exe is much simpler and no WM_COMMAND message is needed. )
Notes:
* Files that are currently open but not specified in foc_link.sub are closed. Only the specified files are opened.
* When a file is closed in BESA Research, the corresponding entry in the foc_link.sub file is deleted.
==Format of foc_link.sub==
For each EEG to be loaded write the following lines to the foc_link.sub file
StartedBy: <Your program name>
EvtFilePath: <path + filename of the evt-File to be loaded for the EEG>
EventCode: [<number>] <number> <number>
ElecFilePath: <path + filename of the elp-File to be loaded for the EEG>
ReviewDateTime: <YYYY-MM-DD/HH:MM:SS>
FilePath: <path + filename of EEG to be loaded>

The first line, StartedBy (followed by a colon and a blank), is an optional tag that can be set to specify the name of your application which calls BESA Research.
The second line, EvtFilePath (followed by a colon and a blank), is an optional tag that can be set to load events specified in an evt-file. If this tag is not defined, only the events found in the EEG data file are loaded.
The third line, EventCode (followed by a colon and a blank), is an optional tag that can be set to define the type and range of your events stored in the event file specified in EvtFilePath.
The first number defines the code (type) of your events (e.g. 1=Trigger). The second number defines the event ID range minimum and the third number stands for the maximum.
If this tag is defined, BESA Research will remove all events from the EEG which IDs are within the defined range. Then the new events are loaded instead. If this tag is not defined, the new events are loaded in addition to existing events. This tag will be ignored if no EvtFilePath is defined.
The fourth line, ElecFilePath (followed by a colon and a blank), is an optional tag that can be set to attach an electrode configuration specified in an elp-file. If this tag is not defined, the original/recorded electrode configuration found in the EEG-Data file is loaded.
The fifth line, ReviewDateTime (followed by a colon and a blank), is an optional tag that can be set to specify a time at which the review should be started. If this tag is not defined, the review starts at the beginning of the file.
The FilePath line must be the last line for each EEG entry and has to be defined. The tag is followed by path+filename (after the obligatory colon and blank). A maximum of 256 characters for path+filename is read.

==Examples==
===Open one EEG data file at the beginning.===

FilePath: D:\EEG\000822WC.eeg

===Open one EEG data file at a defined position.===

ReviewDateTime: 2008-07-02/12:18:12
FilePath: D:\EEG\000822WC.eeg

===Open three EEG data files, position for second data file is specified.===

FilePath: D:\EEG\000822WC.eeg

ReviewDateTime: 2008-07-02/12:18:12
FilePath: D:\EEG\000822WD.eeg

FilePath: D:\EEG\000822WE.eeg

We suggest to separate single EEG entries by an empty line, although this is not required.
===Complete foc_link.sub entry with all possible tags===

StartedBy: BESA Epilepsy
ElecFilePath: C:\ELP-FILES\000717WA-STD.elp
EvtFilePath: C:\EVT-FILES\000717WA-STD.evt
EventCode: 1 51 60
ReviewDateTime: 2008-07-02/14:20:12
FilePath: D:\EEG\000717WA.eeg

[[Category:BESA Research]]

Control of BESA Research by external programs

2016-04-08T11:28:04Z

Andre: Control OF BESA ....

Main Page

2016-04-08T10:18:32Z

Andre: /* BESA recipes */ added Control BESA Research by external programs

=Welcome to the BESA Wiki!=

We just started working on this wiki!

This wiki is designed to help users with typical questions around using BESA to achieve their goals.
Topics are available for the following categories:

== FAQ ==

=== Licensing ===
[[Licensing]]

=== Data Review and Analysis ===

[[Export Single Trial Data]]

[[How to Average EEG channels]]

[[Averaging Across EEG Datasets from Different Recording Systems]]

[[Time Frequency Resolution In BESA]]

[[Change Waveform Colours]]

[[Supported Data Formats]]

=== Matlab interface ===

[[How Do I Configure the Matlab Interface?]]

[[Updating the Matlab Interface after Matlab Upgrade]]

=== BESA Statistics ===

[[Cluster Alpha vs. Neighbor Distance]]

=== Trouble shooting in BESA MRI and BESA Statistics ===

[[MF Error 211]]

== BESA recipes ==

[[Control BESA Research by external programs]]

[[Correcting Volume Conductor Segmentations]]

[[Random Averaging]]

[[Statistical Analysis for More than Two Levels]]

== Coming soon ==
* a collection of useful batches
* and further content we will be publishing on this wiki

Contributions to the Wiki from the community are very welcome! Please create an account with a valid email to edit the BESA Wiki's content.

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Control of BESA Research by external programs

2016-04-08T10:03:34Z

Andre: /* Purpose and Procedure */ minor change

=Control BESA Research by external programs (valid for BESA Research versions 5.2.2 and higher)=

==Purpose and Procedure==
This document describes how to start BESA Research from an external program (a patient database management program or an EEG review program) with a list of one or more files to be opened in BESA Research. It is recommended to create an icon BESA or BESA Research in the external program and to start BESA Research using this icon.
* To start BESA Research from the external program to review EEG data, this program must first write the foc_link.sub file to disk. It must contain the data file(s) to be opened (see [[#Format of foc_link.sub|Format of foc_link.sub]]). Then BESA Research needs to be started as described below in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]].
* If BESA Research is already running, first the file foc_link.sub has to be updated or created.
* If the foc_link.sub file is written to the BESA Research installation folder, BESA Research can either be accessed by executing a WM_COMMAND (see [[#Open EEG data while BESA Research is running|Open EEG data while BESA Research is running]]) or using the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]].
* If the foc_link.sub file is written to another folder, only the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]] can be used.
We recommend using the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]], since this will work in all cases, and the foc_link.sub file can be located in any arbitrary folder.

==Start BESA Research to open EEG data==
Use the following command to start BESA Research with the command line parameter:
<foc_link.sub file path>\foc_link.sub
The foc_link.sub file contains a list of the datasets to be loaded at program start. The file format is described below in [[#Format of foc_link.sub|Format of foc_link.sub]].
For example, to load EEGs in BESA 5.2.2 or higher (e.g. BESA Research 5.3) at program start (assumed to be installed in C:\BESA52 and file foc_link.sub file located in the BESA Research installation folder), apply the following command:

C:\BESA52\BESA.exe C:\BESA52\foc_link.sub
==Open EEG data while BESA Research is running==
If you want to load a different EEG data file while BESA Research is running, simply execute the same command as upon start of BESA Research after updating the file list in foc_link.sub, e.g.
C:\BESA52\BESA.exe C:\BESA52\foc_link.sub
BESA.exe interprets this call from a database or review program. It checks whether BesaMain.exe is already running. If yes, it keeps BesaMain.exe running, closes the old files, and opens the new file(s) listed in foc_link.sub. If not yet running, BESA.exe starts BesaMain.exe with the new file(s) listed in foc_link.sub. Thus, the procedure for changing an EEG file in BESA Research is the same as described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]] for starting BESA Research with the first file(s).

( In older BESA versions (up to version 5.2) a different procedure was required that is still working but not required anymore:
When BESA receives a WM_COMMAND message with Id 3000 (Id = (int)(LOWORD(wParam)), file foc_link.sub in the BESA installation folder was reread. While this feature is still working, it is not recommended anymore because the automatic handling by BESA.exe is much simpler and no WM_COMMAND message is needed. )
Notes:
* Files that are currently open but not specified in foc_link.sub are closed. Only the specified files are opened.
* When a file is closed in BESA Research, the corresponding entry in the foc_link.sub file is deleted.
==Format of foc_link.sub==
For each EEG to be loaded write the following lines to the foc_link.sub file
StartedBy: <Your program name>
EvtFilePath: <path + filename of the evt-File to be loaded for the EEG>
EventCode: [<number>] <number> <number>
ElecFilePath: <path + filename of the elp-File to be loaded for the EEG>
ReviewDateTime: <YYYY-MM-DD/HH:MM:SS>
FilePath: <path + filename of EEG to be loaded>

The first line, StartedBy (followed by a colon and a blank), is an optional tag that can be set to specify the name of your application which calls BESA Research.
The second line, EvtFilePath (followed by a colon and a blank), is an optional tag that can be set to load events specified in an evt-file. If this tag is not defined, only the events found in the EEG data file are loaded.
The third line, EventCode (followed by a colon and a blank), is an optional tag that can be set to define the type and range of your events stored in the event file specified in EvtFilePath.
The first number defines the code (type) of your events (e.g. 1=Trigger). The second number defines the event ID range minimum and the third number stands for the maximum.
If this tag is defined, BESA Research will remove all events from the EEG which IDs are within the defined range. Then the new events are loaded instead. If this tag is not defined, the new events are loaded in addition to existing events. This tag will be ignored if no EvtFilePath is defined.
The fourth line, ElecFilePath (followed by a colon and a blank), is an optional tag that can be set to attach an electrode configuration specified in an elp-file. If this tag is not defined, the original/recorded electrode configuration found in the EEG-Data file is loaded.
The fifth line, ReviewDateTime (followed by a colon and a blank), is an optional tag that can be set to specify a time at which the review should be started. If this tag is not defined, the review starts at the beginning of the file.
The FilePath line must be the last line for each EEG entry and has to be defined. The tag is followed by path+filename (after the obligatory colon and blank). A maximum of 256 characters for path+filename is read.

==Examples==
===Open one EEG data file at the beginning.===

FilePath: D:\EEG\000822WC.eeg

===Open one EEG data file at a defined position.===

ReviewDateTime: 2008-07-02/12:18:12
FilePath: D:\EEG\000822WC.eeg

===Open three EEG data files, position for second data file is specified.===

FilePath: D:\EEG\000822WC.eeg

ReviewDateTime: 2008-07-02/12:18:12
FilePath: D:\EEG\000822WD.eeg

FilePath: D:\EEG\000822WE.eeg

We suggest to separate single EEG entries by an empty line, although this is not required.
===Complete foc_link.sub entry with all possible tags===

StartedBy: BESA Epilepsy
ElecFilePath: C:\ELP-FILES\000717WA-STD.elp
EvtFilePath: C:\EVT-FILES\000717WA-STD.evt
EventCode: 1 51 60
ReviewDateTime: 2008-07-02/14:20:12
FilePath: D:\EEG\000717WA.eeg

[[Category:BESA Research]]

Control of BESA Research by external programs

2016-04-08T09:59:20Z

Andre: fixed some section links

=Control BESA Research by external programs (valid for BESA Research versions 5.2.2 and higher)=

==Purpose and Procedure==
This document describes how to start BESA Research from an external program (a patient database management program or an EEG review program) with a list of one or more files to be opened in BESA Research. It is recommended to create an icon BESA or BESA Research in the external program and to start BESA Research using this icon.
* To start BESA Research from the external program to review EEG data, this program must first write the foc_link.sub file to disk. It must contain the data file(s) to be opened (see [[#Format of foc_link.sub|Format of foc_link.sub]]). Then BESA Research needs to be started as described below in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]].
* If BESA Research is already running, first the file foc_link.sub has to be updated or created.
* If the foc_link.sub file is written to the BESA Research installation folder, BESA Research can either be accessed by executing a WM_COMMAND (see [[#Open EEG data while BESA Research is running|Open EEG data while BESA Research is running]]) or using the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]].
* If the foc_link.sub file is written to another folder, only the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]] can be used.
We recommend using the procedure described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]] in all cases, since this will work in all cases, and the foc_link.sub file can be located in any arbitrary folder.

==Start BESA Research to open EEG data==
Use the following command to start BESA Research with the command line parameter:
<foc_link.sub file path>\foc_link.sub
The foc_link.sub file contains a list of the datasets to be loaded at program start. The file format is described below in [[#Format of foc_link.sub|Format of foc_link.sub]].
For example, to load EEGs in BESA 5.2.2 or higher (e.g. BESA Research 5.3) at program start (assumed to be installed in C:\BESA52 and file foc_link.sub file located in the BESA Research installation folder), apply the following command:

C:\BESA52\BESA.exe C:\BESA52\foc_link.sub
==Open EEG data while BESA Research is running==
If you want to load a different EEG data file while BESA Research is running, simply execute the same command as upon start of BESA Research after updating the file list in foc_link.sub, e.g.
C:\BESA52\BESA.exe C:\BESA52\foc_link.sub
BESA.exe interprets this call from a database or review program. It checks whether BesaMain.exe is already running. If yes, it keeps BesaMain.exe running, closes the old files, and opens the new file(s) listed in foc_link.sub. If not yet running, BESA.exe starts BesaMain.exe with the new file(s) listed in foc_link.sub. Thus, the procedure for changing an EEG file in BESA Research is the same as described in [[#Start BESA Research to open EEG data|Start BESA Research to open EEG data]] for starting BESA Research with the first file(s).

( In older BESA versions (up to version 5.2) a different procedure was required that is still working but not required anymore:
When BESA receives a WM_COMMAND message with Id 3000 (Id = (int)(LOWORD(wParam)), file foc_link.sub in the BESA installation folder was reread. While this feature is still working, it is not recommended anymore because the automatic handling by BESA.exe is much simpler and no WM_COMMAND message is needed. )
Notes:
* Files that are currently open but not specified in foc_link.sub are closed. Only the specified files are opened.
* When a file is closed in BESA Research, the corresponding entry in the foc_link.sub file is deleted.
==Format of foc_link.sub==
For each EEG to be loaded write the following lines to the foc_link.sub file
StartedBy: <Your program name>
EvtFilePath: <path + filename of the evt-File to be loaded for the EEG>
EventCode: [<number>] <number> <number>
ElecFilePath: <path + filename of the elp-File to be loaded for the EEG>
ReviewDateTime: <YYYY-MM-DD/HH:MM:SS>
FilePath: <path + filename of EEG to be loaded>

The first line, StartedBy (followed by a colon and a blank), is an optional tag that can be set to specify the name of your application which calls BESA Research.
The second line, EvtFilePath (followed by a colon and a blank), is an optional tag that can be set to load events specified in an evt-file. If this tag is not defined, only the events found in the EEG data file are loaded.
The third line, EventCode (followed by a colon and a blank), is an optional tag that can be set to define the type and range of your events stored in the event file specified in EvtFilePath.
The first number defines the code (type) of your events (e.g. 1=Trigger). The second number defines the event ID range minimum and the third number stands for the maximum.
If this tag is defined, BESA Research will remove all events from the EEG which IDs are within the defined range. Then the new events are loaded instead. If this tag is not defined, the new events are loaded in addition to existing events. This tag will be ignored if no EvtFilePath is defined.
The fourth line, ElecFilePath (followed by a colon and a blank), is an optional tag that can be set to attach an electrode configuration specified in an elp-file. If this tag is not defined, the original/recorded electrode configuration found in the EEG-Data file is loaded.
The fifth line, ReviewDateTime (followed by a colon and a blank), is an optional tag that can be set to specify a time at which the review should be started. If this tag is not defined, the review starts at the beginning of the file.
The FilePath line must be the last line for each EEG entry and has to be defined. The tag is followed by path+filename (after the obligatory colon and blank). A maximum of 256 characters for path+filename is read.

==Examples==
===Open one EEG data file at the beginning.===

FilePath: D:\EEG\000822WC.eeg

===Open one EEG data file at a defined position.===

ReviewDateTime: 2008-07-02/12:18:12
FilePath: D:\EEG\000822WC.eeg

===Open three EEG data files, position for second data file is specified.===

FilePath: D:\EEG\000822WC.eeg

ReviewDateTime: 2008-07-02/12:18:12
FilePath: D:\EEG\000822WD.eeg

FilePath: D:\EEG\000822WE.eeg

We suggest to separate single EEG entries by an empty line, although this is not required.
===Complete foc_link.sub entry with all possible tags===

StartedBy: BESA Epilepsy
ElecFilePath: C:\ELP-FILES\000717WA-STD.elp
EvtFilePath: C:\EVT-FILES\000717WA-STD.evt
EventCode: 1 51 60
ReviewDateTime: 2008-07-02/14:20:12
FilePath: D:\EEG\000717WA.eeg

[[Category:BESA Research]]

Control of BESA Research by external programs

2016-04-08T09:40:31Z

Andre: migrated existing description to wiki

=Control BESA Research by external programs (valid for BESA Research versions 5.2.2 and higher)=

==Purpose and Procedure==
This document describes how to start BESA Research from an external program (a patient database management program or an EEG review program) with a list of one or more files to be opened in BESA Research. It is recommended to create an icon BESA or BESA Research in the external program and to start BESA Research using this icon.
* To start BESA Research from the external program to review EEG data, this program must first write the foc_link.sub file to disk. It must contain the data file(s) to be opened (see Chapter 4). Then BESA Research needs to be started as described below in Chapter 2.
* If BESA Research is already running, first the file foc_link.sub has to be updated or created.
* If the foc_link.sub file is written to the BESA Research installation folder, BESA Research can either be accessed by executing a WM_COMMAND (see Chapter 3) or using the procedure described in Chapter 2.
* If the foc_link.sub file is written to another folder, only the procedure described in Chapter 2 can be used.
We recommend using the procedure described in Chapter 2 in all cases, since this will work in all cases, and the foc_link.sub file can be located in any arbitrary folder.

==Start BESA Research to open EEG data==
Use the following command to start BESA Research with the command line parameter:
<foc_link.sub file path>\foc_link.sub
The foc_link.sub file contains a list of the datasets to be loaded at program start. The file format is described below in Chapter 4.
For example, to load EEGs in BESA 5.2.2 or higher (e.g. BESA Research 5.3) at program start (assumed to be installed in C:\BESA52 and file foc_link.sub file located in the BESA Research installation folder), apply the following command:

C:\BESA52\BESA.exe C:\BESA52\foc_link.sub
==Open EEG data while BESA Research is running==
If you want to load a different EEG data file while BESA Research is running, simply execute the same command as upon start of BESA Research after updating the file list in foc_link.sub, e.g.
C:\BESA52\BESA.exe C:\BESA52\foc_link.sub
BESA.exe interprets this call from a database or review program. It checks whether BesaMain.exe is already running. If yes, it keeps BesaMain.exe running, closes the old files, and opens the new file(s) listed in foc_link.sub. If not yet running, BESA.exe starts BesaMain.exe with the new file(s) listed in foc_link.sub. Thus, the procedure for changing an EEG file in BESA Research is the same as described in Chapter 2 for starting BESA Research with the first file(s).

( In older BESA versions (up to version 5.2) a different procedure was required that is still working but not required anymore:
When BESA receives a WM_COMMAND message with Id 3000 (Id = (int)(LOWORD(wParam)), file foc_link.sub in the BESA installation folder was reread. While this feature is still working, it is not recommended anymore because the automatic handling by BESA.exe is much simpler and no WM_COMMAND message is needed. )
Notes:
* Files that are currently open but not specified in foc_link.sub are closed. Only the specified files are opened.
* When a file is closed in BESA Research, the corresponding entry in the foc_link.sub file is deleted.
* Format of foc_link.sub
For each EEG to be loaded write the following lines to the foc_link.sub file
StartedBy: <Your program name>
EvtFilePath: <path + filename of the evt-File to be loaded for the EEG>
EventCode: [<number>] <number> <number>
ElecFilePath: <path + filename of the elp-File to be loaded for the EEG>
ReviewDateTime: <YYYY-MM-DD/HH:MM:SS>
FilePath: <path + filename of EEG to be loaded>

The first line, StartedBy (followed by a colon and a blank), is an optional tag that can be set to specify the name of your application which calls BESA Research.
The second line, EvtFilePath (followed by a colon and a blank), is an optional tag that can be set to load events specified in an evt-file. If this tag is not defined, only the events found in the EEG data file are loaded.
The third line, EventCode (followed by a colon and a blank), is an optional tag that can be set to define the type and range of your events stored in the event file specified in EvtFilePath.
The first number defines the code (type) of your events (e.g. 1=Trigger). The second number defines the event ID range minimum and the third number stands for the maximum.
If this tag is defined, BESA Research will remove all events from the EEG which IDs are within the defined range. Then the new events are loaded instead. If this tag is not defined, the new events are loaded in addition to existing events. This tag will be ignored if no EvtFilePath is defined.
The fourth line, ElecFilePath (followed by a colon and a blank), is an optional tag that can be set to attach an electrode configuration specified in an elp-file. If this tag is not defined, the original/recorded electrode configuration found in the EEG-Data file is loaded.
The fifth line, ReviewDateTime (followed by a colon and a blank), is an optional tag that can be set to specify a time at which the review should be started. If this tag is not defined, the review starts at the beginning of the file.
The FilePath line must be the last line for each EEG entry and has to be defined. The tag is followed by path+filename (after the obligatory colon and blank). A maximum of 256 characters for path+filename is read.

==Examples==
===Open one EEG data file at the beginning.===

FilePath: D:\EEG\000822WC.eeg

===Open one EEG data file at a defined position.===

ReviewDateTime: 2008-07-02/12:18:12
FilePath: D:\EEG\000822WC.eeg

===Open three EEG data files, position for second data file is specified.===

FilePath: D:\EEG\000822WC.eeg

ReviewDateTime: 2008-07-02/12:18:12
FilePath: D:\EEG\000822WD.eeg

FilePath: D:\EEG\000822WE.eeg

We suggest to separate single EEG entries by an empty line, although this is not required.
===Complete foc_link.sub entry with all possible tags===

StartedBy: BESA Epilepsy
ElecFilePath: C:\ELP-FILES\000717WA-STD.elp
EvtFilePath: C:\EVT-FILES\000717WA-STD.evt
EventCode: 1 51 60
ReviewDateTime: 2008-07-02/14:20:12
FilePath: D:\EEG\000717WA.eeg

[[Category:BESA Research]]

Random Averaging

2016-02-11T15:53:26Z

Andre: Removed Signature on top of the page.

== Abstract ==
The idea of this tutorial is to provide a procedure for random averaging of row data containing triggers. The advantage of random averaging is that the result is not only one average over the trials but many different averages of the same data with different choice of trials and these averages can be statistically analyzed in order to get a statistically verified differences between the signal before and the signal after the trigger point. This can be applied e.g. in the source space and it can be used to determine brain regions with a statistically significant activity against baseline. All steps in this article are demonstrated on a file from the examples of BESA Research - "S1.cnt".

== Export the single trial data in simple binary file format ==
Load from the examples of BESA Research the file "S1.cnt" in the folder "ERP-Auditory-Intensity". After the file was loaded select menu "File -> Export...". The "Export data" dialog opens (see Figure 1).
[[File:ExportDataDialog.png|thumb|500px|Figure 1 The "Export data"-dialog]]
In that dialog select "Epochs around triggers" in the section "Data to export". The two buttons "Interval..." and "Triggers..." become active. Then click on "Interval..." to set appropriate values for the time interval around the trigger and after that click on "Triggers..." in order to select trigger for the random averaging. Please make sure to select only one trigger (see Figure 2) else the generated random averages will contain mixed data from all selected triggers. In the "Export data"-dialog click "OK" to export the data.
[[File:SelectTriggerDialog.png|thumb|500px|Figure 2 "Select trigger"-dialog]]

== Use the external tool BesaRandomAveraging.exe to generate the random averages ==
There exists a tool called "BesaRandomAveraging.exe" which is designed for that to load the exported single trial data and to generate random averages. This tool is based on a Python script called "BesaRandomAveraging.py" which is open source. Both, the source and the binary can be downloaded from here [ftp://h1772544.stratoserver.net/public/Python/BESA_PYTHON.zip] . The usage of the tool is as follows:
<source lang="dos">
BesaRandomAveraging.exe -f <inputfile> ...
-n <number of averages> -t <number of trials>
</source>
where '''''<inputfile>''''' is the absolute path (directory + filename) to the file containing the exported single trial data, '''''<number of averages>''''' is the number of random averages to create and '''''<number of trials used for averaging>''''' is the number of trials which are selected for each average.

'''Example:'''
<source lang="dos">
BesaRandomAveraging.exe -f N:\\Python\\data\\ ...
S1-export.dat -n 20 -t 50
</source>
This command line will generate 20 different averages using sample of 50 trials for every average.
It is possible to start the tool from the DOS prompt or directly from BESA Research (see Figure 3) using the following batch command:
<source lang="c">GENRunProcess(...)</source>
[[File:RunExternalTool.png|thumb|500px|Figure 3 Dialog for the batch command "GENRunProcess(...)"]]

== Perform source analysis on the averages ==
Once the random averages are created we want to perform source analysis on them. For this purpose we are going to use batch in order to save time. The following batch can be used for the source analysis using LORETA:
<source lang="c">
MAINFilter(LC:0.50-6dB-f,HC:45.00-24dB-z,NF:off,BP:off)
MAINMarkBlock(WholeSegment,-,1,SendToSA)
SAimageLORETA(NoImageWeights,ForceRecompute)
SAimageExport(%basename%_LORETA.dat,All,ASCII,-)
SAexit()
</source>
The first line sets the filter, the second marks the entire interval and sends it to the source analysis module, the third computes LORETA over the entire interval, the fourth exports the LORETA results as an ASCII-file and the last just exits the source analysis module.
Now we have the LORETA results for the entire time interval, however, we need additional results to compare with. This could be either a control condition or LORETA results from the baseline interval. In this tutorial we choose to use the baseline interval. In that case we should use another batch script which is very similar to the previous one in order to calculate LORETA only for the baseline interval:
<source lang="c">
MAINFilter(LC:0.50-6dB-f,HC:45.00-24dB-z,NF:off,BP:off)
MAINMarkBlock(WholeSegment,-,1,SendToSA)
SAfitInterval(-100,0,FitInterval)
SAimageLORETA(NoImageWeights,ForceRecompute)
SAimageExport(%basename%_LORETA.dat,All,ASCII,-)
SAexit()
</source>
The only difference with respect to the previous script is the command '''''SAfitInterval(-100,0,FitInterval)''''' which sets only the baseline interval [-100 0] for the source localization.

== Calculate root-mean-square (RMS) over the time points in the baseline in order to get only one source image for the baseline interval ==
Now the LORETA source reconstruction files are generated and we want to compare the evoked response and the response in the baseline in order to get the regions in the brain which are statistically significant. For this purpose we have to choose how to do that. One possible problem is that the baseline interval is not necessarily exactly as long as the interval containing the evoked response of interest. Consequently, it is more convenient to use baseline interval which is as long as we need it. In order to achieve that we calculate the root-mean-square over the time for LORETA images calculated in the baseline interval. In that way we get for every random average one LORETA image representing the localization results for the baseline. After that we can stretch this image to as many time points as we need and save the 4D matrix in an ASCII file. These steps can be performed with a Matlab script:
<source lang="matlab">

%% create constant baseline

addpath('N:\BESA_MATLAB\BesaIO\besa_matlab_readers')
addpath('N:\BESA_MATLAB\BesaIO\ersam2besa')

DataPathSignal = 'N:\Python\data\LoretaData';
DataPathBaseline = 'N:\Python\data\Baseline';
DataPathConstBaseline = 'N:\Python\data\ConstantBaseline';

FirstTimeSample = -100.0; % ms
TimeStep = 4; % ms
ImageMethod = 'Standard LORETA';

FileNames = ...
{'S1-export_new15_LORETA.dat', 'S1-export_new4_LORETA.dat', ...
'S1-export_new16_LORETA.dat', 'S1-export_new5_LORETA.dat', ...
'S1-export_new0_LORETA.dat', 'S1-export_new17_LORETA.dat', ...
'S1-export_new6_LORETA.dat', 'S1-export_new10_LORETA.dat', ...
'S1-export_new18_LORETA.dat', 'S1-export_new7_LORETA.dat', ...
'S1-export_new11_LORETA.dat', 'S1-export_new19_LORETA.dat', ...
'S1-export_new8_LORETA.dat', 'S1-export_new12_LORETA.dat', ...
'S1-export_new1_LORETA.dat', 'S1-export_new9_LORETA.dat', ...
'S1-export_new13_LORETA.dat', 'S1-export_new2_LORETA.dat', ...
'S1-export_new14_LORETA.dat', 'S1-export_new3_LORETA.dat'};

NumFiles = length(FileNames);

for f=1:NumFiles

CurrFilename = FileNames{f};

CompletePathBaseline = fullfile(DataPathBaseline, CurrFilename);
CompletePathSignal = fullfile(DataPathSignal, CurrFilename);
ConstantBaselineData = fullfile(DataPathConstBaseline, CurrFilename);

BaselineData = readBESAimage(CompletePathBaseline);
SignalData = readBESAimage(CompletePathSignal);

NumTimeSamples = size(SignalData.Data, 4);

% Average baseline over time
% data4 = squeeze(mean(BaselineData.Data, 4));
data4 = squeeze(rms(BaselineData.Data, 4));
data5 = repmat(data4, [1 1 1 NumTimeSamples]);
data6 = permute(data5, [4 1 2 3]);

besa_save4DimageData(ConstantBaselineData, data6, ...
min(SignalData.Coordinates.X), min(SignalData.Coordinates.Y), ...
min(SignalData.Coordinates.Z), max(SignalData.Coordinates.X), ...
max(SignalData.Coordinates.Y), max(SignalData.Coordinates.Z), ...
length(SignalData.Coordinates.X), length(SignalData.Coordinates.Y), ...
length(SignalData.Coordinates.Z), ImageMethod, ...
FirstTimeSample, TimeStep)

end
</source>
The external functions used in this script are part of our open source tools "besa_matlab_readers" and "ersam2besa" which can be downloaded from our ftp-server here: [ftp://h1772544.stratoserver.net/public/Matlab/].

== Perform statistical comparison with the results ==
After all source reconstruction files were generated it remains to compare the evoked responses against the baseline responses. This can be done with BESA Statistics using either paired t-test or within ANOVA projects.

Main Page

2015-12-09T10:27:37Z

Andre: very minor changes ~~~~

=Welcome to the BESA Wiki!=

We just started working on this wiki!
Soon you will be able to access:
* tutorials
* FAQs
* a collection of useful batches
* and further content we will be publishing on this wiki

Contributions to the Wiki from the community are very welcome! Please create an account with a valid email to edit the BESA Wiki's content.

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Main Page

2015-12-08T21:32:28Z

Andre: minor improvements ~~~~

=Welcome to the BESA Wiki!=

We just started working on this wiki!
Soon you will be able to access:
* a collection of various tutorials showing examples of some of the BESA workflows
* a collection of FAQs
* and further contents we will be publishing

Contributions to the Wiki are very welcome! Please create an account with a valid email to edit the BESA Wiki's content.

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

Main Page

2015-12-07T13:52:46Z

Andre: First test on creating the main page.

Welcome to BESA Wiki!

[[Create an account]] to edit the BESA Wiki's content.

Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
* [//www.mediawiki.org/wiki/Localisation#Translation_resources Localise MediaWiki for your language]

User talk:Andre

2015-12-07T13:31:00Z

Andre: test

This is a test.