BESA® Wiki - User contributions [en]

BESA Research Batch Processing

2024-03-11T13:54:31Z

Dominik:

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



== Combine Conditions and Batch Module: Introduction ==

Functions of this module are started by selecting the menu operations "'''ERP / Combine Conditions...'''" and "'''Process / Batch Scripts...'''".

* '''Combine Condition Scripts''' provides various operations on BESA averages.
* '''Batch Scripts''' provides batch operations on all data files.
* Note that a batch script can also be performed on the current file by selecting "'''Process / Run Batch...'''" or by typing the shortcut key "'''R'''".

== File List Tab ==

Define a list of files on which the operations will be performed. The tab is the same for Combine Conditions Scripts and for Batch Scripts. Combine Conditions Scripts only allows you to open BESA average files (e.g. '''<nowiki>*.fsg</nowiki>''' and '''<nowiki>*.avr</nowiki>''', but also '''.mul''', '''.raw''', '''.swf''', and '''.foc''' if the files have a defined pre-stimulus interval), whereas Batch Scripts allows you to open any data file whose format is known to BESA Research.

When the Combine-Conditions or the Batch module is started, all currently opened (Combine-Conditions: averages only) files are displayed in the list.

To the right of each file name, the number of electrodes, total number of channels, and the sampling rate used in the file are displayed. In the Combine-Conditions module, the number of Epochs (segments) and the number of differently-named conditions are also shown.

'''Add files to the list'''

* Press the '''Add File ''' button.
* Drag one or more files from Windows Explorer onto the window.

'''Remove files from the list'''

* Right click on the file name and confirm the delete operation in the resulting dialog.
* Mark one or more file names in the list (e.g. hold down the''' Ctrl''' key to mark multiple files). Right click to obtain the context menu and select "'''Delete'''", or just press the '''Del '''key.

'''Reorder files within the current file list'''

* Right click on the file name and select "'''''Move Up'''''" or "'''''Move Down'''''".
* Mark one or more file names in the list (e.g. hold down the '''Ctr'''l key to mark multiple files). Right click to obtain the context menu and select "'''''Move Up'''''" or "'''''Move Down'''''", or hold down the''' Ctrl''' key '''and '''press the '''Up''' and '''Down arrows'''.

'''Sort the current file list alphabetically'''

* Click on the File bar above the list

'''Save the current file list'''

* Press the '''Save File List''' button.

'''Load a file list'''

* Press the '''Load File List''' button, or the '''Load Previous''' button to load the most recently used file list.

'''Which conditions are read from a source file? (Combine-Conditions module only)'''

* Normally, all conditions are read from a source file. To exclude one or more segments from operations in the Combine Conditions module, mark the segments as artifacts in the main program display. It is sufficient for the beginning or the end of an artifact interval to be within the segment for the segment to be excluded.

'''File list from Combine Conditions:'''

[[Image:Batch processing (1).png]]

'''Don't try to open here... (Batch only)'''

By default, this checkbox is unchecked.

In the checked state, BESA Research doesn't check if it can open the file. Use this function '''only''' if the file is ASCII and you want to use the '''ImportASCII '''batch command.

'''File List from Batch Scripts''':

[[Image:Batch processing (2).png]]

== Batch Processing ==

=== Batch Processing Scripts ===

With Batch Scripts, you can define a set of operations (e.g. Artifact Scan, Average, etc.) and apply these to several data files.

These operations include

* Load Paradigm
* Artifact Scan
* Average
* Export (and Merge)
* File Open (switch to another data file)
* Set filters
* Specify a montage (used, for example, for export to current montage)
* Run automatic eye and EKG artifact correction
* Define artifact topographies
* Turn artifact correction and view on and off
* Read and write events
* Edit default block epoch (for export around triggers)
* Edit triggers (for export around triggers)
* Mark a block for export, or send the block to Source Analysis or Top View
* Convert patterns to triggers
* Attach auxiliary files (e.g. elp, sfp) to the data file
* Send to MATLAB
* Specify display configurations for the BESA Research Main, SA, and Top View windows
* and more - see the full list of [[#Batch Commands|Batch Commands]]

An additional set of commands are available for operations in the '''Source Analysis Module''', allowing to load, create and fit dipole models, and save the results.

A further set of commands apply to '''Time-Frequency Analysis''', allowing to start TFC, change the display, save results, and run the beamformer or DICS analyses on a selected time-frequency range.

[[Image:Batch commands1.png]]

These operations will be extended in future program releases.

The module includes two tabbed windows:

* '''File List''': Define a list of files on which the operations will be performed.
* '''Batch''': Define or load '''batch commands'''. Run the batch.

=== Batch Tab ===

Load or define batch commands, and then apply them to the files in the File List.

[[Image:Batch processing (4).png]]

'''Add Command'''

* Press '''Add Command''' to add a new command to the batch. The following dialog is opened, showing the available commands:

[[Image:Batch commands1.png]]

* Select the desired command and press '''OK''' or double-click on the command. A dialog box is opened, allowing to specify individual command parameters.
* If you click on "Apply at beginning of batch" or "Apply at end of batch", the command will only be run at the beginning or the end of a batch. You can use this, for example, at the end of a batch to start a MATLAB script to perform statistics on the results of the batch.

'''Load and Save Batch'''

* Press '''Load Batch''' to load a previously defined batch or '''Save Batch''' to save the current batch to a file ('''<nowiki>*.bbat</nowiki>''').

'''Load Previous'''

* Press '''Load Previous''' to load the most recently used batch file. Whenever a batch is run, the current set of commands is written to the file '''Previous.bbat in''' the '''Scripts/Batch''' subdirectory. This file is loaded when you press '''Load Previous'''.

'''Clear All'''

* Clears all commands from the window.

'''View Log File'''

* Each time a batch is run, BESA Research adds information about the batch to a log file, with headings showing the date and time the batch was started. The file is opened automatically in Internet Explorer if errors occurred during processing. Otherwise you may open the file by pressing the '''View Log File''' button here or in the dialog that is displayed at the end of batch processing. 
* The log file is saved in xml format, and a JavaScript is used to format the display in web browsers. JavaScript should be enabled in the browser to obtain an optimal display of the results. If JavaScript is enabled, the log file is displayed as a list of headings for each batch. Click on a heading to display the results of the corresponding batch.
* To open the log file in the Notepad, hold the''' Shift '''key down when pressing the '''View Log File''' button.

'''Batch Command List'''

* Double-click on a command to edit it. See [[#Batch Commands|Batch Commands]] for descriptions of the dialogs that are opened to edit each command.
* Right click on a command to open a context menu allowing more options.

[[Image:Batch processing (5).png]]

* '''Delete''', '''Move Up''', '''and Move Down''' can also be applied to multiple selections.
* If you have made a multiple selection, the '''Del '''button will delete all the marked commands. '''Ctrl '''plus '''Up''' or '''Down''' '''cursor keys''' will move the marked commands up or down.
* '''Toggle Comment''' will add or remove a semicolon (;) in front of the command, to deactivate or reactivate the command.
* '''Toggle Command Only at Start/End''' will add or remove the text "Start_" or "End_" in front of the command. With these prefixes, the command will only be performed when the first file ("Start_") or the last file ("End_") in the file list is being processed.

'''Single Step Mode'''

* Check this item to step through the batch, one command at a time. A dialog is opened after each command, allowing to run the next command, continue the batch without single steps, or stop running the batch. See the'' “Pause''” command for further details.
* During a batch, press and hold down the '''Pause''' or '''Delete''' key to interrupt the batch and enter Single Step Mode. Press and hold down the '''Esc''' key to cancel the batch.

'''Changes in batch written to database'''

* Checked by default. If this item is unchecked, file display settings, such as Montage setting and Artifact correction display, are not written to the database. When the file is next opened in BESA Research, the settings made in the batch are not retained.

'''Leave files in the file list open after running the batch'''

* If this item is checked, files in the file list will remain open after the batch. This is useful, for instance, if you want to open a set of files, specifying the same montage and/or filter settings for each file.

Press '''OK''' to start running the batch. Each command is then applied in succession to each file in the File List.

Note that, while a batch is running press and hold down the''' Pause''' or '''Delete''' key to interrupt the batch and enter Single Step Mode. Press and hold down the '''Esc''' key to cancel the batch.

=== The log file ===

A protocol of each batch is written to the log file '''Batch.txt.''' (e.g. C:\Users\Public\Documents\BESA\Research_7_1\Scripts\Log\Batch.txt)

When you press the '''View Log File''' button, the file is opened in the Batch Log dialog. The Batch Log dialog will be opened automatically if there was an error during batch processing, unless you have used the ''BatchError'' batch command to suppress this behaviour.

'''Backup of the log file'''

When the log file is written, a backup of the previous version is written to '''Batch.txt.bak'''.

If the size of the log file exceeds 200 KB, it is renamed to '''Batch.txt_date_time''' (e.g. '''Batch.txt_2004-10-08_10-53-32'''), and a new version of '''Batch.txt''' is created.

=== Placeholders ===

A powerful feature of the batch commands is the ability to define file names and specify standard paths using placeholders. These are text strings enclosed by percentage (%) signs. They can be used in all batch commands where file names are specified.

'''Basename'''

{| class="wikitable"
! Placeholder !! Description !! Example
|-
|style="text-align:center;" width="10%"|'''%basename%'''
|width="40%"|replaced by the basename of the currently opened file.
|width="40%"|If the data file is named "f-spike.fsg", "%basename%-export.fsg" will be interpreted as "f-spike-export.fsg".
|-
|style="text-align:center;"|'''%basename-n%'''
|replaced by the basename of the currently opened file, but removing the last "n" characters from the name.
|If the data file is named "dongle-BB.fsg", "%basename-3%" will be replaced by "dongle", because the last 3 characters of the basename have been removed.
|-
|style="text-align:center;"|'''%-nbasename%'''
|replaced by the basename of the currently opened file, but removing the first "n" characters from the name.
|If the data file is named "BB-dongle.fsg", "%-3basename%" will be replaced by "dongle", because the first 3 characters of the basename have been removed.
|-
|style="text-align:center;"|'''%orgbasename%'''
|replace by basename of the current file in the file list (it has the same meaning as %basename% if no MAINFileOpen batch command was used in command list)
|
|-
|style="text-align:center;"|'''%base%'''
|replace by basename of the current file without the path
|
|-
|style="text-align:center;"|'''%orgbase%'''
|replace by basename of the current file in the file list without the path
|-
|style="text-align:center;"|'''%ext%'''
|replace by extension of the current file
|
|-
|style="text-align:center;"|'''%orgext%'''
|replace by extension of the current file in the file list
|
|-
|style="text-align:center;"|'''%basefolder%'''
|replace by folder of the current file
|
|-
|style="text-align:center;"|'''%orgbasefolder%'''
|replace by folder of the current file in the file list
|
|-
|style="text-align:center;"|'''%t%'''
|Log batch command only: time since start of batch on current file
|
|-
|style="text-align:center;"|'''%T%'''
|Log batch command only: current date and time
|
|-
|style="text-align:center;"|'''%label%'''
|Replace label of the most recent marked block by the block label, not including no. of averages
|
|-
|style="text-align:center;"|'''%LABEL%'''
| Replace label of the most recent marked block by the block label, including no. of averages

|
|-
|style="text-align:center;"|'''%scripts%'''
|replaced by the path to the Scripts folder.
|"%scripts%Batch" is where batches are saved by default; "%scripts%MATLAB" is the location of the standard MATLAB scripts used by BESA Research.
|-
|style="text-align:center;"|'''%montages%'''
|replaced by the path to the Montages folder.
|
|-
|style="text-align:center;"|'''%examples%'''
|replaced by the path to the Examples folder.
|
|}



'''Placeholders for folders'''

The following placeholders are the same as those used in the [Folders] section of '''Besa.ini''':

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

* '''Windows 10 (English)'''

<div style="margin-left:1.27cm;margin-right:0cm;"> '''%localapp%''' = ""C:\Users[user]\AppData\Local\BESA\Research_7_1", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as ""Desktop[user]\AppData\Local\BESA\Research_7_1".</div>

<div style="margin-left:1.27cm;margin-right:0cm;"> '''%publicprog%''' = "Documents\BESA\Research_7_1".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%privateprog%''' = ""C:\Users\[user]\Documents\BESA\Research_7_1", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as "Desktop\[User]\Documents\BESA\Research_7_1".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%progdir%''' = the BESA Research root folder. In a default installation, this is "C:\Program Files\BESA\Research_7_1".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%besaroot%''' is the same as''' %progdir%'''</div>

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

<div style="margin-left:1.27cm;margin-right:0cm;">'''%localapp%''' = "C:\Users\[user]\AppData\Local\BESA\Research_7_1", where [user] is the logon name of the current user. This folder is directly accessible from the Desktop as "Desktop\[user]\AppData\Local\BESA\Research_7_1".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%publicprog%''' = "C:\Users\Public\Public Documents\BESA\Research_7_1". This folder is directly accessible from the Windows Explorer under "Libraries\Documents\Public Documents\BESA\Research_7_1".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%privateprog%''' = "C:\Users\[user]\Documents\BESA\Research_7_1", where [user] is the logon name of the current user. This folder is directly accessible from the Windows Explorer as ""Libraries\Documents\My Documents\Research_7_1" or "Desktop\[User]\My Documents\BESA\Research_7_1".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%progdir%''' = the BESA Research root folder. In a default installation, this is "C:\Program Files\BESA\Research_7_1".</div>

<div style="margin-left:1.27cm;margin-right:0cm;">'''%besaroot%''' is the same as''' %progdir%  '''</div>

=== Batch Commands ===

Batch commands are selected when the "'''Add Command'''" button is pressed in the "Batch" Tab. The commands are subdivided into five categories: General commands, commands for the Main module, for the Source Analysis module, imaging commands in the Source Analysis module, and commands for Time-Frequency Analysis. The commands have prefixes,''' GEN''', '''MAIN''',''' SA''', '''SAIMAGE''', and''' TFC'''), which identify the category. For compatibility with older program versions, old batches without the prefixes are accepted.

Detailed descriptions of each batch command are available in the electronic help chapter “''Batch Processing and Combining Conditions / Batch Processing / Batch Commands”.''

'''General commands''' - prefixed with "'''GEN'''" (can be used anywhere):

{| cellspacing="8" style
| style="width: 180pt"| GENBatchError || used to change program behavior when errors occur
|-
| GENBatchWindowPosition || set the position of the batch window relative to the main window
|-
| GENComment || comment in the batch script: no batch functionality
|-
| GENMATLABcommand || send a command string to MATLAB
|-
| GENMATLABwaitForVariable || tells BESA to wait until Matlab has created a variable with the specified name.
|-
| GENPause || pause batch operations, allowing step-by-step operations
|-
| GENFor/GENEndFor|| a programming language-like FOR loop
|-
| GENRunProcess || runs a command-line process, e.g. an external program to perform part of the data analysis in the batch
|-
| GENsaveBitmap || save a screenshot of the Source Analysis or the 3D window
|-
| SetVariable || the value of the variable is inserted into subsequent batch commands where the text contains the name flanked by % signs
|-
| GENWindowPosition || set window size and positions to a selection of standard settings, e.g. for bitmap export
|}

'''Commands for the Main Module''' - prefixed with "'''MAIN'''":

{| cellspacing="8"
| style="width: 180pt"| MAINArtifactCorrect || run automatic artifact correction
|-
| MAINArtifactMethod || specify the method for artifact correction
|-
| MAINArtifactOn || turn artifact correction an artifact view on or off
|-
| MAINArtifact Scan || run an artifact scan as from the Paradigm Dialog
|-
| MAINAuxiliaryFiles || associate auxiliary files (e.g. *.''ela'', *.''sfp'') with the data file
|-
| MAINAverage || average the data
|-
| MAINBaseline || specify the parameters for baseline correction
|-
| MAINDefineArtifactTopography || define an artifact topography
|-
| MAINEditDefaultEpoch || edit the default block epoch
|-
| MAINEventRead || read events from an ASCII event file
|-
| MAINEventWrite || write events to an ASCII event file
|-
| MAINExport || export or append data in the selected target format
|-
| MAINExportToBESAConnectivity || export data segments to BESA Connectivity
|-
| MAINFFT || calculates the FFT spectrum of the marked data interval
|-
| MAINFFTmean || starts an averaging procedure that calculates the mean spectral properties in pre-defined regions
|-
| MAINFFTsave || saves FFT data (generated using the ''FFT Average option'' in the ''Average ''command) to disk (*.''fma)''
|-
| MAINFileOpen || close the current file and open a new file to which the remaining batch commands will be applied
|-
| MAINFileClose || close the currently open file in a batch, provided it is not the current file in the File List
|-
| MAINFilter || set filters
|-
| MAINfMRIArtifact || turns on the fMRI artifact removal
|-
| MAINGoTo || jumps with the cursor to the specified time point
|-
| MAINICA || starts ICA decomposition of data on the current screen
|-
| MAINICAsave || saves selected ICA components as topographies in a file
|-
| MAINICAselect || opens component selection dialog for managing ICA components
|-
| MAINImportASCII || import an ASCII file into a ''<nowiki>*.fsg</nowiki>'' file.
|-
| MAINMarkBlock || mark a data block (optionally send to Source Analysis)
|-
| MAINMarkChannels || mark one or more channels, as given by the list
|-
| MAINMaxInInterval || within the current marked block, search for the largest absolute value on the specified channel
|-
| MAINMontage || change the montage (used by the Export command when saving to current montage)
|-
| MAINParadigm || load a paradigm file
|-
| MAINPatternToTrigger || convert a tag into a trigger
|-
| MAINPolygraphicFilters || sets filters for polygraphic or added channels
|-
| MAINScale || set amplitude and time scales
|-
| MAINSearchAverageView || start search average view
|-
| MAINSendToMATLAB || send data to MATLAB
|-
| MAINSMTApply || load and apply Schmitt trigger settings file to the data set
|-
| MAINSplineConstant || set the spline constant used in spherical spline maps and channel interpolation
|-
| MAINTriggerRecode || the command recodes a specified trigger number to a new number
|-
| MAINTriggerSelect || edit the trigger list (cf. ''Edit / Trigger Values''...)
|-
| MAINTriggerTagDelete || delete one or more triggers or tags
|-
| MAINViewAverageBuffer || turn on the Average Buffer View and place the specified buffer number to the left in the display
|-
| MAINViewChannelType || select the channel type to display, and select channel types for mapping, export, etc
|-
| MAINViewSelected || turns selected view on or off
|}

'''General commands for Source Analysis''' - prefixed with "'''SA'''" (but see also ''MarkBlock'', which is used to send a block of data to SA and open the SA window):

{| cellspacing="8"
| style="width: 180pt"| SAAddSource || add a dipole or regional source to a model
|-
| SAChannelTypeForFit || switch between EEG, magnetometers or axial gradiometers, and planar gradiometers
|-
| SAConvertSource || convert a source from dipole to regional source, or from regional source to dipole
|-
| SAcorticalClara || run Cortical CLARA
|-
| SAcorticalLoreta || run Cortical LORETA
|-
| SADelete || delete current solution or all solutions or remove current fit interval or cursor
|-
| SADICS || start DICS computation (if DICS has been precomputed in the time-frequency image command)
|-
| SADisplayMRI || switch MRI display on/off and select small or large window
|-
| SAElectrodeConfiguration || equivalent to pressing the Org or Std button in the Channel box of the Source analysis window
|-
| SAExit || close Source Module
|-
| SAFit || start fit
|-
| SAFitConstraint || set fit constraints, e.g. Residual Variance, Energy, Maximum Distance, Image Weighting, and their weights.
|-
| SAFitInterval || set fit or baseline interval
|-
| SAHeadModel || set the head model
|-
| SALabelSource || set the label of the specified source number
|-
| SAMinimumNorm || run a minimum norm analysis
|-
| SANewSolution || open a new solution
|-
| SAOpenSolution || open a solution from a file
|-
| SAPCA || toggle PCA display of data or residual, and transfer a selected number of components to the source model
|-
| SARegularization || set the regularization values both for discrete and distributed source images
|-
| SASaveBitmap || save a screenshot of the Source Analysis or the 3D window
|-
| SASaveLeadfields || save the leadfields of the current source model
|-
| SASaveModelWaveforms || save model waveforms
|-
| SASaveResidualWaveforms || save residual waveforms
|-
| SASaveRVandGFPWaveforms || save residual variance and global field power waveforms
|-
| SASaveSolution || save the current solution
|-
| SASaveSourceMontage || save a source montage
|-
| SASaveSourceWaveforms || save source waveforms
|-
| SASendToMATLAB || send data, model, source waveforms, images, etc. to Matlab
|-
| SASetCursor || set the cursor
|-
| SASetDefaultSourceType || set the default source type (dipole or regional source)
|-
| SASetOrActivateSource || Turn specified source on or off, or enable/disable source for fitting
|-
| SASetOrientation || set orientation (of regional source)
|-
| SASwitchCondition || switch to a specified condition
|}

'''Commands for Distributed 3D Volume Images'''

{| cellspacing="8"
| style="width: 180pt"| SAIMAGEBeamformer || switch between Single Source and Bilateral Beamformer image
|-
| SAIMAGEBeamformerTimeDomain || start beamformer computation in the time domain
|-
| SAimageBrainAtlas || turns on the Brain Atlas overlay on volumetric image
|-
| SAIMAGECLARA || generate CLARA image
|-
| SAIMAGEClip || clip image values under a threshold
|-
| SAIMAGEExport || save the results of minimum norm or 3D imaging method
|-
| SAIMAGEGotoMax || set the crosshair cursor at the nth maximum in the image
|-
| SAIMAGEImport || load a 3D volume image from file
|-
| SAimageImportFMRI || import fMRI image to Source Analysis Module
|-
| SAIMAGELAURA || create LAURA image
|-
| SAIMAGELORETA || create LORETA image
|-
| SAIMAGESLoreta || create sLORETA image
|-
| SAimageSESAME || start SESAME computation
|-
| SAIMAGESSLOFO || create SSLOFO image
|-
| SAIMAGEUser-Defined || create user-defined image
|-
| SAIMAGESaveLeadfields || save the leadfields of all the voxel sources in a 3D image
|-
| SAIMAGEClip || clip current 3D image
|-
| SAIMAGESmooth || smooth current 3D image
|-
| SAIMAGESetCrosshair || set the position of the crosshair in the 3D image
|}

'''Commands for Time-Frequency Analysis''' ('''TFC''')

{| cellspacing="8"
| style="width: 180pt"| TFCStartTFAnalysis ||(previously TFCgo) start TFC analysis using the current paradigm settings
|-
| TFCdisplay || change the TFC display (e.g. power/amplitude, coherence)
|-
| TFCsave || save numerical results to an ASCII file, or save a screenshot of the TFC window
|-
| TFCimage || start beamformer analysis on a selected time-frequency range
|-
| TFCSendToMATLAB || send TF results or single-trial data to MATLAB
|}

=== How to Average Your Data in a Batch ===

Using batch processing, several files from an experiment can be averaged at a time.

Here we summarize the steps required:

'''Before running the batch'''

* Create the paradigm, and save the paradigm file.
* Open each individual data file to check the data:
** Make sure auxiliary files are defined and loaded properly, and the data are displayed correctly.
** Eyeball the data.
** Define bad (and interpolated) channels.
** Mark artifact time ranges.
** If required, set up artifact correction for the file.
** The data file can be closed again after this step.

'''Preparing the batch'''

* Open at least one file and select ''Process / Batch Scripts''.... The file(s) should be displayed in the file list. Alternatively, just select ''Process / Batch Scripts...,'' and add the files by
** pressing the '''Add File''' button
** dragging the files from Windows Explorer
** Opening a previously saved list with ''Load File List''

* You can delete files from the list (press '''Del''') or edit the file sequence using the right click context menu.
* Select the ''Batch Tab''.
* Add commands to your script. For averaging, these would normally be
** '''Paradigm''' -- to load the paradigm file
** '''Artifact Scan''' -- to run the artifact scan
** '''Average''' -- to perform the average

* Save these commands (press '''Save Batch''').
* Test the commands on the files in the current file list: press '''OK'''
* Look at the log file (press '''View Log File''') to check the results of averaging.
* Look at the data averages to make sure they have been done correctly.
* Repeat these steps until averaging is working properly.

'''Running the batch'''

* Select ''Process / Batch Scripts''....
* Open the files you want to average in the batch in the file list:
** Any files that were open in BESA are included in the list
** Files can be added using the '''Add File''' button
** You may drag one or more files from Windows Explorer to the file list
** Alternatively, load a previously saved file list.

* Edit the file list, e.g. delete unwanted files (use the '''Del''' key or the right click context menu), or reorder the files (use '''Ctrl + cursor keys''' or context menu).
* Note that the order of files in the list specifies the order in which they will be processed in the batch script. This order will be important if all results are saved to the same target file. Otherwise the file sequence is not important.
* Optionally, save the file list (press '''Save Batch'''
* Select the ''Batch Tab'', and load the previously defined batch script with ''Load Batch''.
* Press '''OK''' to run the batch.

=== How to Merge and Compress raw data ===

Using the Export command in a batch, several data files can be merged into a single data file in BESA's data format ('''<nowiki>*.foc</nowiki>''').

This can be useful if data from one subject have been collected in several data blocks, and you want to analyze all data blocks together.

Optionally, to save space, data can be saved in compressed format.

'''Files can be merged:'''

* if they have identical channel configurations, or
* there are at least 16 EEG channels, and the export format is Standard 81 (i.e. EEG channels are interpolated to 81 standard locations).

'''How to merge files:'''

* Select '''Process / Batch Scripts...'''
* Add all the files that are to be merged to the file list:
** Any files that were open in BESA Research are included in the list
** Files can be added using the '''Add File''' button
** You may drag one or more files from Windows Explorer to the file list
** Alternatively, load a previously saved file list (''Load File List'').
* Rearrange the files in the file list to the sequence in which they should be merged.
* Select the ''Batch Tab ''and insert an "''Export"'' command, as described below.

The following dialog shows a possible configuration of the ''Export'' command:

[[Image:Batch processing (4).gif]]

* The parameters shown in the Information box are the settings chosen in the ''Export Dialog'' when the '''Select Options''' button has been pressed.
* '''Append if file already exists''' must be checked in order to merge the files.
* The '''target file name''' must be fixed, i.e. don't use the '''%basename%''' variable, because that will result in a different target file name for each source file.
* There are two variables that can be used for the segment label:
** '''%filename%''' will insert the basename of the source file into the segment label.
** '''%c%''' will insert the file number into the segment label. The number gives the position of the file in the file list. For instance, "File %c%" will generate the label "File 2" for the second file in the list.

=== Example: Data averaging in the auditory intensity experiment ===

In this example, two raw data files, '''s1.cnt''' and '''s2.cnt''', from the auditory intensity experiment will be batch averaged.

Please note that there are further tutorials covering this experiment. The first file is contaminated by many eyeblinks, and more epochs would be averaged if eye correction were used (see Viewlet demonstration on artifact correction on the BESA website). However, in this tutorial, we will just use artifact rejection.

'''A. Various ways of creating a File List'''

1. '''Files that were open in BESA Research are automatically added to the File List.''' Start BESA Research and open the files '''s1.cnt '''and '''s2.cnt '''in the directory ''Examples\ERP-Auditory-Intensity''.

2. Select ''Process / Batch Scripts''.... You should see the file names in the '''''File List Tab''''' something like this:

[[Image:Batch processing (5).gif]]

3. You can resort the files in the file list alphabetically by clicking onto the '''''File List column header''''':

[[Image:Batch processing (6).gif]]

Alternatively, you can mark any file, hold down the '''Ctrl '''key and press the '''Up''' or '''Down arrow '''to move the file name up or down the list. This is the sequence in which files will be processed in the batch.

[[Image:Batch processing (7).gif]]

4. Press '''Save File List''' and save the list you have created to '''ERP-Aud-Ex1.flist'''.

5. Highlight both names and press the''' Del '''button to remove them from the list.

6. '''Files can be dragged from Windows Explorer'''. Start Windows Explorer and navigate to the ''ERP-Auditory-Intensity'' subdirectory of your BESA Research examples folder (located in the ''Public Documents'' folder of your computer). Click on '''s1.cnt''' and drag it with the mouse onto the '''''File List Tab'''''. Let go of the mouse. BESA Research opens the file, and displays the name in the File List. Repeat for '''s2.cnt.'''

7. Highlight both names and press the '''Del '''button to remove them from the list.

8. '''Files can be added using the ''Add File'' button'''. Press '''Add File''' and navigate to the ''Examples\ERP-Auditory-Intensity'' subdirectory. Select '''s1.cnt'''. Press '''Ctrl''' and select '''s2.cnt'''. Both names should then be displayed in the ''File Open'' dialog. Press '''OK''' to add the files to the file list.

9. Highlight both names and press the '''Del''' button to remove them from the list.

10. '''Files can be loaded from a previously saved file list'''. Press '''Load File List '''and select '''ERP-Aud-Ex1.flist''', the list you saved in step 6 above.

'''B. Setting up the batch'''

1. We will add three commands, '''Paradigm''', '''Artifact Scan''', and '''Average''', to create a batch that will be applied to the two files in the file list.

2. Click on the '''Batch Tab'''.

[[Image:Batch processing (8).gif]]

3. Press the '''Add Command''' button to obtain the ''Select Command'' window:

[[Image:Batch processing (9).gif]]

4. Click on '''Paradigm''' and then on '''OK''' (alternatively, double-click on '''Paradigm'''). Hit '''Browse''', navigate to the ''Auditory'' folder, and select '''AEP_Intensity.pdg''', the paradigm for the auditory intensity experiment.

[[Image:Batch processing (10).gif]]

5. Press '''OK''' to obtain the ''Load Paradigm Task'' window.

[[Image:Batch processing (11).gif]]

6. Press '''OK''', and the first task in the batch is ready, and listed in the Batch Command window. If you want to modify the command, double-click on it to open the above window, that allows to browse for a different paradigm file.

[[Image:Batch processing (12).gif]]

7. Next, we add the '''Artifact Scan''' command. Click on the '''Add Command''' button, and select ''Artifact Scan.''

[[Image:Batch processing (13).gif]]

8. Press '''OK''' to open the ''Artifact Scan Task'' window. We want to be able to view the results of the scan, and adjust thresholds and bad channels if necessary. Therefore, check the ''Wait after scan'' checkbox.

[[Image:Batch processing (14).gif]]

9. Press '''OK''' to close the ''Artifact Scan Task'' window. Our batch now contains two commands.

[[Image:Batch processing (15).gif]]

10. Finally, we will add an '''Average''' command. Press the '''Add Command''' button and select ''Average''. Press '''OK''' to open the ''Average Task ''window.

[[Image:Batch processing (16).gif]]

11. With the default settings, the average would be saved to the same directory as the data. The file name mask is set by default so that in this example the two averages would be saved to '''s1-av.fsg '''and '''s2-av.fsg'''. We will save the averaged files to subdirectory ''"Averages''" of the data directory. Uncheck the ''Use default target'' check box, change the File name mask to '''%basename%_av-test''' in order not to overwrite the predefined files.

[[Image:Batch processing (17).gif]]

12. Press '''OK '''to close the ''Average Task'' window. Our batch is now complete.

[[Image:Batch processing (18).gif]]

13. We will now save the batch so that it can be used again. Press the '''Save Batch''' button, and save to the file '''ERP-Aud-ex1.bbat'''. Note that an easy way to generate new averaging batches is to load a previously save batch and edit the commands -- it may only be necessary to edit the '''Paradigm''' command to select the relevant paradigm file, and maybe to adjust the target directory in the '''Average''' command.

14. Press '''OK''' in the ''Batch'' Window to start the batch running. As requested, the batch pauses after the artifact scan:.

[[Image:Batch processing (19).gif]]

You may now adjust the number of rejected trials, e.g. by moving the vertical red bar to the left or exclude bad channels.

15. Press '''OK''' to continue with averaging.

[[Image:Batch processing (20).gif]]

16. Note that, in the background, the ''Batch Running'' window is providing feedback about the current file and current task.

[[Image:Batch processing (6).jpg|400px]]

17. The batch will stop again after the next artifact scan. Press '''OK''' to allow the batch to run to the end.

[[Image:Batch processing (21).gif|400px]]

18. Press '''View Log''' to view the batch log.

19. The batch log gives feedback about the number of epochs that were averaged for each file.

20. Finally, press '''OK''' to return to the main BESA Research display. Open the averages in the ''Averages'' subdirectory to confirm that they were generated properly.

=== Example: Merging files using the Export Command ===

Here we will demonstrate the use of the '''Export '''command to merge two files. We will combine the two averages from the previous example (Data averaging in the auditory intensity experiment) into one target file.

'''A. Generate the file list'''

# Start BESA Research and load the two data files '''S1_av-test.fsg''' and '''S2_av-test.fsg''' that were saved in the previous example.
# Select ''Process / Batch Scripts....''The two file names should be displayed in the file list.
# In the file list, make sure that '''s1_av-test.fsg '''is the first file in the list. If it is not, highlight the file, and move it up using '''Ctrl+up''', or right click and select ''Move Up'' in the context menu.

'''B. Generate the batch'''

1. Press the '''Add Command''' button, and select the '''Export''' command.

2. Press '''OK''' to open the ''Export Task'' window.

[[Image:Batch processing (24).gif]]

3. Press the '''Select Options'''... button to open the ''Export Dialog''.

[[Image:Batch processing (25).gif]]

4. Since we are combining averages, select ''Hires (no compression)'' in the '''Target data format''' drop-down list (If we were merging raw data files, it is better to select compression. Press '''OK '''to close the dialog. Check'' Append if file already exists'', so that the files will be merged. Enter '''s1+s2''' in the target file name mask edit box. This ensures that both files will be saved to the same target: '''S1+S2.fsg'''.

[[Image:Batch processing (26).gif]]

5. Press '''OK '''to close the ''Export Task'' window. The '''Export '''command is displayed.  

[[Image:Batch processing (27).gif]]

6. Optionally, you may save the batch file by pressing '''Save Batch'''.

7. Press '''OK''' to run the batch, and '''OK''' in the ''Batch Completed'' window to return to the BESA main window.

8. Finally, open the file '''S1+S2.fsg''' to confirm that it contains the two merged files.

'''C. Merge raw data'''

# Repeat the above task to merge the two raw data files '''S1.cnt''' and '''S2.cnt''' into a single target file '''S1+S2.foc'''. In this case, select one of the compression options as the target data format. Note that you would not normally want to merge two files from different subjects. However, several data blocks from the same subject can conveniently be merged using this method.

Note that ''<nowiki>*.fsg</nowiki>'' files can also be merged using the ''Combine Conditions'' dialog. 

== Combine Conditions, Channels ==

=== Combine Condition Scripts ===

With the Combine-Conditions module you can do a variety of operations on BESA averages (files with the extension '''<nowiki>*.fsg</nowiki>''', and other segment files, such as '''<nowiki>*.mul</nowiki>''', '''<nowiki>*.avr</nowiki>''', '''<nowiki>*.swf</nowiki>'''):

* Create grand averages
* Combine averages (add, subtract, weighted/unweighted)
* Merge files
* Exclude unwanted averages
* Rename conditions
* Rename or resort channels
* Generate averages or differences over selected channels
* Transform the data: standard interpolated 81 electrodes, change sampling rate, change interval
* Determine peaks, mean amplitudes, or integrals on data averages
* These operations can be performed on one or more files simultaneously. Results of an operation are stored in a single target file.

The module includes four tabbed windows:

* File List: Define a list of files on which the operations will be performed.
* Condition List: List the condition names, define target condition names, and how input conditions are combined into target conditions.
* Channel List: List the channel names, define target channel names, and how input channels are combined into target channels.
* Run Scripts: Define global options for the output (e.g. spatial interpolation, resampling, copy/merge or average, peak analysis). Start the operation.
* Note that in all four tabs, configurations can be saved for future use, and the '''Load Previous''' button restores the most recently used configuration.

=== Condition List Tab ===

List the condition names, define target condition names, and how input conditions are combined into target conditions.

The first column of the list box shows a list of all the condition names found in the source files.

Rows of the list box define the source conditions. Columns define the target conditions.

'''Initial setting'''

When first selecting the tab, each column shows each condition name found in the source files (as in the example below). In the list box, there is a "+1" along the diagonal. The result of this selection is that target conditions will have the same name as source conditions. Right click on source condition labels to view properties (e.g. no. of samples, time range, sampling rate).

[[Image:Batch processing (28).gif]]

'''Editing the condition list'''

* Target condition names can be edited, inserted or deleted by clicking on the label at the top of each column.
* Click on a box within the list to toggle between "+1", "-1" and blank. These correspond to the operations:
** "+1" = add
** "-1" = subtract
** blank = do nothing
* Right click on a box for further operations: conditions can be weighted by a given factor other than 1.

'''Divide result by sum of PLUS factors'''

* Normally, when creating an average over conditions, the sum is divided by the number of conditions or a weighted average is generated (see below).  If "''Divide the result by the sum of PLUS factors''" is unchecked, the conditions will be summed rather than averaged.
* Note that, when making differences between conditions, no such division is required. BESA Research will uncheck the checkbox automatically if subtraction ("-1") is specified somewhere in the condition list.

'''Weighting of averages'''

* Below the list, click on the ''Weighted Average'' row to toggle "YES" and "NO". "YES" means that averages will be weighted by the number of epochs contributing to the average. For instance, if average A contained 100 epochs and average B contained 200 epochs, the weighted average will be computed as

<div style="margin-left:1cm;margin-right:0cm;">(100 * A +  200 * B) / (100 + 200)</div>

<div style="margin-left:1cm;margin-right:0cm;">Select "NO" for an unweighted average. For the above example, the average is computed as</div>

<div style="margin-left:1cm;margin-right:0cm;">(A + B) / 2</div>

<div style="margin-left:1cm;margin-right:0cm;">Weighted averages are not permitted if one of the boxes contains a negative value.</div>

* Values other than +1 or -1 in the boxes apply a different kind of weighting. For instance, we want to compute the difference between the means of conditions A, B, C and D, E. Use a right-click to specify the fraction 1/3 for each of A, B, and C, and -1/2 for each of D and E (see example below).

[[Image:Batch processing (29).gif]]

'''Save the current condition list'''

* Press the '''Save Condition List''' button.

'''Load a condition list'''

* Press the '''Load Condition List''' button.

'''Load previous settings'''

* Press the '''Load Previous''' button

'''Feedback'''

* Conditions that have different numbers of electrodes (averaging across different files) can only be combined if channels are interpolated to a standard set of electrodes.
* Conditions that have different durations or sampling rates can only be combined if the sampling rate and durations are made the same.
* Feedback about the above situations is displayed by the presence of tick marks above the list box.

=== Channel List Tab ===

List the channel names, define target channel names, and how input channels are combined into target channels.

Note that this tab is very similar in usage to the '''Condition List Tab'''. Note also that some of the functions performed in this tab could also be done in the Montage Editor. It may be a matter of convenience whether you choose to perform these operations here or in the Montage Editor.

The first column of the list box shows a list of all the channel names found in the source files.

Rows of the list box define the ''source'' channel. Columns define the'' target'' channel.

'''Initial setting'''

When first selecting the tab, each column shows each channel name found in the source files (as in the example below). In the list box, there is a "+1" along the diagonal. The result of this selection is that target channel will have the same name as source channel.

'''Combining files'''

If files with different channel configurations are included in the File List, the rows and columns of the Channel List Tab will only contain the labels for the channels that are in common among the files.

If the files in the File List have a different sequence of channels, the sequence of the first file in the list will be adopted in the Channel List.

Thus, for the initial setting, unless the "''Ignore Settings in this Tab''" checkbox is checked, the target grand average or peak/amplitude analysis, etc. will be applied using only channels that are in common among the input files, and using the channel sequence of the first file in the File List. By changing the target channels or by changing the entries in the Channel List, new channels consisting of averages or differences can be generated.

'''What can the Channel List be used for?'''

Some examples:

* Reorder or relabel channels
* Create channel differences
* Create averages over channel groups, e.g. for peak analysis
* Extract a selection of channels for peak analysis or mean amplitudes
* Create grand averages across files with different channel configurations, just using channels in common among the files

[[Image:Batch processing (30).gif]]

'''Editing the channel list'''

* Target channel names can be edited, inserted or deleted by clicking on the label at the top of each column.
* Click on a box within the list to toggle between "+1", "-1" and blank. These correspond to the operations:
** "+1" = add
** "-1" = subtract
** blank = do nothing
* Right click on a box for further operations: channels can be weighted by a given factor other than 1.

'''Divide result by sum of PLUS factors'''

* Normally, when creating an average over channels, the sum is divided by the number of channels or a weighted average is generated (see below).  If "Divide result by the sum of PLUS factors" is unchecked, the channels will be summed rather than averaged.
* Note that, when making differences between channels, no such division is required. BESA Research will uncheck the checkbox automatically if subtraction ("-1") is specified somewhere in the channel list.

'''Save the current channel list'''

* Press the '''Save Channel List''' button.

'''Load a channel list'''

* Press the '''Load Channel List '''button.

'''Load previous settings'''

* Press the '''Load Previous''' button

=== Run Scripts Tab ===

Define global options for the output (e.g. spatial interpolation, resampling, copy/merge or average, peak detection. Start the operation.

[[Image:Batch processing (7).jpg]]

'''Load or Save Settings'''

* You can save the current settings of this tab to a file (*.run) which can be loaded later.
* When you run the script, the current settings are saved automatically to a file "'''PreviousSettings.run'''".

'''Load Previous'''

* Press this button to load the previous settings (from "'''PreviousSettings.run'''").

'''Averages to Generate'''

* '''Generate separate averages for each source file'''. Averages are performed over conditions within the source file, and are then appended to the target file.
* '''Combine data from source files'''. Conditions are combined over all source files into a single target average.
* '''No averages, just copy'''. Files are copied and merged to the target file. Use this option for renaming conditions, merging files, removing unwanted averages (see below), changing the sampling rate and interval.
* '''Peaks and mean amplitudes'''. Specify time ranges for peaks, mean amplitudes, or integrals (areas).
* Note: When generating or copying averages (first three options), filters and baseline settings are turned off. For Peaks and mean amplitudes, filters and baseline settings are specified in the dialog.

'''Spatial Interpolation'''

* '''Interpolate to Standard 81 electrodes'''. The target file will contain only electrodes (other channels are omitted), using the Standard 81 configuration (as in other export functions within BESA Research). This cannot be selected if the source data contain less than 16 EEG channels.
* '''Interpolate Bad Channels'''. Bad electrode channels in the source file will be interpolated. If the above option is deselected and bad channels exist in one or more of the source files, this option is always on.

BESA Research can interpolate EEG, and MEG if the sensors are axial gradiometers or magnetometers. If other channels are marked as bad in one or more of the source files, these will be defined as bad in the target file. This applies to MEG planar gradiometers, to polygraphic data, and to ICR channels.

'''Temporal Interpolation'''

* '''Spline to New Sampling Rate and Interval'''. Data can be converted to a new sampling rate, and the interval can be changed.
** If the sampling rate is reduced, the data will be low-pass filtered at 1/3 sampling frequency before reduction.
** If the sampling interval is changed, the prestimulus and poststimulus intervals are limited by the smallest intervals in the conditions contributing to the averages. These limits are shown below the edit boxes.

'''Peaks and Mean Amplitudes'''

[[Image:Batch processing (31).gif]]

'''Peaks:'''

* Select the time range between which peaks are to be determined.
* Select the montage on which the peaks are to be determined.
* Define the filter settings.
* Define the baseline settings.
* Specify whether peaks are to be defined at one latency: if so, select the channel on which peaks are to be detected.
* Specify whether you want to find positive or negative peaks.

'''Mean amplitudes and areas:'''

* Select the time range over which the mean amplitudes or areas are to be determined.
* Select the montage on which the mean amplitudes or areas are to be determined.
* Define the filter settings.
* Note that when computing areas, data are first rectified (made positive) and then summed over the time range.

'''Output options of the analysis:'''

* A single ASCII file that contains the result of the analysis for all data sets, conditions, and channels including header and information lines.
* A sparse output suitable for import in SPSS. Each variable (e.g. a latency, a channel amplitude) constitutes one column of the output file.
* Direct transfer to MATLAB into a struct besa_peak. For more information on the data transfer from BESA Research to MATLAB, please refer to help chapter ''“The MATLAB interface”.''

'''Starting the Operation'''

* Press '''OK''' to start the operation. After the operation is completed, and the "Open target file in BESA" box is checked, BESA Research will open the target file.  "Open target file in BESA" cannot be checked if "Peaks and mean amplitudes" was selected - then the result of the operation will be an ASCII file or a MATLAB transfer.
* You will be asked for the name of the target file (unless a MATLAB transfer of peak data has been performed).

'''Restrictions'''

* Depending on source file configurations, not all options above are selectable. For instance, if two files contain different numbers of electrodes, and the "''Ignore Settings in this Tab''" checkbox is checked in the '''''Channel List''''' Tab, spatial interpolation to Standard 81 is enforced in the target. Similarly, if different sampling rates are used in different files, temporal interpolation is enforced.
* You are not allowed to add files to the file list if the channel configuration is different, and the data cannot be combined with Standard 81 interpolation. Since Standard 81 interpolation is only possible for EEG, multiple files without EEG can only be loaded if they have the same number of channels.

=== How to Create Grand Averages ===

* Open the files you want to average in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...).''
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions. To average across different conditions, click in the list boxes to obtain "+1" for each source condition to combine, and rename the target condition to define a meaningful name for the average.
* Click on the '''Run Scripts Tab'''.
* If you have more than one file, specify whether averages should be generated across files ('''Combine data from source files''') or within files ('''Generate separate averages for each source file''').
* Select other options if required (spatial or temporal resampling).
* Press '''OK'''.

=== How to Generate Differences Between Conditions ===

* Open the files you want to operate on in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...).''
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions. To create differences, click in the list boxes to obtain "+1" for one of the source conditions, and "-1" for the source condition to subtract, and rename the target condition to define a meaningful name for the difference.
* Click on the '''Run Scripts Tab'''.
* If you have more than one file, specify whether averages should be generated across files ('''Combine data from source files''') or within files ('''Generate separate averages for each source file''').
* Select other options if required (spatial or temporal resampling).
* Press '''OK'''. An average of the differences is generated. If only one example of each condition exists, e.g. in a grand average file, the result is the difference between conditions.

=== How to Merge Files ===

* Open the files you want to merge in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions''...).
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions.
* Click on the '''Run Scripts Tab'''. Select "''No averages, just copy''".
* Press '''OK'''.

'''Notes'''

* If the source files have different electrode configurations, use the Standard 81 configuration for the target.
* If the source files have different sampling rates or intervals, use Temporal Interpolation.

=== How to Remove Unwanted Averages ===

'''Removing one or more unwanted segments'''

* Normally, all conditions are read from a source file. To exclude one or more segments from operations in the Combine Conditions module, mark the segments as artifacts in the main program display. It is sufficient for the beginning or the end of an artifact interval to be within the segment for the segment to be excluded.
* Open the file you want to operate on in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...).''
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions.
* Click on the '''Run Scripts Tab'''. Select "''No averages, just copy''".
* Press''' OK'''.
* The target file contains the copied data without the conditions that were marked as averages.

'''Removing one or more unwanted conditions (by label)'''

* Open the file you want to operate on in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...).''
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions.
* Deselect the target conditions you want to omit (replace the "+1" by a blank).
* Click on the '''Run Scripts Tab'''. Select "''No averages, just copy''".
* Press''' OK'''.
* The target file contains the copied data without the conditions that were marked as artifacts.

=== How to Rename Conditions ===

* Open the file you want to operate on in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions''...).
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions. Click on column headings to rename the target conditions.
* Click on the''' Run Scripts Tab'''. Select "''No averages, just copy''".
* Press '''OK'''.
* The target file contains the copied data with the renamed conditions.

=== How to Change the Sampling Rate ===

* Open the file(s) you want to change in BESA Research.
* Start the Combine Conditions Module (''ERP / Combine Conditions...'').
* Click on the '''Condition List Tab'''. By default, the target conditions receive the same name as the source conditions.
* Click on the '''Run Scripts Tab'''. Select "''No averages, just copy''".
* Select "''Spline to New Sampling Rate and Interval''" and type the new sampling rate into the edit box.
* Press '''OK'''.

=== Example: Create grand average and combinations of conditions ===

In this example, we will generate a grand average of the results of the Auditory Intensity Experiment. The experiment includes averages from five different stimulus intensities. We will create a grand average over each intensity, but also include means over the two lowest and the two highest intensities, and the difference between these two combinations.

'''A. File selection'''

# Start BESA Research and open files '''S1_av.fsg - S10_av.fsg''' in the ''Examples\ERP-Auditory-Intensity'' folder. The files contain the individual averaged data of the 10 subjects who participated in this study.
# Select ''ERP / Combine Conditions...'' The file list should display the two files, with feedback about the number of averages and conditions. 8 epochs are found. See the ''“Data averaging in the auditory intensity'' ''experiment”'' example for examples how to manipulate the file list.

[[Image:Batch processing (32).gif]]

'''B. Define conditions'''

1. Click on the '''Condition List Tab'''. The initial window defines target conditions with the same name as the source conditions. To generate the grand average over these conditions we could proceed without further changes to the '''Run Scripts Tab'''. However, we want to modify the condition list and create a condition that contains the grand averaged difference between the''' High''' and '''Low''' conditions.

[[Image:Batch processing (8).jpg]]

2. Click on the '''All '''column label. In the resulting window, rename condition '''All''' to''' Difference'''. Then press '''OK'''.

[[Image:Batch processing (33).gif]]

3. The last column is now labeled '''Difference.''' Left-click twice onto the ‘'''+1’''' entry that links this condition to the '''All '''input condition. This will remove the link and leave the field blank. To define the ‘Difference’ condition as the average of ‘High’ minus ‘Low’ over subjects, left-click once into the field linking input '''High''' with target '''Difference''' to generate an entry ‘'''+1’''' in this field. Left-click twice into the field linking input '''Low '''with target '''Difference''' to generate an entry '-'''1'''’.

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

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

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

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<div style="margin-left:1.27cm;margin-right:0cm;">[[Image:Batch processing (35).gif]]</div>

4. Press '''Save Condition List''' and save the list to '''ERP-aud-ex1.clist'''. This condition combination can thus be loaded later using the '''Load Condition List''' button.

'''C. Run the script'''

# Click on the '''Run Script Tab'''.
# The default tab settings are ready for generating the grand average ('''Combine data from source file''' and '''Open target file in BESA''' should be checked). Just press '''OK'''. Enter '''All_Subjects_cc-test.fsg''' as file name and press''' Save'''.

The resulting file contains the 8 target conditions, 60db, 70dB, 80dB, 90dB, 100dB, Low, High, and Difference.

=== Example: Average files from different experiments ===

This example is intended to illustrate several features of the ''Combine Conditions'' Dialog, such as electrode interpolation and resampling. We will combine an average from the Auditory Intensity experiment with one from the P300 auditory experiment. In this particular case, it is not a very meaningful thing to do, but it shows what is possible. For instance, the same experiment may have been performed using different sampling rates or electrode combinations. This example shows how such data may be combined.

'''A. File selection'''

# Start BESA Research and open the file '''All_Subjects_GA.fsg''' in the ''Examples\ERP-Auditory-Intensity'' folder. The file contains the grand average data from the auditory intensity experiment.
# Open the file '''RareFrequentResponseLeft.fsg''' in the ''Examples\ERP-P300-Auditory'' folder. This file contains averages from the P300 auditory experiment.
# Select ''ERP / Combine Conditions... ''Note that the files have different sampling rates and different numbers of electrodes.

[[Image:Batch processing (36).gif]]

'''B. Define conditions'''

1. Click on the '''Condition List Tab'''. Note that the feedback text at the bottom of the window displays the text "Standard 81 interpolation required to generate average; Across files: resampling or change in time range required to generate average". The condition labels show all the names from both files.

[[Image:Batch processing (37).gif]]

2. We will exclude most conditions, and just combine the most similar conditions from the two experiments: the "Standard" and the "80dB" conditions. Click on the title of the first column,''' Blink'''. Select “''Delete all conditions to the right of this column”'', and press '''OK'''.

[[Image:Batch processing (38).gif]]

3. Click on the title again, and rename the target condition to "Standard".

[[Image:Batch processing (39).gif]]

4. Click twice in the first line to remove the "+1" entry there. Click once in the third row ("Frequent"), and in the 7th row ("80dB"), to display "+1" at each entry. Thus, just two of the conditions will be combined into one target condition.

[[Image:Batch processing (40).gif]]

'''C. Run the script'''

1. Click on the '''Run Script Tab'''.

[[Image:Batch processing (41).gif]]

2. Note that '''Interpolate to Standard 81 electrodes''' is checked and grayed: since two different electrode sets are to be combined, we can only do this by interpolating electrodes. Also, both '''Spline to new sampling rate''' and '''Clip interval '''are checked and grayed. Again, these settings are required in order to be able to average the two data files together. The sampling rate is set to the higher of the two selections. The time range is set to the largest possible range that can be clipped from the two data sets. For now, leave these settings as they are, and press '''OK'''. Save the target to '''TestCombineExpts_CC-std81.fsg'''.

{{BESAManualNav}}

Discrete Sources

2024-03-11T13:28:03Z

Dominik:

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

== Overview ==

A source is used to model the electro-magnetic activity caused by patches of simultaneously active neurons. There are three types of sources in BESA:

* [[Image:singleDipole.png|40px]] [[#Single Dipole | single dipoles]],
* [[Image:regionalSource.png|40px]] [[#Regional Source | regional sources]],
* [[Image:spatialComponent.png|40px]] [[#Spatial Component | spatial components]].

In case of MRI-coregistered datasets the [[#Confidence Ellipsoid and Error Rim | confidence ellipsoid and error rim]] can be displayed for single dipoles and regional sources.

== Single Dipole ==

[[Image:singleDipole.png|40px]] A single dipole source (abbreviation: ''SD'' or ''Dip'') can be regarded as an electric current dipole, which is used for the physical modeling of the physiological activity. It is described by a location and an orientation, and the source waveform describes its amplitude over time.

'''Selected Source'''

A source is selected by clicking onto the source plot in the head box or by clicking onto the source waveform in the source box. It is deselected by selecting another source or by clicking beneath any source plot in the head box.

The selected source is marked with a circle around its source plots in the head box, with a golden halo in the 3D window and a colored rectangle around its On/Off and Fit/No fit button in the source box. If a source is selected its parameters are displayed in the parameter box.

== Regional Source ==

[[Image:regionalSource.png|40px]] A regional source (abbreviation: ''RS'') is a source which describes all activity originating in the vicinity of its location. It can be regarded as a source with three (MEG spherical head models: two) [[#Single Dipole| single dipoles]] (called components) at the same location but with orthogonal orientations.

[[Image:orientedRegionalSource.png|40px]] A regional source can be rotated such that one of the single orientations of its components explains a maximum of activity at a specified sample. If a regional source has been rotated, the orientation of each component is displayed in the [[Source_Analysis_Functions_of_the_Window#Head_Box | head box]], otherwise only the source body is displayed.

== Spatial Component ==

[[Image:spatialComponent.png|40px]] A spatial component (abbreviation: ''SpC'') is a source represented by a principal vector. This principal vector results from a Principal Component Analysis (PCA) or Independent Component Analysis (ICA) of the covariance data matrix, from the RAP-Music algorithm, or from the measured data at the cursor sample. It describes the contribution of the source at the sensors. The topography of a spatial component need not be of dipolar nature.

If the spatial component results from a PCA, ICA, or the cursor sample, its location is reconstructed by an approximation. Spatial components created by RAP-Music have exactly defined location and orientation but can consist of two components (with one resulting principal vector).

== Confidence Ellipsoid and Error Rim ==
''(requires BESA Research 7.1 or higher)''

For [[#DSingle Dipole | dipole solutions]] and [[#Regional Source | oriented regional sources]], confidence limits are calculated, displayed, and stored. The last fit interval used for a source is relevant for computing the confidence limit, as well as the baseline interval. These intervals are also stored with the solution. In case of multi-dipole solutions or solutions which include spatial components, the full source model is taken into account for computation. Confidence limits are written to solution files if the coordinate system for export is set to Talairach. For these solutions, an import and display of the solution in BESA MRI is possible (BESA MRI 3.0 or higher). The limit that is computed corresponds to the 95% confidence limit. Computation follows the approach of M. Hämäläinen (Interpretation of neuromagnetic measurements: modeling and statistical considerations, PhD thesis at Helsinki University of Technology 1987, pp 27 ff).

* Note: Confidence limit display in the MRI window is only active if an individual MRI was co-registered.
* Also note that the confidence limit computed requires a baseline interval that is well defined. The baseline interval can be adjusted by clicking on the baseline indicator bar at the top left of the Source Analysis window.
* Confidence limits depend on many factors including the number of active sources, the signal-to-noise ratio, and the fit interval. In particular, the confidence limit does not account for other errors, e.g. head model errors, co-registration errors, or influence of artifacts on the solution. They should be regarded as a guideline and serve as a lower limit to the confidence of the solution, not as an upper limit.

'''The confidence ellipsoid radii are computed as follows:'''

First the data predicted by the model (b) is computed using fitting time point i or the fitting interval, and predicted source strength from the inverse operator applied to measured data.

ji is calculated for the time point. Then the Jabobian J can be defined as change in b when moving the dipole in the three main axes of the ellipsoid, e.g. for the first axis (depicted as x axis here):

[[Image:confidenceEllipsoid_eq01.png]]

where h is sufficiently small.

Then compute the C matrix (3x3) from which radii (∆x,∆y,∆z) for a 95% confidence interval can be defined:

[[Image:confidenceEllipsoid_eq02.png]]

[[Image:confidenceEllipsoid_eq03.png]]

'''References'''

* Hämäläinen, M., 1987. Interpretation of neuromagnetic measurements : modeling and statistical considerations. Helsinki University of Technology.

{{BESAManualNav}}

The Initialization File: BESA.ini

2024-03-11T13:13:20Z

Dominik:

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

== Introduction ==

'''BESA.ini File'''

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

'''Location of BESA.ini'''

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

# '''Private''': each user on a PC should have his/her own private settings. This is normally in ''Documents/BESA/Research_7_1''
# '''Public''': all users should use one setting, but they can edit '''BESA.ini''' to change the settings. This is normally in ''Public Documents/BESA/Research_7_1''
# '''Administrator''': the PC administrator determines the settings. This is normally in ''C:Program Files(x86)/BESA/Research_7_1''

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

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

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

{| class="wikitable"
| [Defaults]
| General settings (filters, scaling, and various other settings)
|-
| [Folders]
| Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)
|-
| [Electrodes]
| Electrode renaming
|-
| [Patterns]
| Rename patterns in the '''Tags''' menu
|-
| [Artifacts]
| Settings for artifact correction
|-
| [KEYCONTROLS]
| Function key definitions
|-
| [Search]
| Default parameters for search
|-
| [FFT]
| Frequency band definitions
|-
| [Printer]
| Printer control
|-
| [Calibration]
| Calibration control
|-
| [Video]
| Digital video control
|-
| [Mapping]
| Mapping control
|-
| [Updates]
| Options for program updates
|-
| [Matlab]
| Settings for the MATLAB interface
|-
| [fMRI]
| Settings for the fMRI arfifact removal
|-
| [Montages]
| A setting for a default source montage
|}

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

== Defaults ==

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

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

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

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

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

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

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

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

'''MegScale=200''' scale of MEG/GRA channels in [fT or fT/cm]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'''Notes'''

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

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

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

== Folders ==

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

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

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

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

'''The Variables'''

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

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

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

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

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

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

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

'''Placeholders'''

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

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

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

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

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

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program Files (x86)\BESA\Research_7_0''".

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

== Electrodes ==

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

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

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

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

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

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

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

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

PG1=LO1 define X3 as lateral orbital eye electrode left

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

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

X9=Rsp define X9 channel to be a respiratory channel

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

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

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

== Patterns ==

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

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

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

Pattern1=Spike

Pattern2=Sharp Wave

== Artifacts ==

'''Artifact default settings:'''

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

== Search ==

Default settings for pattern search.

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

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

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

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

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

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

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

'''LowPassFreq = 35 Hz'''

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

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

'''CorrelationThresholdNoMarked = 60%'''

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

'''CorrelationThresholdOneMarked = 85%'''

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

'''CorrelationThresholdFourMarked = 65%'''

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

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

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

'''WriteAfterSearchCheckBox = No'''

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

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

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

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

== KeyControls ==

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

'''Fn=function''' or

'''Del=function'''

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

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

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

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

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

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

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

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

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

'''Batches and Montages:'''

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

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

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

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

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

== FFT ==

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

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

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

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

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

'''FFTBand7=Off'''

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

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

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

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

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

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

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

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

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

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

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

'''FFTHighBand3=14'''

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

'''FFTHighBand4=30'''

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

'''FFTHighBand5=50'''

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

== Printer ==

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

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

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

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

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

== Calibration ==

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

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

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

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

== Video ==

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

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

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

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

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

== Mapping ==

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

'''UseBitmapDrawing=Off'''

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

'''Use3DVBlending=Auto'''

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

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

'''UseDoubleBuffering=On'''

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

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

== Matlab ==

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

'''Platform=64'''

Set '''Platform=32''' if you want to use the x86t version of MATLAB.

== Updates ==

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

'''DaysBetweenUpdateChecks=7'''

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

'''CheckNetworkDongle=Off'''

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

'''LocalPath'''

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

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

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

Download server

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

Path on the server to UpdateVersions.txt.

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

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

'''History'''

Path on the server to general history file

== FMRI ==

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

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

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

These values indicate:

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

== Montage ==

'''The section [Montage] allows to specify an initial montage that is set the first time when the source (Src), recorded (Rec), virtual (Vir) or user (Usr) montage button is pressed. If BESA.ini does not specify a montage, pressing the corresponding button opens the drop-down menu offering all the available montages for the current montage type.'''

'''Source=25s''' specifies that when the Src button in the control ribbon is pressed for the first time, the source montage "25s" will be selected.

'''Recorded=Original Recording''' specifies that when the Rec button in the control ribbon is pressed for the first time, the source montage "Original Recording" will be selected.

'''Virtual=Triple Banana''' specifies that when the Vir button in the control ribbon is pressed for the first time, the source montage "Triple Banana" will be selected.

'''User=CA25''' specifies that when the Usr button in the control ribbon is pressed for the first time, the source montage "CA25" will be selected.

== Reader-Specific Settings ==

 
=== BrainLab ===

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

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

=== Bio-Logic ===

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:

* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>

* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

=== EDF+/BDF/Trackit ===

'''TriggerScan=On'''

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

=== EGI ===

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

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

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

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

Set to “no” if you don’t want to treat DIN events separately. Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

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

This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

=== Harmonie ===

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

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

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

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

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

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

=== Neuroscan Keys ===

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

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

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

=== NKT2100 ===

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

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

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

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

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

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

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

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

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

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

=== Vangard ===

'''AlwaysOpenFileSelect=Yes'''

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

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

=== XLTEK ===

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

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

[[Category:Research Manual]]

{{BESAManualNav}}

Source Analysis 3D Imaging

2024-03-11T12:21:27Z

Dominik:

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


== Overview ==

BESA Research features a set of new functions that provide 3D images that are displayed superimposed to the individual subject's anatomy. This chapter introduces these different images and describe their properties and applications.

The 3D images can be divided into three categories:

'''Volume images:'''

* '''The Multiple Source Beamformer (MSBF)''' is a tool for imaging brain activity. It is applied in the time-domain or time-frequency domain. The beamformer technique in time-frequency domain can image not only evoked, but also induced activity, which is not visible in time-domain averages of the data.
* '''Dynamic Imaging of Coherent Sources (DICS)''' can find coherence between any two pairs of voxels in the brain or between an external source and brain voxels. DICS requires time-frequency-transformed data and can find coherence for evoked and induced activity.

The following imaging methods provide an image of brain activity based on a distributed multiple source model:
* '''CLARA''' is an iterative application of LORETA images, focusing the obtained 3D image in each iteration step.
* '''LAURA '''uses a spatial weighting function that has the form of a local autoregressive function.
* '''LORETA''' has the 3D Laplacian operator implemented as spatial weighting prior.
* '''sLORETA''' is an unweighted minimum norm that is standardized by the resolution matrix.
* '''swLORETA '''is equivalent to sLORETA, except for an additional depth weighting.
* '''SSLOFO '''is an iterative application of standardized minimum norm images with consecutive shrinkage of the source space.
* A '''User-defined volume image''' allows to experiment with the different imaging techniques. It is possible to specify user-defined parameters for the family of distributed source images to create a new imaging technique.
* Bayesian source imaging: '''SESAME''' uses a semi-automated Bayesian approach to estimate the number of dipoles along with their parameters.

'''Surface image:'''

* The '''Surface Minimum Norm Image'''. If no individual MRI is available, the minimum norm image is displayed on a standard brain surface and computed for standard source locations. If available, an individual brain surface is used to construct the distributed source model and to image the brain activity.
* '''Cortical LORETA'''. Unlike classical LORETA, cortical LORETA is not computed in a 3D volume, but on the cortical surface.
* '''Cortical CLARA'''. Unlike classical CLARA, cortical CLARA is not computed in a 3D volume, but on the cortical surface.

'''Discrete model probing:'''

These images do not visualize source activity. Rather, they visualize properties of the currently applied discrete source model:
* The '''Multiple Source Probe Scan (MSPS)''' is a tool for the validation of a discrete multiple source model.
* The '''Source Sensitivity image''' displays the sensitivity of a selected source in the current discrete source model and is therefore data independent.

== Multiple Source Beamformer (MSBF) in the Time-frequency Domain ==

 
'''Short mathematical introduction'''

The BESA beamformer is a modified version of the linearly constrained minimum variance vector beamformer in the time-frequency domain as described in [https://dx.doi.org/10.1073/pnas.98.2.694 Gross et al., "Dynamic imaging of coherent sources: Studying neural interactions in the human brain", PNAS 98, 694-699, 2001]. It allows to image evoked and induced oscillatory activity in a user-defined time-frequency range, where time is taken relative to a triggered event.

The computation is based on a transformation of each channel's single trial data from the time domain into the time-frequency domain. This transformation is performed by the BESA Research Source Coherence module and leads to the complex spectral density Si (f,t), where i is the channel index and f and t denote frequency and time, respectively. Complex cross spectral density matrices C are computed for each trial:

<math>\mathrm{C}_{ij}\left( f,t \right) = \mathrm{S}_{i}\left( f,t \right) \cdot \mathrm{S}_{j}^{*}\left( f,t \right)</math>


The output power P of the beamformer for a specific brain region at location r is then computed by the following equation:

<math>\mathrm{P}\left( r \right) = \operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{-1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{-1}</math>


Here, Cr-1 is the inverse of the SVD-regularized average of Cij(f,t) over trials and the time-frequency range of interest; L is the leadfield matrix of the model containing a regional source at target location r and, optionally, additional sources whose interference with the target source is to be minimized; tr'[] is the trace of the [3×3] (MEG:[2×2]) submatrix of the bracketed expression that corresponds to the source at target location r.

In BESA Research, the output power P(r) is normalized with the output power in a reference time-frequency interval Pref(r). A value q ist defined as follows:

<math> \mathrm{q}\left( r \right) =
\begin{cases}
\sqrt{\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}(r)}} - 1 = \sqrt{\frac{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{\text{ref},r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}} - 1, & \text{for }\mathrm{P}(r) \geq \mathrm{P}_{\text{ref}}(r) \\

1 - \sqrt{\frac{\mathrm{P}_{\text{ref}}\left( r \right)}{\mathrm{P}\left( r \right)}} = 1 - \sqrt{\frac{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{\text{ref},r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}}, & \text{for }\mathrm{P}(r) < \mathrm{P}_{\text{ref}}(r)
\end{cases} </math>


Pref can be computed either from the corresponding frequency range in the baseline of the same condition (i.e. the beamformer images event-related power increase or decrease) or from the corresponding time-frequency range in a control condition (i.e. the beamformer images differences between two conditions). The beamformer image is constructed from values q(r) computed for all locations on a grid specified in the '''General Settings tab'''. For MEG data, the innermost grid points within a sphere of approx. 12% of the head diameter are assigned interpolated rather than calculated values).
q-values are shown in %, where where q[%] = q*100. Alternatively to the definition above, q can also be displayed in units of dB:

<math>\mathrm{q}\left\lbrack \text{dB} \right\rbrack = 10 \cdot \log_{10}\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}</math>


A beamformer operator is designed to pass signals from the brain region of interest r without attenuation, while minimizing interference from activity in all other brain regions. Traditional single-source beamformers are known to mislocalize sources if several brain regions have highly correlated activity. Therefore, the BESA beamformer extends the traditional single-source beamformer in order to implicitly suppress activity from possibly correlated brain regions. This is achieved by using a multiple source beamformer calculation that contains not only the leadfields of the source at the location of interest r, but also those of possibly interfering sources. As a default, BESA Research uses a bilateral beamformer, where specifically contributions from the homologue source in the opposite hemisphere are taken into account (the matrix L thus being of dimension N×6 for EEG and N×4 for MEG, respectively, where N is the number of sensors). This allows for imaging of highly correlated bilateral activity in the two hemispheres that commonly occurs during processing of external stimuli.

In addition, the beamformer computation can take into account possibly correlated sources at arbitrary locations that are specified in the current solution. This is achieved by adding their leadfield vectors to the matrix L in the equation above.

'''Applying the Beamformer'''

This chapter illustrates the usage of the BESA beamformer. The displayed figures are generated using the file ''''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''' (see BESA Tutorial 12: "''Time-frequency analysis, Connectivity analysis, and Beamforming''").

'''Starting the beamformer from the time-frequency window'''

The BESA beamformer is applied in the time-frequency domain and therefore requires the Source Coherence module to be enabled. The time-frequency beamformer is especially useful to image in- or decrease of induced oscillatory activity. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot. For instructions on how to initiate a beamformer computation in the time-frequency window, please refer to Chapter '''[[Source_Coherence_How_to...#How_to_Start_the_Beamformer_from_the_Time-Frequency_Window|How to Create Beamformer Images]]'''.

After the beamformer computation has been initiated in the time-frequency window, the source analysis window opens with an enlarged 3D image of the q-value computed with a '''bilateral beamformer'''. The result is superimposed onto the MR image assigned to the data set (individual or standard).

[[Image:SA 3Dimaging (5).png|700px|thumb|c|none|Beamformer image after starting the computation in the Time-Frequency window. A bilateral pair of sources in the auditory cortex accounts for the highly correlated oscillatory induced activity. Only the bilateral beamformer manages to separate these activities; a traditional single-source beamformer would merge the two sources into one image maximum in the head center instead.]]

'''Multiple source beamformer in the Source Analysis window'''

The 3D imaging display is part of the source analysis window. If you press the '''Restore''' button at the right end of the title bar of the 3D window, the window appears at the bottom right of the source analysis window. In the channel box, the averaged (evoked) data of the selected condition is shown. When a control condition was selected, its average is appended to the average of the target condition.

[[Image:SA 3Dimaging (6).png|700px|thumb|c|none|Source Analysis window with beamformer image. The two sources have been added using the '''''Switch to''''' '''''Maximum''''' and '''''Add Source '''''toolbar buttons (see below). Source waveforms are computed from the displayed averaged data. Therefore, they do not represent the activity displayed in the beamformer image, which in this simulation example is induced (i.e. not phase-locked to the trigger)!]]

When starting the beamformer from the time-frequency window, a bilateral beamformer scan is performed. In the source analysis window, the beamformer computation can be repeated taking into account possibly correlated sources that are specified in the current solution. Interfering activities generated by all sources in the current solution that are in the 'On' state are specifically suppressed ('''they enter the matrix L in the beamformer calculation''', see Chapter ''Short mathematical description'' above). The computation can be started from the '''Image''' menu or from the '''Image selector button''' dropdown menu. The '''Image''' menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window.

[[Image:SA 3Dimaging (7).png|700px|thumb|c|none|Multiple source beamformer image calculated in the presence of a source in the left hemisphere. A '''single''' source scan has been performed. The source set in the current solution accounts for the left-hemispheric q-maximum in the data. Accordingly, the beamformer scan reveals only the as yet unmodeled additional activity in the right hemisphere (note the radiological convention in the 3D image display).]]

The beamformer scan can be performed with a '''single''' or a '''bilateral''' source scan. The default scan type depends on the current solution:
* When the beamformer is started from the Time-Frequency window, the Source Analysis window opens with a new solution and a '''bilateral''' beamformer scan is performed.
* When the beamformer is started within the Source Analysis window, the default is
** a scan with a '''single''' source in addition to the sources in the current solution, if at least one source is active.
** a '''bilateral''' scan if no source in the current solution is active.

The default scan type is the multiple source beamformer. The non-default scan type can be enforced using the corresponding ''Volume Image / Beamformer'' entry in the '''Image''' menu.

'''Inserting Sources out of the Beamformer Image'''

The beamformer image can be used to add sources to the current solution. A simple double-click anywhere in the 2D- or 3D-view will generate a non-oriented regional source at the corresponding location. However, a better and easier way to create sources at image maxima and minima is to use the toolbar buttons '''Switch to Maximum''' [[Image:SA 3Dimaging (8).gif]] and '''Add Source''' [[Image:SA 3Dimaging (9).gif]].

Use the '''Switch to Maximum''' button to place the red crosshair of the 3D window onto a local image maximum or minimum. Hitting the '''Add Source''' button creates a regional source at the location of the crosshair and therefore ensures the exact placement of the source at the image extremum. Moreover, the '''Add Source''' button generates an oriented regional source. BESA Research automatically estimates the source orientation that contributes most to the power in the target time-frequency interval (or the reference time-frequency interval, if its power is larger than that in the target interval). The accuracy of this orientation estimate depends largely on the noise content of the data. The smaller the signal-to-noise ratio of the data, the lower is the accuracy of the orientation estimate. '''This feature allows to use the beamformer as a tool to create a source montage for source coherence analysis, where it is of advantage to work with oriented sources'''.

'''Notes:'''

* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image '''menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the''' Image''' menu.
* For scaling options, use the [[Image:SA 3Dimaging (10).gif]] and [[Image:SA 3Dimaging (11).gif]] '''Image Scale toolbar''' buttons.
* Parameters used for the beamformer calculations can be set in the '''Standard Volumes''' of the ''Image Settings dialog box.''

== Dynamic Imaging of Coherent Sources (DICS) ==

 
'''Short mathematical introduction'''

Dynamic Imaging of Coherent Sources (DICS) is a sophisticated method for imaging cortico-cortical coherence in the brain, or coherence between an external reference (e.g. EMG channel) and cortical structures. DICS can be applied to localize evoked as well as induced coherent cortical activity in a user-defined time-frequency range.

DICS was implemented in BESA closely following [https://dx.doi.org/10.1073/pnas.98.2.694 Gross et al., "Dynamic imaging of coherent sources: Studying neural interactions in the human brain", PNAS 98, 694-699, 2001].

The computation is based on a transformation of each channel's single trial data from the time domain into the frequency domain. This transformation is performed by the BESA Research Coherence module and results in the complex spectral density matrix that is used for constructing the spatial filter similar to beamforming.

DICS computation yields a 3-D image, each voxel being assigned a coherence value. Coherence values can be described as a neural activity index and do not have a unit. The neural activity index contrasts coherence in a target time-frequency bin with coherence of the same time-frequency bin in a baseline.

'''DICS for cortico-cortical coherence is computed as follows:'''

Let L(r) be the leadfield in voxel r in the brain and C the complex cross-spectral density matrix. The spatial filter W(r) for the voxel r in the head is defined as follows:

<math>W\left( r \right) = \left\lbrack L^{T}\left( r \right) \cdot C^{- 1} \cdot L\left( r \right) \right\rbrack^{- 1} \cdot L^{T}(r) \cdot C^{- 1}</math>


The cross-spectrum between two locations (voxels) r1 and r2 in the head are calculated with the following equation:

<math>C_{s}\left( r_{1},r_{2} \right) = W\left( r_{1} \right) \cdot C \cdot W^{*T}\left( r_{2} \right),</math>


where <nowiki>*T</nowiki> means the transposed complex conjugate of a matrix. The cross-spectral density can then be calculated from the cross spectrum as follows:

<math>c_{s}\left( r_{1},r_{2} \right) = \lambda_{1}\left\{ C_{s}\left( r_{1},r_{2} \right) \right\},</math>


where λ1{} indicates the largest singular value of the cross spectrum. Once the cross spectral density is estimated, the connectivity¹(CON) between the two brain regions r1 and r2 are calculated as follows:

<math>\text{CON}\left( r_{1},r_{2} \right) = \frac{c_{s}^{\text{sig}}\left( r_{1},r_{2} \right) - c_{s}^{\text{bl}}(r_{1},r_{2})}{c_{s}^{\text{sig}}\left( r_{1},r_{2} \right) + c_{s}^{\text{bl}}(r_{1},r_{2})},</math>


where cssig is the cross-spectral density for the signal of interest between the two brain regions r1 and r2, and csbl is the corresponding cross spectral density for the baseline or the control condition, respectively. In the case DICS is computed with a cortical reference, r1 is the reference region (voxel) and remains constant while r2 scans all the grid points within the brain sequentially. In that way, the connectivity between the reference brain region and all other brain regions is estimated. The value of CON(r1, r2) falls in the interval [-1 1]. If the cross-spectral density for the baseline is 0 the connectivity value will be 1. If the cross-spectral density for the signal is 0 the connectivity value will be -1.

¹ Here, the term connectivity is used rather than coherence, as strictly speaking the coherence equation is defined slightly differently. For simplicity reasons the rest of the tutorial uses the term coherence.

'''DICS for cortico-muscular coherence is computed as follows:'''

When using an external reference, the equation for coherence calculation is slightly different compared to the equation for cortico-cortical coherence. First of all, the cross-spectral density matrix is not only computed for the MEG/EEG channels, but the external reference channel is added. This resulting matrix is Call. In this case, the cross-spectral density between the reference signal and all other MEG/EEG channels is called cref. It is only one column of Call. Hence, the cross-spectrum in voxel r is calculated with the following equation:

<math>C_{s}\left( r \right) = W\left( r \right) \cdot c_{\text{ref}}</math>


and the corresponding cross-spectral density is calculated as the sum of squares of Cs:

<math>c_{s}\left( r \right) = \sum_{i = 1}^{n}{C_{s}\left( r \right)_{i}^{2}},</math>


where n is 2 for MEG and 3 for EEG. This equation can also be described as the squared Euclidean norm of the cross-spectrum:

<math>c_{s}\left( r \right) = \left\| C_{s} \right\|^{2},</math>


The power in voxel r is calculated as in the cortico-cortical case:

<math>p\left( r \right) = \lambda_{1}\left\{ C_{s}(r,r) \right\}.</math>


At last, coherence between the external reference and cortical activity is calculated with the equation:

<math>\text{CON}\left( r \right) = \frac{c_{s}(r)}{p\left( r \right) \cdot C_{\text{all}}(k,k)},</math>


where Call(k, k) is the (k,k)-th diagonal element of the matrix Call.

DICS is particularly useful, if coherence is to be calculated without an a-priory source model (in contrast to source coherence based on pre-defined source montages). However, the recommended analysis strategy for DICS is to use a brain source as a starting point for coherence calculation that is known to contribute to the EEG/MEG signal of interest. For example, one might first run a beamformer on the time-frequency range of interest and use the voxel with the strongest oscillatory activity as a starting point for DICS. The resulting coherence image will again lead to several maxima (ordered by magnitude), which in turn can serve as starting points for DICS calculation. This way, it is possible to detect even weak sources that show coherent activity in the given time-frequency range.

The other significant application for DICS is estimating coherence between an external source and voxels in the brain. For example, an external source can be muscle activity recoded by an electrode placed over the according peripheral region. This way, the direct relationship between muscle activity and brain activation can be measured.

'''Starting DICS computation from the Time-Frequency Window'''

DICS is particularly useful, if coherence in a user-defined time-frequency bin (evoked or induced) is to be calculated between any two brain regions or between an external reference and the brain. DICS runs only on time-frequency decomposed data, so time-frequency analysis needs to be run before starting DICS computation.

To start the DICS computation, left-drag a window over a selected time-frequency bin in the Time-Frequency Window. Right-click and select “Image”. A dialogue will open (see fig. 1) prompting you to specify time and frequency settings as well as the baseline period. It is recommended to use a baseline period of equal length as the data period of interest. Make sure to select “DICS” in the top row and press “'''Go'''”.

[[Image:SA 3Dimaging (21).gif|450px|thumb|c|none|Fig. 1: Time and frequency settings for DICS and MSBF]]

Next, a window will appear allowing you to specify the reference source for coherence calculation (see fig. 2). It is possible to select a channel (e.g. EMG) or a brain source. If a brain source is chosen and no source analysis was computed beforehand, the option “Use current cross-hair position” must be chosen. In case discrete source analysis was computed previously, the selected source can be chosen as the reference for DICS. Please note that DICS can be re-computed with any cross-hair or source position at a later stage.

[[Image:SA 3Dimaging (1).jpg|400px|thumb|c|none|Fig. 2: Possible options for choosing the reference]]

Confirming with “'''OK'''” will start computation of coherence between the selected channel/voxel and all other brain voxels. In case DICS is computed for a reference source in the brain, it can be advantageous to run a beamforming analysis in the selected time-frequency window first and use one of the beamforming maxima as reference for DICS. Fig. 3 shows an example for DICS calculation.

[[Image:SA 3Dimaging (22).gif|500px|thumb|c|none|Fig. 3: Coherence between left-hemispheric auditory areas and the selected voxel in the right auditory cortex.]]

Coherence values range between -1 and 1. If coherence in the signal is much larger than coherence in the baseline (control condition) then the DICS value is going to approach 1. Contrary, if coherence in the baseline is much larger than coherence in the signal, then the DICS value is going to approach -1. At last, if coherence in the signal is equal to coherence in the baseline, then the DICS value is 0.

In case DICS is to be re-computed with a different reference, simply mark the desired reference position by placing the cross-hair in the anatomical view and select “DICS” in the middle panel of the source analysis window (see Fig. 4). In case an external reference is to be selected, click on “DICS” in the middle panel to bring up the DICS dialogue (see. Fig. 2) and select the desired channel. Please note that DICS computation will only be available after running time-frequency analysis.

[[Image:SA 3Dimaging (23).png|700px|thumb|c|none|Fig. 4: Integration of DICS in the Source Analysis window]]

== Multiple Source Beamformer (MSBF) in the Time Domain ==
''This feature requires BESA Research 7.0 or higher.''

'''Short mathematical introduction'''

Beamforming approach can be also applied in the time domain data. This approach was introduced as linearly constrained minimum variance (LCMV) beamformer (Van Veen et al., 1997). It allows to image evoked activity in a user-defined time range, where time is taken relative to a triggered event, and to estimate source waveforms using the calculated spatial weight at locations of interest. For an implementation of the beamformer in the time domain, data covariance matrices are required, while complex cross spectral density matrices are used for the beamformer approaches in the time-frequency domain as described in the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section.

The bilateral beamformer introduced in the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section is also implemented for the time-domain beamformer to take into account contributions from the homologue source in the opposite. This allows for imaging of highly correlated bilateral activity in the two hemispheres that commonly occurs during processing of external stimuli. In addition, the beamformer computation can take into account possibly correlated sources at arbitrary locations.

The beamformer spatial weight W(r) for the voxel r in the brain is defined as follows (Van Veen et al., 1997):

<math>\mathrm{W}(r) = [\mathrm{L}^T(r)\mathrm{C}^{-1}\mathrm{L}(r)]^{-1}\mathrm{L}^T(r)\mathrm{C}^{-1}</math>


where <math>\mathrm{C}^{-1}</math> is the inversed regularized average of covariance matrix over trials, '''L''' is the leadfield matrix of the model containing a regional source at target location r and optionally additional sources whose interference with the target source is to be minimized. The beamformer spatial weight '''W'''(r) can be applied to the measured data to estimate source waveform at a location r (beamformer virtual sensor):

<math>\mathrm{S}(r,t) = \mathrm{W}(r)\mathrm{M}(t)</math>


where '''S'''(r,t) represents the estimated source waveform and '''M'''(t) represents measured EEG or MEG signals. The output power P of the beamformer for a specific brain region at location r is computed by the following equation:

<math>\mathrm{P}(r) = \operatorname{tr^{'}}[\mathrm{W}(r) \cdot \mathrm{C} \cdot \mathrm{W}^T(r)]</math>


where tr’[ ] is the trace of the [3×3] (MEG: [2×2]) submatrix of the bracketed expression that corresponds to the source at target location r.

Beamformer can suppress noise sources that are correlated across sensors. However, uncorrelated noise will be amplified in a spatially non-uniform manner, with increasing distortion with increasing distance from the sensors (Van Veen et al., 1997; Sekihara et al., 2001). For this reason, estimated source power should be normalized by a noise power. In BESA Research, the output power P(r) is normalized with the output power in a baseline interval or with the output power of a uncorrelated noise: P(r) / Pref (r).

The time-domain beamformer image is constructed from values q(r) computed for all locations on a grid specified in the '''General Settings''' tab. A value q(r) is defined as described in
the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section with data covariance matrices instead of cross-spectral density matrices.

'''Applying the Beamformer'''

This chapter illustrates the usage of the BESA beamformer in the time domain. The displayed figures are generated using the file ‘Examples/ERP-Auditory-Intensity/S1.cnt’.

'''''Starting the time-domain beamformer from the Average tab of the Paradigm dialog box'''''

The time-domain beamformer is needed data covariance matrices and therefore requires the ERP module to be enabled. After the beamformer computation has been initiated in the '''Average tab of the Paradigm dialog box''', the source analysis window opens with an enlarged 3D image of the q-value computed with a bilateral beamformer. The result is superimposed onto the MR image assigned to the data set (individual or standard).

[[File:MSBF4.png|500px|thumb|c|none|Beamformer image for auditory evoked data after starting the computation in the '''Average tab of the Paradigm dialog box'''. The bilateral beamformer manages to separate the activities in auditory areas, while a traditional single-source beamformer would merge the two sources into one image maximum in the head center instead.]]

'''''Multiple-source beamformer in the Source Analysis window'''''

The 3D imaging display is part of the source analysis window. In the Channel box, the averaged (evoked) data of the selected condition is shown. Selected covariance intervals in the ERP module can be checked in the Channel box. The red, gray, and blue rectangles indicate signal, baseline, and common interval, respectively.

[[File:MSBF55.png|700px|thumb|c|none|Source Analysis window with beamformer image. The two beamformer virtual sensors have been added using the Switch to Maximum and Add Source toolbar buttons (see below).
Source waveforms are computed using the beamformer spatial weights and the displayed averaged data (the noise normalized weights (5% noise) option was used to compute the beamformer image).]]

When starting the beamformer from the '''Average tab of the Paradigm dialog box''', the bilateral beamformer scan is performed. In the source analysis window, the beamformer computation can be repeated taking into account possibly correlated sources that are specified in the current solution. Interfering activities generated by all sources in the current solution that are in the 'On' state are specifically suppressed (they enter the leadfield matrix L in the beamformer calculation). The computation can be started from the '''Image''' menu or from the Image selector button [[File:MSBF_Button.png|22px|Image: 22 pixels]] dropdown menu. The Image menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window.

[[File:MSBF66.png|700px|thumb|c|none|Multiple-source beamformer image calculated in the presence of a source in the left hemisphere. A single-source scan has been performed instead of a bilateral beamforemr. The source set in the current solution accounts for the left-hemispheric q-maximum in the data. Accordingly, the beamformer scan reveals only the as yet unmodeled additional activity in the right hemisphere (note the radiological convention in the 3D image display). The source waveform of the beamformer virtual sensor in the left hemisphere is not shown since the location (blue square in the figure) is not considered for the multiple-source beamformer.]]

The beamformer scan can be performed with a single or a bilateral source scan. The default scan type depends on the current solution:

When the beamformer is started from the '''Average tab of the Paradigm dialog box''' the Source Analysis window opens with a new solution and a bilateral beamformer scan is performed.

When the beamformer is started within the Source Analysis window, the default is:
* a scan with a single source in addition to the sources in the current solution, if at least one source is active.
* a bilateral scan if no source in the current solution is active.
* a scan with a single source when scalar-type beamformer is selected in the '''beamformer option dialog box'''.

The default scan type is the multiple source beamformer. The non-default scan type can be enforced using the corresponding Volume Image / Beamformer entry in the Image main
menu or in the beamformer option dialog box (only for the time-domain beamformer).

'''Inserting Sources as Beamformer Virtual Sensor out of the Beamformer Image'''

This is similar to the inserting sources out of the beamformer image in Multiple Source Beamformer (MSBF) in the Time-frequency Domain section.

The beamformer image can be used to add beamformer virtual sensors to the current solution. A simple double-click anywhere in the 3D view (not in the 2D view) will generate a source at the corresponding location. A better and easier way to create sources at image maxima and minima is to use the toolbar buttons '''Switch to Maximum''' [[Image:SA 3Dimaging (8).gif]] and '''Add Source''' [[Image:SA 3Dimaging (9).gif]].

This feature allows to use the beamformer as a tool to create a source montage for '''source coherence''' analysis. A source montage file (*.mtg) for beamformer virtual sensors can
be saved using File \ Save Source Montage As… entry.

The time-domain beamformer image can be also used to add regional or dipole sources to the current solution. Press '''N''' key when there is no source in the current source array or there is more than one beamformer virtual sensor. To create a new source array for beamformer virtual sensor, press '''N''' key when there is more than one regional or dipole source in the current source array.

'''Notes'''

* You can hide or re-display the last computed image by selecting ''Hide Image'' entry in the '''Image''' menu.
* The current image can be exported to ASCII, ANALYZE, or BrainVoyager (*.vmp) format from the '''Image''' menu.
* For scaling options, use [[Image:SA 3Dimaging (10).gif]] and [[Image:SA 3Dimaging (11).gif]] '''Image Scale toolbar''' buttons.
* Parameters used for the beamformer calculations can be set in the '''Standard Volume tab of the Image Settings dialog box'''.
* Note that Model, Residual, Order, and Residual variance are not shown for the beamformer virtual sensor type sources.

'''References'''

* Sekihara, K., Nagarajan, S. S., Poeppel, D., Marantz, A., & Miyashita, Y. (2001). Reconstructing spatio-temporal activities of neural sources using an MEG vector beamformer technique. IEEE Transactions on Biomedical Engineering, 48(7), 760–771.

* Van Veen, B. D., Van Drongelen, W., Yuchtman, M., & Suzuki, A. (1997). Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Transactions on Biomedical Engineering, 44(9), 867–880

== CLARA ==

CLARA ('Classical LORETA Analysis Recursively Applied') is an iterative application of weighted LORETA images with a reduced source space in each iteration.

In an initialization step, a LORETA image is calculated. Then in each iteration the following steps are performed:

# The obtained image is spatially smoothed (this step is left out in the first iteration).
# All grid points with amplitudes below a threshold of 1% of the maximum activity are set to zero, thus being effectively eliminated from the source space in the following step.
# The resulting image defines a spatial weighting term (for each voxel the corresponding image amplitude).
# A LORETA image is computed with an additional spatial weighting term for each voxel as computed in step 3. By the default settings in BESA Research, the regularization values used in the iteration steps are slightly higher than that of the initialization LORETA image.

The procedure stops after 2 iterations, and the image computed in the last iteration is displayed. Please note that you can change all parameters by creating a user-defined volume image.

The advantage of CLARA over non-focusing distributed imaging methods is visualized by the figure below. Both images are computed from the N100 response in an auditory oddball experiment (file '''Oddball.fsg''' in subfolder ''fMRI+EEG-RT-Experiment'' of the ''Examples'' folder). The CLARA image is much more focal than the sLORETA image, making it easier to determine the location of the image maxima.

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (24).gif|thumb|350px|sLORETA image]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (25).gif|thumb|350px|CLARA image]] </li>
</ul></div>

'''Notes:'''

* Starting CLARA: CLARA can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]'' for important information on regularization of distributed inverses.

== LAURA ==

LAURA (Local Auto Regressive Average) belongs to the distributed inverse method of the family of weighted minimum norm methods ([https://doi.org/10.1023/A:1012944913650 Grave de Peralta Menendeza et al., "Noninvasive Localization of Electromagnetic Epileptic Activity. I. Method Descriptions and Simulations", BrainTopography 14(2), 131-137, 2001]). LAURA uses a spatial weighting function that includes depth weighting and that term has the form of a local autoregressive function.

The source activity is estimated by applying the general formula for a weighted minimum norm:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T}\left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings.''

In LAURA, V contains both a depth weighting term W and a representation of a local autoregressive function A. V is computed as:

<math>\mathrm{V} = \left( \mathrm{U}^{T} \cdot \mathrm{U} \right)^{-1}</math>


where

<math>\mathrm{U} = \left( \mathrm{W} \cdot \mathrm{A} \right) \otimes \mathrm{I}_{3}</math>


Here, <math>\otimes</math> denotes the Kronecker product. I3 is the [3×3] identity matrix. W is an [s×s] diagonal matrix (with s the number of source locations on the grid), where each diagonal element is the inverse of the maximum singular value of the corresponding regional source's leadfields. The formula for the diagonal components Aii and the off-diagonal components Aik are as follows:

<math>\mathrm{A}_{ii} = \frac{26}{\mathrm{N}_{i}}\sum_{k \subset V_{i}}^{}\frac{1}{\mathrm{d}_{ik}^{2}}</math>


<math>
\mathrm{A}_{ik} =
\begin{cases}
- 1/\operatorname{dist}\left( i,k \right)^{2}, & \text{if } k \subset V_{i} \\
0, & \text{otherwise}
\end{cases}
</math>


Here, Vi is the vicinity around grid point i that includes the 26 direct neighbors.

The LAURA image in BESA Research displays the norm of the 3 components of S at each location r. Using the menu function ''Image / Export Image As... ''you have the option to save this norm of S or alternatively all components separately to disk.

'''Notes:'''

* '''Grid spacing:''' Due to memory limitations, LAURA images require a grid spacing of 7 mm or more.
* '''Computation time:''' Computation speed during the first LAURA image calculation depends on the grid spacing (computation is faster with larger grid spacing). After the first computation of a LAURA image, a '''*.laura''' file is stored in the data folder, containing intermediate results of the LAURA inverse. This file is used during all subsequent LAURA image computations. Thereby, the time needed to obtain the image is substantially reduced.
* '''MEG:''' In the case of MEG data, an additional constraint is implemented in the LAURA algorithm that prevents solutions from containing radial source currents (compare Pascual-Marqui, ISBET Newsletter 1995, 22-29). In MEG, an additional source space regularization is necessary in the inverse matrix operation required compute V
* '''Starting LAURA:''' LAURA can be started from the''' Image''' menu or from the '''Image Selection''' button.
* '''Regularization:''' Please refer to Chapter'' “Regularization of distributed volume images” ''for important information on regularization of distributed inverses.

== LORETA ==

LORETA ("Low Resolution Electromagnetic Tomography") is a distributed inverse method of the family of ''weighted minimum norm'' methods. LORETA was suggested by R.D. Pascual-Marqui (International Journal of Psychophysiology. 1994, 18:49-65). LORETA is characterized by a smoothness constraint, represented by a discrete 3D Laplacian.

The source activity is estimated by applying the general formula for a weighted minimum norm:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T}\left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings.''

In LORETA, V contains both a depth weighting term and a representation of the 3D Laplacian matrix. V is computed as:

<math>\mathrm{V} = \left( \mathrm{U}^{T} \cdot \mathrm{U} \right)^{- 1}</math>


where

<math>\mathrm{U} = \left( \mathrm{W} \cdot \mathrm{A} \right) \otimes \mathrm{I}_{3}</math>


Here, <math>\otimes</math> denotes the Kronecker product. I3 is the [3x3] identity matrix. W is an [sxs] diagonal matrix (with s the number of source locations on the grid), where each diagonal element is the inverse of the maximum singular value of the corresponding regional source's leadfields. A contains the 3D Laplacian and is computed as

<math>\mathrm{A} = \mathrm{Y} - \mathrm{I}_{s}</math>


with Is the [sxs] identity matrix, where s is the number of sources (= three times the number of grid points) and

<math>\mathrm{Y} = \frac{1}{2}\left\{ \mathrm{I}_{s} + \left\lbrack \operatorname{diag}\left( \mathrm{Z} \cdot \left\lbrack 111 \ldots 1 \right\rbrack^{T} \right) \right\rbrack^{- 1} \right\} \cdot \mathrm{Z}</math>


where

<math>
\mathrm{Z}_{ik} =
\begin{cases}
1/6, & \text{if } \operatorname{dist}\left( i,k \right) = 1 \text{ grid point} \\
0, & \text{otherwise}
\end{cases}
</math>


The LORETA image in BESA Research displays the norm of the 3 components of S at each location r. Using the menu function ''Image / Export Image As... ''you have the option to save this norm of S or alternatively all components separately to disk.

'''Notes:'''
* '''Grid spacing:''' Due to memory limitations, LORETA images require a grid spacing of 5 mm or more.
* '''Computation time:''' Computation speed during the first LORETA image calculation depends on the grid spacing (computation is faster with larger grid spacing). After the first computation of a LORETA image, a '''<nowiki>*.loreta</nowiki>''' file is stored in the data folder, containing intermediate results of the LORETA inverse. This file is used during all subsequent LORETA image computations. Thereby, the time needed to obtain the image is substantially reduced.
* '''MEG''': In the case of MEG data, an additional constraint is implemented in the LORETA algorithm that prevents solutions from containing radial source currents (Pascual-Marqui, ISBET Newsletter 1995, 22-29). In MEG, an additional source space regularization is necessary in the inverse matrix operation required compute V.
* '''Starting LORETA:''' LORETA can be started from the''' Image''' menu or from the '''Image Selection '''button.
* '''Regularization:''' Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed source models.

== sLORETA ==

This distributed inverse method consists of a ''standardized, unweighted minimum norm''. The method was originally suggested by R.D. Pascual-Marqui (Methods & Findings in Experimental & Clinical Pharmacology 2002, 24D:5-12) Starting point is an unweighted minimum norm computation:

<math>\mathrm{S}_{\text{MN}}\left( t \right) = \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings''.

This minimum norm estimate is now standardized to produce the sLORETA activity at a certain brain location r:

<math>\mathrm{S}_{\text{sLORETA}, r} = \mathrm{R}_{rr}^{-1/2} \cdot \mathrm{S}_{\text{MN},r}</math>


SsMN,r is the [3x1] (MEG: [2x1]) minimum norm estimate of the 3 (MEG: 2) dipoles at location r. Rrr is the [3x3] (MEG: [2x2]) diagonal block of the resolution matrix R that corresponds to the source components at the target location r. The resolution matrix is defined as:

<math>\mathrm{R} = \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{L}^{T} + \lambda \cdot \mathrm{I} \right)^{-1} \cdot \mathrm{L}</math>


The sLORETA image in BESA Research displays the norm of SsLORETA, r at each location r. Using the menu function ''Image / Export Image As...'' you have the option to save this norm of SsLORETA, r or alternatively all components separately to disk.

'''Notes:'''

* sLORETA can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter [[#Regularization_of_distributed_volume_images|''Regularization of distributed volume images'']] for important information on regularization of distributed inverses.

== swLORETA ==

This distributed inverse method is a ''standardized, depth-weighted minimum norm'' (E. Palmero-Soler et al 2007 Phys. Med. Biol. 52 1783-1800). It differs from sLORETA only by an additional depth weighting.

Starting point is a depth-weighted minimum norm computation:

<math>\mathrm{S}_{\text{MN}}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings''.

V is the diagonal depth weighting matrix. For s grid locations, V is of dimension [3s x 3s] (MEG: [2s x 2s]). Each diagonal element of V is the inverse of the first singular value of the leadfield of the corresponding regional source. Hence, the first 3 (MEG: 2) diagonal elements equal the inverse of the largest eigenvalue of the leadfield matrix of regional source 1, and so on.

This minimum norm estimate is now standardized to produce the swLORETA activity at a certain brain location r:

<math>\mathrm{S}_{\text{swLORETA},r} = \mathrm{R}_{rr}^{-1/2} \cdot \mathrm{S}_{\text{MN},r}</math>


SsMN,r is the [3x1] (MEG: [2x1]) depth-weighted minimum norm estimate of the regional source at location r. Rrr is the [3x3] (MEG: [2x2]) diagonal block of the resolution matrix R that corresponds to the source components at the target location r. The resolution matrix is defined as:

<math>\mathrm{R} = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} + \lambda \cdot \mathrm{I} \right)^{-1} \cdot \mathrm{L}</math>


The swLORETA image in BESA Research displays the norm of SswLORETA, r at each location r. Using the menu function ''Image / Export Image As...'' you have the option to save this norm of SswLORETA, r or alternatively all components separately to disk.

'''Notes:'''

* sLORETA can be started from the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed inverses.

== sSLOFO ==

SSLOFO (standardized shrinking LORETA-FOCUSS) is an iterative application of weighted distributed source images with a reduced source space in each iteration ([https://dx.doi.org/10.1109/TBME.2005.855720 Liu et al., "Standardized shrinking LORETA-FOCUSS (SSLOFO): a new algorithm for spatio-temporal EEG source reconstruction", IEEE Transactions on Biomedical Engineering 52(10), 1681-1691, 2005]).

In an initialization step, an [[#sLORETA | sLORETA]] image is calculated. Then in each iteration the following steps are performed:

# A weighted minimum norm solution is computed according to the formula <math display="inline">\mathrm{S} = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}</math> . Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D is the data at the time point under consideration. V is a diagonal spatial weighting matrix that is computed in the previous iteration step. In the first iteration, the elements of V contain the magnitudes of the initially computed LORETA image.
# Standardization of this weighted minimum norm image is performed with the resolution matrix as in [[#sLORETA | sLORETA]].
# The obtained standardized weighted minimum norm image is being smoothed to get Ssmooth.
# All voxels with amplitudes below a threshold of 1% of the maximum activity get a weight of zero in the next iteration step, thus being effectively eliminated from the source space in the next iteration step.
# For all other voxels, compute the elements of the spatial weighting matrix V to be used in the next iteration as follows: <math display="inline">\mathrm{V}_{ii,\text{next iteration}} = \frac{1}{\left\| \mathrm{L}_{i} \right\|} \cdot \mathrm{S}_{ii,\text{smooth}} \cdot \mathrm{V}_{ii,\text{current iteration}}</math>



The procedure stops after 3 iterations. Please note that you can change all parameters by creating a [[#User-Defined Volume Image | user-defined volume image]].

'''Notes:'''
* '''Starting sSLOFO''': sSLOFO can be started from the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''[[#Regularization of distributed volume images | Regularization of distributed volume images]]'' for important information on regularization of distributed inverses.

== User-Defined Volume Image ==

In addition to the predefined 3D imaging methods in BESA Research, it is possible to create user-defined imaging methods based on the general formula for distributed inverses:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. Custom-defined parameters are:

* '''The spatial weighting matrix V''': This may include depth weighting, image weighting, or cross-voxel weighting with a 3D Laplacian (as in LORETA) or an autoregressive function (as in LAURA).
* '''Regularization''': The term in parentheses is generally regularized. Note that regularization has a strong effect on the obtained results. Please refer to chapter ''Regularization of Distributed Volume Images''for more information.
* '''Standardization''': Optionally, the result of the distributed inverse can be standardized with the resolution matrix (as in sLORETA).
* '''Iterations''': Inverse computations can be applied iteratively. Each iteration is weighted with the image obtained in the previous iteration.

All parameters for the user-defined volume image are specified in the User-Defined Volume Tab of the Image Settings dialog box. Please refer to chapter ''User-Defined Volume Tab'' for details.

'''Notes:'''

* Starting the user-defined volume image: the image calculation can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''Regularization of distributed volume images'' for important information on regularization of distributed inverses.

== Regularization of distributed volume images ==

Distributed source images require the inversion of a term of the form L V LT. This term is generally regularized before its inversion. In BESA Research, selection can be made between two different regularization approaches (parameters are defined in the ''Image Settings dialog box''):

* '''Tikhonov regularization''': In Tikhonov regularization, the term L V LT is inverted as (L V LT +λ I)-1. Here, l is the regularization constant, and I is the identity matrix.
** One way of determining the optimum regularization constant is by minimizing the ''generalized cross'' ''validation error'' (CVE).
** Alternatively, the regularization constant can be specified manually as a percentage of the trace of the matrix L V LT.
* '''TSVD''': In the truncated singular value decomposition (TSVD) approach, an SVD decomposition of L V LT is computed as  L V LT = U S UT, where the diagonal matrix S contains the singular values. All singular values smaller than the specified percentage of the maximum singular values are set to zero. The inverse is computed as U S-1 UT, where the diagonal elements of S-1 are the inverse of the corresponding non-zero diagonal elements of S.

Regularization has a critical effect on the obtained distributed source images. The results may differ completely with different choices of the regularization parameter (see examples below). Therefore, it is important to evaluate the generated image critically with respect to the regularization constant, and to keep in mind the uncertainties resulting from this fact when interpreting the results. The default setting in BESA Research is a TSVD regularization with a 0.03% threshold. However, this value might need to be adjusted to the specific data set at hand.

The following example illustrates the influence of the regularization parameter on the obtained images. The data used here is condition '''St-Cor of dataset Examples \ TFC-Error-Related-Negativity \ Correct+Error.fsg''' at 176 ms following the visual stimulus. Discrete dipole analysis reveals the main activity in the left and right lateral visual cortex at this latency.

[[File:SA 3Dimaging (42).gif|400px|thumb|c|none|Discrete source model at 176 ms: Main activity in the left and right lateral visual cortex, no visual midline activity.]]

LORETA images computed at this latency depend critically on the choice of the regularization constant. The following 3D images are created with TSVD regularization with SVD cutoffs of 0.1%, 0.005%, and 0.0001%, respectively. The volume grid size was 9 mm. The example demonstrates the dramatic effect of regularization and demonstrates the typical tradeoff between too strong regularization (leading to too smeared 3D images that tend to show blurred maxima) and too small regularization (resulting in too superficial 3D images with multiple maxima).

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (44).gif|thumb|350px|'''SVD cutoff 0.1%''': Regularization too strong. No separation between sources, mislocalization towards the middle of the brain.]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (43).gif|thumb|350px|'''SVD cutoff 0.005%''': Appropriate regularization. Separation of the bilateral activities. Location in agreement with the discrete multiple source model.]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (45).gif|thumb|350px|'''SVD cutoff 0.0001%''': Too small regularization. Mislocalization, too superficial 3D image. ]] </li>
</ul></div>

The automatic determination of the regularization constant using the CVE approach does not necessarily result in the optimum regularization parameter either. In this example, the unscaled CVE approach rather resembles the TSVD image with a cutoff of 0.0001%, i.e. regularization is too small. Therefore, it is advisable to compare different settings of the regularization parameter and make the final choice based on the above-mentioned considerations.

== Cortical LORETA ==

Cortical LORETA is principally the same technique as LORETA, however, Cortical LORETA is not computed in a 3D volume, but on the cortical surface.

The cortical reconstruction in BESA Research fed from BESA MRI is a closed 2D surface with no boundaries and a very close approximation of the actual cortical form. It consists of an irregular triangulated grid.

The Laplace operator that is used for identifying a smooth solution in a three-dimensional space is exchanged with a Laplace operator that runs on the two-dimensional cortical surface.

There is a wide variety of 2D Laplace operators with different characteristics. The general form of the discrete Laplace operator is

<math>\Delta f\left( p_{i} \right) = \frac{1}{d_{i}}\sum_{j \in N(i)}^{}{w_{ij}\left\lbrack f\left( p_{i} \right) - f\left( p_{j} \right) \right\rbrack},</math>


where '''pi''' is the '''i-th''' node of the triangular mesh, '''f(pi) '''is the value of a function f defined on the cortical mesh at the node '''pi''', '''wij''' is the weight for the connection between the nodes '''pi''' and '''pj''' and '''di''' is a normalization factor for the '''i-th''' row of the operator. Furthermore, '''N(i)''' is the set of indices corresponding to the direct (also called "1-ring") neighbors of '''pi'''.

BESA offers the choice of three Laplace operators with slightly different characteristics.

* '''Unweighted Graph Laplacian''': This is the simplest operator. It takes into account only the adjacency of the nodes and not the geometry of the mesh:

<math>
w_{ij} =
\begin{cases}
1, & \text{if } p_{i} \text{ and } p_{j} \text{ are connected by an edge} \\
0, & \text{otherwise}
\end{cases}
</math>

<math>d_{i} = 1</math>


[[Image:SA 3Dimaging (4).jpg |450px]]

* '''Weighted Graph Laplacian:''' This operator is similar to the unweighted graph Laplacian but with different weights for the different connections. The connections between nearby nodes get larger weights than the connections between farther nodes:

<math>w_{ij} = \frac{1}{\operatorname{dist}\left( p_{i},p_{j} \right)}</math>

<math>d_{i} = \sum_{j \in N(i)}^{} {\operatorname{dist}\left(p_{i}, p_{j} \right)}</math>


where '''dist''' ('''pi''' , '''pj''') is the distance between the nodes '''pi '''and '''pj'''.

[[Image:SA 3Dimaging (6).jpg|450px]]

* '''Geometric Laplacian with mixed area weights''': This operator takes into account the angles in the corresponding triangles into account as well as the area around the nodes in order to determine the connection weights:

<math>w_{ij} = \frac{\cot\left( \alpha_{ij} \right) + \cot\left( \beta_{ij} \right)}{2}</math>

<math>d_{i} = A_{\text{mixed}}</math>


where '''αij''' and '''βij''' denote the two angles opposite to the edge ('''i , j''') and '''Amixed '''is either the Voronoi area, or 1/2 of the triangle area or 1/4 of the triangle area depending on the type of the triangle.

[[Image:SA 3Dimaging (8).jpg|450px]]

'''Regularization and other parameters:'''

[[Image:CorticalLOR.png‎]]

* '''SVD cutoff''': The regularization for the inverse operator as a percent of the largest singular value.
* '''Depth weighting''': Turn depth weighting on or off.
* '''Laplacian type''': Selection of Laplacian operators (see above).

'''Notes:'''
* '''Starting Cortical LORETA''': Cortical LORETA can be started from the sub-menu '''Surface Image''' of the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]''” for important information on regularization of distributed inverses.

'''References:'''

Please refer to ''Iordanov et al.: LORETA With Cortical Constraint: Choosing an Adequate Surface Laplacian Operator. Front Neurosci 12, Article 746, 2018'', for more information - full article available [https://www.frontiersin.org/articles/10.3389/fnins.2018.00746/full here].

== Cortical CLARA ==

Cortical CLARA is principally the same technique as CLARA, but Cortical CLARA is not computed in a 3D volume, but on the cortical surface. Instead of using a LORETA image as the basis for the iterative application, cortical CLARA uses cortical LORETA.

'''Regularization and other parameters:'''

[[Image:SA 3Dimaging (47).gif]]

* '''SVD cutoff''': The regularization for the inverse operator as a percent of the largest singular value.
* '''Depth weighting''': Turn depth weighting on or off.
* '''Laplacian type''': Selection of Laplacian operators (see Cortical LORETA).
* '''No of iterations''': Number of iterations for CLARA. The more iterations are used, the sparser becomes the solution.
* '''Automatic''': The algorithm tries to determine the number of iterations automatically. The goodness of fit (GOF) is calculated after every iteration and if there is a big jump in the GOF then the algorithm will stop. If no jumps appear during the calculations then CLARA iterates until the specified number of iterations is reached.
* '''Regularize iterations''': If one wants to use different regularization for the CLARA iterations than the value specified as "SVD cutoff", this option should be selected.
* '''Amount to clip from img (%)''': Cortical CLARA uses the solution from the previous iteration as an additional weighting matrix for the current iteration. That weighting matrix is constructed by cutting the "low" activity from the solution. This number specifies how much of the activity should be cut from the previous solution in order to construct the weighting matrix. This value is given as a percentage of the maximal activity. Default value is 10%.

'''Notes:'''

* '''Starting Cortical CLARA:''' Cortical CLARA can be started from the sub-menu '''Surface Image''' of the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]''” for important information on regularization of distributed inverses.

== Cortex Inflation ==

The inflated cortex is a smoothened version of the individual cortical surface with minimal metric distortions (Fischl, B. et al. (1999). Cortical Surface-Based Analysis: II: Inflation, Flattening, and a Surface-Based Coordinate System. ''NeuroImage'', 9(2), 195–207). Gyri and sulci are smoothened out. The original distances between each point on the cortex and its neighbors are, however, mostly preserved.

[[Image:SA 3Dimaging (48).gif]]

''Cortical LORETA map overlaid on top of the inflated cortical surface.''

A lighter gray color overlaid on top of the surface image indicates the location of a gyrus of the individual cortex surface, while a darker gray color indicates the location of a sulcus. The inflated cortical surface can be computed in '''BESA MRI 2.0'''. For more details please refer to the BESA MRI 2.0 help.

== Surface Minimum Norm Image ==

'''Introduction'''

The minimum norm approach is a common method to estimate a distributed electrical current image in the brain at each time sample (Hämäläinen & Ilmoniemi 1984). The source activities of a large number of regional sources are computed. The sources are evenly distributed using 1500 standard locations 10% and 30% below the smoothed standard brain surface (when using the standard MRI) or using between 3000-4000 locations on the individual brain surface defined by the gray-white-matter boundary.

Since the number of sources is much larger than the number of sensors in a minimum norm solution, the inverse problem is highly underdetermined and must be stabilized by a mathematical constraint, the minimum norm. Out of the many current distributions that can account for the recorded sensor data, the solution with the minimum L2 norm, i.e. the minimum total power of the current distribution is displayed in BESA Research.

First, the forward solution (leadfield matrix L) of all sources is calculated in the current head model. Then, the source activities S(t) of all source components are computed from the data matrix D(t) using an inverse regularized by the estimated noise covariance matrix:

<math>\mathrm{S}\left( t \right) = \mathrm{R} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{R} \cdot \mathrm{L}^{T} + \mathrm{C}_N \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed regional source model, CN denotes the noise correlation matrix in sensor space, and R is a weighting matrix in source space. R and CN can be designed in different ways in order to optimize the minimum norm result. The total activity of each regional source is computed as the root mean square of the source activities S(t) of its 3 (MEG:2) components. This total source activity is transformed to a color-coded image of the brain surface. (When the standard brain is used, two sources are assigned to each surface location, located 10% and 30% below the surface, respectively. The color that is displayed on the standard brain surface is the larger of the two corresponding source activities.)

'''Weighting options'''

The minimum norm current imaging techniques of BESA Research provide different weighting strategies. Two weighting approaches are available: Depth weighting and spatio-temporal approaches.
* '''Depth weighting:''' Without depth weighting, deep sources appear very smeared in a minimum-norm reconstruction. With depth weighting, both deep and superficial sources produce a similar, more focal result. If this weighting method is selected, the leadfield of each regional source is scaled with the largest singular value of the SVD (singular value decomposition) of the source's leadfield.
* '''Spatio-temporal weighting''': Spatio-temporal weighting tries to assign large weight to sources that are assumed to be more likely to contribute to the recorded data.
** '''Subspace correlation after single source scan''': This method divides the signal into a signal and a noise subspace. The correlation of the leadfield of a regional source i with the signal subspace (pi) is computed to find out if the source location contributes to the measured data. The weighting matrix R becomes a diagonal matrix. Each of the three (MEG: 2) components of a regional source get the same weighting value pi2. This approach is based on the signal subspace correlation measure introduced by J.C. Mosher, R. M. Leahy (Recursive MUSIC: A Framework for EEG and MEG Source Localization, IEEE Trans. On Biomed. Eng. Vol. 45, No. 11, November 1998)
** '''Dale & Sereno 1993:''' In the approach of Dale and Sereno (J Cogn Neurosci, 1993, 5: 162-176) a signal subspace needs not be defined. The correlation pi of the leadfield of regional source i with the inverse of the data covariance matrix is computed along with the largest singular value λmax of the data covariance matrix. The weighting matrix R is a diagonal matrix with weights: [[Image:SA 3Dimaging (50).gif]]. Each of the three (MEG: 2) components of a regional source receives the same weighting value.

'''Noise regularization'''

Three methods to estimate the channel noise correlation matrix CN are provided by the program:
* '''Use baseline:''' Select this option to estimate the noise from the user-definable baseline. The signal is computed from the data at non-baseline latencies.
* '''Use 15% lowest values:''' The baseline activity is computed from the data at those 15% of all displayed latencies that have the lowest global field power. The signal is computed from all displayed latencies.
* '''Use the full baseline covariance matrix''': This option is only available if a previous beamformer image in the time-domain was calculated. In this case, it can be selected from the general image settings dialog tab. The baseline covariance interval is the one selected for the beamformer, and is indicated by a thin horizontal bar in the channel box.

In each case, the activity (noise or signal, respectively) is defined as root-mean-square across all respective latencies for each channel.

The noise covariance matrix CN is constructed as a diagonal matrix. The entries in the main diagonal are proportional to the noise activity of the individual channels (if selected) or are all equally proportional to the average noise activity over all channels. The noise covariance matrix CN is then scaled such that the ratio of the Frobenius norms of the weighted leadfield projector matrix (LRLT) and the noise covariance matrix CN equals the Signal-to-Noise ratio. This scaling can be multiplied by an additional factor (default=1) to sharpen (<1) or smoothen (>1) the minimum norm image.

'''Applying the Minimum Norm Image'''

The minimum-norm algorithm is started via the ''Surface minimum norm image dialog box'', which is opened from the''' Image''' menu, or by typing the shortcut '''Ctrl-M''': Please refer to Chapter ''“Surface'' ''Minimum Norm Tab”'' for more details.

As opposed to the other 3D images available from the '''Image '''menu, the surface minimum norm image is not computed on a volumetric grid, but rather for locations on the brain surface. Accordingly, the results of the minimum norm image are displayed superimposed to the brain surface mesh rather than to the volumetric MR image.

The figure below shows a minimum norm image computed from the file '''Examples\Epilepsy\Spikes\Spikes-Child4_EEG+MEG_averaged.fsg'''. The EEG spike peak was imaged using the individual brain surface of the subject. A baseline from -300 to -70 ms was used. Minimum norm was computed with depth weighting, Spatio-temporal weighting according to Dale & Sereno 1993 and individual noise weighting with a noise scale factor of 0.01. The minimum norm image reveals the location of the spike generator in the close vicinity of the frontal left-hemispheric lesion in this subject.

[[Image:SA 3Dimaging (51).gif]]

== Multiple Source Probe Scan (MSPS) ==

 
'''Introduction'''

The MSPS function provides a tool for the validation of a given solution. It is based on the following theoretical consideration: If the recorded EEG/MEG data has been modeled adequately, i.e. all active brain regions are represented by a source in the current solution, then any additional probe source added to the solution will not show any activity apart from noise. The only exception occurs if this probe source is placed in close vicinity to one of the sources in the current solution. In that case, the solution's source and the probe source will share the activity of the corresponding brain area. The MSPS applies these considerations by scanning the brain on a pre-defined grid with a regional probe added to the current solution. Grid extent and density can be specified in the Image settings. The power P of the probe source at location r in the signal interval is compared with the power of the probe source in a reference interval, defining a value q:

<math>\mathrm{q}\left( r \right) = \sqrt{\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}} - 1</math>


MSPS can be computed on time domain or time-frequency domain data:
* In the time domain, q(r) is computed from the source waveform of the probe source. Here, P(r) is the mean power of the probe source at location r in the marked latency range, and Pref(r) is the mean probe source power in the user-definable baseline interval.
* In the time-frequency domain, an MSPS image can be computed from the complex cross spectral density matrices. By applying the inverse operator for a source configuration consisting of the current solution and the probe source, the power of the probe source can be computed for the target interval [P(r)] and the reference time-frequency interval [Pref(r)]. In the resulting MSPS image, q-values are shown in %, where q[%] = q*100.

The inverse operator used to determine the probe source power uses different regularization constants for the probe source and the sources in the current solution. The regularization constant of the sources in the current solution can be specified in the Image settings (default 4%). The regularization constant of the probe source is internally set to 0%.

Alternatively to the definition above, q can also be displayed in units of dB:

<math>\mathrm{q}\left\lbrack \text{dB} \right\rbrack = 10 \cdot \log_{10}\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}</math>


Values of q smaller than zero are not shown in the MSPS image.

According to the considerations above, an MSPS of a correct source model should optimally yield image maxima around the sources in the current solution only. If the MSPS image is blurred or shows maxima at locations different from the modeled sources, this indicates a non-sufficient or incorrect solution.

'''Applying the MSPS'''

This chapter illustrates the application of the Multiple Source Probe Scan. The figures are generated with data from file '''Examples/Epilepsy/Spikes/Rolandic-Spike-Child.fsg''' (-300 : +200 ms, filtered from 3 Hz [forward] to 40 Hz [zero-phase]).

'''Time domain versus time-frequency domain MSPS'''

The multiple source probe scan can be computed in the time domain or the time-frequency domain. The latter is possible only when time-frequency domain data is available for the current condition, i.e. if the condition has been created by starting a multiple source beamformer (MSBF) computation from the source coherence window. In this case, evoking the MSPS calculation from the '''Imaging '''button or from the '''Image''' menu will bring up the following dialog window that allows to choose between time- or time-frequency MSPS. If only time domain data is available, this dialog window will not appear and MSPS will be computed in the time domain.

[[Image:SA 3Dimaging (53).gif]]

For a time-frequency domain MSPS, the target and the reference time-frequency interval have been specified already in the Time-Frequency window (see Chapter "''How To Create Beamformer Images''"). For a time-domain MSPS, the target and the reference epoch have to be specified in the Source Analysis window as described below.

'''Time domain MSPS'''

The time-domain MSPS image displays the ratio of the power of a regional probe source in the signal and the baseline interval. The currently set baseline is indicated by a horizontal line in the upper left corner of the channel box.

[[Image:SA 3Dimaging (54).gif|thumb|c|none|330px|The black horizontal bar in the upper part of the channel box (here circled in red) indicates the baseline interval.]]

By default, BESA Research defines the pre-stimulus interval of the current data segment as baseline. The baseline should represent a latency range in which no event-related activity is present in the data. There are several possibilities to modify the baseline interval: by clicking on the horizontal line with the left mouse button or by using the corresponding entry in the '''Condition '''menu or '''Fit Interval''' popup menu.

Mark an interval to define the target epoch, i.e. the time-interval for which the current solution is to be tested. Start the MSPS by selecting it from the '''Image selection '''button or from the '''Image''' menu to start the probe source scan. The''' Image '''menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window. The 3D window opens and displays the scan result.

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (55).png|thumb|c|none|650px|This figure shows the MSPS image applied on the three left-hemispheric sources in the solution ''''Rolandic-Spike-Child-RS2.bsa''''. The baseline is set from -300 ms to -50 ms. The right-hemispheric sources have been switched off. The fit interval is set to the latency range of large overall activity in the data (-43 ms : 117 ms). A realistic FEM model appropriate for the subject's age (12 years, conductivity ratios (cr) 50) is applied. The MSPS image does not show maxima at the modeled source locations and rather shows a spread q-value distribution.]] </li>

<li style="display: inline-block;"> [[File:SA 3Dimaging (56).png|thumb|c|none|650px|The MSPS image for the same latency range when the right-hemispheric sources have been included. The MSPS image appears more focal and shows maxima around the modeled brain regions. This indicates the substantial improvement of the solution by adding the right-hemispheric sources that model the propagation of the epileptic spike from the left to the right hemisphere (note the radiological side convention in the 3D window).]] </li>
</ul></div>

'''Time-Resolved MSPS'''

If the MSPS has been computed on time domain data, the image can be shown separately for each latency in the selected interval. After the MSPS has been computed for the marked epoch, double-click anywhere within this epoch to display the ratio of the probe source magnitude at the selected latency and the mean probe source magnitude in the baseline. Scanning the latency range by moving the cursor (e.g. with the left and right arrow cursor keys) provides a time-resolved MSPS image.

Time-resolved MSPS images are not available if the MSPS has been computed on data in the time-frequency domain.

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (57).png|thumb|c|none|650px|MSPS image of the spike peak activity at 0 ms. The activity mainly occurs in the left hemisphere. This fact is illustrated by the source waveforms and confirmed in the MSPS image, which shows a focal maximum around the location of the red sources.]] </li>

<li style="display: inline-block;"> [[File:SA 3Dimaging (58).png|thumb|c|none|650px|Around +27 ms, the spike has propagated to the right hemisphere. This becomes evident from the waveforms of the blue sources, which show a significant latency lag with respect to the first three sources, and from the MSPS image, which shows the maximum around blue sources at this latency.]] </li>
</ul></div>

'''Notes:'''

* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image''' menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the''' Image''' menu.
* For scaling options, please refer to the '''scaling buttons''' popup menu .
* Parameters used for the MSPS calculations can be set in the ''General Settings tab'' of the ''Image Settings dialog box.''

== Source Sensitivity ==

'''Introduction'''

The 'Source sensitivity' function displays the sensitivity of the selected source in the current source model to activity in other brain regions. Sensitivity is defined as the fraction of power at the scanned brain location that is mapped onto the selected source.

To compute the source sensitivity, unit brain activity is modeled at different locations (probe source) throughout the brain. To this data, the current source model is applied to compute the source waveforms SCM of all modeled sources:

<math>\mathrm{S}_{\text{CM}} = \mathrm{L}_{\text{CM}}^{-1} \cdot \mathrm{L}_{\text{PS}}</math>


Here LCM-1 is the regularized inverse operator for the current model, and LPS is the leadfield of the regional probe source (dimension [Nx3] for EEG and [Nx2] for MEG, respectively, where N is the number of sensors). The source amplitude SSS of the selected source in the model is a 3x3 (MEG: 2x2) sub-matrix of SCM (if the selected source is a regional source) or a 1x3-matrix (MEG: 1x2) (if the selected source is a dipole). The root mean square of the singular values of SCM is defined as the source sensitivity.

The 3D source sensitivity image displays this value for all locations on a grid specified under '''Image/Settings'''. Grid density can be specified in the Image Settings.

'''Applying the Source Sensitivity Image'''

The Source Sensitivity image is evoked from the '''Image''' menu or by pressing the corresponding hot key (default: '''V''').

This function is enabled only when a solution with an active selected source is present in the Source Analysis window. The source sensitivity image then displays the sensitivity of the selected source to activity in other brain regions.

[[Image:SA 3Dimaging (59).png|700px|thumb|c|none|Source Sensitivity image for the selected frontal source (green) in model ''''''High_Intensity_3RS.bsa'''''' in folder 'Examples/ERP_Auditory_Intensity'. The data displayed is the '100dB' condition in file ''''''All_Subjects_cc.fsg''''''. The selected source is sensitive to activity in the frontal brain region (yellow/white), while it is not influenced by activity in the vicinity of the left and right auditory cortex areas, which are modeled by the red and blue source in the model (transparent/gray).]]

'''Notes:'''

* The sensitivity image is independent of the recorded sensor signals. It only depends on the current source model, the sensor configuration, the head model, and the regularization constant.
* If the regularization constant is set to zero, each source has a sensitivity of 100% to activity around its own location. With increasing regularization, the spatial filter becomes less focused, and the sensitivity of a source to activity at its location decreases.
* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image''' menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the '''Image''' menu.

== SESAME ==

''This feature requires BESA Research 7.0 or higher.''

'''SESAME''' (Sequential Semi-Analytic Monte-Carlo Estimation) is a Bayesian approach for estimating sources that uses Markov-Chain Monte-Carlo method for efficient computation of the probability distribution as described in Sommariva, S., & Sorrentino, A. "Sequential Monte Carlo samplers for semi-linear inverse problems and application to magnetoencephalography." Inverse Problems 30.11 (2014): 114020.

It allows to automatically estimate simultaneously the number of dipoles, their locations and time courses requiring virtually no user input. The algorithm is divided in two blocks:

* The first block consists of a Monte Carlo sampling algorithm that produces, with an adaptive number of iterations, a set of samples representing the posterior distribution for the number of dipoles and the dipole locations.
* The second block estimates the source time courses, given the number of dipoles and the dipole locations.

The Monte Carlo algorithm in the first block works by letting a set of weighted samples evolve with each iteration. At each iteration, the samples (a multi-dipole state) approximates the n-th element of a sequence of distributions p1, …, pN, that reaches the desired posterior distribution (pN = p(x|y)). The sequence is built as pN = p(x) p(y|x) α(n), such that α(1) = 0, α(N) = 1. The actual sequence of values of alpha is determined online. Dipole moments are estimated after the number of dipoles and the dipole locations have been estimated with the Monte Carlo procedure. This continues until a steady state is reached.

The SESAME image in BESA Research displays the final probability of source location along with an estimate for number of sources. Using the menu function '''Image / Export Image As...''' you have the option to save this SESAME image.

'''Non-uniform spatial priors for SESAME'''

By default, SESAME uses a uniform prior distribution on the source location. However, when the Weight by Image button at the top of the variance box is pressed and SESAME image is computed, the currently active 3D image will be used as non-uniform spatial priors for the SESAME computation (the positive values in the active 3D image, scaled to the current image maximum, are used as non-uniform spatial priors). The usage of non-uniform priors can effectively increase the source localization accuracy when the prior distribution is correct (A. Viani, G. Luria and A. Sorrentino, "Non-uniform spatial priors for multi-dipole localization from MEG/EEG data," 2022 IEEE International Conference on E-health Networking, Application & Services (HealthCom), Genoa, Italy, 2022, pp. 149-154, doi: 10.1109/HealthCom54947.2022.9982792).
To use this method, a 3D image (e.g. source image or imported fMRI image) should be displayed in the 3D window.
When the computation is finished, the Weight by Image button will be released.

'''Notes:'''

*'''Grid spacing:''' Due to memory and computational limitations, it is recommended to use SESAME with a grid spacing of 5 mm or more.
*'''Fit Interval:''' SESAME requires a fit interval of more than 2 samples to start the computation.
*'''Computation time:''' Computation speed during SESAME calculation depends on the grid spacing (computation is faster with larger grid spacing) and number of channels.

== Brain Atlas ==
''This feature requires BESA Research 7.0 or higher.''

'''Introduction'''

Brain atlas is a priori data that can be applied over any discrete or distributed source image displayed in the 3D window. It is a reference value that strongly depends on the selected brain atlas and should not be used as medical reference since individual brains may differ from the brain atlas. The display settings can be adjusted in 3D Window Tab.

[[Image:BrainAtlas1.png|600px]]

'''Brain Atlases'''

In BESA Research the atlases listed below are provided. '''BESA is not the author of the atlases; please cite the appropriate publications if you use any of the atlases in your publication.'''

[http://atlas.brainnetome.org/bnatlas.html '''Brainnetome'''] 
This is one of the most modern brain probabilistic atlas where structural, functional, and connectivity information was used to perform cortical parcellation. It was introduce by Fan and colleagues (2016), and is still work in progress. The atlas was created using data from 40 healthy adults taking part in the Human Connectome Project. In March 2018, the atlas consists of 246 structures labeled independently for each hemisphere. In BESA we provide the max probability map with labeling. Please visit the Brainnetome webpage to see more details related to the indicated brain regions (i.e. behavioral domains, paradigm classes and regions connectivity).

'''AAL''' 
Automated Anatomical Labeling atlas was created in 2002 by Tzourio-Mazoyer and collegues (2002). It is the mostly used atlas nowadays. The atlas is based on the averaged brain of one subject (young male) who was scanned 27 times. The atlas resolution is 1 mm isometric. The brain sulci were drawn manually on every 2mm slice and then brain regions were automatically assigned. The atlas consists of 116 regions which are asymmetrical between hemispheres. The atlas is implemented as in the [https://www.fil.ion.ucl.ac.uk/spm/ '''SPM12'''] toolbox.

'''Brodmann''' 
The Brodmann map was created by Brodmann (1909). The brain regions were differentiated by cytoarchitecture of each cortical area using the Nissi method of cell staining. The digitalization of the original Brodmann map was performed by Damasio and Damasio (1989). The digitalized atlas consists of 44 fields that are symmetric between hemispheres. BESA used the atlas implementation as in Chris Roden’s [https://people.cas.sc.edu/rorden/mricro/index.html '''MRICro'''] software.

'''AAL2015''' 
Automated Anatomical Labeling revision 2015. This is the updated AAL atlas. In comparison to the previous version (AAL) mainly the frontal lobe shows a higher degree of parcellation (Rolls, Joliot, and Tzourio-Mazoyer 2015). The atlas is implemented as in the [https://www.fil.ion.ucl.ac.uk/spm/ '''SPM12'''] toolbox.

'''Talairach''' 
Atlas was created in 1988 by Talairach and Tournoux (1988) and it is based on the post mortem brain slices of a 60 year old right handed European female. It was created by drawing and matching regions with the Brodmann map. The atlas is available at 5 tissue levels, however we used only the volumetric gyrus level as it is the most known in neuroscience and is the most appropriate for EEG. The atlas consists of 55 regions that are symmetric between hemispheres. The native resolution of the atlas was 0.43x0.43x2-5 mm. Please note that the poor resolution in Z direction is a direct consequence atlas definition, and since it is a post-mortem atlas it will not correctly match the brain template
(noticeable mainly on brain edges). The atlas digitalization was performed by Lancaster and colleagues (2000) resulting in a “golden standard” for neuroscience. The atlas was first implemented in a software called [http://www.talairach.org/daemon.html '''talairach daemon'''].

'''Yeo7 and Yeo17''' 
Yeo7 and Yeo17 are the resting state functional connectivity atlases created by Yeo et al. (2011). For atlas creation 1000 subjects, coregistered using surface-based alignment were used. Two versions of parcellation were used resulting for the 7 and 17 networks (Yeo7 and Yeo17 atlas respectively). In the original publication atlases for two different levels of brain structure coverage were prepared: neocortex and liberal. In BESA products, only one of them (liberal) is available. Note that in comparison to the other atlases, here networks are reflected, rather than the individual brain structures. These atlases are in line with [[BESA_Research_Montage_Editor#Standard_Source_Montage_-_Resting_State_Montages | Resting State Source Montages]].

'''Visualization modes'''

'''Just Labels''' 
Displayed are crosshair coordinates (Talairach or MNI), the currently used brain atlas and the region name where the crosshair is placed. No atlas overlay will be visible on the 3D image.

'''brainCOLOR''' 
All information is displayed as in “Just Labels” mode but also the atlas is visible as an overlay over the MRI. The coloring is performed using the algorithm introduced by Klein and colleagues (Klein et al. 2010). With this method of coloring the regions which are part of the same lobe are colored in a similar color but with different color shade. The shade is computed by the algorithm to make these regions visually differentiable from each other as much as possible.

'''Individual Color''' 
In this mode the native brain atlas color is used if provided by the authors of the brain atlas (i.e. Yeo7). Where this was not available BESA autogenerated colors for the atlas using an approach similar to political map coloring. This approach aims to differentiate most regions that are adjacent to each other and no presumptions on lobes is applied.

'''Contour''' 
Only region contours (borders between atlas regions) are drawn with blue color. This is the default mode in BESA Research.

'''References'''

* Brodmann, Korbinian. 1909. Vergleichende Lokalisationslehre Der Großhirnrinde. Leipzig: Barth. https://www.livivo.de/doc/437605.
* Damasio, Hanna, and Antonio R. Damasio. 1989. Lesion Analysis in Neuropsychology. Oxford University Press, USA.
* Fan, Lingzhong, Hai Li, Junjie Zhuo, Yu Zhang, Jiaojian Wang, Liangfu Chen, Zhengyi Yang, et al. 2016. “The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.” Cerebral Cortex 26 (8): 3508–26. https://doi.org/10.1093/cercor/bhw157.
* Klein, Arno, Andrew Worth, Jason Tourville, Bennett Landman, Tito Dal Canton, Satrajit S. Ghosh, and David Shattuck. 2010. “An Interactive Tool for Constructing Optimal Brain Colormaps.” https://mindboggle.info/braincolor/colormaps/index.html.
* Lancaster, Jack L., Marty G. Woldorff, Lawrence M. Parsons, Mario Liotti, Catarina S. Freitas, Lacy Rainey, Peter V. Kochunov, Dan Nickerson, Shawn A. Mikiten, and Peter T. Fox. 2000. “Automated Talairach Atlas Labels for Functional Brain Mapping.” Human Brain Mapping 10 (3): 120–131.
*Rolls, Edmund T., Marc Joliot, and Nathalie Tzourio-Mazoyer. 2015. “Implementation of a New Parcellation of the Orbitofrontal Cortex in the Automated Anatomical Labeling Atlas.” NeuroImage 122 (November): 1–5. https://doi.org/10.1016/j.neuroimage.2015.07.075.
* Talairach, J, and P Tournoux. 1988. Co-Planar Stereotaxic Atlas of the Human Brain. 3-Dimensional Proportional System: An Approach to Cerebral Imaging. Thieme.
*Thomas Yeo, B. T., F. M. Krienen, J. Sepulcre, M. R. Sabuncu, D. Lashkari, M. Hollinshead, J. L. Roffman, et al. 2011. “The Organization of the Human Cerebral Cortex Estimated by Intrinsic Functional Connectivity.” Journal of Neurophysiology 106 (3): 1125–65. https://doi.org/10.1152/jn.00338.2011.
* Tzourio-Mazoyer, N., B. Landeau, D. Papathanassiou, F. Crivello, O. Etard, N. Delcroix, B. Mazoyer, and M. Joliot. 2002. “Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain.” NeuroImage 15 (1): 273–89. https://doi.org/10.1006/nimg.2001.0978.

== Slice View ==

''This feature requires BESA Research 7.1 or higher.''

A convenient way to review MRI data and export it in graphical form is a multi-slice view. To enable multi-slice view press the toggle multiple view button until the slice view is shown in the 3D window.

[[Image:SliceView1.png|600px]]

In this view discrete sources, [[Source_Analysis_3D_Imaging#Overview | distributed sources]] and [[Source_Analysis_3D_Imaging#Brain Atlas| brain atlas]] can be also be overlayed. The display matrix can be adjusted by slice view controls that are available in the 3D Window tab of the Preferences Dialog Box. One of the following slicing direction can be selected: Transverse, Coronal, Sagittal by pressing the appropriate button in the 3D window toolbar.

By adjusting First slice and Last slice sliders, the span of the volume that will be displayed can be adjusted. The interval between slices can be adjusted by changing the Spacing slider value. The layout of slices will be automatically adjusted to fill the full space of the main window. All values in the sliders are given in mm.

'''Note''': The last slice value will be adjusted to the closest possible number matching the given first slice and spacing value. During multi-slice view the cursor is disabled and no
atlas information is provided.

== Glassbrain ==

''This feature requires BESA Research 7.1 or higher.''

[[Image:Glassbrain.png|600px]]

The glass brain can be enabled or disabled in one of the following ways:

* by pressing the button [[File:Buton GlassBrain.png]] in the toolbar,
* by using the shortcut SHIFT-G or
* by checking the checkbox in Preferences, 3D Display tab.

The transparency value of the glass brain can be adjusted in one of the following ways:

* by a slider/edit box in Preferences, 3D Display tab or
* by using the keyboard shortcut SHIFT-UP (to increase transparency by 10%) or SHIFT-DOWN (to decrease transparency by 10%).

Note that If a distributed solution is displayed together with the glass brain, a notification is displayed in the left bottom corner of 3D window to prevent misconception of the glass brain as a cortical image:

“Volume-based image only", which means that the results of distributed source analysis images are visualized only for the current MRI slice, and are not projected to the displayed surface.

{{BESAManualNav}}

The Initialization File: BESA.ini

2024-03-11T11:44:17Z

Dominik:

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

== Introduction ==

'''BESA.ini File'''

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

'''Location of BESA.ini'''

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

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

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

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

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

{| class="wikitable"
| [Defaults]
| General settings (filters, scaling, and various other settings)
|-
| [Folders]
| Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)
|-
| [Electrodes]
| Electrode renaming
|-
| [Patterns]
| Rename patterns in the '''Tags''' menu
|-
| [Artifacts]
| Settings for artifact correction
|-
| [KEYCONTROLS]
| Function key definitions
|-
| [Search]
| Default parameters for search
|-
| [FFT]
| Frequency band definitions
|-
| [Printer]
| Printer control
|-
| [Calibration]
| Calibration control
|-
| [Video]
| Digital video control
|-
| [Mapping]
| Mapping control
|-
| [Updates]
| Options for program updates
|-
| [Matlab]
| Settings for the MATLAB interface
|-
| [fMRI]
| Settings for the fMRI arfifact removal
|-
| [Montages]
| A setting for a default source montage
|}

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

== Defaults ==

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

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

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

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

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

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

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

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

'''MegScale=200''' scale of MEG/GRA channels in [fT or fT/cm]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'''Notes'''

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

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

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

== Folders ==

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

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

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

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

'''The Variables'''

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

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

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

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

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

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

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

'''Placeholders'''

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

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

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

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

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

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program Files (x86)\BESA\Research_7_0''".

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

== Electrodes ==

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

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

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

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

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

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

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

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

PG1=LO1 define X3 as lateral orbital eye electrode left

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

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

X9=Rsp define X9 channel to be a respiratory channel

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

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

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

== Patterns ==

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

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

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

Pattern1=Spike

Pattern2=Sharp Wave

== Artifacts ==

'''Artifact default settings:'''

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

== Search ==

Default settings for pattern search.

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

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

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

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

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

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

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

'''LowPassFreq = 35 Hz'''

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

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

'''CorrelationThresholdNoMarked = 60%'''

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

'''CorrelationThresholdOneMarked = 85%'''

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

'''CorrelationThresholdFourMarked = 65%'''

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

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

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

'''WriteAfterSearchCheckBox = No'''

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

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

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

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

== KeyControls ==

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

'''Fn=function''' or

'''Del=function'''

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

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

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

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

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

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

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

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

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

'''Batches and Montages:'''

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

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

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

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

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

== FFT ==

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

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

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

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

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

'''FFTBand7=Off'''

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

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

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

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

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

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

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

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

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

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

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

'''FFTHighBand3=14'''

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

'''FFTHighBand4=30'''

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

'''FFTHighBand5=50'''

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

== Printer ==

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

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

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

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

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

== Calibration ==

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

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

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

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

== Video ==

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

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

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

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

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

== Mapping ==

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

'''UseBitmapDrawing=Off'''

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

'''Use3DVBlending=Auto'''

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

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

'''UseDoubleBuffering=On'''

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

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

== Matlab ==

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

'''Platform=64'''

Set '''Platform=32''' if you want to use the x86t version of MATLAB.

== Updates ==

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

'''DaysBetweenUpdateChecks=7'''

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

'''CheckNetworkDongle=Off'''

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

'''LocalPath'''

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

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

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

Download server

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

Path on the server to UpdateVersions.txt.

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

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

'''History'''

Path on the server to general history file

== FMRI ==

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

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

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

These values indicate:

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

== Montage ==

'''The section [Montage] allows to specify an initial montage that is set the first time when the source (Src), recorded (Rec), virtual (Vir) or user (Usr) montage button is pressed. If BESA.ini does not specify a montage, pressing the corresponding button opens the drop-down menu offering all the available montages for the current montage type.'''

'''Source=25s''' specifies that when the Src button in the control ribbon is pressed for the first time, the source montage "25s" will be selected.

'''Recorded=Original Recording''' specifies that when the Rec button in the control ribbon is pressed for the first time, the source montage "Original Recording" will be selected.

'''Virtual=Triple Banana''' specifies that when the Vir button in the control ribbon is pressed for the first time, the source montage "Triple Banana" will be selected.

'''User=CA25''' specifies that when the Usr button in the control ribbon is pressed for the first time, the source montage "CA25" will be selected.

== Reader-Specific Settings ==

 
=== BrainLab ===

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

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

=== Bio-Logic ===

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:

* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>

* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

=== EDF+/BDF/Trackit ===

'''TriggerScan=On'''

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

=== EGI ===

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

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

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

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

Set to “no” if you don’t want to treat DIN events separately. Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

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

This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

=== Harmonie ===

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

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

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

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

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

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

=== Neuroscan Keys ===

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

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

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

=== NKT2100 ===

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

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

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

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

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

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

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

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

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

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

=== Vangard ===

'''AlwaysOpenFileSelect=Yes'''

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

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

=== XLTEK ===

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

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

[[Category:Research Manual]]

{{BESAManualNav}}

The Initialization File: BESA.ini

2024-03-11T11:32:18Z

Dominik:

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

== Introduction ==

'''BESA.ini File'''

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

'''Location of BESA.ini'''

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

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

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

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

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

{| class="wikitable"
| [Defaults]
| General settings (filters, scaling, and various other settings)
|-
| [Folders]
| Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)
|-
| [Electrodes]
| Electrode renaming
|-
| [Patterns]
| Rename patterns in the '''Tags''' menu
|-
| [Artifacts]
| Settings for artifact correction
|-
| [KEYCONTROLS]
| Function key definitions
|-
| [Search]
| Default parameters for search
|-
| [FFT]
| Frequency band definitions
|-
| [Printer]
| Printer control
|-
| [Calibration]
| Calibration control
|-
| [Video]
| Digital video control
|-
| [Mapping]
| Mapping control
|-
| [Updates]
| Options for program updates
|-
| [Matlab]
| Settings for the MATLAB interface
|-
| [fMRI]
| Settings for the fMRI arfifact removal
|-
| [Montages]
| A setting for a default source montage
|}

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

== Defaults ==

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

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

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

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

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

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

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

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

'''MegScale=200''' scale of MEG/GRA channels in [fT or fT/cm]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'''Notes'''

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

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

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

== Folders ==

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

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

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

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

'''The Variables'''

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

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

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

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

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

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

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

'''Placeholders'''

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

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

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

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

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

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program Files (x86)\BESA\Research_7_0''".

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

== Electrodes ==

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

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

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

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

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

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

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

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

PG1=LO1 define X3 as lateral orbital eye electrode left

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

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

X9=Rsp define X9 channel to be a respiratory channel

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

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

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

== Patterns ==

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

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

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

Pattern1=Spike

Pattern2=Sharp Wave

== Artifacts ==

'''Artifact default settings:'''

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

== Search ==

Default settings for pattern search.

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

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

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

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

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

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

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

'''LowPassFreq = 35 Hz'''

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

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

'''CorrelationThresholdNoMarked = 60%'''

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

'''CorrelationThresholdOneMarked = 85%'''

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

'''CorrelationThresholdFourMarked = 65%'''

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

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

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

'''WriteAfterSearchCheckBox = No'''

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

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

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

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

== KeyControls ==

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

'''Fn=function''' or

'''Del=function'''

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

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

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

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

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

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

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

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

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

'''Batches and Montages:'''

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

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

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

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

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

== FFT ==

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

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

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

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

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

'''FFTBand7=Off'''

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

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

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

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

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

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

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

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

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

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

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

'''FFTHighBand3=14'''

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

'''FFTHighBand4=30'''

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

'''FFTHighBand5=50'''

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

== Printer ==

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

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

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

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

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

== Calibration ==

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

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

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

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

== Video ==

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

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

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

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

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

== Mapping ==

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

'''UseBitmapDrawing=Off'''

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

'''Use3DVBlending=Auto'''

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

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

'''UseDoubleBuffering=On'''

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

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

== Matlab ==

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

'''Platform=64'''

Set '''Platform=32''' if you want to use the x86t version of MATLAB.

== Updates ==

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

'''DaysBetweenUpdateChecks=7'''

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

'''CheckNetworkDongle=Off'''

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

'''LocalPath'''

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

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

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

ftp download server

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

Path on the server to UpdateVersions.txt.

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

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

'''History'''

Path on the server to general history file

== FMRI ==

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

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

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

These values indicate:

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

== Montage ==

'''The section [Montage] allows to specify an initial montage that is set the first time when the source (Src), recorded (Rec), virtual (Vir) or user (Usr) montage button is pressed. If BESA.ini does not specify a montage, pressing the corresponding button opens the drop-down menu offering all the available montages for the current montage type.'''

'''Source=25s''' specifies that when the Src button in the control ribbon is pressed for the first time, the source montage "25s" will be selected.

'''Recorded=Original Recording''' specifies that when the Rec button in the control ribbon is pressed for the first time, the source montage "Original Recording" will be selected.

'''Virtual=Triple Banana''' specifies that when the Vir button in the control ribbon is pressed for the first time, the source montage "Triple Banana" will be selected.

'''User=CA25''' specifies that when the Usr button in the control ribbon is pressed for the first time, the source montage "CA25" will be selected.

== Reader-Specific Settings ==

 
=== BrainLab ===

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

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

=== Bio-Logic ===

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:

* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>

* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

=== EDF+/BDF/Trackit ===

'''TriggerScan=On'''

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

=== EGI ===

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

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

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

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

Set to “no” if you don’t want to treat DIN events separately. Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

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

This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

=== Harmonie ===

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

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

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

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

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

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

=== Neuroscan Keys ===

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

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

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

=== NKT2100 ===

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

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

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

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

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

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

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

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

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

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

=== Vangard ===

'''AlwaysOpenFileSelect=Yes'''

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

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

=== XLTEK ===

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

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

[[Category:Research Manual]]

{{BESAManualNav}}

The Initialization File: BESA.ini

2024-03-11T11:30:30Z

Dominik:

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

== Introduction ==

'''BESA.ini File'''

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

'''Location of BESA.ini'''

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

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

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

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

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

{| class="wikitable"
| [Defaults]
| General settings (filters, scaling, and various other settings)
|-
| [Folders]
| Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)
|-
| [Electrodes]
| Electrode renaming
|-
| [Patterns]
| Rename patterns in the '''Tags''' menu
|-
| [Artifacts]
| Settings for artifact correction
|-
| [KEYCONTROLS]
| Function key definitions
|-
| [Search]
| Default parameters for search
|-
| [FFT]
| Frequency band definitions
|-
| [Printer]
| Printer control
|-
| [Calibration]
| Calibration control
|-
| [Video]
| Digital video control
|-
| [Mapping]
| Mapping control
|-
| [Updates]
| Options for program updates
|-
| [Matlab]
| Settings for the MATLAB interface
|-
| [fMRI]
| Settings for the fMRI arfifact removal
|-
| [Montages]
| A setting for a default source montage
|}

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

== Defaults ==

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

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

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

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

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

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

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

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

'''MegScale=200''' scale of MEG/GRA channels in [fT or fT/cm]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'''Notes'''

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

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

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

== Folders ==

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

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

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

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

'''The Variables'''

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

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

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

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

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

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

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

'''Placeholders'''

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

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

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

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

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

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program Files (x86)\BESA\Research_7_0''".

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

== Electrodes ==

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

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

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

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

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

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

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

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

PG1=LO1 define X3 as lateral orbital eye electrode left

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

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

X9=Rsp define X9 channel to be a respiratory channel

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

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

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

== Patterns ==

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

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

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

Pattern1=Spike

Pattern2=Sharp Wave

== Artifacts ==

'''Artifact default settings:'''

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

== Search ==

Default settings for pattern search.

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

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

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

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

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

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

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

'''LowPassFreq = 35 Hz'''

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

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

'''CorrelationThresholdNoMarked = 60%'''

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

'''CorrelationThresholdOneMarked = 85%'''

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

'''CorrelationThresholdFourMarked = 65%'''

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

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

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

'''WriteAfterSearchCheckBox = No'''

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

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

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

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

== KeyControls ==

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

'''Fn=function''' or

'''Del=function'''

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

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

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

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

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

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

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

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

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

'''Batches and Montages:'''

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

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

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

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

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

== FFT ==

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

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

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

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

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

'''FFTBand7=Off'''

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

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

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

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

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

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

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

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

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

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

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

'''FFTHighBand3=14'''

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

'''FFTHighBand4=30'''

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

'''FFTHighBand5=50'''

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

== Printer ==

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

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

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

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

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

== Calibration ==

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

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

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

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

== Video ==

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

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

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

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

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

== Mapping ==

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

'''UseBitmapDrawing=Off'''

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

'''Use3DVBlending=Auto'''

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

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

'''UseDoubleBuffering=On'''

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

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

== Matlab ==

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

'''Platform=64'''

Set '''Platform=32''' if you want to use the x86t version of MATLAB.

== Updates ==

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

'''DaysBetweenUpdateChecks=7'''

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

'''CheckNetworkDongle=Off'''

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

'''LocalPath'''

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

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

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

ftp download server

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

Path on the server to UpdateVersions.txt.

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

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

'''History'''

Path on the server to general history file

== FMRI ==

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

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

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

These values indicate:

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

== Montage ==

'''This section allows to specify an initial montage that is set the first time when the source (Src), recorded (Rec), virtual (Vir) or user (Usr) montage button is pressed. If BESA.ini does not specify a montage, pressing the corresponding button opens the drop-down menu offering all the available montages for the current montage type.'''

'''Source=25s''' specifies that when the Src button in the control ribbon is pressed for the first time, the source montage "25s" will be selected.

'''Recorded=Original Recording''' specifies that when the Rec button in the control ribbon is pressed for the first time, the source montage "Original Recording" will be selected.

'''Virtual=Triple Banana''' specifies that when the Vir button in the control ribbon is pressed for the first time, the source montage "Triple Banana" will be selected.

'''User=CA25''' specifies that when the Usr button in the control ribbon is pressed for the first time, the source montage "CA25" will be selected.

== Reader-Specific Settings ==

 
=== BrainLab ===

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

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

=== Bio-Logic ===

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:

* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>

* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

=== EDF+/BDF/Trackit ===

'''TriggerScan=On'''

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

=== EGI ===

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

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

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

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

Set to “no” if you don’t want to treat DIN events separately. Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

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

This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

=== Harmonie ===

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

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

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

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

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

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

=== Neuroscan Keys ===

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

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

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

=== NKT2100 ===

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

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

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

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

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

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

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

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

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

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

=== Vangard ===

'''AlwaysOpenFileSelect=Yes'''

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

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

=== XLTEK ===

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

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

[[Category:Research Manual]]

{{BESAManualNav}}

The Initialization File: BESA.ini

2024-03-11T11:26:16Z

Dominik:

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

== Introduction ==

'''BESA.ini File'''

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

'''Location of BESA.ini'''

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

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

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

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

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

{| class="wikitable"
| [Defaults]
| General settings (filters, scaling, and various other settings)
|-
| [Folders]
| Folders used by BESA Research (Examples, Montages, Scripts, Settings,...)
|-
| [Electrodes]
| Electrode renaming
|-
| [Patterns]
| Rename patterns in the '''Tags''' menu
|-
| [Artifacts]
| Settings for artifact correction
|-
| [KEYCONTROLS]
| Function key definitions
|-
| [Search]
| Default parameters for search
|-
| [FFT]
| Frequency band definitions
|-
| [Printer]
| Printer control
|-
| [Calibration]
| Calibration control
|-
| [Video]
| Digital video control
|-
| [Mapping]
| Mapping control
|-
| [Updates]
| Options for program updates
|-
| [Matlab]
| Settings for the MATLAB interface
|-
| [fMRI]
| Settings for the fMRI arfifact removal
|-
| [Montages]
| A setting for a default source montage
|}

'''Reader-specific settings'''

[BrainLab]

[Bio-Logic]

[EDF+] [BDF] [Trackit]

[EGI]

[Harmonie]

[NeuroScan Keys]

[NKT2100]

[Vangard]

[XLTEK]

== Defaults ==

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

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

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

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

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

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

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

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

'''MegScale=200''' scale of MEG/GRA channels in [fT or fT/cm]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

'''Notes'''

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

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

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

== Folders ==

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

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

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

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

'''The Variables'''

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

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

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

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

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

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

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

'''Placeholders'''

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

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

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

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

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

'''%progdir%''' = the BESA Research root folder. In a default installation, this is "''C:\Program Files (x86)\BESA\Research_7_0''".

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

== Electrodes ==

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

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

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

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

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

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

X1=ECG1 define X1 channel to be ECG1

X2=ECG2 define X2 channel to be ECG2

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

PG1=LO1 define X3 as lateral orbital eye electrode left

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

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

X9=Rsp define X9 channel to be a respiratory channel

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

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

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

== Patterns ==

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

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

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

Pattern1=Spike

Pattern2=Sharp Wave

== Artifacts ==

'''Artifact default settings:'''

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

== Search ==

Default settings for pattern search.

'''Default Settings for the ''Search/Options ''Dialog box:'''

'''CorrelationThreshold''' = '''75%'''

'''AmplitudeThreshold = 100 µV'''

'''GradientThreshold = 25'''

'''Default Settings for the ''Search/Average/View'' (SAV) Dialog box:'''

'''PreCursor = -250 ms'''

'''PostCursor = 150 ms'''

'''HighPassFreq = 2 Hz'''

'''HighPassSlope = 12 dB/Octave'''

'''HighPassType = 0 (0 = zero phase, 1 = forward, 2 = backward'''

'''LowPassFreq = 35 Hz'''

'''LowPassSlope = 24 dB/Octave'''

'''LowPassType = 0 (0 = zero phase, 1 = forward, 2 = backward)'''

'''CorrelationThresholdNoMarked = 60%'''

Default correlation threshold if no channel labels are marked when the SAV Dialog is opened.

'''CorrelationThresholdOneMarked = 85%'''

Default correlation threshold if one channel label is marked when the SAV Dialog is opened.

'''CorrelationThresholdFourMarked = 65%'''

Default correlation threshold if between two channel labels are marked when the SAV Dialog is opened.

'''SelectedViewWindowWidthMultiplier = 300%'''

'''WriteAfterSearch = No'''

If set to "Yes", a File Save dialog will open, to allow to save the search average to a file (as with the SAW function).

'''WriteAfterSearchCheckBox = No'''

If set to "Yes", an additional checkbox "Write after search" is displayed at the bottom of the SAV Dialog, allowing to choose whether or not to write the search average after a search:

[[Image:ST Besa ini (1).gif ‎ ]]

'''PreserveDefaults = Yes'''

If set to "No", the SAV Dialog will open with the same boxes checked as the last time the dialog was opened during the current session.

If set to "Yes", the default frequency, buffer width, selected view after search, and default threshold are always checked when the dialog is opened.

== KeyControls ==

In the [KeyControls] section you can specify functions that can be allocated to '''function keys''' or to the ''Del'' key. Specify using the form:

'''Fn=function''' or

'''Del=function'''

where "''n''" is a number between 2 and 12 (F1 is reserved for Help). For example:

    F2 = Batch1

Possible functions are:

'''Setting or removing events:'''

'''Pattern''n''''', where ''n''<nowiki>=1-5: Sets the tag number </nowiki>''n'' at the cursor latency.

'''Epochfast:''' sets one boundary of an epoch at the cursor latency, but does not open the epoch text box to define a label.

'''Marker:'''  sets a marker at the cursor latency.

'''Comment:''' sets a comment at the cursor latency and opens the comment box to enter text.

'''Epoch:''' sets one boundary of an epoch at the cursor latency and opens the epoch text box to enter a label.

'''Artifact:''' sets one boundary of an artifact segment at the cursor latency.

'''Delete:'''  deletes a tag at the cursor latency

'''Batches and Montages:'''

'''Batch''n''''', where n=1-12: Runs a predefined batch file corresponding to the number ''n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a batch, pressing it will open a ''File Open Dialog'' to select a batch. The setting you have chosen will be retained across BESA Research sessions. Holding the '''<shift>''' key while pressing the '''function key''' will always open the dialog. Hold the''' <ctrl> '''key with the function key to open the associated batch in the batch edit dialog.</div>

'''Montage''n''''', where n=1-12: Sets a montage corresponding to the number'' n''.

<div style="margin-left:0.953cm;margin-right:0cm;">If a key has not yet been associated with a montage, pressing it will generate a message asking you to associate a montage as follows: Holding the '''<shift> '''key while pressing the '''function key''' will remove the current association, and substitute it with the current montage.</div>

The default settings after program installation are listed in the online help chapter ''Review / Reference / Controls / Mouse and Keyboard / Keyboard Controls''.

== FFT ==

'''Default settings provided for section [FFT]:'''

These settings define the setup in the Spectral Analysis section of the BESA Research program (FFT window, see the chapter "''Spectral Analysis / FFT''"). Up to 7 frequency bands may be defined. Five are defined by default.

'''FFTBand1=On''' FFT Bands 1-5 are defined

'''FFTBand2=On'''

'''FFTBand3=On'''

'''FFTBand4=On'''

'''FFTBand5=On'''

'''FFTBand6=Off''' FFT Bands 6-7 are not defined

'''FFTBand7=Off'''

'''FFTNameBand1=Delta''' Names of the defined bands

'''FFTNameBand2=Theta'''

'''FFTNameBand3=Alpha'''

'''FFTNameBand4=Beta'''

'''FFTNameBand5=Gamma'''

'''FFTColorBand1=RGB(0,0,0)'''  Default color of each band

'''FFTColorBand2=RGB(0,128,64)'''

'''FFTColorBand3=RGB(128,0,0)'''

'''FFTColorBand4=RGB(255,0,0)'''

'''FFTColorBand5=RGB(255,128,0)'''

'''FFTColorBand6=RGB(255,192,0)'''

'''FFTColorBand7=RGB(255,255,0)'''

'''FFTLowBand1=1''' Delta from 1-4 Hz

'''FFTHighBand1=4'''

'''FFTLowBand2=4''' Theta from 4-8 Hz

'''FFTHighBand2=8'''

'''FFTLowBand3=8''' Alpha from 8-14 Hz

'''FFTHighBand3=14'''

'''FFTLowBand4=14''' Beta from 14-30 Hz

'''FFTHighBand4=30'''

'''FFTLowBand5=30''' Gamma from 30-50 Hz

'''FFTHighBand5=50'''

These values are best set from within BESA Research, using the '''Options''' menu in the FFT window (see the chapter "''Spectral Analysis / FFT / FFT Options Menu''"). Current settings are stored after each session and retrieved in the next session.

== Printer ==

'''Default settings provided for section [Printer]:'''

'''PrinterMarginPercent=100''' controls size of printout

'''PrinterColors=256''' set to 1/2 for black&white, 0/256 for color printers

'''PrinterLineMode=1''' set to 2 for thicker lines and to save printer memory

'''PrinterMapResolution=1''' set to 2, 3, 4 to save printer memory and increase speed

== Calibration ==

'''Default settings provided for section [Calibration]:'''

'''AutoCalibration=Off''' On: automatic calibration of signals >= 4 cycles

'''MicrovoltCalibration=50''' peak voltage of calibration signal

If calibration is set to'' On'', the menu item ''Calibration ''will appear in the''' Process '''menu. Position your current screen at an epoch containing at least 4 regular cycles of the calibration signal (in all channels!) and select Calibration.

== Video ==

'''Default settings provided for section [Video]:'''

'''DVCFilePath=C:\DVC\DVPlay.exe''' holds the path to the digital video player

'''DVCCommandLineArguments=/S:3 /M:P /T:M'''  arguments to be passed to the digital video player

'''CursorPagingOffsetLeft=0.2  '''

'''CursorPagingOffsetRight=0.8'''

'''CursorMinDistToBorderBeforePaging=0.02'''

'''PageDisplayIfCursorIsBelowVideo=1'''

'''MappingRepetitionRateWithVideoInMS=100'''  gives the number of milliseconds between two maps if the mapping window is open while the video is running. If the graphics board encounters problems during the display, this value should be increased.

== Mapping ==

'''Default settings provided for section [Mapping]:'''

'''UseBitmapDrawing=Off'''

Set this to "On" if 3D maps show a strange pattern of black triangular shapes (this is frequently observed with modern Intel On-Board graphics controllers, and is a result of inadequate drivers for OpenGL).

'''Use3DVBlending=Auto'''

Set this to "Off" if the 3D view in the Montage Editor or the Source Analysis window does not show up properly (this may happen with some older graphics cards).

Set this to "On" if the 3D view in the Montage Editor or the Source Analysis window shows a ragged surface boundary.

'''UseDoubleBuffering=On'''

Set this to "Off" to disable double buffering mechanism that prevents the screen from flickering while paging through data and dragging window (''this feature requires BESA Research 7.1 or higher'').

Note: '''MapSmoothing''', the default map smoothing parameter, can be specified in the '''[Defaults]''' section.

== Matlab ==

'''Default settings for the [Matlab] section:'''

'''Platform=32'''

Set '''Platform=64''' if you want to use the 64-bit version of MATLAB.

== Updates ==

This section is not normally required, but the variables here can be altered or defined to determine how BESA Research checks for dongle and program updates.

'''DaysBetweenUpdateChecks=7'''

Sets the number of days between automatic checks for updates. Set the value to 0 to check every time BESA Research is started. Set to -1 to turn off automatic update checks.

'''CheckNetworkDongle=Off'''

For the network administrator: If set to "On", BESA Research will check the dongle on the network for updates. Otherwise the state of the network dongle will be ignored.

'''LocalPath'''

For the network administrator. This can be set to a path on the local network to the BESA update files, so that users can obtain their updates locally. The path is given to the text file "'''UpdateVersions.txt'''" (e.g. ''LocalPath=\\transtec-sak\zarascratch\BESA\Updates\UpdateVersions.txt''), which contains further details for the program to obtain its updates. If you want to use this feature, please contact us at [mailto:support@besa.de support@besa.de].

The following variables are not required, because BESA Research has the paths hardwired:

'''FTP1 (also FTP2, FTP3)'''

ftp download server

'''Path1 (also Path2, Path3)'''

Path on the server to UpdateVersions.txt.

'''HaspPath1 (also HaspPath2, HaspPath3)'''

Path on the server to HASP (dongle) update files.

'''History'''

Path on the server to general history file

== FMRI ==

''(requires Besa Research 7.0 or higher)''

These settings define the default parameters for the fMRI artifact removal in the BESA Research (see [[BESA_Research_Artifact_Correction#fMRI_artifact_removal|fMRI artifact removal]] chapter for further details). For example:

<syntaxhighlight lang="text">
[FMRI]
FMRIRemovalMode=1
TRDelay=200
TRLength=800
NumberOfAverages=21
fMRImoveThreshold=0.15
FMRITRID=8015
ScansToSkip=0
</syntaxhighlight>

These values indicate:

* '''FMRIRemovalMode''': Removal method (0: Turned off; 1: Allen et al, 2000; 2: Allen et al., 2000 Modified; 3: Moosmann et al.,2003)
* '''TRDelay''': Delay between marker and start of volume acquisition [ms]
* '''NumberOfAverages''': Number of artifact occurrence averages
* '''fMRImoveThreshold''': Movement threshold [mm]
* '''FMRITRID''': fMRI Trigger code
* '''ScansToSkip''': Number of scans to skip

== Montage ==

'''This section allows to specify an initial montage that is set the first time when the source (Src), recorded (Rec), virtual (Vir) or user (Usr) montage button is pressed. If BESA.ini does not specify a montage, pressing the corresponding button opens the drop-down menu offering all the available montages for the current montage type.'''

'''Source=25s''' specifies that when the Src button in the control ribbon is pressed for the first time, the source montage "25s" will be selected.

'''Recorded=Original Recording''' specifies that when the Rec button in the control ribbon is pressed for the first time, the source montage "Original Recording" will be selected.

'''Virtual=Triple Banana''' specifies that when the Vir button in the control ribbon is pressed for the first time, the source montage "Triple Banana" will be selected.

'''User=CA25''' specifies that when the Usr button in the control ribbon is pressed for the first time, the source montage "CA25" will be selected.

== Reader-Specific Settings ==

 
=== BrainLab ===

'''Default settings provided for section [BrainLab]:'''

'''BrainLabFormat=New''' this entry ensures that the newer BrainLab file format can be read by BESA Research.

=== Bio-Logic ===

'''FileSelect=Yes'''

If there are several Bio-Logic files in a data folder, the reader can check if the files have the same settings. There are three possible options:

* Open a dialog to ask if the files should be treated as a single data set, or as individual, separate files.

[[Image:ST Besa ini (2).jpg ‎]]

<div style="margin-left:0.953cm;margin-right:0cm;">in this case, use '''FileSelect=Yes''' (this is the default setting) Note that the choice made in the dialog will apply to the file(s) within a BESA Research session. For a given file and session, the dialog will only be opened once, even if the file is closed and reopened.</div>

* Always concatenate such files into a single data set. In this case use '''FileSelect=All'''
* Always open the files as single, separate files. In this case use '''FileSelect=Single'''

=== EDF+/BDF/Trackit ===

'''TriggerScan=On'''

Set '''TriggerScan=Off '''to prevent BESA Research from scanning the file for triggers. This is done separately for EDF+, BDF, and Trackit files in sections '''[EDF+], [BDF],''' and '''[Trackit]''' in the '''BESA.ini''' file.

=== EGI ===

The treatment of DIN events can be modified in the''' [EGI] '''section:

'''CombineDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you want to treat DIN events separately, and not generate combined values.

'''SeparateDINevents'''<nowiki>=yes/no    (default is “yes”)</nowiki>

Set to “no” if you don’t want to treat DIN events separately. Thus, using the above two parameters, you can choose whether you want to treat DIN events as combined, separate, both, or completely ignored.

'''CombineDINeventsPrefix'''<nowiki>=dinComb</nowiki>

This defines the text preceding the number when DIN events are combined. The default is “dinComb”.</div>

=== Harmonie ===

'''Default settings provided for section [Harmonie] (Stellate Harmonie systems):'''

'''SeizurePreEpoch=60''' length of the epoch preceding a seizure detection in s

'''SeizurePostEpoch=60''' length of the epoch following a seizure detection in s

'''PushButtonPreEpoch=60''' length of the epoch preceding a push button detection

'''PushButtonPostEpoch=60''' length of the epoch following a push button detection

When BESA Research encounters a seizure detection event or a push button detection event in a Stellate Harmonie file, it automatically sets an epoch around the event, which makes it convenient to view just those epochs for analysis. The length of the epochs preceding and following the events can be adjusted in the '''.ini''' file.

=== Neuroscan Keys ===

'''Note that there is a setting "NeuroScanDataNumberOfBits" in the [Defaults] section of BESA.ini that is used for distinguishing the data format of Neuroscan files (16 or 32-bit).'''

'''Default settings provided for section [NeuroScan Keys] (NeuroScan systems):'''

Event1=Movement Text corresponding to keyboard events 1 through 10

Event2=Blink

Event3=Talking

Event4=Cough

Event5=Muscle

Event6=Jaw

Event7=Sneeze

Event8=Swallow

Event9=Eye movement

Event10=Hiccup

=== NKT2100 ===

'''Default settings provided for section [NKT2100] (Nihon Kohden EEG 21xx systems):'''

'''TriggerScan=On'''   Set to "Off" to prevent a scan for trigger events.

'''Country=NotKanji''' set to NotKanji for non-Kanji characters else to Kanji

'''KanjiCharSize=16''' Kanji character size

'''KanjiPrinterCharSize=32''' Kanji printer character size

'''EEG_Sensitivity=50''' default sensitivity of Nihon Kohden EEG-2100 system

'''DC_Sensitivity=50''' default sensitivity of Nihon Kohden DAE-2100 system

'''QJ_Sensitivity=100''' default sensitivity of Nihon Kohden QJ-403 system

'''Mark_Sensitivity=100''' default sensitivity of EEG-2100 marker channels

These settings need to be changed only if the manufacturer has specified different gains for your system. Otherwise do not alter these settings.

=== Vangard ===

'''AlwaysOpenFileSelect=Yes'''

If "Yes" is selected, each time a Vangard file is opened, a dialog box will open, asking for a selection of the segment type to display.

If "No" is selected, the selection dialog is opened whenever a Vangard file is opened for the first time, or if the ''Channel and digitized head surface point information dialog box'' is opened (e.g. with '''ctrl-L''' or ''File/Head Surface Points and Sensors/Load Coordinate Files...'' ).

=== XLTEK ===

'''TriggerScan=Off '''Set to "On" to scan the data file for trigger events

'''MontageNo=2''' Set to 1 or 2. If two montages for the data file are defined, this variable determines whether the first or the second alternative should be used.

[[Category:Research Manual]]

{{BESAManualNav}}

Integration with MRI and fMRI

2021-11-25T13:14:21Z

Dominik:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher BESA MRI
|version = BESA Research 6.1 or higher BESA MRI 2.0 or higher
}}



== Introduction ==

Both for developing and evaluating dipole source models of EEG or MEG activity, it is useful to have access to structural MRI or fMRI data.

The BESA MRI software allows to preprocess structural MRI data so that the individual anatomical information contained in the MRI can be utilized in BESA Research.

BESA MRI makes it possible ...

*... to align the EEG and MEG sensors with the structural MRI data.

*... to read and display the aligned, individual Talairach structural MRIs directly in the BESA Research Source Analysis module. In this way, source analysis results can be presented on top of the aligned MRIs, which allows us to evaluate the anatomical regions to which the reconstructed sources may correspond.

*... to use an individual, realistically shaped FEM or BEM head model for source analysis in BESA Research. FEM and BEM head models take into account the individual volume conduction properties of the subject's head derived from the structural MRI data. This allows for more accurate source analysis (Yvert 1997, Lanfer 2012).

*... overlay source analysis results obtained in BESA Research with fMRI data.

*... use fMRI BOLD regions or MRI structures to initialize dipole models.

*... use fMRI image to constrain EEG/MEG source localization

*... send discrete source analysis results from BESA Research to BESA MRI to visualize them in both Talairach and subject-specific (ACPC) coordinates.

The chapters below describe the steps necessary to integrate the MRI and fMRI data with BESA Research.

It is also possible to use BESA Research with BrainVoyager. Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website:
[https://www.brainvoyager.com/downloads/downloads.html BrainVoyager Downloads].

'''Aligning Coordinate Systems'''

* For a given BESA data set, the electrode and other head surface points need to be aligned to the MRI coordinates.
* The basic steps necessary to align the EEG electrode locations, the MEG sensors and the MRI are described in Section [[Integration_with_MRI_and_fMRI#Setting_Up_Coregistration_Using_BrainVoyager|How Coregistration is done]].
* Detailed instructions on how to align EEG / MEG and MRI data using BESA MRI can be found in the coregistration quick guide which is available on the BESA homepage ([http://www.besa.de/downloads/quick-guides/ Quick Guides]).
* Detailed instructions on how to align EEG / MEG and MRI data using BrainVoyager are described in Section [[Integration_with_MRI_and_fMRI#Setting_Up_Coregistration_Using_BrainVoyager|How To set up Coregistration between BESA and BrainVoyager]].
* In BESA Research, all necessary settings with regard to the alignment are made in the [[Integration_with_MRI_and_fMRI#The_Coregistration_Dialog|Coregistration Dialog]].
* Requirements with respect to the MRI data for a good coregistration can be found in Section [[#MRI_Requirements_for_Good_Coregistration|MRI Requirements for Good Coregistration]].
* Requirements with respect to EEG and MEG data for a good coregistration can be found in Section [[#EEG/MEG Data Requirements for Good Coregistration|EEG/MEG Data Requirements for Good Coregistration]].

'''Generating an individual, realistically shaped FEM head model'''

* The generation of a FEM head model that can be used in BESA Research is done in BESA MRI as an additional step following the EEG / MEG to MRI coregistration.
* Detailed instructions on how to generate the FEM head model can be found in the coregistration quick guide which is available on the BESA homepage ([http://www.besa.de/downloads/quick-guides/ Quick Guides]).

'''Co-locating dipoles and MRI locations'''

* After aligning the EEG / MEG and the MRI data it is possible to co-locate dipoles and MRI locations. This means, it is possible to visualize the dipoles and to specify the dipole parameters in the MRI coordinate system.
* [[Integration_with_MRI_and_fMRI#Co-locating_Sources_and_MRI_in_the_BESA_Research_Source_Module|How to Co-locate sources and MRI in the BESA Research Source Module]] describes how in the BESA Research Source Analysis module dipoles can directly be visualized in the space of the individual MRI.
* [[Integration_with_MRI_and_fMRI#Send_a_Dipole_from_BESA_Research_to_BrainVoyager|How to Send a discrete Solution to BESA MRI]] describes how to export the current solution to the co-registered MRI and open it in BESA MRI.

'''References'''

Lanfer, B., I. Paul-Jordanov, M. Scherg, and C. H. Wolters. “Influence of Interior Cerebrospinal Fluid Compartments on EEG Source Analysis.” In Proceedings BMT 2012, Vol. 57. Jena: De Gruyter, 2012. doi:10.1515/bmt-2012-4020.

Yvert, B., O. Bertrand, M. Thévenet, J. F. Echallier, and J. Pernier. “A Systematic Evaluation of the Spherical Model Accuracy in EEG Dipole Localization.” Electroencephalography and Clinical Neurophysiology 102, no. 5 (May 1997): 452–59. doi:16/S0921-884X(97)96611-X.

== How Coregistration is done ==

This section outlines the basic steps to coregister the EEG / MEG data to an individual MRI. These steps are necessary to load an individual MRI into BESA Research.

'''What happens:'''

* EEG / MEG sensor locations and the MRI data are defined in different coordinate systems. Setting up coregistration is the process of aligning the two coordinate systems.
* BESA Research uses the ''Coregistration Dialog'' to coordinate the alignment procedure.
* Alignment is done with the ''AC-PC-transformed MRI''.
* BESA Research displays the ''Talairach-transformed MRI'' in the source analysis module.
* A coregistration file (with the extension "'''.sfh'''") is used to mediate between BESA Research and BESA MRI (or BrainVoyagerQX):
* BESA Research writes the coregistration file which contains the coordinates of head surface points (fiducials, electrodes, other digitized surface points).
* The coordinates are read into BESA MRI (or BrainVoyager), and aligned with the AC-PC-transformed MRI. The alignment information is then appended to the ''coregistration file''. The names of the AC-PC MRI ('''<nowiki>*.vmr</nowiki>''') and the surface mesh ('''<nowiki>*.srf</nowiki>'''), and, if available, the Talairach transformation, are also appended.
* BESA Research reads the coregistration file and appends the name of the Talairach-transformed MRI and head surface. If a brain surface has been created, this is also appended.
* Subsequently, BESA Research reads the coregistration file automatically when loading the data file.
* In the BESA Research source module, the individual MRI is displayed instead of the standard MRI. Talairach coordinates of dipoles are the "real" Talairach coordinates as defined, e.g., in BrainVoyager.

'''The steps you have to take (once for each data set):'''

* From the BESA Research ''Coregistration Dialog'', write a coregistration file. Switch to BESA MRI (or BrainVoyagerQX).
* If BESA MRI is used follow the steps in the coregistration quickguide which is available on the BESA homepage ([http://www.besa.de/downloads/quick-guides/ Quick Guides]).
* If BrainVoyager is used follow the steps in Section “''How to set up coregistration between BESA and BrainVoyager”.''
* Back in BESA Research, reload the altered '''coregistration file'''. When using BESA MRI the file names of the generated surface and volume data files will be automatically filled in. When using BrainVoyager file names are only filled in automatically when the files are named according to the file naming conventions. Otherwise, file names have to be set manually.
* The coregistration file is now associated with the data file in the BESA Research database and will be used automatically the next time the file is opened in BESA Research. If the database entry is cleared, and the data are reloaded, you must make sure the coregistration file is also loaded (either using the ''Coregistration Dialog'' or the ''Channel and digitized head surface point information Dialog'').

== Alignment of BESA and MRICoordinate Systems ==

=== The Coregistration Dialog ===

The dialog is opened either from the ''Channel and digitized head surface point information'' ('''Ctrl-L''') ''dialog ''by pressing the '''Edit/Coreg''' button, or from the main menu ("'''File/MRI Coregistration...'''").

'''Note:''' If the coregistration dialog is invoked from an EEG data set in which no digitized electrode coordinates are available (i.e. standard electrode positions located on a sphere are assumed), BESA Research presents a warning message, saying that for MRI coregistration realistic electrode coordinates produce better results. BESA Research has a list of such realistic standard coordinates (i.e. located on a pre-defined standard head surface) for various electrodes available in file '''Default.sfp''', which is located in the Standard Electrode folder. If all electrodes in the dataset are listed in this file, a dialog window suggests to apply this file to the current data set, i.e. to switch from standard sphere coordinates to the standard realistic electrode coordinates in file '''Default.sfp'''. If the suggestion is accepted, '''default.sfp''' is assigned to the dataset (see Channel and digitized head surface point information ('''Ctrl-L''') dialog).

'''The Dialog:'''

[[Image:MRI Integration (1).gif ‎]]

* Press the '''Select MRI prog''' button to select your preferred MRI program. The current choice is between ''BESA MRI.exe'' and ''BrainVoyagerQX.exe''. The path to the MRI program is saved (in ''System\BESA.set'') and will be remembered by BESA Research. The top right hand button (now showing '''BESA MRI''') shows the current selection.
* Press the '''BESA MRI''' button to start the process of aligning the BESA Research and MRI coordinate systems. If no coregistration ('''<nowiki>*.sfh</nowiki>''') file is defined in the dialog (empty ''Surface coregistration file edit box''), BESA Research will first prompt for a file name. We recommend saving this file to the folder where the MRIs are kept. The MRI program will then be started. When you return to the ''Coregistration Dialog'', BESA Research checks if the ''Coregistration File'' has changed. If so, the dialog is updated with the new information.
* Press the top '''Browse... '''button to select a preexisting ''Coregistration File''.
* The entries in the edit boxes below show the files that will be used in the BESA Research Source Analysis module when the individual MRI is loaded. When using BESA MRI the file names will be automatically filled in. If you are using BrainVoagerQX and you are following our (and the BrainVoyagerQX) recommended naming conventions for files, and the files exist, then the names will be filled in automatically after you have completed the alignment procedure in BrainVoyagerQX. Otherwise you may have to browse for the files.
* Below the edit boxes the FEM field states whether all necessary information for the individual FEM head model were found in the coregistration file. If the field says ''Individual FEM for EEG'' ''defined!'' then all necessary data was found and the individual FEM EEG head model can be used in the BESA Research Source Analysis module. A similar message indicates whether the FEM MEG head model is available.
* Note that the MRI and the surfaces are Talairach-transformed! Alignment between BESA Research and the individual MRI is done with the MRI transformed to the AC-PC coordinate system, but the BESA Research Source Analysis module uses the Talairach-transformed image data and surfaces.

<div style="color:#ff0000;"></div>

=== Setting Up Coregistration Using BrainVoyager ===

It is assumed that you know how to load an MRI as a 3D data set into BrainVoyagerQX, and how to clean the image so that regions outside the head are black. We also assume knowledge of how to create AC-PC-aligned and Talairach-transformed MRIs.

Perform the following steps:

* BESA Research. Start the ''Coregistration Dialog''. Export the Coregistration File (head surface points) from your data by pressing the '''BrainVoyagerQX''' button in the dialog. Save the file to the directory where your MRI is located. BrainVoyagerQX is started.
* BrainVoyagerQX. Load the MRI corresponding to the EEG/MEG data. For optimal performance, the MRI should be cleaned so that regions outside the head are black. Prepare an AC-PC-transformed MRI and a Talairach MRI. For each, generate a surface mesh. Save these files following our recommended naming conventions (see chapter [[Integration_with_MRI_and_fMRI#MRI_file_Name_Conventions|MRI File Name Conventions]]). Save the Talairach coordinate file ('''<nowiki>*.tal</nowiki>'''). If these steps have already been performed, load the ACPC MRI and load the ACPC mesh. If you want to generate a brain surface mesh, see chapter [[Integration_with_MRI_and_fMRI#How_to_Generate_a_Brain_Surface_Mesh|How to Generate a Brain Surface Mesh]].
* BrainVoyagerQX. Load the Coregistration File (''EEG-MEG BESA/Load Surface Points''). The points will be displayed, but they are not aligned to the head:

[[Image:MRI Integration (2).gif ‎]]

* BrainVoyagerQX. Define fiducial points on the head surface. Right click on the 3D head display and select the ''Fiducials Dialog'' in the drop-down menu:

[[Image:MRI Integration (3).gif ‎]] [[Image:MRI Integration (4).gif ‎]]

* BrainVoyagerQX. Rotate the head (by holding the '''Shift '''button down and clicking and dragging with the mouse) so that the Nasion is clearly visible. Move the mouse to the Nasion, and press '''Ctrl+Left Click'''. The coordinates of the Nasion are inserted into the dialog. Repeat for the left preauricular point, and then for the right preauricular point.

[[Image:MRI Integration (5).gif ‎]]

Note: if you have defined your fiducials differently in your BESA Research data (e.g. ear holes), click on the corresponding points in the MRI. If you have additional head surface points (step 8), accuracy in pinpointing the fiducials is not critical.

* BrainVoyagerQX. In the Fiducials Dialog, press the '''Fit fiducials''' button. The head surface points are now more or less aligned to the head.

[[Image:MRI Integration (6).gif ‎]]

* BrainVoyagerQX. Now select '''''EEG-MEG BESA/Fit Surface Points...'''''

[[Image:MRI Integration (7).gif ‎]]

If you do not see the right half of the dialog, press the '''Advanced >>''' button.

* Specify the distances of the digitization points from the skin. In the illustration above, the digitization points for electrodes are estimated to be 8 mm from the surface of the head. For the purpose of accurate alignment, the distance of digitization points from skin section of the dialog needs to be filled in correctly. We recommend that "Restrain solution around fiducials" is checked, and a reasonable limit (here 3 mm) of the restraint is defined. Then press '''OK'''.

[[Image:MRI Integration (8).gif ‎]]

BrainVoyager fits the points to the head, stretching x, y, and z coordinates to obtain a better fit than before.

Note: The fit performed during this step accounts for scaling inequalities between the x, y, and z axes in the MRI. Coregistration gains in accuracy over the use of fiducials alone a) because more head surface points are used, and b) because the scaling inequalities are accounted for.

* Alignment is now completed. If you only want to display the structural MRI in the BESA Source Module, you can return to the BESA Coregistration Dialog.
* BESA Research. When you switch back to the Coregistration Dialog, BESA Research will try to fill in the names of the Talairach MRI and surface meshes. If the names are not filled in, use the '''Browse...''' buttons to select the MRI and surface meshes. Press '''OK''' to save the Coregistration File. Alignment is completed!

The alignment steps need only be performed once for a given MRI and EEG/MEG data set. Otherwise, after starting BrainVoyager, just load the MRI, the surface mesh, and the surface points (see [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done |How to Set Up Coregistration with BrainVoyager after Alignment has been Done]]). Now the following actions are possible: see chapters

* [[Integration_with_MRI_and_fMRI#Co-locating_Sources_and_MRI_in_the_BESA_Research_Source_Module|How to Co-Locate Sources and MRI in the BESA Research Source Module]]
* [[Integration_with_MRI_and_fMRI#Send_a_Dipole_from_BESA_Research_to_BrainVoyager|How to Send a Dipole from BESA Research to BrainVoyager]]
* [[Integration_with_MRI_and_fMRI#Define_a_Dipole_in_BESA_Research_at_a_Location_Defined_in_the_MRI|How to Define a Dipole in BESA Research at a Location Defined in the MRI]]

=== MRI file Name Conventions ===

If you follow the naming conventions for file names as described here, BESA Research detects the file names it requires, and the ''Coregistration Dialog'' is filled in automatically.

Please note that BESA MRI automatically uses these naming conventions for the generated files.

* '''The AC-PC MRI file name''' should end with "'''_ACPC.vmr'''", and the corresponding surface mesh name should end with "'''_ACPC.srf'''". After alignment, BrainVoyagerQX writes these names to the Coregistration File.
* '''The Talairach MRI file name '''should end with "'''_TAL.vmr'''", and the corresponding surface mesh name should end with "'''_TAL.srf'''". If defined, the brain surface mesh should end with "'''_TAL_WM.srf'''" ('''WM''' = '''w'''hite '''m'''atter).
* '''How BESA Research finds the Talairach files.''' When BESA Research rereads the Coregistration File after alignment of the coordinate systems, it finds the ACPC file names and defines the corresponding TAL file names. If these files exist, the names are entered into the Coregistration Dialog. For instance, if the Coregistration File contains the name "'''MRI''' '''PB_ACPC.vmr'''", BESA Research will look for the files "'''MRI_PB_TAL.vmr'''", "'''MRI_PB_TAL.srf'''", and "'''MRI_PB_TAL_WM.srf'''". If these files exist, they are entered into the dialog.
* '''Older BrainVoyager version.''' If you use BrainVoyager.exe to align coordinate systems, the file names are not saved with the Coregistration File. In this case, browse for the Talairach or the ACPC MRI from the Coregistration Dialog. BESA Research will use the rules as described above to insert the correct file names into the dialog.
* '''Missing Talairach coordinates.''' If, after aligning coordinate systems, the Talairach coordinates are missing from the Coregistration File (you forgot to load the Talairach coordinates in BrainVoyagerQX, or you used BrainVoyager.exe), BESA Research will look for a file ending with "'''_ACPC.tal'''", and read the coordinates from this file. You can also browse for a '''<nowiki>*.tal</nowiki>''' file in the Coregistration Dialog. For instance, if the MRI file is named "'''MRI_PB_ACPC.vmr'''" or "'''MR_''' '''PB_TAL.vmr'''", BESA Research will look for "'''MRI_PB_ACPC.tal'''" to find the Talairach coordinates.
* '''File names in the Coregistration File are saved relative to the Coregistration File location, if they are in the same folder.''' If the MRIs are in the same folder as the Coregistration File they will be recorded as ".\filename" (e.g. "'''.\MRI PB_tal.vmr'''"). This means that you can copy the Coregistration File together with the MRIs and meshes to a different folder, and BESA Research will be able to locate the files when the Coregistration File is opened. If the MRIs are saved in a different folder from the Coregistration File, the absolute paths are saved in the file. If the files are moved to new locations, you will have to restart the Coregistration Dialog and redefine the file locations.

=== How to Generate a Brain Surface Mesh ===

BESA Research is able to compute surface images, such as (Cortical LORETA, Cortical CLARA, Minimum Norm) using an individual cortex surface as the source space. A suitable cortex surface for this purpose can be effortlessly created using BESA MRI. Alternatively, BrainVoyager can be used for the creation of the brain surface mesh.

'''BESA MRI'''
* The brain surface generation is performed as one work step of the BESA MRI segmentation workflow.
* The cortex surface reconstruction is done using a robust and accurate automatic segmentation procedure.
* Details on how to generate the brain surface mesh in BESA MRI can be found in the coregistration quickguide which is available on the BESA homepage: [http://www.besa.de/downloads/quick-guides/ Quick Guides].

'''BrainVoyager'''
* BrainVoyagerQX provides a semiautomatic procedure to generate meshes for the brain surface of the Talairach MRI. Please refer to the BrainVoyager Help to find out how to do this.
* The result of the BrainVoyager procedure is two meshes, one for the left and one for the right hemisphere.
* BESA Research requires a single mesh. Therefore, load first one mesh (''Meshes/Load Mesh..''.), and append the other mesh (''Meshes/Add Mesh...''). Merge these two meshes (''Meshes/Merge'' ''meshes in surface window'') and then save the result (''Meshes/Save Mesh...''). If possible, use the recommended name conventions for the resulting file (file name ends in "'''_TAL_WM.srf"). '''For instance, if the Talairach MRI is named "'''MRI PB_TAL.vmr'''", name the brain surface mesh "'''MRI PB_TAL_WM.srf'''".
* See also the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [http://brainvoyager.com/Downloads.html BrainVoyager Downloads].

== Co-locating Dipoles and MRI Locations ==

=== Co-locating Sources and MRI in the BESA Research Source Module ===

If the alignment procedure using BESA MRI (or BrainVoyager) has been completed then you can load the individual structural MRI in the Source Module by pressing ''''A'''' or using a mouse right click and selecting '''''Display MRI'''''.

Sources in the current model are then overlayed onto the individual MRI.

A double-click at any location in the MRI will define a new source at the corresponding location in the BESA Research head model.

[[Image:MRI Integration (9).gif ‎]]

=== Coregistration with BrainVoyager after Alignment has been Done ===

Alignment between BESA Research and BrainVoyager is only required once for a given BESA Research data set and the corresponding MRI. At a later time, if you want to Co-locate sources between BESA Research and BrainVoyager, perform the following steps in BrainVoyager:
* Load the MRI.
* Load the head surface mesh (''Meshes/Load Mesh..''.).
* Load the Coregistration File (''EEG-MEG BESA/Load Surface Points..''.).

BrainVoyager is now ready for Co-location.

=== Send a Dipole from BESA Research to BrainVoyager ===

First, start BrainVoyager(QX). This can be done from the BESA Research Source Module by pressing the '''BrainVoyager '''button. Note that in the Source Module, the ''Options / Preferences / BrainVoyager'' tab allows to define the path to BrainVoyager.

In BrainVoyager, [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done|set up coregistration]].

In the BESA Research Source Module, highlight the dipole of interest.

In the BESA Research Source Module, click on the '''BrainVoyager''' button.

Program control will automatically switch to BrainVoyager. The head will be cut at the section corresponding to the dipole of interest.

[[Image:MRI Integration (10).gif‎|200px]]

Note that all dipoles in the current model are sent to BrainVoyager. The highlighted dipole (here, the red dipole) determines the plane at which the head will be cut.

Note that the dipoles are visible in both the surface module and in the 2D view:

[[Image:MRI Integration (11).gif|400px]]

=== Define a Dipole in BESA Research at a Location Defined in the MRI ===

First set up coregistration (see chapter [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done|Coregistration with BrainVoyager after Alignment has been Done]]).

In the BrainVoyager 2D MRI view, place the mouse over the point at which you would like to define a dipole. Right click at this point. If this point lies within an fRMI cluster, BrainVoyager will automatically determine its center and use it as a seeding point instead. Press '''Send Seed Point To BESA....'''

[[Image:MRI Integration (12).gif ‎]]

The following Dialog is opened:

[[Image:MRI Integration (13).gif ‎]]

Press '''Send to BESA'''.

The BESA Source Analysis window appears. The new dipole or regional source (depending on the setting in the ‘Options’ dialog in the Source Analysis window is now displayed at the corresponding location. If a dipole is seeded, BESA automatically fits its orientation. For further adjustment of the model, you may need to refit the orientation, e.g. at a certain time range, or in the presence of other sources.

Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [http://brainvoyager.com/Downloads.html BrainVoyager Downloads].

== Reference ==

=== The Coregistration File (*.sfh) ===

This file is used to mediate between BESA Research and BESA MRI (or BrainVoyager(QX)). When it is first written by BESA Research, it contains a list of the digitized head surface points (fiducials, electrodes, other digitized points), e.g.

<source lang="dos">
NrOfPoints: 68
Fid_Nz 0.00000 103.10000 0.00000 3 255 128 255
Fid_T9 -78.40000 0.00000 0.00000 3 255 128 255
Fid_T10 73.00000 0.00000 0.00000 3 255 128 255
Ele_E1 -28.70000 23.90000 122.30000 3 255 0 0
Ele_E2 -80.40000 19.80000 75.90000 3 255 0 0
Ele_E3 -84.00000 37.90000 9.00000 3 255 0 0
Ele_E4 -17.60000 92.90000 89.10000 3 255 0 0

...

Ele_E63 -6.80000 -104.00000 54.40000 3 255 0 0
Ele_E64 -42.80000 -46.90000 115.60000 3 255 0 0
Ele_Cz' -2.10000 2.20000 131.10000 3 255 0 0
</source>

Each line contains a label, the coordinates in the Head Coordinate system, and parameters specifying the size and color of the sensor or head surface point as displayed in BESA MRI (or BrainVoyager).

After aligning the coordinate systems, BESA MRI (or BrainVoyagerQX) appends lines defining the transformation between the BESA Research and the MRI coordinate systems:

<pre>
# Trans-data(in BV-coords): 3 translation, 3 rotation (in grad), 3 scale
37.435 15.811 2.820 0.025 1.938 8.779 1.009 0.973 0.977
Fiducials:
41.7873 148.0180 128.0844
154.7772 169.4783 204.1080
147.0154 168.9746 54.1266
Midpoint (in BV-coords):
128.0000 128.0000 128.0000
Volume: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_acpc.vmr
Surface: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_acpc.srf
AC: 128 128 128
PC: 154 128 128
AP: 58 128 128
PP: 241 129 130
SP: 154 50 128
IP: 128 172 128
RP: 128 128 60
LP: 165 128 198
</pre>

Note: Older versions of BrainVoyager.exe do not append the lines starting with "Volume". In addition, the Talairach coordinates (starting at "AC: ...") are not appended if they were not loaded in BrainVoyagerQX.

Finally, when the Coregistration Dialog in BESA Research has found the Talairach MRI and surface meshes, and you press the OK button, BESA Research appends the additional file names:

<pre>
TalVolume: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_tal.vmr
TalSurface: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_tal.srf
TalBrainSurface: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_tal_wm.srf
</pre>

BESA MRI already inserts the correct file names into the coregistration file when doing the coregistration. When also an EEG or MEG FEM head model is generated then additional lines are appended to the coregistration file containing the file names of the generated FEM data files.

=== MRI Requirements for Good Coregistration ===

We recommend a high quality T1-weighted anatomical image with 1 mm³ voxels (e.g. 256 x 256 saggital scan with 1 mm spacing).

In order to define the surface mesh, a clear contrast between the head surface and the outside of the head (T1-weighting) is required. Noise and measurement artifacts can influence the representation of the scalp surface. When doing the coregistration in BrainVoyager improvements in noisy images often can be achieved by cleaning up the image after first reading it using the tools provided by BrainVoyager.

For coregistration with head surface points, it is useful to include the whole head in the image, including nose and ears. If surface points on the nose are included with the EEG/MEG data set, these points help to stabilize the fit of head surface points to the surface mesh.

=== EEG/MEG Data Requirements for Good Coregistration ===

We recommend several (30 or more) digitized head surface points in addition to the fiducials, including points on the nose (nose tip and sides). These points may include electrodes. In the case of electrodes, it is important to measure the distance from the scalp to the digitization point, i.e. the electrode thickness.

[[Category:Research Manual]]

{{BESAManualNav}}

Integration with MRI and fMRI

2021-11-25T13:10:20Z

Dominik:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher BESA MRI
|version = BESA Research 6.1 or higher BESA MRI 2.0 or higher
}}



== Introduction ==

Both for developing and evaluating dipole source models of EEG or MEG activity, it is useful to have access to structural MRI or fMRI data.

The BESA MRI software allows to preprocess structural MRI data so that the individual anatomical information contained in the MRI can be utilized in BESA Research.

BESA MRI makes it possible ...

*... to align the EEG and MEG sensors with the structural MRI data.

*... to read and display the aligned, individual Talairach structural MRIs directly in the BESA Research Source Analysis module. In this way, source analysis results can be presented on top of the aligned MRIs, which allows us to evaluate the anatomical regions to which the reconstructed sources may correspond.

*... to use an individual, realistically shaped FEM or BEM head model for source analysis in BESA Research. FEM and BEM head models take into account the individual volume conduction properties of the subject's head derived from the structural MRI data. This allows for more accurate source analysis (Yvert 1997, Lanfer 2012).

*... overlay source analysis results obtained in BESA Research with fMRI data.

*... use fMRI BOLD regions or MRI structures to initialize dipole models.

*... use fMRI image to constrain EEG/MEG source localization

*... send discrete source analysis results from BESA Research to BESA MRI to visualize them in both Talairach and subject-specific (ACPC) coordinates.

The chapters below describe the steps necessary to integrate the MRI and fMRI data with BESA Research.

It is also possible to use BESA Research with BrainVoyager. Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website:
[https://www.brainvoyager.com/downloads/downloads.html BrainVoyager Downloads].

'''Aligning Coordinate Systems'''

* For a given BESA data set, the electrode and other head surface points need to be aligned to the MRI coordinates.
* The basic steps necessary to align the EEG electrode locations, the MEG sensors and the MRI are described in Section [[Integration_with_MRI_and_fMRI#Setting_Up_Coregistration_Using_BrainVoyager|How Coregistration is done]].
* Detailed instructions on how to align EEG / MEG and MRI data using BESA MRI can be found in the coregistration quick guide which is available on the BESA homepage ([http://www.besa.de/downloads/quick-guides/ Quick Guides]).
* Detailed instructions on how to align EEG / MEG and MRI data using BrainVoyager are described in Section [[Integration_with_MRI_and_fMRI#Setting_Up_Coregistration_Using_BrainVoyager|How To set up Coregistration between BESA and BrainVoyager]].
* In BESA Research, all necessary settings with regard to the alignment are made in the [[Integration_with_MRI_and_fMRI#The_Coregistration_Dialog|Coregistration Dialog]].
* Requirements with respect to the MRI data for a good coregistration can be found in Section [[#MRI_Requirements_for_Good_Coregistration|MRI Requirements for Good Coregistration]].
* Requirements with respect to EEG and MEG data for a good coregistration can be found in Section [[#EEG/MEG Data Requirements for Good Coregistration|EEG/MEG Data Requirements for Good Coregistration]].

'''Generating an individual, realistically shaped FEM head model'''

* The generation of a FEM head model that can be used in BESA Research is done in BESA MRI as an additional step following the EEG / MEG to MRI coregistration.
* Detailed instructions on how to generate the FEM head model can be found in the coregistration quick guide which is available on the BESA homepage ([http://www.besa.de/downloads/quick-guides/ Quick Guides]).

'''Co-locating dipoles and MRI locations'''

* After aligning the EEG / MEG and the MRI data it is possible to co-locate dipoles and MRI locations. This means, it is possible to visualize the dipoles and to specify the dipole parameters in the MRI coordinate system.
* [[Integration_with_MRI_and_fMRI#Co-locating_Sources_and_MRI_in_the_BESA_Research_Source_Module|How to Co-locate sources and MRI in the BESA Research Source Module]] describes how in the BESA Research Source Analysis module dipoles can directly be visualized in the space of the individual MRI.
* [[Integration_with_MRI_and_fMRI#Send_a_Dipole_from_BESA_Research_to_BrainVoyager|How to Send a Dipole from BESA Research to BrainVoyager]] describes how to send a source model from BESA Research to BrainVoyager for further inspection.

'''References'''

Lanfer, B., I. Paul-Jordanov, M. Scherg, and C. H. Wolters. “Influence of Interior Cerebrospinal Fluid Compartments on EEG Source Analysis.” In Proceedings BMT 2012, Vol. 57. Jena: De Gruyter, 2012. doi:10.1515/bmt-2012-4020.

Yvert, B., O. Bertrand, M. Thévenet, J. F. Echallier, and J. Pernier. “A Systematic Evaluation of the Spherical Model Accuracy in EEG Dipole Localization.” Electroencephalography and Clinical Neurophysiology 102, no. 5 (May 1997): 452–59. doi:16/S0921-884X(97)96611-X.

== How Coregistration is done ==

This section outlines the basic steps to coregister the EEG / MEG data to an individual MRI. These steps are necessary to load an individual MRI into BESA Research.

'''What happens:'''

* EEG / MEG sensor locations and the MRI data are defined in different coordinate systems. Setting up coregistration is the process of aligning the two coordinate systems.
* BESA Research uses the ''Coregistration Dialog'' to coordinate the alignment procedure.
* Alignment is done with the ''AC-PC-transformed MRI''.
* BESA Research displays the ''Talairach-transformed MRI'' in the source analysis module.
* A coregistration file (with the extension "'''.sfh'''") is used to mediate between BESA Research and BESA MRI (or BrainVoyagerQX):
* BESA Research writes the coregistration file which contains the coordinates of head surface points (fiducials, electrodes, other digitized surface points).
* The coordinates are read into BESA MRI (or BrainVoyager), and aligned with the AC-PC-transformed MRI. The alignment information is then appended to the ''coregistration file''. The names of the AC-PC MRI ('''<nowiki>*.vmr</nowiki>''') and the surface mesh ('''<nowiki>*.srf</nowiki>'''), and, if available, the Talairach transformation, are also appended.
* BESA Research reads the coregistration file and appends the name of the Talairach-transformed MRI and head surface. If a brain surface has been created, this is also appended.
* Subsequently, BESA Research reads the coregistration file automatically when loading the data file.
* In the BESA Research source module, the individual MRI is displayed instead of the standard MRI. Talairach coordinates of dipoles are the "real" Talairach coordinates as defined, e.g., in BrainVoyager.

'''The steps you have to take (once for each data set):'''

* From the BESA Research ''Coregistration Dialog'', write a coregistration file. Switch to BESA MRI (or BrainVoyagerQX).
* If BESA MRI is used follow the steps in the coregistration quickguide which is available on the BESA homepage ([http://www.besa.de/downloads/quick-guides/ Quick Guides]).
* If BrainVoyager is used follow the steps in Section “''How to set up coregistration between BESA and BrainVoyager”.''
* Back in BESA Research, reload the altered '''coregistration file'''. When using BESA MRI the file names of the generated surface and volume data files will be automatically filled in. When using BrainVoyager file names are only filled in automatically when the files are named according to the file naming conventions. Otherwise, file names have to be set manually.
* The coregistration file is now associated with the data file in the BESA Research database and will be used automatically the next time the file is opened in BESA Research. If the database entry is cleared, and the data are reloaded, you must make sure the coregistration file is also loaded (either using the ''Coregistration Dialog'' or the ''Channel and digitized head surface point information Dialog'').

== Alignment of BESA and MRICoordinate Systems ==

=== The Coregistration Dialog ===

The dialog is opened either from the ''Channel and digitized head surface point information'' ('''Ctrl-L''') ''dialog ''by pressing the '''Edit/Coreg''' button, or from the main menu ("'''File/MRI Coregistration...'''").

'''Note:''' If the coregistration dialog is invoked from an EEG data set in which no digitized electrode coordinates are available (i.e. standard electrode positions located on a sphere are assumed), BESA Research presents a warning message, saying that for MRI coregistration realistic electrode coordinates produce better results. BESA Research has a list of such realistic standard coordinates (i.e. located on a pre-defined standard head surface) for various electrodes available in file '''Default.sfp''', which is located in the Standard Electrode folder. If all electrodes in the dataset are listed in this file, a dialog window suggests to apply this file to the current data set, i.e. to switch from standard sphere coordinates to the standard realistic electrode coordinates in file '''Default.sfp'''. If the suggestion is accepted, '''default.sfp''' is assigned to the dataset (see Channel and digitized head surface point information ('''Ctrl-L''') dialog).

'''The Dialog:'''

[[Image:MRI Integration (1).gif ‎]]

* Press the '''Select MRI prog''' button to select your preferred MRI program. The current choice is between ''BESA MRI.exe'' and ''BrainVoyagerQX.exe''. The path to the MRI program is saved (in ''System\BESA.set'') and will be remembered by BESA Research. The top right hand button (now showing '''BESA MRI''') shows the current selection.
* Press the '''BESA MRI''' button to start the process of aligning the BESA Research and MRI coordinate systems. If no coregistration ('''<nowiki>*.sfh</nowiki>''') file is defined in the dialog (empty ''Surface coregistration file edit box''), BESA Research will first prompt for a file name. We recommend saving this file to the folder where the MRIs are kept. The MRI program will then be started. When you return to the ''Coregistration Dialog'', BESA Research checks if the ''Coregistration File'' has changed. If so, the dialog is updated with the new information.
* Press the top '''Browse... '''button to select a preexisting ''Coregistration File''.
* The entries in the edit boxes below show the files that will be used in the BESA Research Source Analysis module when the individual MRI is loaded. When using BESA MRI the file names will be automatically filled in. If you are using BrainVoagerQX and you are following our (and the BrainVoyagerQX) recommended naming conventions for files, and the files exist, then the names will be filled in automatically after you have completed the alignment procedure in BrainVoyagerQX. Otherwise you may have to browse for the files.
* Below the edit boxes the FEM field states whether all necessary information for the individual FEM head model were found in the coregistration file. If the field says ''Individual FEM for EEG'' ''defined!'' then all necessary data was found and the individual FEM EEG head model can be used in the BESA Research Source Analysis module. A similar message indicates whether the FEM MEG head model is available.
* Note that the MRI and the surfaces are Talairach-transformed! Alignment between BESA Research and the individual MRI is done with the MRI transformed to the AC-PC coordinate system, but the BESA Research Source Analysis module uses the Talairach-transformed image data and surfaces.

<div style="color:#ff0000;"></div>

=== Setting Up Coregistration Using BrainVoyager ===

It is assumed that you know how to load an MRI as a 3D data set into BrainVoyagerQX, and how to clean the image so that regions outside the head are black. We also assume knowledge of how to create AC-PC-aligned and Talairach-transformed MRIs.

Perform the following steps:

* BESA Research. Start the ''Coregistration Dialog''. Export the Coregistration File (head surface points) from your data by pressing the '''BrainVoyagerQX''' button in the dialog. Save the file to the directory where your MRI is located. BrainVoyagerQX is started.
* BrainVoyagerQX. Load the MRI corresponding to the EEG/MEG data. For optimal performance, the MRI should be cleaned so that regions outside the head are black. Prepare an AC-PC-transformed MRI and a Talairach MRI. For each, generate a surface mesh. Save these files following our recommended naming conventions (see chapter [[Integration_with_MRI_and_fMRI#MRI_file_Name_Conventions|MRI File Name Conventions]]). Save the Talairach coordinate file ('''<nowiki>*.tal</nowiki>'''). If these steps have already been performed, load the ACPC MRI and load the ACPC mesh. If you want to generate a brain surface mesh, see chapter [[Integration_with_MRI_and_fMRI#How_to_Generate_a_Brain_Surface_Mesh|How to Generate a Brain Surface Mesh]].
* BrainVoyagerQX. Load the Coregistration File (''EEG-MEG BESA/Load Surface Points''). The points will be displayed, but they are not aligned to the head:

[[Image:MRI Integration (2).gif ‎]]

* BrainVoyagerQX. Define fiducial points on the head surface. Right click on the 3D head display and select the ''Fiducials Dialog'' in the drop-down menu:

[[Image:MRI Integration (3).gif ‎]] [[Image:MRI Integration (4).gif ‎]]

* BrainVoyagerQX. Rotate the head (by holding the '''Shift '''button down and clicking and dragging with the mouse) so that the Nasion is clearly visible. Move the mouse to the Nasion, and press '''Ctrl+Left Click'''. The coordinates of the Nasion are inserted into the dialog. Repeat for the left preauricular point, and then for the right preauricular point.

[[Image:MRI Integration (5).gif ‎]]

Note: if you have defined your fiducials differently in your BESA Research data (e.g. ear holes), click on the corresponding points in the MRI. If you have additional head surface points (step 8), accuracy in pinpointing the fiducials is not critical.

* BrainVoyagerQX. In the Fiducials Dialog, press the '''Fit fiducials''' button. The head surface points are now more or less aligned to the head.

[[Image:MRI Integration (6).gif ‎]]

* BrainVoyagerQX. Now select '''''EEG-MEG BESA/Fit Surface Points...'''''

[[Image:MRI Integration (7).gif ‎]]

If you do not see the right half of the dialog, press the '''Advanced >>''' button.

* Specify the distances of the digitization points from the skin. In the illustration above, the digitization points for electrodes are estimated to be 8 mm from the surface of the head. For the purpose of accurate alignment, the distance of digitization points from skin section of the dialog needs to be filled in correctly. We recommend that "Restrain solution around fiducials" is checked, and a reasonable limit (here 3 mm) of the restraint is defined. Then press '''OK'''.

[[Image:MRI Integration (8).gif ‎]]

BrainVoyager fits the points to the head, stretching x, y, and z coordinates to obtain a better fit than before.

Note: The fit performed during this step accounts for scaling inequalities between the x, y, and z axes in the MRI. Coregistration gains in accuracy over the use of fiducials alone a) because more head surface points are used, and b) because the scaling inequalities are accounted for.

* Alignment is now completed. If you only want to display the structural MRI in the BESA Source Module, you can return to the BESA Coregistration Dialog.
* BESA Research. When you switch back to the Coregistration Dialog, BESA Research will try to fill in the names of the Talairach MRI and surface meshes. If the names are not filled in, use the '''Browse...''' buttons to select the MRI and surface meshes. Press '''OK''' to save the Coregistration File. Alignment is completed!

The alignment steps need only be performed once for a given MRI and EEG/MEG data set. Otherwise, after starting BrainVoyager, just load the MRI, the surface mesh, and the surface points (see [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done |How to Set Up Coregistration with BrainVoyager after Alignment has been Done]]). Now the following actions are possible: see chapters

* [[Integration_with_MRI_and_fMRI#Co-locating_Sources_and_MRI_in_the_BESA_Research_Source_Module|How to Co-Locate Sources and MRI in the BESA Research Source Module]]
* [[Integration_with_MRI_and_fMRI#Send_a_Dipole_from_BESA_Research_to_BrainVoyager|How to Send a Dipole from BESA Research to BrainVoyager]]
* [[Integration_with_MRI_and_fMRI#Define_a_Dipole_in_BESA_Research_at_a_Location_Defined_in_the_MRI|How to Define a Dipole in BESA Research at a Location Defined in the MRI]]

=== MRI file Name Conventions ===

If you follow the naming conventions for file names as described here, BESA Research detects the file names it requires, and the ''Coregistration Dialog'' is filled in automatically.

Please note that BESA MRI automatically uses these naming conventions for the generated files.

* '''The AC-PC MRI file name''' should end with "'''_ACPC.vmr'''", and the corresponding surface mesh name should end with "'''_ACPC.srf'''". After alignment, BrainVoyagerQX writes these names to the Coregistration File.
* '''The Talairach MRI file name '''should end with "'''_TAL.vmr'''", and the corresponding surface mesh name should end with "'''_TAL.srf'''". If defined, the brain surface mesh should end with "'''_TAL_WM.srf'''" ('''WM''' = '''w'''hite '''m'''atter).
* '''How BESA Research finds the Talairach files.''' When BESA Research rereads the Coregistration File after alignment of the coordinate systems, it finds the ACPC file names and defines the corresponding TAL file names. If these files exist, the names are entered into the Coregistration Dialog. For instance, if the Coregistration File contains the name "'''MRI''' '''PB_ACPC.vmr'''", BESA Research will look for the files "'''MRI_PB_TAL.vmr'''", "'''MRI_PB_TAL.srf'''", and "'''MRI_PB_TAL_WM.srf'''". If these files exist, they are entered into the dialog.
* '''Older BrainVoyager version.''' If you use BrainVoyager.exe to align coordinate systems, the file names are not saved with the Coregistration File. In this case, browse for the Talairach or the ACPC MRI from the Coregistration Dialog. BESA Research will use the rules as described above to insert the correct file names into the dialog.
* '''Missing Talairach coordinates.''' If, after aligning coordinate systems, the Talairach coordinates are missing from the Coregistration File (you forgot to load the Talairach coordinates in BrainVoyagerQX, or you used BrainVoyager.exe), BESA Research will look for a file ending with "'''_ACPC.tal'''", and read the coordinates from this file. You can also browse for a '''<nowiki>*.tal</nowiki>''' file in the Coregistration Dialog. For instance, if the MRI file is named "'''MRI_PB_ACPC.vmr'''" or "'''MR_''' '''PB_TAL.vmr'''", BESA Research will look for "'''MRI_PB_ACPC.tal'''" to find the Talairach coordinates.
* '''File names in the Coregistration File are saved relative to the Coregistration File location, if they are in the same folder.''' If the MRIs are in the same folder as the Coregistration File they will be recorded as ".\filename" (e.g. "'''.\MRI PB_tal.vmr'''"). This means that you can copy the Coregistration File together with the MRIs and meshes to a different folder, and BESA Research will be able to locate the files when the Coregistration File is opened. If the MRIs are saved in a different folder from the Coregistration File, the absolute paths are saved in the file. If the files are moved to new locations, you will have to restart the Coregistration Dialog and redefine the file locations.

=== How to Generate a Brain Surface Mesh ===

BESA Research is able to compute surface images, such as (Cortical LORETA, Cortical CLARA, Minimum Norm) using an individual cortex surface as the source space. A suitable cortex surface for this purpose can be effortlessly created using BESA MRI. Alternatively, BrainVoyager can be used for the creation of the brain surface mesh.

'''BESA MRI'''
* The brain surface generation is performed as one work step of the BESA MRI segmentation workflow.
* The cortex surface reconstruction is done using a robust and accurate automatic segmentation procedure.
* Details on how to generate the brain surface mesh in BESA MRI can be found in the coregistration quickguide which is available on the BESA homepage: [http://www.besa.de/downloads/quick-guides/ Quick Guides].

'''BrainVoyager'''
* BrainVoyagerQX provides a semiautomatic procedure to generate meshes for the brain surface of the Talairach MRI. Please refer to the BrainVoyager Help to find out how to do this.
* The result of the BrainVoyager procedure is two meshes, one for the left and one for the right hemisphere.
* BESA Research requires a single mesh. Therefore, load first one mesh (''Meshes/Load Mesh..''.), and append the other mesh (''Meshes/Add Mesh...''). Merge these two meshes (''Meshes/Merge'' ''meshes in surface window'') and then save the result (''Meshes/Save Mesh...''). If possible, use the recommended name conventions for the resulting file (file name ends in "'''_TAL_WM.srf"). '''For instance, if the Talairach MRI is named "'''MRI PB_TAL.vmr'''", name the brain surface mesh "'''MRI PB_TAL_WM.srf'''".
* See also the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [http://brainvoyager.com/Downloads.html BrainVoyager Downloads].

== Co-locating Dipoles and MRI Locations ==

=== Co-locating Sources and MRI in the BESA Research Source Module ===

If the alignment procedure using BESA MRI (or BrainVoyager) has been completed then you can load the individual structural MRI in the Source Module by pressing ''''A'''' or using a mouse right click and selecting '''''Display MRI'''''.

Sources in the current model are then overlayed onto the individual MRI.

A double-click at any location in the MRI will define a new source at the corresponding location in the BESA Research head model.

[[Image:MRI Integration (9).gif ‎]]

=== Coregistration with BrainVoyager after Alignment has been Done ===

Alignment between BESA Research and BrainVoyager is only required once for a given BESA Research data set and the corresponding MRI. At a later time, if you want to Co-locate sources between BESA Research and BrainVoyager, perform the following steps in BrainVoyager:
* Load the MRI.
* Load the head surface mesh (''Meshes/Load Mesh..''.).
* Load the Coregistration File (''EEG-MEG BESA/Load Surface Points..''.).

BrainVoyager is now ready for Co-location.

=== Send a Dipole from BESA Research to BrainVoyager ===

First, start BrainVoyager(QX). This can be done from the BESA Research Source Module by pressing the '''BrainVoyager '''button. Note that in the Source Module, the ''Options / Preferences / BrainVoyager'' tab allows to define the path to BrainVoyager.

In BrainVoyager, [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done|set up coregistration]].

In the BESA Research Source Module, highlight the dipole of interest.

In the BESA Research Source Module, click on the '''BrainVoyager''' button.

Program control will automatically switch to BrainVoyager. The head will be cut at the section corresponding to the dipole of interest.

[[Image:MRI Integration (10).gif‎|200px]]

Note that all dipoles in the current model are sent to BrainVoyager. The highlighted dipole (here, the red dipole) determines the plane at which the head will be cut.

Note that the dipoles are visible in both the surface module and in the 2D view:

[[Image:MRI Integration (11).gif|400px]]

=== Define a Dipole in BESA Research at a Location Defined in the MRI ===

First set up coregistration (see chapter [[Integration_with_MRI_and_fMRI#Coregistration_with_BrainVoyager_after_Alignment_has_been_Done|Coregistration with BrainVoyager after Alignment has been Done]]).

In the BrainVoyager 2D MRI view, place the mouse over the point at which you would like to define a dipole. Right click at this point. If this point lies within an fRMI cluster, BrainVoyager will automatically determine its center and use it as a seeding point instead. Press '''Send Seed Point To BESA....'''

[[Image:MRI Integration (12).gif ‎]]

The following Dialog is opened:

[[Image:MRI Integration (13).gif ‎]]

Press '''Send to BESA'''.

The BESA Source Analysis window appears. The new dipole or regional source (depending on the setting in the ‘Options’ dialog in the Source Analysis window is now displayed at the corresponding location. If a dipole is seeded, BESA automatically fits its orientation. For further adjustment of the model, you may need to refit the orientation, e.g. at a certain time range, or in the presence of other sources.

Detailed instructions on (f)MRI import and processing in Brain Voyager is provided by the '''BrainVoyager Getting Started Guide''' that can be downloaded from the Brain Innovation website: [http://brainvoyager.com/Downloads.html BrainVoyager Downloads].

== Reference ==

=== The Coregistration File (*.sfh) ===

This file is used to mediate between BESA Research and BESA MRI (or BrainVoyager(QX)). When it is first written by BESA Research, it contains a list of the digitized head surface points (fiducials, electrodes, other digitized points), e.g.

<source lang="dos">
NrOfPoints: 68
Fid_Nz 0.00000 103.10000 0.00000 3 255 128 255
Fid_T9 -78.40000 0.00000 0.00000 3 255 128 255
Fid_T10 73.00000 0.00000 0.00000 3 255 128 255
Ele_E1 -28.70000 23.90000 122.30000 3 255 0 0
Ele_E2 -80.40000 19.80000 75.90000 3 255 0 0
Ele_E3 -84.00000 37.90000 9.00000 3 255 0 0
Ele_E4 -17.60000 92.90000 89.10000 3 255 0 0

...

Ele_E63 -6.80000 -104.00000 54.40000 3 255 0 0
Ele_E64 -42.80000 -46.90000 115.60000 3 255 0 0
Ele_Cz' -2.10000 2.20000 131.10000 3 255 0 0
</source>

Each line contains a label, the coordinates in the Head Coordinate system, and parameters specifying the size and color of the sensor or head surface point as displayed in BESA MRI (or BrainVoyager).

After aligning the coordinate systems, BESA MRI (or BrainVoyagerQX) appends lines defining the transformation between the BESA Research and the MRI coordinate systems:

<pre>
# Trans-data(in BV-coords): 3 translation, 3 rotation (in grad), 3 scale
37.435 15.811 2.820 0.025 1.938 8.779 1.009 0.973 0.977
Fiducials:
41.7873 148.0180 128.0844
154.7772 169.4783 204.1080
147.0154 168.9746 54.1266
Midpoint (in BV-coords):
128.0000 128.0000 128.0000
Volume: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_acpc.vmr
Surface: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_acpc.srf
AC: 128 128 128
PC: 154 128 128
AP: 58 128 128
PP: 241 129 130
SP: 154 50 128
IP: 128 172 128
RP: 128 128 60
LP: 165 128 198
</pre>

Note: Older versions of BrainVoyager.exe do not append the lines starting with "Volume". In addition, the Talairach coordinates (starting at "AC: ...") are not appended if they were not loaded in BrainVoyagerQX.

Finally, when the Coregistration Dialog in BESA Research has found the Talairach MRI and surface meshes, and you press the OK button, BESA Research appends the additional file names:

<pre>
TalVolume: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_tal.vmr
TalSurface: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_tal.srf
TalBrainSurface: C:\BESA\Examples\ERP P300-Auditory\MRI_PB_tal_wm.srf
</pre>

BESA MRI already inserts the correct file names into the coregistration file when doing the coregistration. When also an EEG or MEG FEM head model is generated then additional lines are appended to the coregistration file containing the file names of the generated FEM data files.

=== MRI Requirements for Good Coregistration ===

We recommend a high quality T1-weighted anatomical image with 1 mm³ voxels (e.g. 256 x 256 saggital scan with 1 mm spacing).

In order to define the surface mesh, a clear contrast between the head surface and the outside of the head (T1-weighting) is required. Noise and measurement artifacts can influence the representation of the scalp surface. When doing the coregistration in BrainVoyager improvements in noisy images often can be achieved by cleaning up the image after first reading it using the tools provided by BrainVoyager.

For coregistration with head surface points, it is useful to include the whole head in the image, including nose and ears. If surface points on the nose are included with the EEG/MEG data set, these points help to stabilize the fit of head surface points to the surface mesh.

=== EEG/MEG Data Requirements for Good Coregistration ===

We recommend several (30 or more) digitized head surface points in addition to the fiducials, including points on the nose (nose tip and sides). These points may include electrodes. In the case of electrodes, it is important to measure the distance from the scalp to the digitization point, i.e. the electrode thickness.

[[Category:Research Manual]]

{{BESAManualNav}}

Source Analysis Functions of the Window

2021-11-25T13:02:00Z

Dominik:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = BESA Research 6.1 or higher
}}

== Overview ==

The Source Analysis module window is subdivided into six main parts (boxes) which will be explained briefly in the following sections:
* The Channel Box (left)
* The Variance Box (top center)
* The Source Box (bottom center)
* The Parameter Box (top right)
* The Head Box (mid right)
* The 3D Window (bottom right)

Note that the 3D window will not normally appear automatically (unless specified in the '''Options / Preferences''' menu), and the head box will take up more space if the 3D window is not displayed.

[[Image:Functions SAwindow (1).gif ]]


The '''title bar''' contains information about the data file, the filename, the condition name, the filter settings, and the selected time interval.

Most of the functions and commands can be chosen from the main '''menu bar''' below the title bar. However, all important commands are also available via a right mouse click. Whenever you right-click, a context-sensitive popup menu will appear containing the available commands.

A detailed description of the commands of the '''menu bar''' and the different popup menus is given in the online help ''Reference ''chapter.

At the bottom, you will notice the '''status bar''', which gives information about the current mouse position (latency or 3D position) and the current cursor location or the fit interval(s). (See the section on the '''status bar''' in the online help ''Reference ''chapter).

The individual size of the boxes can be modified: Try placing the mouse over the vertical double line that separates the source box and the head box. The horizontal arrow that appears indicates that you can move this separator by dragging with the left mouse button.

The same is possible for the horizontal double line bounding the variance box.

== Channel Box ==

The channel box normally shows the signals at each channel. The display depends on the state of the push buttons at the top of the channel box.

The figure below shows an example with the display of the measured data waveforms (violet) and the residual waveforms (red) at each channel. The channel labels are displayed to the left of each waveform.

An overplot of all waveforms is displayed above the single waveforms (labeled ''All'').

[[Image:Functions SAwindow (2).gif]]


Below the first row of buttons, there is a '''description of the current condition''' containing the condition name, the filter settings and the condition epoch. Below the condition epoch, the baseline of the current condition is displayed as horizontal black/red line.

At the bottom, you see the''' figure legend '''describing the used colors and the number of displayed channels (or PCA components).

The '''Channel buttons''' at the top of the channels box specify which waveforms are displayed.

* The''' Data''' button toggles the display of the data (measured signals) of the visible channels (violet waveforms). If you double click on this button the''' Model '''and''' Residual''' buttons are released and the channels are re-sorted by the amplitude of the measured data.
* Press the '''Model''' button to toggle the display of the modeled data (blue waveforms). The modeled data are calculated from the waveforms of the active sources in the current solution using the currently chosen head model. (The source waveforms are displayed in the source box, the head model is set and displayed in the parameter box.) Pressing the '''Model '''button toggles between the display of all active sources (button is labeled '''M-A''') and the display of the model waveforms which result from the contributions of all sources whose Fit/No fit button is pressed (button is labeled M-F). Note that the '''Residual''' button is released if the '''Model''' button is pressed without holding the '''Control-key'''.
* Press the''' Residual''' button to toggle the residual (unexplained) signal (red waveforms), i.e. the difference between measured and modeled data. If you double click on this button the '''Data''' and '''Model''' buttons are released and the channels are re-sorted by the amplitude of the residual. Note that the''' Model''' button is released if the''' Residual''' button is pressed without holding the '''Control-key.'''
* The '''Sort''' button (fourth button from the left) changes the ordering of the channels. Pushing this button switches between original order (button is labeled '''Order''' or '''Ord'''.), sorting by the amplitude of the measured data (||Data|| or ||D||), and sorting by the amplitude of the residual (||Res.|| or ||R||). In practice, by using one of the sorting modes ||Data|| or ||Residual||, you will only have to display the first few channels during the fitting procedure, since the channels with the largest signals are shown at the top.
* Use the '''P.C.A.''' button to start a Principal Components Analysis (PCA) over the marked fit interval(s) (if no fit interval is set the PCA is computed over the whole epoch). The percentage variance accounted for by each component is shown at the left of each waveform. When the PCA is displayed, data, model, and residual waveforms are not visible. Note that if the '''Residual '''button is down and the '''Data''' button is up, the PCA is computed for the residual data and not the measured data.
* The button at the far right is the '''EEG/MEG/MEEG''' button. Pushing this button toggles between the data sets (EEG, MEG and MEEG) of the current condition, if combined EEG and MEG have been recorded. The label of the button shows which data set is currently displayed.
For combined recordings, it is possible to combine EEG and MEG for fitting. In this case, each channel is normalized by the signal in the defined baseline interval. Changing the baseline interval leads to a re-computation of data in this case. In order to use MEEG, the head models of EEG and MEG need to match to ensure a common source space (e.g. spherical head models for both, or individual FEM / BEM for both). Adjust the head models individually for the EEG and MEG modes first before entering MEEG mode.

At the top left below the''' Data''' button, the '''Switch Condition''' buttons (labeled with two arrows) enable fast switching between different conditions. They are enabled only if at least two conditions have been loaded.

Below the '''Switch Condition''' buttons, the '''Toggle Electrode Configuration''' button toggles between using the original channels (button is labeled '''Org''') or using an interpolated montage of 81 electrodes at standard locations (button is labeled '''Std'''). This montage allows comparison of different subjects at standard electrode locations. Note: If MEG channels are displayed this button is not available.

The channel box is bounded at the right by three scroll bars. Use the topmost one to change the number of displayed channels. The scroll bar below ('''select displayed channels''') can be used to scroll through the channels. The bottom one, consisting only of two arrows, changes the amplitude scaling of the displayed signals ('''scale waveforms''').

The '''MAG''' and '''GRD''' buttons at the bottom of the channel box appear only if an MEG data set containing both magnetometer and gradiometer sensors is displayed, or if MEEG mode is active. The buttons are used to toggle the display of the magnetometer and gradiometer channels. In case of the '''MEEG''' mode, '''EEG''' and either of '''MAG''' and '''GRD''' buttons (or both) are displayed. Combination of any MEG mode with the EEG data can then be toggled in that way.

In the figure above you see one '''fit interval''', shown in a darker color. The fit interval is used for fitting, computing the PCA, and more.

'''Using the Mouse'''

In the channel box, it is possible to set the cursor or a fit interval with the left mouse button. If you click on the text in the top left corner, you may change the condition name. By clicking on the baseline, a new baseline interval can be specified.

If you click the right mouse button somewhere in the channel box, the '''Channel Box popup menu''' appears with commands specific to this box.

== Variance Box ==

The variance box shows the global field power (blue) and the residual variance (red) in logarithmic scaling, relative to the maximum global field power.
* '''The global field power''': the sum of squares of the activity over all channels of the current data set
* '''The residual variance''': the sum of squares of the unexplained signal

Note that the global field power is scaled from bottom to top, whereas the residual variance is scaled from top to bottom. The corresponding waveform scales at the left of the variance box are given in percent.

[[Image:Functions SAwindow (3).gif]]


At the top left, the '''residual variance''' (RV) over all samples inside the fit interval(s) is displayed (labeled '''R.V'''.). Below, the minimum residual variance inside the fit intervals (labeled '''Best''') is shown. If no fit interval is selected, values for the whole epoch are given. If a cursor is set, the RV over the whole epoch and the value of the RV at the cursor sample are displayed (labeled '''Curs'''.).

At the top right, second row, you see the current value of the '''regularization constant''', a parameter used to reduce the interaction between sources. (You can set the regularization constant with the '''Regularization''' '''Constant: X%''' menu entry in the '''Options''' menu or by clicking on the current value.)

The '''Fit Criterion buttons''' at the top of the variance box toggle the corresponding fit criteria on and off. Starting from the left the buttons represent the residual variance criterion, the energy criterion, the minimum distance criterion, and the residual variance - q value (S/N) criterion. You will find additional information in the section '''Fit Criterion Buttons''' in the online help ''Reference'' chapter.

'''Using the Mouse'''

In the variance box, it is possible to set the cursor or a fit interval with the left mouse button. If you click on the regularization constant ('''RC'''), you may set a new value.

If you click the right mouse button somewhere in the variance box, the '''Variance Box popup menu''' appears with commands specific to this box.

== Source Box ==

The source box shows the source waveforms of the current solution. The source waveforms are computed over the whole epoch of the current data set using the currently chosen head model. (The head model is set and displayed in the parameter box.) If no solution is available the source box is empty.

A single dipole or a spatial component has one source waveform, a regional source has three waveforms for EEG and two for MEG (one waveform for each component). A spatial component is labeled SC just below its waveform.

[[Image:Functions SAwindow (4).gif]]

(Click on the region of interest to view a description)

At the top of the source box you will find the following buttons:

* The '''All on''' button activates or deactivates all sources (switches all sources on or off). Spatial components whose principal vector does not match with the current data set cannot be activated.
* The '''All fit''' button enables all active sources (not spatial components) for fitting.
* The''' Start fit '''button fits the enabled sources within the specified fit interval(s). If no fit interval is set the sources the whole epoch is used for fitting, if a cursor is set they are fitted only at the cursor sample. Another way to start fitting is given by the ''Fit Enabled Sources''... entry in the standard popup menu.
* The '''Image selection button''' button allows for a quick computation of a 3D image. The type of the image to be computed is shown in the button label. By default, this is the previously computed 3D image. For details on the available image types in BESA Research, please refer to chapter 3D imaging. When you click on this button while keeping CTRL button pressed the new computation will be performed applying weighting based on current image. When you click on this button while keeping SHIFT button pressed the computation will be performed from scratch (leadfields will be re initialized)

* The '''BrainVoyager '''button will start the BrainVoyager program. If the BrainVoyager path has not been set correctly the BrainVoyager tab of the ''Preferences ''dialog box is displayed to allow you to set the valid path. If the BrainVoyager program is already running the current solution is sent to BrainVoyager for display in the structural MRT image (c.f. ''Integration with MRI/fMRI'').

Each source waveform has two push buttons assigned to it:

* The '''On/Off''' buttons to the left of the source waveforms activate or deactivate the associated sources. Spatial components whose principal vector does not match with the current data set cannot be activated. If a source is inactive, it does not contribute to the model.
* The '''Fit/No fit '''buttons below the '''On/Off''' buttons enable or disable the associated source for fitting. If a source is selected, it is enabled for fitting automatically. On the other hand, a source is automatically selected if you push the corresponding '''Fit/No fit''' button. Note that spatial components have no '''Fit/No fit''' button since they cannot be enabled for fitting. You can enable several sources for fitting by keeping the '''Control-key''' on your keyboard pressed and pushing the '''Fit/No fit''' buttons of the sources you would like to fit simultaneously. If the model waveforms of fit enabled sources are displayed in the channel box (the '''Model''' button in the channel box shows ''M-F''), or if the model data of fit enabled sources are mapped in the 3D window, only sources whose '''Fit/No fit''' button is down are taken into account for the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map.
* The '''Map/No map''' buttons are visible only if the model waveforms of fit enabled sources are displayed in the channel box (the''' Model''' button in the channel box shows ''M-F'') or if the model data of fit enabled sources are mapped in the 3D window. They are available for spatial components only, since other sources use the '''Fit/No fit''' buttons to enable/disable the source for mapping or to display the model waveforms. Only spatial components whose '''Map/No map''' button is down are taken into account in the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map. You can enable several sources for mapping by keeping the '''Control-key''' on your keyboard pressed and pushing the '''Map/No map '''buttons (for spatial components) or '''Fit/No fit''' buttons (for other source types) of the sources you would like to contribute to the model waveforms or model map.

Use the '''Waveform Scale''' buttons (labeled with two arrows) at the bottom right of the source box to adjust the waveform amplitude scale. If you hold the '''Control-key''' in combination, the scale is reset to default.

'''Using the Mouse'''

Click on a source waveform if you want to select the associated source. The selected source is marked by a colored rectangle around its '''On/Off''' and '''Fit/No fit''' buttons.

If the current solution contains more than one sources you can change the source order by dragging the baseline of the source waveform up and down.

As in the Channel Box, you can set the cursor or a fit interval with the left mouse button.

You may double click on the '''source label''' to specify a new label.

If you click the right mouse button somewhere in the source box, the '''Source Box''' popup menu appears with commands specific to this box.

If you click the right mouse button on a source label or source number at the right-hand side of the source waveforms, the '''Source Label''' popup menu is displayed.

== Parameter Box ==

The parameter box shows either the parameters of the current head model or of the selected source.

'''If no source is selected the parameter box looks like the figure below:'''

[[Image:Functions SAwindow (5).gif]]


The top row shows the currently selected head model. The default model for EEG is the 4-shell ellipsoidal model. Different EEG models can be selected using the ''Head Model Selection'' list.

For EEG, you can select a standardized Realistic Head Model Approximation based on finite elements (FEM) with different conductivity ratios of brain to skull and anisotropies. For a detailed description of the different head models see chapter ''Head Models''.

If the current channel type is MEG (as indicated by the '''EEG/MEG''' button in the '''channel box'''), the spherical MEG head model (Sarvas, 1987) and the individual FEM head model are available. Please note, that the individual FEM head model first has to be created in BESA MRI.

The '''head radius''' in millimeters which is used in the head models is given in the first text field labeled head. If the head radius is computed from the individual head it cannot be modified.

The '''head model parameters '''of the different head compartments are given in the text fields: The thicknesses of the scalp, of the bone, and of the cerebral spinal fluid (csf) are displayed in the second, third and fourth text fields of the upper row. The relative conductivities of brain, scalp, bone, and csf are displayed in the bottom row. Click onto the text fields to edit the current value.

If you click the right mouse button on a text filed while at least one head model parameter differs from its default value, the '''Head Model Text Field''' popup menu appears which allows to reset values to the default.

'''Note:''' The head model parameters are used in the ''4 shell ellipsoidal'' and ''Polynomial'' ''4 shells'' head models only.

'''If a source is selected, the parameter box looks like this:'''

[[Image:Functions SAwindow (6).gif]]


The coordinate system which is used to display or modify the source coordinates can be switched with the '''Coordinate System''' button at the top left. The following coordinate systems are available:

* '''(Cartesian) head coordinates''': Defined by three reference points on the head known as ''fiducials''. The unit is millimeter. The button is labeled '''Cart./HC'''.

* '''Talairach coordinates''':
*# Talairach coordinates calculated using the individual MRI information of the current condition. The button is labeled '''Talairach'''.
*# Approximate ''Talairach coordinates'' estimated by a default transformation to the BESA Research standard brain that is used for the 3D anatomical view if an individual MRI is not available for the current condition. The button is labeled '''Tal.''' (''appr''.). For additional information, please see the chapter [[Integration with MRI and fMRI]]),

* '''MNI coordinates''':
*# MNI coordinates (SPM convention) calculated using the individual MRI information of the current condition. The button is labeled '''MNI'''.
*# Approximate MNI coordinates estimated by a default transformation to the BESA Research standard brain that is used for the 3D anatomical view if an individual MRI is not available for the current condition. The button is labeled '''MNI (appr.)'''. For additional information, please see the chapter [[Integration with MRI and fMRI]]),

* '''(Cartesian) unit sphere coordinates''' (BESA coordinates): Defined by the best fit sphere. The button is labeled '''Cart./US'''.

* '''Polar unit sphere coordinates''' (polar BESA coordinates): Same coordinate system as above, but the coordinates are given in'' polar coordinates''. The button is labeled '''Polar/US'''.

Note: A detailed description of the coordinate systems is given in the chapter [[Electrodes and Surface Locations]].

To the left of the '''Coordinate System''' button the location and orientation coordinates of the selected source are given in the text fields labeled as follows:

* '''x-loc''', '''y-loc''', and '''z-loc''': Location of the selected source in cartesian coordinates.
* '''x-ori''', '''y-ori''', and '''z-ori''': Orientation of the selected source in cartesian coordinates (the length of the vector specified by the three orientation coordinates is 1)
* '''ecc''', '''theta''', and '''phi''': Location of the selected source in polar coordinates (eccentricity, azimuth, and polar angle), visible only if polar coordinates are displayed.
* '''o-the''' and '''o-phi''': Orientation of the selected source in polar coordinates (azimuth and polar angle). These text fields are visible only if polar coordinates are displayed.

The second and third row shows the '''current location and orientation constraints''' for the selected source. Four states are possible:

* '''Free:''' No constraint is set. The source location/orientation can be fitted.
* '''Fixed''': The source location/orientation is fixed during the next fit and will not be modified.
* '''Symmetric to''' (available for the source location only): The source location is set symmetric (mirrored into the other hemisphere) to the referenced source which is specified in the middle text field. The offsets to the symmetric location of the referenced source are given in the text field to the right.
* '''Bound to''' (available for the source location only): The source location is bound to the referenced source which is specified in the middle text field. The offsets to the location of the specified source are given in the text field to the right.

If you click onto the middle text field of the referenced source or the text field containing the location offset, the ''Set source constraint ''dialog box will open which allows to modify the referenced source and the location offset.

'''Using the Mouse'''

A left mouse click in the ''parameter ''box will toggle the display of the selected source parameters and the display of the head model parameters.

If you click the right mouse button somewhere in the parameter box, the '''Parameter Box popup menu''' appears with specific commands to this box.

Click on the '''source label''' to specify a new label.

== Head Box ==

The Head Box shows six head schemes with the sources of the current solution. Each of the three standard views is displayed twice from opposite directions: First row sagittal view from left (left scheme) and from right (right scheme), second row transversal top view (left) and transversal view from bottom (right), and third row coronal view from behind (left) and frontal coronal view (right).

Note: If the ''3D window'' is open the appearance of the head box is different. Only two head schemes are displayed. You will find more information at the end of this page.

[[Image:Functions SAwindow (7).gif]]

A source is plotted in one view only if it is located in the forward hemisphere or slightly in the back hemisphere, so that, e.g. for the sagittal view (first row), a source is plotted only in the left head scheme if it is located in the left hemisphere, and not in the right top head scheme (in the figure below all sources except for the green one).

Note: You can specify the depth up to which sources are plotted in the back hemisphere (the so-called ''source transparency'') in the'' Boxes'' Tab of the ''Preferences ''dialog box.

If the cursor is set, the size of the source plot depends on the strength of the source (the amplitude of the source waveform) at the cursor.

The '''description and filename''' of the current solution is given at the top of the head box. If the solution has not been stored yet the text ''New solution...'' is displayed. If any modifications of the solution have not yet been saved, this is indicated by appending the text ''"modified"'' to the filename. Set a new description by clicking on the text with the left mouse button.

The '''Switch Solution''' buttons at the top left corner, marked with small arrows, allow to switch between solutions. They are enabled only if there are at least two solutions. If you right click on these buttons while they are enabled the '''Switch Solution '''popup menu opens which allows for changing to a specified solution.

The '''Hold''' button below the '''Switch Solution''' buttons becomes important if more than one condition has been uploaded or the condition has more than one data set. It toggles between two settings:
* '''Up:''' When the user switches between data sets or conditions, it will also be switched to the solution which was last modified when the new data set was active.
* '''Down:''' When the user switches between conditions, the current solution will not be changed.

Clicking on the ''''+' '''button at the top right creates a new solution and copies the current solution to the new one. If the solution which was copied already has a file path (i.e. has been loaded or saved before), the file path of the new solution is modified such that it does not specify an existing file.

The button is disabled if no solution is available.

Note: The entry ''New Copy of Displayed Solution'' in the '''Solution''' menu provides the same functionality.

The '''Source Plot Scale''' buttons at the bottom right of the head box are used to adjust the size of the source plots. Note that two different settings are stored: One for the source display if the cursor has been set, one for the display without cursor. If you hold the '''Control-key''' in combination, the scale is reset to default.

'''Using the Mouse'''

A double-click on one of the head schemes creates a new source at that location. The type of the new source can be specified using the menu entry '''Options/Default Source Type'''. A double click on an existing source deletes it.

If a source is under the mouse the mouse changes to [[Image:|top]]. A single click with the left button turns the source under the mouse into the selected source. A double click deletes the source.

If the source under the mouse can be moved the mouse changes to [[Image:|top]]. You can move the source by dragging with the left mouse button (spatial components may not be moved). The source location is bound to the limits which have been set in the ''Limit of source location section'' in the'' Preferences'' dialog box.

If the orientation of a source can be modified the mouse changes to [[Image:|top]]( single dipoles only). Drag the vertex of the orientation to rotate the dipole. Use the '''Shift-key''' in combination if you want to rotate the orientation in the specified view only.

Note: If you want to drag the orientation even if it is hidden use the '''Control-key''' in combination.

If you double click on the filename of the solution, which is given at the top of the head box, a text box is displayed in which you may enter a description. If a solution description has been set, it is displayed instead of the filename. This description will be stored when the solution is saved.

If you click the right mouse button somewhere in the head box, the '''Head Box''' popup menu appears with commands specific to this box.

'''Head box display if the 3D window is open'''

If the ''3D window'' is open the appearance of the head box is different. Only two head schemes are displayed.

[[Image:Functions SAwindow (11).gif]]

The '''Flip Head Scheme''' buttons (labeled '''Flp''') at the bottom right and left of the window flip the associated head scheme. E.g. clicking onto the left '''Flp''' button in this image would switch the sagittal view from the left to the sagittal view from the right.

Use the '''Shift Head Scheme''' buttons (second and third button to the left, marked with small arrows) to scroll the head schemes until you see your desired view.

The '''Transparency scroll bar '''in the mid bottom changes the source transparency. A source is plotted in one view only if it is located in the forward hemisphere or as far in the back hemisphere as set by the transparency value - the depth up to which sources are plotted in the back hemisphere. Please see additional information in the section ''Source Transparency'', (''Preferences'' dialog box), use the '''Back''' button of the Windows® help to jump back to this page.

== 3D Window ==

The 3D window is opened if a 3D map (fig. 1) or the anatomical view of an individual MRI or the BESA Research standard Brain (fig. 2) is displayed. It also opens if any of the 3D volume imaging or 3D surface imaging methods are used. (Use the popup menu entries '''Display MRI''' or '''Display 3D Maps'''.)

<div><ul>
<li style="display: inline-block;"> [[File:3D_Window_-_Cortical_Map.png|thumb|425px|Fig. 1]] </li>
<li style="display: inline-block;"> [[File:3D_Window_-_Rolandic.png|thumb|425px|Fig. 2]] </li>
</ul></div>


The sources of the current solution are displayed in the anatomical view (fig. 2), or in the cortical imaging view if this is activated via the popup menu using the right mouse button. The selected source is displayed with a golden halo around the source body. If EEG/MEG data is coregistered with MRI the confidence elipsoids and error rims are displayed around fitted sources

The '''3D window toolbar''' is explained in details in the ''3D Window Toolbar'' section in the BESA help ''Reference'' chapter.

'''Using the Keyboard'''

A number of key combinations are useful for navigation/display in the 3D window if the 3D window is active. The most important commands with their default keys are listed here. Note that you can change the default keys in the ''Define hot keys'' dialog box, which also allows to specify additional key commands.

Command default key(s) and effects:

* '''Decrement/Increment scale''' '''Num-, Num+:''' Decrements/Increments the map scale in the 3D map or the source plot size in the anatomical view.
* '''Move down/left/right/up''' '''Numpad-2, Numpad-4, Numpad-6, Numpad-8''': If a source is selected, the source is moved within the current slice in steps of one millimeter in the corresponding direction. If no source is selected, the slicing center is moved instead. This only applies to the anatomical view.
* '''Slice backwards/forward''' '''Down, Up''': If a source is selected the source is moved into the next slice, one millimeter out of or into the current anatomical view. If no source is selected the slicing center is sliced down or up instead. This only applies to the anatomical view.
* '''Switch to specific slice''' '''Shift-C, Shift-S, Shift-T''': Switches to the coronal, sagittal, or transversal slice (anatomical view only).
* '''Display 3D maps''' '''M''': Switches from the anatomical view to the 3D map. Works only if the cursor has been set.
* '''Display standard MRI''' '''A''': Switches from the 3D map to the anatomical view.
* '''Display brain atlas overlay''' ''' ''Shift-A''''': Toggles on or off brain atlas overlay on anatomical view.

'''Using the Mouse'''

Whenever an action with the left mouse button is possible the mouse cursor will change from the standard arrow to a special icon. The following mouse actions are possible:

'''New source'''

A double click on a surface (skin or brain) or inside an anatomical view will insert a new source at the associated 3D location. The type of the new source can be specified using the menu entry '''Options/Default Source Type'''.

'''Delete source'''

A double click on an existing source will delete the source after a confirmation box is closed with ''Yes''.

[[Image:Functions SAwindow (14).gif]] '''Rotate'''

Dragging with the left mouse button will rotate the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Rotation Mode''' button of the '''3D window toolbar '''or the '''Shift-key''' have to be pressed.

[[Image:Functions SAwindow (15).gif]] '''Zoom'''

Dragging with the left mouse button will zoom the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Zoom Mode''' button of the '''3D window toolbar''' or the '''Shift-''' and '''Control-key''' have to be pressed.

[[Image:Functions SAwindow (16).gif]] '''Move'''

Dragging with the left mouse button will rotate the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Move Mode''' button of the''' 3D window toolbar '''or the '''Control-key''' have to be pressed.

[[Image:Functions SAwindow (17).gif]] '''Slice Vertically'''

Dragging with the left mouse button will slice the current slicing center up and down. This action is available on the anatomical view only. The '''Slice Mode''' button of the '''3D window toolbar''' or the '''Alternate-key''' have to be pressed in combination.

[[Image:Functions SAwindow (18).gif]] '''Slice Horizontally'''

Dragging with the left mouse button will slice the current slicing center horizontally. This action is available on the 2D anatomical views only. The '''Slice Mode''' button of the '''3D window toolbar''' or the '''Alternate-key''' must not be pressed.

[[Image:Functions SAwindow (19).gif]] '''Set Slicing Center to Source Location'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

This action is available on the anatomical view only if a source is under the mouse and this source must not be moved (e.g. a spatial component).

[[Image:Functions SAwindow (9).gif]] '''Move Source'''

A single click with the left mouse button will select the source under the mouse (if not already selected). A double click will delete the source.

Dragging with the left mouse button will move the source horizontally to the displayed slice.

This action is available only if a source is under the mouse, this source may be moved (no spatial component), and the '''Move Mode''' button of the '''3D window toolbar''' or the '''Control-key''' are pressed.

[[Image:Functions SAwindow (20).gif]] '''Move Source and Slice Horizontally'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

Dragging with the left mouse button will move the source horizontally to the displayed slice and set the current slicing center to the new source location.

This action is available only if a source is under the mouse, this source may be moved (no spatial component) and the '''Move Mode''' button, the '''Slice Mode '''button (of the '''3D window toolbar'''), the '''Control-''' and '''Alternate-key''' are not pressed.

[[Image:Functions SAwindow (21).gif]] '''Move Source and Slice Vertically'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

Dragging with the left mouse button will move the source vertically to the displayed slice and set the current slicing center to the new source location.

This action is available only if a source is under the mouse, this source may be moved (no spatial component) and the '''Slice Mode''' button of the '''3D window toolbar''' or the '''Alternate-key''' are pressed.

If you click the right mouse button somewhere in the 3D window, the '''3D Window''' popup menu appears with commands specific to this window.

{{BESAManualNav}}

Source Analysis Functions of the Window

2021-11-25T12:52:08Z

Dominik:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = BESA Research 6.1 or higher
}}

== Overview ==

The Source Analysis module window is subdivided into six main parts (boxes) which will be explained briefly in the following sections:
* The Channel Box (left)
* The Variance Box (top center)
* The Source Box (bottom center)
* The Parameter Box (top right)
* The Head Box (mid right)
* The 3D Window (bottom right)

Note that the 3D window will not normally appear automatically (unless specified in the '''Options / Preferences''' menu), and the head box will take up more space if the 3D window is not displayed.

[[Image:Functions SAwindow (1).gif ]]


The '''title bar''' contains information about the data file, the filename, the condition name, the filter settings, and the selected time interval.

Most of the functions and commands can be chosen from the main '''menu bar''' below the title bar. However, all important commands are also available via a right mouse click. Whenever you right-click, a context-sensitive popup menu will appear containing the available commands.

A detailed description of the commands of the '''menu bar''' and the different popup menus is given in the online help ''Reference ''chapter.

At the bottom, you will notice the '''status bar''', which gives information about the current mouse position (latency or 3D position) and the current cursor location or the fit interval(s). (See the section on the '''status bar''' in the online help ''Reference ''chapter).

The individual size of the boxes can be modified: Try placing the mouse over the vertical double line that separates the source box and the head box. The horizontal arrow that appears indicates that you can move this separator by dragging with the left mouse button.

The same is possible for the horizontal double line bounding the variance box.

== Channel Box ==

The channel box normally shows the signals at each channel. The display depends on the state of the push buttons at the top of the channel box.

The figure below shows an example with the display of the measured data waveforms (violet) and the residual waveforms (red) at each channel. The channel labels are displayed to the left of each waveform.

An overplot of all waveforms is displayed above the single waveforms (labeled ''All'').

[[Image:Functions SAwindow (2).gif]]


Below the first row of buttons, there is a '''description of the current condition''' containing the condition name, the filter settings and the condition epoch. Below the condition epoch, the baseline of the current condition is displayed as horizontal black/red line.

At the bottom, you see the''' figure legend '''describing the used colors and the number of displayed channels (or PCA components).

The '''Channel buttons''' at the top of the channels box specify which waveforms are displayed.

* The''' Data''' button toggles the display of the data (measured signals) of the visible channels (violet waveforms). If you double click on this button the''' Model '''and''' Residual''' buttons are released and the channels are re-sorted by the amplitude of the measured data.
* Press the '''Model''' button to toggle the display of the modeled data (blue waveforms). The modeled data are calculated from the waveforms of the active sources in the current solution using the currently chosen head model. (The source waveforms are displayed in the source box, the head model is set and displayed in the parameter box.) Pressing the '''Model '''button toggles between the display of all active sources (button is labeled '''M-A''') and the display of the model waveforms which result from the contributions of all sources whose Fit/No fit button is pressed (button is labeled M-F). Note that the '''Residual''' button is released if the '''Model''' button is pressed without holding the '''Control-key'''.
* Press the''' Residual''' button to toggle the residual (unexplained) signal (red waveforms), i.e. the difference between measured and modeled data. If you double click on this button the '''Data''' and '''Model''' buttons are released and the channels are re-sorted by the amplitude of the residual. Note that the''' Model''' button is released if the''' Residual''' button is pressed without holding the '''Control-key.'''
* The '''Sort''' button (fourth button from the left) changes the ordering of the channels. Pushing this button switches between original order (button is labeled '''Order''' or '''Ord'''.), sorting by the amplitude of the measured data (||Data|| or ||D||), and sorting by the amplitude of the residual (||Res.|| or ||R||). In practice, by using one of the sorting modes ||Data|| or ||Residual||, you will only have to display the first few channels during the fitting procedure, since the channels with the largest signals are shown at the top.
* Use the '''P.C.A.''' button to start a Principal Components Analysis (PCA) over the marked fit interval(s) (if no fit interval is set the PCA is computed over the whole epoch). The percentage variance accounted for by each component is shown at the left of each waveform. When the PCA is displayed, data, model, and residual waveforms are not visible. Note that if the '''Residual '''button is down and the '''Data''' button is up, the PCA is computed for the residual data and not the measured data.
* The button at the far right is the '''EEG/MEG/MEEG''' button. Pushing this button toggles between the data sets (EEG, MEG and MEEG) of the current condition, if combined EEG and MEG have been recorded. The label of the button shows which data set is currently displayed.
For combined recordings, it is possible to combine EEG and MEG for fitting. In this case, each channel is normalized by the signal in the defined baseline interval. Changing the baseline interval leads to a re-computation of data in this case. In order to use MEEG, the head models of EEG and MEG need to match to ensure a common source space (e.g. spherical head models for both, or individual FEM / BEM for both). Adjust the head models individually for the EEG and MEG modes first before entering MEEG mode.

At the top left below the''' Data''' button, the '''Switch Condition''' buttons (labeled with two arrows) enable fast switching between different conditions. They are enabled only if at least two conditions have been loaded.

Below the '''Switch Condition''' buttons, the '''Toggle Electrode Configuration''' button toggles between using the original channels (button is labeled '''Org''') or using an interpolated montage of 81 electrodes at standard locations (button is labeled '''Std'''). This montage allows comparison of different subjects at standard electrode locations. Note: If MEG channels are displayed this button is not available.

The channel box is bounded at the right by three scroll bars. Use the topmost one to change the number of displayed channels. The scroll bar below ('''select displayed channels''') can be used to scroll through the channels. The bottom one, consisting only of two arrows, changes the amplitude scaling of the displayed signals ('''scale waveforms''').

The '''MAG''' and '''GRD''' buttons at the bottom of the channel box appear only if an MEG data set containing both magnetometer and gradiometer sensors is displayed, or if MEEG mode is active. The buttons are used to toggle the display of the magnetometer and gradiometer channels. In case of the '''MEEG''' mode, '''EEG''' and either of '''MAG''' and '''GRD''' buttons (or both) are displayed. Combination of any MEG mode with the EEG data can then be toggled in that way.

In the figure above you see one '''fit interval''', shown in a darker color. The fit interval is used for fitting, computing the PCA, and more.

'''Using the Mouse'''

In the channel box, it is possible to set the cursor or a fit interval with the left mouse button. If you click on the text in the top left corner, you may change the condition name. By clicking on the baseline, a new baseline interval can be specified.

If you click the right mouse button somewhere in the channel box, the '''Channel Box popup menu''' appears with commands specific to this box.

== Variance Box ==

The variance box shows the global field power (blue) and the residual variance (red) in logarithmic scaling, relative to the maximum global field power.
* '''The global field power''': the sum of squares of the activity over all channels of the current data set
* '''The residual variance''': the sum of squares of the unexplained signal

Note that the global field power is scaled from bottom to top, whereas the residual variance is scaled from top to bottom. The corresponding waveform scales at the left of the variance box are given in percent.

[[Image:Functions SAwindow (3).gif]]


At the top left, the '''residual variance''' (RV) over all samples inside the fit interval(s) is displayed (labeled '''R.V'''.). Below, the minimum residual variance inside the fit intervals (labeled '''Best''') is shown. If no fit interval is selected, values for the whole epoch are given. If a cursor is set, the RV over the whole epoch and the value of the RV at the cursor sample are displayed (labeled '''Curs'''.).

At the top right, second row, you see the current value of the '''regularization constant''', a parameter used to reduce the interaction between sources. (You can set the regularization constant with the '''Regularization''' '''Constant: X%''' menu entry in the '''Options''' menu or by clicking on the current value.)

The '''Fit Criterion buttons''' at the top of the variance box toggle the corresponding fit criteria on and off. Starting from the left the buttons represent the residual variance criterion, the energy criterion, the minimum distance criterion, and the residual variance - q value (S/N) criterion. You will find additional information in the section '''Fit Criterion Buttons''' in the online help ''Reference'' chapter.

'''Using the Mouse'''

In the variance box, it is possible to set the cursor or a fit interval with the left mouse button. If you click on the regularization constant ('''RC'''), you may set a new value.

If you click the right mouse button somewhere in the variance box, the '''Variance Box popup menu''' appears with commands specific to this box.

== Source Box ==

The source box shows the source waveforms of the current solution. The source waveforms are computed over the whole epoch of the current data set using the currently chosen head model. (The head model is set and displayed in the parameter box.) If no solution is available the source box is empty.

A single dipole or a spatial component has one source waveform, a regional source has three waveforms for EEG and two for MEG (one waveform for each component). A spatial component is labeled SC just below its waveform.

[[Image:Functions SAwindow (4).gif]]

At the top of the source box you will find the following buttons:

* The '''All on''' button activates or deactivates all sources (switches all sources on or off). Spatial components whose principal vector does not match with the current data set cannot be activated.
* The '''All fit''' button enables all active sources (not spatial components) for fitting.
* The''' Start fit '''button fits the enabled sources within the specified fit interval(s). If no fit interval is set the sources the whole epoch is used for fitting, if a cursor is set they are fitted only at the cursor sample. Another way to start fitting is given by the ''Fit Enabled Sources''... entry in the standard popup menu.
* The '''Image selection button''' button allows for a quick computation of a 3D image. The type of the image to be computed is shown in the button label. By default, this is the previously computed 3D image. For details on the available image types in BESA Research, please refer to chapter 3D imaging. When you click on this button while keeping CTRL button pressed the new computation will be performed applying weighting based on current image. When you click on this button while keeping SHIFT button pressed the computation will be performed from scratch (leadfields will be re initialized)

* The '''BrainVoyager '''button will start the BrainVoyager program. If the BrainVoyager path has not been set correctly the BrainVoyager tab of the ''Preferences ''dialog box is displayed to allow you to set the valid path. If the BrainVoyager program is already running the current solution is sent to BrainVoyager for display in the structural MRT image (c.f. ''Integration with MRI/fMRI'').

Each source waveform has two push buttons assigned to it:

* The '''On/Off''' buttons to the left of the source waveforms activate or deactivate the associated sources. Spatial components whose principal vector does not match with the current data set cannot be activated. If a source is inactive, it does not contribute to the model.
* The '''Fit/No fit '''buttons below the '''On/Off''' buttons enable or disable the associated source for fitting. If a source is selected, it is enabled for fitting automatically. On the other hand, a source is automatically selected if you push the corresponding '''Fit/No fit''' button. Note that spatial components have no '''Fit/No fit''' button since they cannot be enabled for fitting. You can enable several sources for fitting by keeping the '''Control-key''' on your keyboard pressed and pushing the '''Fit/No fit''' buttons of the sources you would like to fit simultaneously. If the model waveforms of fit enabled sources are displayed in the channel box (the '''Model''' button in the channel box shows ''M-F''), or if the model data of fit enabled sources are mapped in the 3D window, only sources whose '''Fit/No fit''' button is down are taken into account for the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map.
* The '''Map/No map''' buttons are visible only if the model waveforms of fit enabled sources are displayed in the channel box (the''' Model''' button in the channel box shows ''M-F'') or if the model data of fit enabled sources are mapped in the 3D window. They are available for spatial components only, since other sources use the '''Fit/No fit''' buttons to enable/disable the source for mapping or to display the model waveforms. Only spatial components whose '''Map/No map''' button is down are taken into account in the waveform or map display. Otherwise the associated source will not contribute to the model waveforms or model map. You can enable several sources for mapping by keeping the '''Control-key''' on your keyboard pressed and pushing the '''Map/No map '''buttons (for spatial components) or '''Fit/No fit''' buttons (for other source types) of the sources you would like to contribute to the model waveforms or model map.

Use the '''Waveform Scale''' buttons (labeled with two arrows) at the bottom right of the source box to adjust the waveform amplitude scale. If you hold the '''Control-key''' in combination, the scale is reset to default.

'''Using the Mouse'''

Click on a source waveform if you want to select the associated source. The selected source is marked by a colored rectangle around its '''On/Off''' and '''Fit/No fit''' buttons.

If the current solution contains more than one sources you can change the source order by dragging the baseline of the source waveform up and down.

As in the Channel Box, you can set the cursor or a fit interval with the left mouse button.

You may double click on the '''source label''' to specify a new label.

If you click the right mouse button somewhere in the source box, the '''Source Box''' popup menu appears with commands specific to this box.

If you click the right mouse button on a source label or source number at the right-hand side of the source waveforms, the '''Source Label''' popup menu is displayed.

== Parameter Box ==

The parameter box shows either the parameters of the current head model or of the selected source.

'''If no source is selected the parameter box looks like the figure below:'''

[[Image:Functions SAwindow (5).gif]]


The top row shows the currently selected head model. The default model for EEG is the 4-shell ellipsoidal model. Different EEG models can be selected using the ''Head Model Selection'' list.

For EEG, you can select a standardized Realistic Head Model Approximation based on finite elements (FEM) with different conductivity ratios of brain to skull and anisotropies. For a detailed description of the different head models see chapter ''Head Models''.

If the current channel type is MEG (as indicated by the '''EEG/MEG''' button in the '''channel box'''), the spherical MEG head model (Sarvas, 1987) and the individual FEM head model are available. Please note, that the individual FEM head model first has to be created in BESA MRI.

The '''head radius''' in millimeters which is used in the head models is given in the first text field labeled head. If the head radius is computed from the individual head it cannot be modified.

The '''head model parameters '''of the different head compartments are given in the text fields: The thicknesses of the scalp, of the bone, and of the cerebral spinal fluid (csf) are displayed in the second, third and fourth text fields of the upper row. The relative conductivities of brain, scalp, bone, and csf are displayed in the bottom row. Click onto the text fields to edit the current value.

If you click the right mouse button on a text filed while at least one head model parameter differs from its default value, the '''Head Model Text Field''' popup menu appears which allows to reset values to the default.

'''Note:''' The head model parameters are used in the ''4 shell ellipsoidal'' and ''Polynomial'' ''4 shells'' head models only.

'''If a source is selected, the parameter box looks like this:'''

[[Image:Functions SAwindow (6).gif]]


The coordinate system which is used to display or modify the source coordinates can be switched with the '''Coordinate System''' button at the top left. The following coordinate systems are available:

* '''(Cartesian) head coordinates''': Defined by three reference points on the head known as ''fiducials''. The unit is millimeter. The button is labeled '''Cart./HC'''.

* '''Talairach coordinates''':
*# Talairach coordinates calculated using the individual MRI information of the current condition. The button is labeled '''Talairach'''.
*# Approximate ''Talairach coordinates'' estimated by a default transformation to the BESA Research standard brain that is used for the 3D anatomical view if an individual MRI is not available for the current condition. The button is labeled '''Tal.''' (''appr''.). For additional information, please see the chapter [[Integration with MRI and fMRI]]),

* '''MNI coordinates''':
*# MNI coordinates (SPM convention) calculated using the individual MRI information of the current condition. The button is labeled '''MNI'''.
*# Approximate MNI coordinates estimated by a default transformation to the BESA Research standard brain that is used for the 3D anatomical view if an individual MRI is not available for the current condition. The button is labeled '''MNI (appr.)'''. For additional information, please see the chapter [[Integration with MRI and fMRI]]),

* '''(Cartesian) unit sphere coordinates''' (BESA coordinates): Defined by the best fit sphere. The button is labeled '''Cart./US'''.

* '''Polar unit sphere coordinates''' (polar BESA coordinates): Same coordinate system as above, but the coordinates are given in'' polar coordinates''. The button is labeled '''Polar/US'''.

Note: A detailed description of the coordinate systems is given in the chapter [[Electrodes and Surface Locations]].

To the left of the '''Coordinate System''' button the location and orientation coordinates of the selected source are given in the text fields labeled as follows:

* '''x-loc''', '''y-loc''', and '''z-loc''': Location of the selected source in cartesian coordinates.
* '''x-ori''', '''y-ori''', and '''z-ori''': Orientation of the selected source in cartesian coordinates (the length of the vector specified by the three orientation coordinates is 1)
* '''ecc''', '''theta''', and '''phi''': Location of the selected source in polar coordinates (eccentricity, azimuth, and polar angle), visible only if polar coordinates are displayed.
* '''o-the''' and '''o-phi''': Orientation of the selected source in polar coordinates (azimuth and polar angle). These text fields are visible only if polar coordinates are displayed.

The second and third row shows the '''current location and orientation constraints''' for the selected source. Four states are possible:

* '''Free:''' No constraint is set. The source location/orientation can be fitted.
* '''Fixed''': The source location/orientation is fixed during the next fit and will not be modified.
* '''Symmetric to''' (available for the source location only): The source location is set symmetric (mirrored into the other hemisphere) to the referenced source which is specified in the middle text field. The offsets to the symmetric location of the referenced source are given in the text field to the right.
* '''Bound to''' (available for the source location only): The source location is bound to the referenced source which is specified in the middle text field. The offsets to the location of the specified source are given in the text field to the right.

If you click onto the middle text field of the referenced source or the text field containing the location offset, the ''Set source constraint ''dialog box will open which allows to modify the referenced source and the location offset.

'''Using the Mouse'''

A left mouse click in the ''parameter ''box will toggle the display of the selected source parameters and the display of the head model parameters.

If you click the right mouse button somewhere in the parameter box, the '''Parameter Box popup menu''' appears with specific commands to this box.

Click on the '''source label''' to specify a new label.

== Head Box ==

The Head Box shows six head schemes with the sources of the current solution. Each of the three standard views is displayed twice from opposite directions: First row sagittal view from left (left scheme) and from right (right scheme), second row transversal top view (left) and transversal view from bottom (right), and third row coronal view from behind (left) and frontal coronal view (right).

Note: If the ''3D window'' is open the appearance of the head box is different. Only two head schemes are displayed. You will find more information at the end of this page.

[[Image:Functions SAwindow (7).gif]]

A source is plotted in one view only if it is located in the forward hemisphere or slightly in the back hemisphere, so that, e.g. for the sagittal view (first row), a source is plotted only in the left head scheme if it is located in the left hemisphere, and not in the right top head scheme (in the figure below all sources except for the green one).

Note: You can specify the depth up to which sources are plotted in the back hemisphere (the so-called ''source transparency'') in the'' Boxes'' Tab of the ''Preferences ''dialog box.

If the cursor is set, the size of the source plot depends on the strength of the source (the amplitude of the source waveform) at the cursor.

The '''description and filename''' of the current solution is given at the top of the head box. If the solution has not been stored yet the text ''New solution...'' is displayed. If any modifications of the solution have not yet been saved, this is indicated by appending the text ''"modified"'' to the filename. Set a new description by clicking on the text with the left mouse button.

The '''Switch Solution''' buttons at the top left corner, marked with small arrows, allow to switch between solutions. They are enabled only if there are at least two solutions. If you right click on these buttons while they are enabled the '''Switch Solution '''popup menu opens which allows for changing to a specified solution.

The '''Hold''' button below the '''Switch Solution''' buttons becomes important if more than one condition has been uploaded or the condition has more than one data set. It toggles between two settings:
* '''Up:''' When the user switches between data sets or conditions, it will also be switched to the solution which was last modified when the new data set was active.
* '''Down:''' When the user switches between conditions, the current solution will not be changed.

Clicking on the ''''+' '''button at the top right creates a new solution and copies the current solution to the new one. If the solution which was copied already has a file path (i.e. has been loaded or saved before), the file path of the new solution is modified such that it does not specify an existing file.

The button is disabled if no solution is available.

Note: The entry ''New Copy of Displayed Solution'' in the '''Solution''' menu provides the same functionality.

The '''Source Plot Scale''' buttons at the bottom right of the head box are used to adjust the size of the source plots. Note that two different settings are stored: One for the source display if the cursor has been set, one for the display without cursor. If you hold the '''Control-key''' in combination, the scale is reset to default.

'''Using the Mouse'''

A double-click on one of the head schemes creates a new source at that location. The type of the new source can be specified using the menu entry '''Options/Default Source Type'''. A double click on an existing source deletes it.

If a source is under the mouse the mouse changes to [[Image:|top]]. A single click with the left button turns the source under the mouse into the selected source. A double click deletes the source.

If the source under the mouse can be moved the mouse changes to [[Image:|top]]. You can move the source by dragging with the left mouse button (spatial components may not be moved). The source location is bound to the limits which have been set in the ''Limit of source location section'' in the'' Preferences'' dialog box.

If the orientation of a source can be modified the mouse changes to [[Image:|top]]( single dipoles only). Drag the vertex of the orientation to rotate the dipole. Use the '''Shift-key''' in combination if you want to rotate the orientation in the specified view only.

Note: If you want to drag the orientation even if it is hidden use the '''Control-key''' in combination.

If you double click on the filename of the solution, which is given at the top of the head box, a text box is displayed in which you may enter a description. If a solution description has been set, it is displayed instead of the filename. This description will be stored when the solution is saved.

If you click the right mouse button somewhere in the head box, the '''Head Box''' popup menu appears with commands specific to this box.

'''Head box display if the 3D window is open'''

If the ''3D window'' is open the appearance of the head box is different. Only two head schemes are displayed.

[[Image:Functions SAwindow (11).gif]]

The '''Flip Head Scheme''' buttons (labeled '''Flp''') at the bottom right and left of the window flip the associated head scheme. E.g. clicking onto the left '''Flp''' button in this image would switch the sagittal view from the left to the sagittal view from the right.

Use the '''Shift Head Scheme''' buttons (second and third button to the left, marked with small arrows) to scroll the head schemes until you see your desired view.

The '''Transparency scroll bar '''in the mid bottom changes the source transparency. A source is plotted in one view only if it is located in the forward hemisphere or as far in the back hemisphere as set by the transparency value - the depth up to which sources are plotted in the back hemisphere. Please see additional information in the section ''Source Transparency'', (''Preferences'' dialog box), use the '''Back''' button of the Windows® help to jump back to this page.

== 3D Window ==

The 3D window is opened if a 3D map (fig. 1) or the anatomical view of an individual MRI or the BESA Research standard Brain (fig. 2) is displayed. It also opens if any of the 3D volume imaging or 3D surface imaging methods are used. (Use the popup menu entries '''Display MRI''' or '''Display 3D Maps'''.)

<div><ul>
<li style="display: inline-block;"> [[File:3D_Window_-_Cortical_Map.png|thumb|425px|Fig. 1]] </li>
<li style="display: inline-block;"> [[File:3D_Window_-_Rolandic.png|thumb|425px|Fig. 2]] </li>
</ul></div>


The sources of the current solution are displayed in the anatomical view (fig. 2), or in the cortical imaging view if this is activated via the popup menu using the right mouse button. The selected source is displayed with a golden halo around the source body. If EEG/MEG data is coregistered with MRI the confidence elipsoids and error rims are displayed around fitted sources

The '''3D window toolbar''' is explained in details in the ''3D Window Toolbar'' section in the BESA help ''Reference'' chapter.

'''Using the Keyboard'''

A number of key combinations are useful for navigation/display in the 3D window if the 3D window is active. The most important commands with their default keys are listed here. Note that you can change the default keys in the ''Define hot keys'' dialog box, which also allows to specify additional key commands.

Command default key(s) and effects:

* '''Decrement/Increment scale''' '''Num-, Num+:''' Decrements/Increments the map scale in the 3D map or the source plot size in the anatomical view.
* '''Move down/left/right/up''' '''Numpad-2, Numpad-4, Numpad-6, Numpad-8''': If a source is selected, the source is moved within the current slice in steps of one millimeter in the corresponding direction. If no source is selected, the slicing center is moved instead. This only applies to the anatomical view.
* '''Slice backwards/forward''' '''Down, Up''': If a source is selected the source is moved into the next slice, one millimeter out of or into the current anatomical view. If no source is selected the slicing center is sliced down or up instead. This only applies to the anatomical view.
* '''Switch to specific slice''' '''Shift-C, Shift-S, Shift-T''': Switches to the coronal, sagittal, or transversal slice (anatomical view only).
* '''Display 3D maps''' '''M''': Switches from the anatomical view to the 3D map. Works only if the cursor has been set.
* '''Display standard MRI''' '''A''': Switches from the 3D map to the anatomical view.
* '''Display brain atlas overlay''' ''' ''Shift-A''''': Toggles on or off brain atlas overlay on anatomical view.

'''Using the Mouse'''

Whenever an action with the left mouse button is possible the mouse cursor will change from the standard arrow to a special icon. The following mouse actions are possible:

'''New source'''

A double click on a surface (skin or brain) or inside an anatomical view will insert a new source at the associated 3D location. The type of the new source can be specified using the menu entry '''Options/Default Source Type'''.

'''Delete source'''

A double click on an existing source will delete the source after a confirmation box is closed with ''Yes''.

[[Image:Functions SAwindow (14).gif]] '''Rotate'''

Dragging with the left mouse button will rotate the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Rotation Mode''' button of the '''3D window toolbar '''or the '''Shift-key''' have to be pressed.

[[Image:Functions SAwindow (15).gif]] '''Zoom'''

Dragging with the left mouse button will zoom the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Zoom Mode''' button of the '''3D window toolbar''' or the '''Shift-''' and '''Control-key''' have to be pressed.

[[Image:Functions SAwindow (16).gif]] '''Move'''

Dragging with the left mouse button will rotate the current view. This action is available on a 3D map or on the 3D view of the anatomical view. The '''Move Mode''' button of the''' 3D window toolbar '''or the '''Control-key''' have to be pressed.

[[Image:Functions SAwindow (17).gif]] '''Slice Vertically'''

Dragging with the left mouse button will slice the current slicing center up and down. This action is available on the anatomical view only. The '''Slice Mode''' button of the '''3D window toolbar''' or the '''Alternate-key''' have to be pressed in combination.

[[Image:Functions SAwindow (18).gif]] '''Slice Horizontally'''

Dragging with the left mouse button will slice the current slicing center horizontally. This action is available on the 2D anatomical views only. The '''Slice Mode''' button of the '''3D window toolbar''' or the '''Alternate-key''' must not be pressed.

[[Image:Functions SAwindow (19).gif]] '''Set Slicing Center to Source Location'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

This action is available on the anatomical view only if a source is under the mouse and this source must not be moved (e.g. a spatial component).

[[Image:Functions SAwindow (9).gif]] '''Move Source'''

A single click with the left mouse button will select the source under the mouse (if not already selected). A double click will delete the source.

Dragging with the left mouse button will move the source horizontally to the displayed slice.

This action is available only if a source is under the mouse, this source may be moved (no spatial component), and the '''Move Mode''' button of the '''3D window toolbar''' or the '''Control-key''' are pressed.

[[Image:Functions SAwindow (20).gif]] '''Move Source and Slice Horizontally'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

Dragging with the left mouse button will move the source horizontally to the displayed slice and set the current slicing center to the new source location.

This action is available only if a source is under the mouse, this source may be moved (no spatial component) and the '''Move Mode''' button, the '''Slice Mode '''button (of the '''3D window toolbar'''), the '''Control-''' and '''Alternate-key''' are not pressed.

[[Image:Functions SAwindow (21).gif]] '''Move Source and Slice Vertically'''

A single click with the left mouse button will select the source under the mouse (if not already selected) and set the current slicing center to the source location. A double click will delete the source.

Dragging with the left mouse button will move the source vertically to the displayed slice and set the current slicing center to the new source location.

This action is available only if a source is under the mouse, this source may be moved (no spatial component) and the '''Slice Mode''' button of the '''3D window toolbar''' or the '''Alternate-key''' are pressed.

If you click the right mouse button somewhere in the 3D window, the '''3D Window''' popup menu appears with commands specific to this window.

{{BESAManualNav}}

Source Analysis 3D Imaging

2021-11-25T12:38:55Z

Dominik:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = BESA Research 6.1 or higher
}}


== Overview ==

BESA Research features a set of new functions that provide 3D images that are displayed superimposed to the individual subject's anatomy. This chapter introduces these different images and describe their properties and applications.

The 3D images can be divided into three categories:

'''Volume images:'''

* '''The Multiple Source Beamformer (MSBF)''' is a tool for imaging brain activity. It is applied in the time-domain or time-frequency domain. The beamformer technique in time-frequency domain can image not only evoked, but also induced activity, which is not visible in time-domain averages of the data.
* '''Dynamic Imaging of Coherent Sources (DICS)''' can find coherence between any two pairs of voxels in the brain or between an external source and brain voxels. DICS requires time-frequency-transformed data and can find coherence for evoked and induced activity.

The following imaging methods provide an image of brain activity based on a distributed multiple source model:
* '''CLARA''' is an iterative application of LORETA images, focusing the obtained 3D image in each iteration step.
* '''LAURA '''uses a spatial weighting function that has the form of a local autoregressive function.
* '''LORETA''' has the 3D Laplacian operator implemented as spatial weighting prior.
* '''sLORETA''' is an unweighted minimum norm that is standardized by the resolution matrix.
* '''swLORETA '''is equivalent to sLORETA, except for an additional depth weighting.
* '''SSLOFO '''is an iterative application of standardized minimum norm images with consecutive shrinkage of the source space.
* A '''User-defined volume image''' allows to experiment with the different imaging techniques. It is possible to specify user-defined parameters for the family of distributed source images to create a new imaging technique.
* Bayesian source imaging: '''SESAME''' uses a semi-automated Bayesian approach to estimate the number of dipoles along with their parameters.

'''Surface image:'''

* The '''Surface Minimum Norm Image'''. If no individual MRI is available, the minimum norm image is displayed on a standard brain surface and computed for standard source locations. If available, an individual brain surface is used to construct the distributed source model and to image the brain activity.
* '''Cortical LORETA'''. Unlike classical LORETA, cortical LORETA is not computed in a 3D volume, but on the cortical surface.
* '''Cortical CLARA'''. Unlike classical CLARA, cortical CLARA is not computed in a 3D volume, but on the cortical surface.

'''Discrete model probing:'''

These images do not visualize source activity. Rather, they visualize properties of the currently applied discrete source model:
* The '''Multiple Source Probe Scan (MSPS)''' is a tool for the validation of a discrete multiple source model.
* The '''Source Sensitivity image''' displays the sensitivity of a selected source in the current discrete source model and is therefore data independent.

== Multiple Source Beamformer (MSBF) in the Time-frequency Domain ==

 
'''Short mathematical introduction'''

The BESA beamformer is a modified version of the linearly constrained minimum variance vector beamformer in the time-frequency domain as described in [https://dx.doi.org/10.1073/pnas.98.2.694 Gross et al., "Dynamic imaging of coherent sources: Studying neural interactions in the human brain", PNAS 98, 694-699, 2001]. It allows to image evoked and induced oscillatory activity in a user-defined time-frequency range, where time is taken relative to a triggered event.

The computation is based on a transformation of each channel's single trial data from the time domain into the time-frequency domain. This transformation is performed by the BESA Research Source Coherence module and leads to the complex spectral density Si (f,t), where i is the channel index and f and t denote frequency and time, respectively. Complex cross spectral density matrices C are computed for each trial:

<math>\mathrm{C}_{ij}\left( f,t \right) = \mathrm{S}_{i}\left( f,t \right) \cdot \mathrm{S}_{j}^{*}\left( f,t \right)</math>


The output power P of the beamformer for a specific brain region at location r is then computed by the following equation:

<math>\mathrm{P}\left( r \right) = \operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{-1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{-1}</math>


Here, Cr-1 is the inverse of the SVD-regularized average of Cij(f,t) over trials and the time-frequency range of interest; L is the leadfield matrix of the model containing a regional source at target location r and, optionally, additional sources whose interference with the target source is to be minimized; tr'[] is the trace of the [3×3] (MEG:[2×2]) submatrix of the bracketed expression that corresponds to the source at target location r.

In BESA Research, the output power P(r) is normalized with the output power in a reference time-frequency interval Pref(r). A value q ist defined as follows:

<math> \mathrm{q}\left( r \right) =
\begin{cases}
\sqrt{\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}(r)}} - 1 = \sqrt{\frac{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{\text{ref},r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}} - 1, & \text{for }\mathrm{P}(r) \geq \mathrm{P}_{\text{ref}}(r) \\

1 - \sqrt{\frac{\mathrm{P}_{\text{ref}}\left( r \right)}{\mathrm{P}\left( r \right)}} = 1 - \sqrt{\frac{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{\text{ref},r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}}, & \text{for }\mathrm{P}(r) < \mathrm{P}_{\text{ref}}(r)
\end{cases} </math>


Pref can be computed either from the corresponding frequency range in the baseline of the same condition (i.e. the beamformer images event-related power increase or decrease) or from the corresponding time-frequency range in a control condition (i.e. the beamformer images differences between two conditions). The beamformer image is constructed from values q(r) computed for all locations on a grid specified in the '''General Settings tab'''. For MEG data, the innermost grid points within a sphere of approx. 12% of the head diameter are assigned interpolated rather than calculated values).
q-values are shown in %, where where q[%] = q*100. Alternatively to the definition above, q can also be displayed in units of dB:

<math>\mathrm{q}\left\lbrack \text{dB} \right\rbrack = 10 \cdot \log_{10}\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}</math>


A beamformer operator is designed to pass signals from the brain region of interest r without attenuation, while minimizing interference from activity in all other brain regions. Traditional single-source beamformers are known to mislocalize sources if several brain regions have highly correlated activity. Therefore, the BESA beamformer extends the traditional single-source beamformer in order to implicitly suppress activity from possibly correlated brain regions. This is achieved by using a multiple source beamformer calculation that contains not only the leadfields of the source at the location of interest r, but also those of possibly interfering sources. As a default, BESA Research uses a bilateral beamformer, where specifically contributions from the homologue source in the opposite hemisphere are taken into account (the matrix L thus being of dimension N×6 for EEG and N×4 for MEG, respectively, where N is the number of sensors). This allows for imaging of highly correlated bilateral activity in the two hemispheres that commonly occurs during processing of external stimuli.

In addition, the beamformer computation can take into account possibly correlated sources at arbitrary locations that are specified in the current solution. This is achieved by adding their leadfield vectors to the matrix L in the equation above.

'''Applying the Beamformer'''

This chapter illustrates the usage of the BESA beamformer. The displayed figures are generated using the file ''''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''' (see BESA Tutorial 12: "''Time-frequency analysis, Connectivity analysis, and Beamforming''").

'''Starting the beamformer from the time-frequency window'''

The BESA beamformer is applied in the time-frequency domain and therefore requires the Source Coherence module to be enabled. The time-frequency beamformer is especially useful to image in- or decrease of induced oscillatory activity. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot. For instructions on how to initiate a beamformer computation in the time-frequency window, please refer to Chapter '''[[Source_Coherence_How_to...#How_to_Start_the_Beamformer_from_the_Time-Frequency_Window|How to Create Beamformer Images]]'''.

After the beamformer computation has been initiated in the time-frequency window, the source analysis window opens with an enlarged 3D image of the q-value computed with a '''bilateral beamformer'''. The result is superimposed onto the MR image assigned to the data set (individual or standard).

[[Image:SA 3Dimaging (5).gif]]

''Beamformer image after starting the computation in the Time-Frequency window. A bilateral pair of sources in the auditory cortex accounts for the highly correlated oscillatory induced activity. Only the bilateral beamformer manages to separate these activities; a traditional single-source beamformer would merge the two sources into one image maximum in the head center instead.''

'''Multiple source beamformer in the Source Analysis window'''

The 3D imaging display is part of the source analysis window. If you press the '''Restore''' button at the right end of the title bar of the 3D window, the window appears at the bottom right of the source analysis window. In the channel box, the averaged (evoked) data of the selected condition is shown. When a control condition was selected, its average is appended to the average of the target condition.

[[Image:SA 3Dimaging (6).gif]]

''Source Analysis window with beamformer image. The two sources have been added using the '''''Switch to''''' '''''Maximum''''' and '''''Add Source '''''toolbar buttons (see below). Source waveforms are computed from the displayed averaged data. Therefore, they do not represent the activity displayed in the beamformer image, which in this simulation example is induced (i.e. not phase-locked to the trigger)!''

When starting the beamformer from the time-frequency window, a bilateral beamformer scan is performed. In the source analysis window, the beamformer computation can be repeated taking into account possibly correlated sources that are specified in the current solution. Interfering activities generated by all sources in the current solution that are in the 'On' state are specifically suppressed ('''they enter the matrix L in the beamformer calculation''', see Chapter ''Short mathematical description'' above). The computation can be started from the '''Image''' menu or from the '''Image selector button''' dropdown menu. The '''Image''' menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window.

[[Image:SA 3Dimaging (7).gif]]

''Multiple source beamformer image calculated in the presence of a source in the left hemisphere. A '''single''' source scan has been performed. The source set in the current solution accounts for the left-hemispheric q-maximum in the data. Accordingly, the beamformer scan reveals only the as yet unmodeled additional activity in the right hemisphere (note the radiological convention in the 3D image display).''

The beamformer scan can be performed with a '''single''' or a '''bilateral''' source scan. The default scan type depends on the current solution:
* When the beamformer is started from the Time-Frequency window, the Source Analysis window opens with a new solution and a '''bilateral''' beamformer scan is performed.
* When the beamformer is started within the Source Analysis window, the default is
** a scan with a '''single''' source in addition to the sources in the current solution, if at least one source is active.
** a '''bilateral''' scan if no source in the current solution is active.

The default scan type is the multiple source beamformer. The non-default scan type can be enforced using the corresponding ''Volume Image / Beamformer'' entry in the '''Image''' menu.

'''Inserting Sources out of the Beamformer Image'''

The beamformer image can be used to add sources to the current solution. A simple double-click anywhere in the 2D- or 3D-view will generate a non-oriented regional source at the corresponding location. However, a better and easier way to create sources at image maxima and minima is to use the toolbar buttons '''Switch to Maximum''' [[Image:SA 3Dimaging (8).gif]] and '''Add Source''' [[Image:SA 3Dimaging (9).gif]].

Use the '''Switch to Maximum''' button to place the red crosshair of the 3D window onto a local image maximum or minimum. Hitting the '''Add Source''' button creates a regional source at the location of the crosshair and therefore ensures the exact placement of the source at the image extremum. Moreover, the '''Add Source''' button generates an oriented regional source. BESA Research automatically estimates the source orientation that contributes most to the power in the target time-frequency interval (or the reference time-frequency interval, if its power is larger than that in the target interval). The accuracy of this orientation estimate depends largely on the noise content of the data. The smaller the signal-to-noise ratio of the data, the lower is the accuracy of the orientation estimate. '''This feature allows to use the beamformer as a tool to create a source montage for source coherence analysis, where it is of advantage to work with oriented sources'''.

'''Notes:'''

* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image '''menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the''' Image''' menu.
* For scaling options, use the [[Image:SA 3Dimaging (10).gif]] and [[Image:SA 3Dimaging (11).gif]] '''Image Scale toolbar''' buttons.
* Parameters used for the beamformer calculations can be set in the '''Standard Volumes''' of the ''Image Settings dialog box.''

== Dynamic Imaging of Coherent Sources (DICS) ==

 
'''Short mathematical introduction'''

Dynamic Imaging of Coherent Sources (DICS) is a sophisticated method for imaging cortico-cortical coherence in the brain, or coherence between an external reference (e.g. EMG channel) and cortical structures. DICS can be applied to localize evoked as well as induced coherent cortical activity in a user-defined time-frequency range.

DICS was implemented in BESA closely following [https://dx.doi.org/10.1073/pnas.98.2.694 Gross et al., "Dynamic imaging of coherent sources: Studying neural interactions in the human brain", PNAS 98, 694-699, 2001].

The computation is based on a transformation of each channel's single trial data from the time domain into the frequency domain. This transformation is performed by the BESA Research Coherence module and results in the complex spectral density matrix that is used for constructing the spatial filter similar to beamforming.

DICS computation yields a 3-D image, each voxel being assigned a coherence value. Coherence values can be described as a neural activity index and do not have a unit. The neural activity index contrasts coherence in a target time-frequency bin with coherence of the same time-frequency bin in a baseline.

'''DICS for cortico-cortical coherence is computed as follows:'''

Let L(r) be the leadfield in voxel r in the brain and C the complex cross-spectral density matrix. The spatial filter W(r) for the voxel r in the head is defined as follows:

<math>W\left( r \right) = \left\lbrack L^{T}\left( r \right) \cdot C^{- 1} \cdot L\left( r \right) \right\rbrack^{- 1} \cdot L^{T}(r) \cdot C^{- 1}</math>


The cross-spectrum between two locations (voxels) r1 and r2 in the head are calculated with the following equation:

<math>C_{s}\left( r_{1},r_{2} \right) = W\left( r_{1} \right) \cdot C \cdot W^{*T}\left( r_{2} \right),</math>


where <nowiki>*T</nowiki> means the transposed complex conjugate of a matrix. The cross-spectral density can then be calculated from the cross spectrum as follows:

<math>c_{s}\left( r_{1},r_{2} \right) = \lambda_{1}\left\{ C_{s}\left( r_{1},r_{2} \right) \right\},</math>


where λ1{} indicates the largest singular value of the cross spectrum. Once the cross spectral density is estimated, the connectivity¹(CON) between the two brain regions r1 and r2 are calculated as follows:

<math>\text{CON}\left( r_{1},r_{2} \right) = \frac{c_{s}^{\text{sig}}\left( r_{1},r_{2} \right) - c_{s}^{\text{bl}}(r_{1},r_{2})}{c_{s}^{\text{sig}}\left( r_{1},r_{2} \right) + c_{s}^{\text{bl}}(r_{1},r_{2})},</math>


where cssig is the cross-spectral density for the signal of interest between the two brain regions r1 and r2, and csbl is the corresponding cross spectral density for the baseline or the control condition, respectively. In the case DICS is computed with a cortical reference, r1 is the reference region (voxel) and remains constant while r2 scans all the grid points within the brain sequentially. In that way, the connectivity between the reference brain region and all other brain regions is estimated. The value of CON(r1, r2) falls in the interval [-1 1]. If the cross-spectral density for the baseline is 0 the connectivity value will be 1. If the cross-spectral density for the signal is 0 the connectivity value will be -1.

¹ Here, the term connectivity is used rather than coherence, as strictly speaking the coherence equation is defined slightly differently. For simplicity reasons the rest of the tutorial uses the term coherence.

'''DICS for cortico-muscular coherence is computed as follows:'''

When using an external reference, the equation for coherence calculation is slightly different compared to the equation for cortico-cortical coherence. First of all, the cross-spectral density matrix is not only computed for the MEG/EEG channels, but the external reference channel is added. This resulting matrix is Call. In this case, the cross-spectral density between the reference signal and all other MEG/EEG channels is called cref. It is only one column of Call. Hence, the cross-spectrum in voxel r is calculated with the following equation:

<math>C_{s}\left( r \right) = W\left( r \right) \cdot c_{\text{ref}}</math>


and the corresponding cross-spectral density is calculated as the sum of squares of Cs:

<math>c_{s}\left( r \right) = \sum_{i = 1}^{n}{C_{s}\left( r \right)_{i}^{2}},</math>


where n is 2 for MEG and 3 for EEG. This equation can also be described as the squared Euclidean norm of the cross-spectrum:

<math>c_{s}\left( r \right) = \left\| C_{s} \right\|^{2},</math>


The power in voxel r is calculated as in the cortico-cortical case:

<math>p\left( r \right) = \lambda_{1}\left\{ C_{s}(r,r) \right\}.</math>


At last, coherence between the external reference and cortical activity is calculated with the equation:

<math>\text{CON}\left( r \right) = \frac{c_{s}(r)}{p\left( r \right) \cdot C_{\text{all}}(k,k)},</math>


where Call(k, k) is the (k,k)-th diagonal element of the matrix Call.

DICS is particularly useful, if coherence is to be calculated without an a-priory source model (in contrast to source coherence based on pre-defined source montages). However, the recommended analysis strategy for DICS is to use a brain source as a starting point for coherence calculation that is known to contribute to the EEG/MEG signal of interest. For example, one might first run a beamformer on the time-frequency range of interest and use the voxel with the strongest oscillatory activity as a starting point for DICS. The resulting coherence image will again lead to several maxima (ordered by magnitude), which in turn can serve as starting points for DICS calculation. This way, it is possible to detect even weak sources that show coherent activity in the given time-frequency range.

The other significant application for DICS is estimating coherence between an external source and voxels in the brain. For example, an external source can be muscle activity recoded by an electrode placed over the according peripheral region. This way, the direct relationship between muscle activity and brain activation can be measured.

'''Starting DICS computation from the Time-Frequency Window'''

DICS is particularly useful, if coherence in a user-defined time-frequency bin (evoked or induced) is to be calculated between any two brain regions or between an external reference and the brain. DICS runs only on time-frequency decomposed data, so time-frequency analysis needs to be run before starting DICS computation.

To start the DICS computation, left-drag a window over a selected time-frequency bin in the Time-Frequency Window. Right-click and select “Image”. A dialogue will open (see fig. 1) prompting you to specify time and frequency settings as well as the baseline period. It is recommended to use a baseline period of equal length as the data period of interest. Make sure to select “DICS” in the top row and press “'''Go'''”.

[[Image:SA 3Dimaging (21).gif|450px|thumb|c|none|Fig. 1: Time and frequency settings for DICS and MSBF]]

Next, a window will appear allowing you to specify the reference source for coherence calculation (see fig. 2). It is possible to select a channel (e.g. EMG) or a brain source. If a brain source is chosen and no source analysis was computed beforehand, the option “Use current cross-hair position” must be chosen. In case discrete source analysis was computed previously, the selected source can be chosen as the reference for DICS. Please note that DICS can be re-computed with any cross-hair or source position at a later stage.

[[Image:SA 3Dimaging (1).jpg|400px|thumb|c|none|Fig. 2: Possible options for choosing the reference]]

Confirming with “'''OK'''” will start computation of coherence between the selected channel/voxel and all other brain voxels. In case DICS is computed for a reference source in the brain, it can be advantageous to run a beamforming analysis in the selected time-frequency window first and use one of the beamforming maxima as reference for DICS. Fig. 3 shows an example for DICS calculation.

[[Image:SA 3Dimaging (22).gif|500px|thumb|c|none|Fig. 3: Coherence between left-hemispheric auditory areas and the selected voxel in the right auditory cortex.]]

Coherence values range between -1 and 1. If coherence in the signal is much larger than coherence in the baseline (control condition) then the DICS value is going to approach 1. Contrary, if coherence in the baseline is much larger than coherence in the signal, then the DICS value is going to approach -1. At last, if coherence in the signal is equal to coherence in the baseline, then the DICS value is 0.

In case DICS is to be re-computed with a different reference, simply mark the desired reference position by placing the cross-hair in the anatomical view and select “DICS” in the middle panel of the source analysis window (see Fig. 4). In case an external reference is to be selected, click on “DICS” in the middle panel to bring up the DICS dialogue (see. Fig. 2) and select the desired channel. Please note that DICS computation will only be available after running time-frequency analysis.

[[Image:SA 3Dimaging (23).gif|700px|thumb|c|none|Fig. 4: Integration of DICS in the Source Analysis window]]

== Multiple Source Beamformer (MSBF) in the Time Domain ==
''This feature requires BESA Research 7.0 or higher.''

'''Short mathematical introduction'''

Beamforming approach can be also applied in the time domain data. This approach was introduced as linearly constrained minimum variance (LCMV) beamformer (Van Veen et al., 1997). It allows to image evoked activity in a user-defined time range, where time is taken relative to a triggered event, and to estimate source waveforms using the calculated spatial weight at locations of interest. For an implementation of the beamformer in the time domain, data covariance matrices are required, while complex cross spectral density matrices are used for the beamformer approaches in the time-frequency domain as described in the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section.

The bilateral beamformer introduced in the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section is also implemented for the time-domain beamformer to take into account contributions from the homologue source in the opposite. This allows for imaging of highly correlated bilateral activity in the two hemispheres that commonly occurs during processing of external stimuli. In addition, the beamformer computation can take into account possibly correlated sources at arbitrary locations.

The beamformer spatial weight W(r) for the voxel r in the brain is defined as follows (Van Veen et al., 1997):

<math>\mathrm{W}(r) = [\mathrm{L}^T(r)\mathrm{C}^{-1}\mathrm{L}(r)]^{-1}\mathrm{L}^T(r)\mathrm{C}^{-1}</math>


where <math>\mathrm{C}^{-1}</math> is the inversed regularized average of covariance matrix over trials, '''L''' is the leadfield matrix of the model containing a regional source at target location r and optionally additional sources whose interference with the target source is to be minimized. The beamformer spatial weight '''W'''(r) can be applied to the measured data to estimate source waveform at a location r (beamformer virtual sensor):

<math>\mathrm{S}(r,t) = \mathrm{W}(r)\mathrm{M}(t)</math>


where '''S'''(r,t) represents the estimated source waveform and '''M'''(t) represents measured EEG or MEG signals. The output power P of the beamformer for a specific brain region at location r is computed by the following equation:

<math>\mathrm{P}(r) = \operatorname{tr^{'}}[\mathrm{W}(r) \cdot \mathrm{C} \cdot \mathrm{W}^T(r)]</math>


where tr’[ ] is the trace of the [3×3] (MEG: [2×2]) submatrix of the bracketed expression that corresponds to the source at target location r.

Beamformer can suppress noise sources that are correlated across sensors. However, uncorrelated noise will be amplified in a spatially non-uniform manner, with increasing distortion with increasing distance from the sensors (Van Veen et al., 1997; Sekihara et al., 2001). For this reason, estimated source power should be normalized by a noise power. In BESA Research, the output power P(r) is normalized with the output power in a baseline interval or with the output power of a uncorrelated noise: P(r) / Pref (r).

The time-domain beamformer image is constructed from values q(r) computed for all locations on a grid specified in the '''General Settings''' tab. A value q(r) is defined as described in
the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section with data covariance matrices instead of cross-spectral density matrices.

'''Applying the Beamformer'''

This chapter illustrates the usage of the BESA beamformer in the time domain. The displayed figures are generated using the file ‘Examples/ERP-Auditory-Intensity/S1.cnt’.

'''''Starting the time-domain beamformer from the Average tab of the Paradigm dialog box'''''

The time-domain beamformer is needed data covariance matrices and therefore requires the ERP module to be enabled. After the beamformer computation has been initiated in the '''Average tab of the Paradigm dialog box''', the source analysis window opens with an enlarged 3D image of the q-value computed with a bilateral beamformer. The result is superimposed onto the MR image assigned to the data set (individual or standard).

[[File:MSBF4.png|500px|thumb|c|none|Beamformer image for auditory evoked data after starting the computation in the '''Average tab of the Paradigm dialog box'''. The bilateral beamformer manages to separate the activities in auditory areas, while a traditional single-source beamformer would merge the two sources into one image maximum in the head center instead.]]

'''''Multiple-source beamformer in the Source Analysis window'''''

The 3D imaging display is part of the source analysis window. In the Channel box, the averaged (evoked) data of the selected condition is shown. Selected covariance intervals in the ERP module can be checked in the Channel box. The red, gray, and blue rectangles indicate signal, baseline, and common interval, respectively.

[[File:MSBF55.png|700px|thumb|c|none|Source Analysis window with beamformer image. The two beamformer virtual sensors have been added using the Switch to Maximum and Add Source toolbar buttons (see below).
Source waveforms are computed using the beamformer spatial weights and the displayed averaged data (the noise normalized weights (5% noise) option was used to compute the beamformer image).]]

When starting the beamformer from the '''Average tab of the Paradigm dialog box''', the bilateral beamformer scan is performed. In the source analysis window, the beamformer computation can be repeated taking into account possibly correlated sources that are specified in the current solution. Interfering activities generated by all sources in the current solution that are in the 'On' state are specifically suppressed (they enter the leadfield matrix L in the beamformer calculation). The computation can be started from the '''Image''' menu or from the Image selector button [[File:MSBF_Button.png|22px|Image: 22 pixels]] dropdown menu. The Image menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window.

[[File:MSBF66.png|700px|thumb|c|none|Multiple-source beamformer image calculated in the presence of a source in the left hemisphere. A single-source scan has been performed instead of a bilateral beamforemr. The source set in the current solution accounts for the left-hemispheric q-maximum in the data. Accordingly, the beamformer scan reveals only the as yet unmodeled additional activity in the right hemisphere (note the radiological convention in the 3D image display). The source waveform of the beamformer virtual sensor in the left hemisphere is not shown since the location (blue square in the figure) is not considered for the multiple-source beamformer.]]

The beamformer scan can be performed with a single or a bilateral source scan. The default scan type depends on the current solution:

When the beamformer is started from the '''Average tab of the Paradigm dialog box''' the Source Analysis window opens with a new solution and a bilateral beamformer scan is performed.

When the beamformer is started within the Source Analysis window, the default is:
* a scan with a single source in addition to the sources in the current solution, if at least one source is active.
* a bilateral scan if no source in the current solution is active.
* a scan with a single source when scalar-type beamformer is selected in the '''beamformer option dialog box'''.

The default scan type is the multiple source beamformer. The non-default scan type can be enforced using the corresponding Volume Image / Beamformer entry in the Image main
menu or in the beamformer option dialog box (only for the time-domain beamformer).

'''Inserting Sources as Beamformer Virtual Sensor out of the Beamformer Image'''

This is similar to the inserting sources out of the beamformer image in Multiple Source Beamformer (MSBF) in the Time-frequency Domain section.

The beamformer image can be used to add beamformer virtual sensors to the current solution. A simple double-click anywhere in the 3D view (not in the 2D view) will generate a source at the corresponding location. A better and easier way to create sources at image maxima and minima is to use the toolbar buttons '''Switch to Maximum''' [[Image:SA 3Dimaging (8).gif]] and '''Add Source''' [[Image:SA 3Dimaging (9).gif]].

This feature allows to use the beamformer as a tool to create a source montage for '''source coherence''' analysis. A source montage file (*.mtg) for beamformer virtual sensors can
be saved using File \ Save Source Montage As… entry.

The time-domain beamformer image can be also used to add regional or dipole sources to the current solution. Press '''N''' key when there is no source in the current source array or there is more than one beamformer virtual sensor. To create a new source array for beamformer virtual sensor, press '''N''' key when there is more than one regional or dipole source in the current source array.

'''Notes'''

* You can hide or re-display the last computed image by selecting ''Hide Image'' entry in the '''Image''' menu.
* The current image can be exported to ASCII, ANALYZE, or BrainVoyager (*.vmp) format from the '''Image''' menu.
* For scaling options, use [[Image:SA 3Dimaging (10).gif]] and [[Image:SA 3Dimaging (11).gif]] '''Image Scale toolbar''' buttons.
* Parameters used for the beamformer calculations can be set in the '''Standard Volume tab of the Image Settings dialog box'''.
* Note that Model, Residual, Order, and Residual variance are not shown for the beamformer virtual sensor type sources.

'''References'''

* Sekihara, K., Nagarajan, S. S., Poeppel, D., Marantz, A., & Miyashita, Y. (2001). Reconstructing spatio-temporal activities of neural sources using an MEG vector beamformer technique. IEEE Transactions on Biomedical Engineering, 48(7), 760–771.

* Van Veen, B. D., Van Drongelen, W., Yuchtman, M., & Suzuki, A. (1997). Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Transactions on Biomedical Engineering, 44(9), 867–880

== CLARA ==

CLARA ('Classical LORETA Analysis Recursively Applied') is an iterative application of weighted LORETA images with a reduced source space in each iteration.

In an initialization step, a LORETA image is calculated. Then in each iteration the following steps are performed:

# The obtained image is spatially smoothed (this step is left out in the first iteration).
# All grid points with amplitudes below a threshold of 1% of the maximum activity are set to zero, thus being effectively eliminated from the source space in the following step.
# The resulting image defines a spatial weighting term (for each voxel the corresponding image amplitude).
# A LORETA image is computed with an additional spatial weighting term for each voxel as computed in step 3. By the default settings in BESA Research, the regularization values used in the iteration steps are slightly higher than that of the initialization LORETA image.

The procedure stops after 2 iterations, and the image computed in the last iteration is displayed. Please note that you can change all parameters by creating a user-defined volume image.

The advantage of CLARA over non-focusing distributed imaging methods is visualized by the figure below. Both images are computed from the N100 response in an auditory oddball experiment (file '''Oddball.fsg''' in subfolder ''fMRI+EEG-RT-Experiment'' of the ''Examples'' folder). The CLARA image is much more focal than the sLORETA image, making it easier to determine the location of the image maxima.

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (24).gif|thumb|350px|sLORETA image]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (25).gif|thumb|350px|CLARA image]] </li>
</ul></div>

'''Notes:'''

* Starting CLARA: CLARA can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]'' for important information on regularization of distributed inverses.

== LAURA ==

LAURA (Local Auto Regressive Average) belongs to the distributed inverse method of the family of weighted minimum norm methods ([https://doi.org/10.1023/A:1012944913650 Grave de Peralta Menendeza et al., "Noninvasive Localization of Electromagnetic Epileptic Activity. I. Method Descriptions and Simulations", BrainTopography 14(2), 131-137, 2001]). LAURA uses a spatial weighting function that includes depth weighting and that term has the form of a local autoregressive function.

The source activity is estimated by applying the general formula for a weighted minimum norm:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T}\left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings.''

In LAURA, V contains both a depth weighting term W and a representation of a local autoregressive function A. V is computed as:

<math>\mathrm{V} = \left( \mathrm{U}^{T} \cdot \mathrm{U} \right)^{-1}</math>


where

<math>\mathrm{U} = \left( \mathrm{W} \cdot \mathrm{A} \right) \otimes \mathrm{I}_{3}</math>


Here, <math>\otimes</math> denotes the Kronecker product. I3 is the [3×3] identity matrix. W is an [s×s] diagonal matrix (with s the number of source locations on the grid), where each diagonal element is the inverse of the maximum singular value of the corresponding regional source's leadfields. The formula for the diagonal components Aii and the off-diagonal components Aik are as follows:

<math>\mathrm{A}_{ii} = \frac{26}{\mathrm{N}_{i}}\sum_{k \subset V_{i}}^{}\frac{1}{\mathrm{d}_{ik}^{2}}</math>


<math>
\mathrm{A}_{ik} =
\begin{cases}
- 1/\operatorname{dist}\left( i,k \right)^{2}, & \text{if } k \subset V_{i} \\
0, & \text{otherwise}
\end{cases}
</math>


Here, Vi is the vicinity around grid point i that includes the 26 direct neighbors.

The LAURA image in BESA Research displays the norm of the 3 components of S at each location r. Using the menu function ''Image / Export Image As... ''you have the option to save this norm of S or alternatively all components separately to disk.

'''Notes:'''

* '''Grid spacing:''' Due to memory limitations, LAURA images require a grid spacing of 7 mm or more.
* '''Computation time:''' Computation speed during the first LAURA image calculation depends on the grid spacing (computation is faster with larger grid spacing). After the first computation of a LAURA image, a '''*.laura''' file is stored in the data folder, containing intermediate results of the LAURA inverse. This file is used during all subsequent LAURA image computations. Thereby, the time needed to obtain the image is substantially reduced.
* '''MEG:''' In the case of MEG data, an additional constraint is implemented in the LAURA algorithm that prevents solutions from containing radial source currents (compare Pascual-Marqui, ISBET Newsletter 1995, 22-29). In MEG, an additional source space regularization is necessary in the inverse matrix operation required compute V
* '''Starting LAURA:''' LAURA can be started from the''' Image''' menu or from the '''Image Selection''' button.
* '''Regularization:''' Please refer to Chapter'' “Regularization of distributed volume images” ''for important information on regularization of distributed inverses.

== LORETA ==

LORETA ("Low Resolution Electromagnetic Tomography") is a distributed inverse method of the family of ''weighted minimum norm'' methods. LORETA was suggested by R.D. Pascual-Marqui (International Journal of Psychophysiology. 1994, 18:49-65). LORETA is characterized by a smoothness constraint, represented by a discrete 3D Laplacian.

The source activity is estimated by applying the general formula for a weighted minimum norm:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T}\left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings.''

In LORETA, V contains both a depth weighting term and a representation of the 3D Laplacian matrix. V is computed as:

<math>\mathrm{V} = \left( \mathrm{U}^{T} \cdot \mathrm{U} \right)^{- 1}</math>


where

<math>\mathrm{U} = \left( \mathrm{W} \cdot \mathrm{A} \right) \otimes \mathrm{I}_{3}</math>


Here, <math>\otimes</math> denotes the Kronecker product. I3 is the [3x3] identity matrix. W is an [sxs] diagonal matrix (with s the number of source locations on the grid), where each diagonal element is the inverse of the maximum singular value of the corresponding regional source's leadfields. A contains the 3D Laplacian and is computed as

<math>\mathrm{A} = \mathrm{Y} - \mathrm{I}_{s}</math>


with Is the [sxs] identity matrix, where s is the number of sources (= three times the number of grid points) and

<math>\mathrm{Y} = \frac{1}{2}\left\{ \mathrm{I}_{s} + \left\lbrack \operatorname{diag}\left( \mathrm{Z} \cdot \left\lbrack 111 \ldots 1 \right\rbrack^{T} \right) \right\rbrack^{- 1} \right\} \cdot \mathrm{Z}</math>


where

<math>
\mathrm{Z}_{ik} =
\begin{cases}
1/6, & \text{if } \operatorname{dist}\left( i,k \right) = 1 \text{ grid point} \\
0, & \text{otherwise}
\end{cases}
</math>


The LORETA image in BESA Research displays the norm of the 3 components of S at each location r. Using the menu function ''Image / Export Image As... ''you have the option to save this norm of S or alternatively all components separately to disk.

'''Notes:'''
* '''Grid spacing:''' Due to memory limitations, LORETA images require a grid spacing of 5 mm or more.
* '''Computation time:''' Computation speed during the first LORETA image calculation depends on the grid spacing (computation is faster with larger grid spacing). After the first computation of a LORETA image, a '''<nowiki>*.loreta</nowiki>''' file is stored in the data folder, containing intermediate results of the LORETA inverse. This file is used during all subsequent LORETA image computations. Thereby, the time needed to obtain the image is substantially reduced.
* '''MEG''': In the case of MEG data, an additional constraint is implemented in the LORETA algorithm that prevents solutions from containing radial source currents (Pascual-Marqui, ISBET Newsletter 1995, 22-29). In MEG, an additional source space regularization is necessary in the inverse matrix operation required compute V.
* '''Starting LORETA:''' LORETA can be started from the''' Image''' menu or from the '''Image Selection '''button.
* '''Regularization:''' Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed source models.

== sLORETA ==

This distributed inverse method consists of a ''standardized, unweighted minimum norm''. The method was originally suggested by R.D. Pascual-Marqui (Methods & Findings in Experimental & Clinical Pharmacology 2002, 24D:5-12) Starting point is an unweighted minimum norm computation:

<math>\mathrm{S}_{\text{MN}}\left( t \right) = \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings''.

This minimum norm estimate is now standardized to produce the sLORETA activity at a certain brain location r:

<math>\mathrm{S}_{\text{sLORETA}, r} = \mathrm{R}_{rr}^{-1/2} \cdot \mathrm{S}_{\text{MN},r}</math>


SsMN,r is the [3x1] (MEG: [2x1]) minimum norm estimate of the 3 (MEG: 2) dipoles at location r. Rrr is the [3x3] (MEG: [2x2]) diagonal block of the resolution matrix R that corresponds to the source components at the target location r. The resolution matrix is defined as:

<math>\mathrm{R} = \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{L}^{T} + \lambda \cdot \mathrm{I} \right)^{-1} \cdot \mathrm{L}</math>


The sLORETA image in BESA Research displays the norm of SsLORETA, r at each location r. Using the menu function ''Image / Export Image As...'' you have the option to save this norm of SsLORETA, r or alternatively all components separately to disk.

'''Notes:'''

* sLORETA can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter [[#Regularization_of_distributed_volume_images|''Regularization of distributed volume images'']] for important information on regularization of distributed inverses.

== swLORETA ==

This distributed inverse method is a ''standardized, depth-weighted minimum norm'' (E. Palmero-Soler et al 2007 Phys. Med. Biol. 52 1783-1800). It differs from sLORETA only by an additional depth weighting.

Starting point is a depth-weighted minimum norm computation:

<math>\mathrm{S}_{\text{MN}}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings''.

V is the diagonal depth weighting matrix. For s grid locations, V is of dimension [3s x 3s] (MEG: [2s x 2s]). Each diagonal element of V is the inverse of the first singular value of the leadfield of the corresponding regional source. Hence, the first 3 (MEG: 2) diagonal elements equal the inverse of the largest eigenvalue of the leadfield matrix of regional source 1, and so on.

This minimum norm estimate is now standardized to produce the swLORETA activity at a certain brain location r:

<math>\mathrm{S}_{\text{swLORETA},r} = \mathrm{R}_{rr}^{-1/2} \cdot \mathrm{S}_{\text{MN},r}</math>


SsMN,r is the [3x1] (MEG: [2x1]) depth-weighted minimum norm estimate of the regional source at location r. Rrr is the [3x3] (MEG: [2x2]) diagonal block of the resolution matrix R that corresponds to the source components at the target location r. The resolution matrix is defined as:

<math>\mathrm{R} = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} + \lambda \cdot \mathrm{I} \right)^{-1} \cdot \mathrm{L}</math>


The swLORETA image in BESA Research displays the norm of SswLORETA, r at each location r. Using the menu function ''Image / Export Image As...'' you have the option to save this norm of SswLORETA, r or alternatively all components separately to disk.

'''Notes:'''

* sLORETA can be started from the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed inverses.

== sSLOFO ==

SSLOFO (standardized shrinking LORETA-FOCUSS) is an iterative application of weighted distributed source images with a reduced source space in each iteration ([https://dx.doi.org/10.1109/TBME.2005.855720 Liu et al., "Standardized shrinking LORETA-FOCUSS (SSLOFO): a new algorithm for spatio-temporal EEG source reconstruction", IEEE Transactions on Biomedical Engineering 52(10), 1681-1691, 2005]).

In an initialization step, an [[#sLORETA | sLORETA]] image is calculated. Then in each iteration the following steps are performed:

# A weighted minimum norm solution is computed according to the formula <math display="inline">\mathrm{S} = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}</math> . Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D is the data at the time point under consideration. V is a diagonal spatial weighting matrix that is computed in the previous iteration step. In the first iteration, the elements of V contain the magnitudes of the initially computed LORETA image.
# Standardization of this weighted minimum norm image is performed with the resolution matrix as in [[#sLORETA | sLORETA]].
# The obtained standardized weighted minimum norm image is being smoothed to get Ssmooth.
# All voxels with amplitudes below a threshold of 1% of the maximum activity get a weight of zero in the next iteration step, thus being effectively eliminated from the source space in the next iteration step.
# For all other voxels, compute the elements of the spatial weighting matrix V to be used in the next iteration as follows: <math display="inline">\mathrm{V}_{ii,\text{next iteration}} = \frac{1}{\left\| \mathrm{L}_{i} \right\|} \cdot \mathrm{S}_{ii,\text{smooth}} \cdot \mathrm{V}_{ii,\text{current iteration}}</math>



The procedure stops after 3 iterations. Please note that you can change all parameters by creating a [[#User-Defined Volume Image | user-defined volume image]].

'''Notes:'''
* '''Starting sSLOFO''': sSLOFO can be started from the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''[[#Regularization of distributed volume images | Regularization of distributed volume images]]'' for important information on regularization of distributed inverses.

== User-Defined Volume Image ==

In addition to the predefined 3D imaging methods in BESA Research, it is possible to create user-defined imaging methods based on the general formula for distributed inverses:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. Custom-defined parameters are:

* '''The spatial weighting matrix V''': This may include depth weighting, image weighting, or cross-voxel weighting with a 3D Laplacian (as in LORETA) or an autoregressive function (as in LAURA).
* '''Regularization''': The term in parentheses is generally regularized. Note that regularization has a strong effect on the obtained results. Please refer to chapter ''Regularization of Distributed Volume Images''for more information.
* '''Standardization''': Optionally, the result of the distributed inverse can be standardized with the resolution matrix (as in sLORETA).
* '''Iterations''': Inverse computations can be applied iteratively. Each iteration is weighted with the image obtained in the previous iteration.

All parameters for the user-defined volume image are specified in the User-Defined Volume Tab of the Image Settings dialog box. Please refer to chapter ''User-Defined Volume Tab'' for details.

'''Notes:'''

* Starting the user-defined volume image: the image calculation can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''Regularization of distributed volume images'' for important information on regularization of distributed inverses.

== Regularization of distributed volume images ==

Distributed source images require the inversion of a term of the form L V LT. This term is generally regularized before its inversion. In BESA Research, selection can be made between two different regularization approaches (parameters are defined in the ''Image Settings dialog box''):

* '''Tikhonov regularization''': In Tikhonov regularization, the term L V LT is inverted as (L V LT +λ I)-1. Here, l is the regularization constant, and I is the identity matrix.
** One way of determining the optimum regularization constant is by minimizing the ''generalized cross'' ''validation error'' (CVE).
** Alternatively, the regularization constant can be specified manually as a percentage of the trace of the matrix L V LT.
* '''TSVD''': In the truncated singular value decomposition (TSVD) approach, an SVD decomposition of L V LT is computed as  L V LT = U S UT, where the diagonal matrix S contains the singular values. All singular values smaller than the specified percentage of the maximum singular values are set to zero. The inverse is computed as U S-1 UT, where the diagonal elements of S-1 are the inverse of the corresponding non-zero diagonal elements of S.

Regularization has a critical effect on the obtained distributed source images. The results may differ completely with different choices of the regularization parameter (see examples below). Therefore, it is important to evaluate the generated image critically with respect to the regularization constant, and to keep in mind the uncertainties resulting from this fact when interpreting the results. The default setting in BESA Research is a TSVD regularization with a 0.03% threshold. However, this value might need to be adjusted to the specific data set at hand.

The following example illustrates the influence of the regularization parameter on the obtained images. The data used here is condition '''St-Cor of dataset Examples \ TFC-Error-Related-Negativity \ Correct+Error.fsg''' at 176 ms following the visual stimulus. Discrete dipole analysis reveals the main activity in the left and right lateral visual cortex at this latency.

[[File:SA 3Dimaging (42).gif|400px|thumb|c|none|Discrete source model at 176 ms: Main activity in the left and right lateral visual cortex, no visual midline activity.]]

LORETA images computed at this latency depend critically on the choice of the regularization constant. The following 3D images are created with TSVD regularization with SVD cutoffs of 0.1%, 0.005%, and 0.0001%, respectively. The volume grid size was 9 mm. The example demonstrates the dramatic effect of regularization and demonstrates the typical tradeoff between too strong regularization (leading to too smeared 3D images that tend to show blurred maxima) and too small regularization (resulting in too superficial 3D images with multiple maxima).

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (44).gif|thumb|350px|'''SVD cutoff 0.1%''': Regularization too strong. No separation between sources, mislocalization towards the middle of the brain.]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (43).gif|thumb|350px|'''SVD cutoff 0.005%''': Appropriate regularization. Separation of the bilateral activities. Location in agreement with the discrete multiple source model.]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (45).gif|thumb|350px|'''SVD cutoff 0.0001%''': Too small regularization. Mislocalization, too superficial 3D image. ]] </li>
</ul></div>

The automatic determination of the regularization constant using the CVE approach does not necessarily result in the optimum regularization parameter either. In this example, the unscaled CVE approach rather resembles the TSVD image with a cutoff of 0.0001%, i.e. regularization is too small. Therefore, it is advisable to compare different settings of the regularization parameter and make the final choice based on the above-mentioned considerations.

== Cortical LORETA ==

Cortical LORETA is principally the same technique as LORETA, however, Cortical LORETA is not computed in a 3D volume, but on the cortical surface.

The cortical reconstruction in BESA Research fed from BESA MRI is a closed 2D surface with no boundaries and a very close approximation of the actual cortical form. It consists of an irregular triangulated grid.

The Laplace operator that is used for identifying a smooth solution in a three-dimensional space is exchanged with a Laplace operator that runs on the two-dimensional cortical surface.

There is a wide variety of 2D Laplace operators with different characteristics. The general form of the discrete Laplace operator is

<math>\Delta f\left( p_{i} \right) = \frac{1}{d_{i}}\sum_{j \in N(i)}^{}{w_{ij}\left\lbrack f\left( p_{i} \right) - f\left( p_{j} \right) \right\rbrack},</math>


where '''pi''' is the '''i-th''' node of the triangular mesh, '''f(pi) '''is the value of a function f defined on the cortical mesh at the node '''pi''', '''wij''' is the weight for the connection between the nodes '''pi''' and '''pj''' and '''di''' is a normalization factor for the '''i-th''' row of the operator. Furthermore, '''N(i)''' is the set of indices corresponding to the direct (also called "1-ring") neighbors of '''pi'''.

BESA offers the choice of three Laplace operators with slightly different characteristics.

* '''Unweighted Graph Laplacian''': This is the simplest operator. It takes into account only the adjacency of the nodes and not the geometry of the mesh:

<math>
w_{ij} =
\begin{cases}
1, & \text{if } p_{i} \text{ and } p_{j} \text{ are connected by an edge} \\
0, & \text{otherwise}
\end{cases}
</math>

<math>d_{i} = 1</math>


[[Image:SA 3Dimaging (4).jpg |450px]]

* '''Weighted Graph Laplacian:''' This operator is similar to the unweighted graph Laplacian but with different weights for the different connections. The connections between nearby nodes get larger weights than the connections between farther nodes:

<math>w_{ij} = \frac{1}{\operatorname{dist}\left( p_{i},p_{j} \right)}</math>

<math>d_{i} = \sum_{j \in N(i)}^{} {\operatorname{dist}\left(p_{i}, p_{j} \right)}</math>


where '''dist''' ('''pi''' , '''pj''') is the distance between the nodes '''pi '''and '''pj'''.

[[Image:SA 3Dimaging (6).jpg|450px]]

* '''Geometric Laplacian with mixed area weights''': This operator takes into account the angles in the corresponding triangles into account as well as the area around the nodes in order to determine the connection weights:

<math>w_{ij} = \frac{\cot\left( \alpha_{ij} \right) + \cot\left( \beta_{ij} \right)}{2}</math>

<math>d_{i} = A_{\text{mixed}}</math>


where '''αij''' and '''βij''' denote the two angles opposite to the edge ('''i , j''') and '''Amixed '''is either the Voronoi area, or 1/2 of the triangle area or 1/4 of the triangle area depending on the type of the triangle.

[[Image:SA 3Dimaging (8).jpg|450px]]

'''Regularization and other parameters:'''

[[Image:CorticalLOR.png‎]]

* '''SVD cutoff''': The regularization for the inverse operator as a percent of the largest singular value.
* '''Depth weighting''': Turn depth weighting on or off.
* '''Laplacian type''': Selection of Laplacian operators (see above).

'''Notes:'''
* '''Starting Cortical LORETA''': Cortical LORETA can be started from the sub-menu '''Surface Image''' of the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]''” for important information on regularization of distributed inverses.

'''References:'''

Please refer to ''Iordanov et al.: LORETA With Cortical Constraint: Choosing an Adequate Surface Laplacian Operator. Front Neurosci 12, Article 746, 2018'', for more information - full article available [https://www.frontiersin.org/articles/10.3389/fnins.2018.00746/full here].

== Cortical CLARA ==

Cortical CLARA is principally the same technique as CLARA, but Cortical CLARA is not computed in a 3D volume, but on the cortical surface. Instead of using a LORETA image as the basis for the iterative application, cortical CLARA uses cortical LORETA.

'''Regularization and other parameters:'''

[[Image:SA 3Dimaging (47).gif]]

* '''SVD cutoff''': The regularization for the inverse operator as a percent of the largest singular value.
* '''Depth weighting''': Turn depth weighting on or off.
* '''Laplacian type''': Selection of Laplacian operators (see Cortical LORETA).
* '''No of iterations''': Number of iterations for CLARA. The more iterations are used, the sparser becomes the solution.
* '''Automatic''': The algorithm tries to determine the number of iterations automatically. The goodness of fit (GOF) is calculated after every iteration and if there is a big jump in the GOF then the algorithm will stop. If no jumps appear during the calculations then CLARA iterates until the specified number of iterations is reached.
* '''Regularize iterations''': If one wants to use different regularization for the CLARA iterations than the value specified as "SVD cutoff", this option should be selected.
* '''Amount to clip from img (%)''': Cortical CLARA uses the solution from the previous iteration as an additional weighting matrix for the current iteration. That weighting matrix is constructed by cutting the "low" activity from the solution. This number specifies how much of the activity should be cut from the previous solution in order to construct the weighting matrix. This value is given as a percentage of the maximal activity. Default value is 10%.

'''Notes:'''

* '''Starting Cortical CLARA:''' Cortical CLARA can be started from the sub-menu '''Surface Image''' of the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]''” for important information on regularization of distributed inverses.

== Cortex Inflation ==

The inflated cortex is a smoothened version of the individual cortical surface with minimal metric distortions (Fischl, B. et al. (1999). Cortical Surface-Based Analysis: II: Inflation, Flattening, and a Surface-Based Coordinate System. ''NeuroImage'', 9(2), 195–207). Gyri and sulci are smoothened out. The original distances between each point on the cortex and its neighbors are, however, mostly preserved.

[[Image:SA 3Dimaging (48).gif]]

''Cortical LORETA map overlaid on top of the inflated cortical surface.''

A lighter gray color overlaid on top of the surface image indicates the location of a gyrus of the individual cortex surface, while a darker gray color indicates the location of a sulcus. The inflated cortical surface can be computed in '''BESA MRI 2.0'''. For more details please refer to the BESA MRI 2.0 help.

== Surface Minimum Norm Image ==

'''Introduction'''

The minimum norm approach is a common method to estimate a distributed electrical current image in the brain at each time sample (Hämäläinen & Ilmoniemi 1984). The source activities of a large number of regional sources are computed. The sources are evenly distributed using 1500 standard locations 10% and 30% below the smoothed standard brain surface (when using the standard MRI) or using between 3000-4000 locations on the individual brain surface defined by the gray-white-matter boundary.

Since the number of sources is much larger than the number of sensors in a minimum norm solution, the inverse problem is highly underdetermined and must be stabilized by a mathematical constraint, the minimum norm. Out of the many current distributions that can account for the recorded sensor data, the solution with the minimum L2 norm, i.e. the minimum total power of the current distribution is displayed in BESA Research.

First, the forward solution (leadfield matrix L) of all sources is calculated in the current head model. Then, the source activities S(t) of all source components are computed from the data matrix D(t) using an inverse regularized by the estimated noise covariance matrix:

<math>\mathrm{S}\left( t \right) = \mathrm{R} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{R} \cdot \mathrm{L}^{T} + \mathrm{C}_N \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed regional source model, CN denotes the noise correlation matrix in sensor space, and R is a weighting matrix in source space. R and CN can be designed in different ways in order to optimize the minimum norm result. The total activity of each regional source is computed as the root mean square of the source activities S(t) of its 3 (MEG:2) components. This total source activity is transformed to a color-coded image of the brain surface. (When the standard brain is used, two sources are assigned to each surface location, located 10% and 30% below the surface, respectively. The color that is displayed on the standard brain surface is the larger of the two corresponding source activities.)

'''Weighting options'''

The minimum norm current imaging techniques of BESA Research provide different weighting strategies. Two weighting approaches are available: Depth weighting and spatio-temporal approaches.
* '''Depth weighting:''' Without depth weighting, deep sources appear very smeared in a minimum-norm reconstruction. With depth weighting, both deep and superficial sources produce a similar, more focal result. If this weighting method is selected, the leadfield of each regional source is scaled with the largest singular value of the SVD (singular value decomposition) of the source's leadfield.
* '''Spatio-temporal weighting''': Spatio-temporal weighting tries to assign large weight to sources that are assumed to be more likely to contribute to the recorded data.
** '''Subspace correlation after single source scan''': This method divides the signal into a signal and a noise subspace. The correlation of the leadfield of a regional source i with the signal subspace (pi) is computed to find out if the source location contributes to the measured data. The weighting matrix R becomes a diagonal matrix. Each of the three (MEG: 2) components of a regional source get the same weighting value pi2. This approach is based on the signal subspace correlation measure introduced by J.C. Mosher, R. M. Leahy (Recursive MUSIC: A Framework for EEG and MEG Source Localization, IEEE Trans. On Biomed. Eng. Vol. 45, No. 11, November 1998)
** '''Dale & Sereno 1993:''' In the approach of Dale and Sereno (J Cogn Neurosci, 1993, 5: 162-176) a signal subspace needs not be defined. The correlation pi of the leadfield of regional source i with the inverse of the data covariance matrix is computed along with the largest singular value λmax of the data covariance matrix. The weighting matrix R is a diagonal matrix with weights: [[Image:SA 3Dimaging (50).gif]]. Each of the three (MEG: 2) components of a regional source receives the same weighting value.

'''Noise regularization'''

Three methods to estimate the channel noise correlation matrix CN are provided by the program:
* '''Use baseline:''' Select this option to estimate the noise from the user-definable baseline. The signal is computed from the data at non-baseline latencies.
* '''Use 15% lowest values:''' The baseline activity is computed from the data at those 15% of all displayed latencies that have the lowest global field power. The signal is computed from all displayed latencies.
* '''Use the full baseline covariance matrix''': This option is only available if a previous beamformer image in the time-domain was calculated. In this case, it can be selected from the general image settings dialog tab. The baseline covariance interval is the one selected for the beamformer, and is indicated by a thin horizontal bar in the channel box.

In each case, the activity (noise or signal, respectively) is defined as root-mean-square across all respective latencies for each channel.

The noise covariance matrix CN is constructed as a diagonal matrix. The entries in the main diagonal are proportional to the noise activity of the individual channels (if selected) or are all equally proportional to the average noise activity over all channels. The noise covariance matrix CN is then scaled such that the ratio of the Frobenius norms of the weighted leadfield projector matrix (LRLT) and the noise covariance matrix CN equals the Signal-to-Noise ratio. This scaling can be multiplied by an additional factor (default=1) to sharpen (<1) or smoothen (>1) the minimum norm image.

'''Applying the Minimum Norm Image'''

The minimum-norm algorithm is started via the ''Surface minimum norm image dialog box'', which is opened from the''' Image''' menu, or by typing the shortcut '''Ctrl-M''': Please refer to Chapter ''“Surface'' ''Minimum Norm Tab”'' for more details.

As opposed to the other 3D images available from the '''Image '''menu, the surface minimum norm image is not computed on a volumetric grid, but rather for locations on the brain surface. Accordingly, the results of the minimum norm image are displayed superimposed to the brain surface mesh rather than to the volumetric MR image.

The figure below shows a minimum norm image computed from the file '''Examples\Epilepsy\Spikes\Spikes-Child4_EEG+MEG_averaged.fsg'''. The EEG spike peak was imaged using the individual brain surface of the subject. A baseline from -300 to -70 ms was used. Minimum norm was computed with depth weighting, Spatio-temporal weighting according to Dale & Sereno 1993 and individual noise weighting with a noise scale factor of 0.01. The minimum norm image reveals the location of the spike generator in the close vicinity of the frontal left-hemispheric lesion in this subject.

[[Image:SA 3Dimaging (51).gif]]

== Multiple Source Probe Scan (MSPS) ==

 
'''Introduction'''

The MSPS function provides a tool for the validation of a given solution. It is based on the following theoretical consideration: If the recorded EEG/MEG data has been modeled adequately, i.e. all active brain regions are represented by a source in the current solution, then any additional probe source added to the solution will not show any activity apart from noise. The only exception occurs if this probe source is placed in close vicinity to one of the sources in the current solution. In that case, the solution's source and the probe source will share the activity of the corresponding brain area. The MSPS applies these considerations by scanning the brain on a pre-defined grid with a regional probe added to the current solution. Grid extent and density can be specified in the Image settings. The power P of the probe source at location r in the signal interval is compared with the power of the probe source in a reference interval, defining a value q:

<math>\mathrm{q}\left( r \right) = \sqrt{\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}} - 1</math>


MSPS can be computed on time domain or time-frequency domain data:
* In the time domain, q(r) is computed from the source waveform of the probe source. Here, P(r) is the mean power of the probe source at location r in the marked latency range, and Pref(r) is the mean probe source power in the user-definable baseline interval.
* In the time-frequency domain, an MSPS image can be computed from the complex cross spectral density matrices. By applying the inverse operator for a source configuration consisting of the current solution and the probe source, the power of the probe source can be computed for the target interval [P(r)] and the reference time-frequency interval [Pref(r)]. In the resulting MSPS image, q-values are shown in %, where q[%] = q*100.

The inverse operator used to determine the probe source power uses different regularization constants for the probe source and the sources in the current solution. The regularization constant of the sources in the current solution can be specified in the Image settings (default 4%). The regularization constant of the probe source is internally set to 0%.

Alternatively to the definition above, q can also be displayed in units of dB:

<math>\mathrm{q}\left\lbrack \text{dB} \right\rbrack = 10 \cdot \log_{10}\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}</math>


Values of q smaller than zero are not shown in the MSPS image.

According to the considerations above, an MSPS of a correct source model should optimally yield image maxima around the sources in the current solution only. If the MSPS image is blurred or shows maxima at locations different from the modeled sources, this indicates a non-sufficient or incorrect solution.

'''Applying the MSPS'''

This chapter illustrates the application of the Multiple Source Probe Scan. The figures are generated with data from file '''Examples/Epilepsy/Spikes/Rolandic-Spike-Child.fsg''' (-300 : +200 ms, filtered from 3 Hz [forward] to 40 Hz [zero-phase]).

'''Time domain versus time-frequency domain MSPS'''

The multiple source probe scan can be computed in the time domain or the time-frequency domain. The latter is possible only when time-frequency domain data is available for the current condition, i.e. if the condition has been created by starting a multiple source beamformer (MSBF) computation from the source coherence window. In this case, evoking the MSPS calculation from the '''Imaging '''button or from the '''Image''' menu will bring up the following dialog window that allows to choose between time- or time-frequency MSPS. If only time domain data is available, this dialog window will not appear and MSPS will be computed in the time domain.

[[Image:SA 3Dimaging (53).gif]]

For a time-frequency domain MSPS, the target and the reference time-frequency interval have been specified already in the Time-Frequency window (see Chapter "''How To Create Beamformer Images''"). For a time-domain MSPS, the target and the reference epoch have to be specified in the Source Analysis window as described below.

'''Time domain MSPS'''

The time-domain MSPS image displays the ratio of the power of a regional probe source in the signal and the baseline interval. The currently set baseline is indicated by a horizontal line in the upper left corner of the channel box.

[[Image:SA 3Dimaging (54).gif|thumb|c|none|330px|The black horizontal bar in the upper part of the channel box (here circled in red) indicates the baseline interval.]]

By default, BESA Research defines the pre-stimulus interval of the current data segment as baseline. The baseline should represent a latency range in which no event-related activity is present in the data. There are several possibilities to modify the baseline interval: by clicking on the horizontal line with the left mouse button or by using the corresponding entry in the '''Condition '''menu or '''Fit Interval''' popup menu.

Mark an interval to define the target epoch, i.e. the time-interval for which the current solution is to be tested. Start the MSPS by selecting it from the '''Image selection '''button or from the '''Image''' menu to start the probe source scan. The''' Image '''menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window. The 3D window opens and displays the scan result.

<div><ul>
<li style="display: inline-block;"> [[Image:SA 3Dimaging (55).gif|thumb|c|none|650px|This figure shows the MSPS image applied on the three left-hemispheric sources in the solution ''''Rolandic-Spike-Child-RS2.bsa''''. The baseline is set from -300ms to -50 ms. The right-hemispheric sources have been switched off. The fit interval is set to the latency range of large overall activity in the data (-43 ms : 117 ms). A realistic FEM model appropriate for the subject's age (12 years, conductivity ratios (cr) 50) is applied. The MSPS image does not show maxima at the modeled source locations and rather shows a spread q-value distribution.]] </li>

<li style="display: inline-block;"> [[Image:SA 3Dimaging (56).gif|thumb|c|none|650px|The MSPS image for the same latency range when the right-hemispheric sources have been included. The MSPS image appears more focal and shows maxima around the modeled brain regions. This indicates the substantial improvement of the solution by adding the right-hemispheric sources that model the propagation of the epileptic spike from the left to the right hemisphere (note the radiological side convention in the 3D window).]] </li>
</ul></div>

'''Time-Resolved MSPS'''

If the MSPS has been computed on time domain data, the image can be shown separately for each latency in the selected interval. After the MSPS has been computed for the marked epoch, double-click anywhere within this epoch to display the ratio of the probe source magnitude at the selected latency and the mean probe source magnitude in the baseline. Scanning the latency range by moving the cursor (e.g. with the left and right arrow cursor keys) provides a time-resolved MSPS image.

Time-resolved MSPS images are not available if the MSPS has been computed on data in the time-frequency domain.

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (57).gif|thumb|450px|MSPS image of the spike peak activity at 0ms. The activity mainly occurs in the left hemisphere. This fact is illustrated by the source waveforms and confirmed in the MSPS image, which shows a focal maximum around the location of the red sources.]] </li>

<li style="display: inline-block;"> [[File:SA 3Dimaging (58).gif|thumb|450px|Around +27 ms, the spike has propagated to the right hemisphere. This becomes evident from the waveforms of the blue sources, which show a significant latency lag with respect to the first three sources, and from the MSPS image, which shows the maximum around blue sources at this latency.]] </li>
</ul></div>



'''Notes:'''

* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image''' menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the''' Image''' menu.
* For scaling options, please refer to the '''scaling buttons''' popup menu .
* Parameters used for the MSPS calculations can be set in the ''General Settings tab'' of the ''Image Settings dialog box.''

== Source Sensitivity ==

'''Introduction'''

The 'Source sensitivity' function displays the sensitivity of the selected source in the current source model to activity in other brain regions. Sensitivity is defined as the fraction of power at the scanned brain location that is mapped onto the selected source.

To compute the source sensitivity, unit brain activity is modeled at different locations (probe source) throughout the brain. To this data, the current source model is applied to compute the source waveforms SCM of all modeled sources:

<math>\mathrm{S}_{\text{CM}} = \mathrm{L}_{\text{CM}}^{-1} \cdot \mathrm{L}_{\text{PS}}</math>


Here LCM-1 is the regularized inverse operator for the current model, and LPS is the leadfield of the regional probe source (dimension [Nx3] for EEG and [Nx2] for MEG, respectively, where N is the number of sensors). The source amplitude SSS of the selected source in the model is a 3x3 (MEG: 2x2) sub-matrix of SCM (if the selected source is a regional source) or a 1x3-matrix (MEG: 1x2) (if the selected source is a dipole). The root mean square of the singular values of SCM is defined as the source sensitivity.

The 3D source sensitivity image displays this value for all locations on a grid specified under '''Image/Settings'''. Grid density can be specified in the Image Settings.

'''Applying the Source Sensitivity Image'''

The Source Sensitivity image is evoked from the '''Image''' menu or by pressing the corresponding hot key (default: '''V''').

This function is enabled only when a solution with an active selected source is present in the Source Analysis window. The source sensitivity image then displays the sensitivity of the selected source to activity in other brain regions.

[[Image:SA 3Dimaging (59).gif]]

''Source Sensitivity image for the selected frontal source (green) in model ''''''High_Intensity_3RS.bsa'''''' in folder 'Examples/ERP_Auditory_Intensity'. The data displayed is the '100dB' condition in file ''''''All_Subjects_cc.fsg''''''. The selected source is sensitive to activity in the frontal brain region (yellow/white), while it is not influenced by activity in the vicinity of the left and right auditory cortex areas, which are modeled by the red and blue source in the model (transparent/gray).''

'''Notes:'''

* The sensitivity image is independent of the recorded sensor signals. It only depends on the current source model, the sensor configuration, the head model, and the regularization constant.
* If the regularization constant is set to zero, each source has a sensitivity of 100% to activity around its own location. With increasing regularization, the spatial filter becomes less focused, and the sensitivity of a source to activity at its location decreases.
* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image''' menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the '''Image''' menu.

== SESAME ==
''This feature requires BESA Research 7.0 or higher.''

'''SESAME''' (Sequential Semi-Analytic Monte-Carlo Estimation) is a Bayesian approach for estimating sources that uses Markov-Chain Monte-Carlo method for efficient computation of the probability distribution as described in Sommariva, S., & Sorrentino, A. "Sequential Monte Carlo samplers for semi-linear inverse problems and application to magnetoencephalography." Inverse Problems 30.11 (2014): 114020.

It allows to automatically estimate simultaneously the number of dipoles, their locations and time courses requiring virtually no user input. The algorithm is divided in two blocks:

* The first block consists of a Monte Carlo sampling algorithm that produces, with an adaptive number of iterations, a set of samples representing the posterior distribution for the number of dipoles and the dipole locations.
* The second block estimates the source time courses, given the number of dipoles and the dipole locations.

The Monte Carlo algorithm in the first block works by letting a set of weighted samples evolve with each iteration. At each iteration, the samples (a multi-dipole state) approximates the n-th element of a sequence of distributions p1, …, pN, that reaches the desired posterior distribution (pN = p(x|y)). The sequence is built as pN = p(x) p(y|x) α(n), such that α(1) = 0, α(N) = 1. The actual sequence of values of alpha is determined online. Dipole moments are estimated after the number of dipoles and the dipole locations have been estimated with the Monte Carlo procedure. This continues until a steady state is reached.

The SESAME image in BESA Research displays the final probability of source location along with an estimate for number of sources. Using the menu function '''Image / Export Image As...''' you have the option to save this SESAME image.

'''Notes:'''

*'''Grid spacing:''' Due to memory and computational limitations, it is recommended to use SESAME with a grid spacing of 5 mm or more.
*'''Fit Interval:''' SESAME requires a fit interval of more than 2 samples to start the computation.
*'''Computation time:''' Computation speed during SESAME calculation depends on the grid spacing (computation is faster with larger grid spacing) and number of channels.

== Brain Atlas ==
''This feature requires BESA Research 7.0 or higher.''

'''Introduction'''

Brain atlas is a priori data that can be applied over any discrete or distributed source image displayed in the 3D window. It is a reference value that strongly depends on the selected brain atlas and should not be used as medical reference since individual brains may differ from the brain atlas. The display settings can be adjusted in 3D Window Tab.

[[Image:BrainAtlas1.png|600px]]

'''Brain Atlases'''

In BESA Research the atlases listed below are provided. '''BESA is not the author of the atlases; please cite the appropriate publications if you use any of the atlases in your publication.'''

[http://atlas.brainnetome.org/bnatlas.html '''Brainnetome'''] 
This is one of the most modern brain probabilistic atlas where structural, functional, and connectivity information was used to perform cortical parcellation. It was introduce by Fan and colleagues (2016), and is still work in progress. The atlas was created using data from 40 healthy adults taking part in the Human Connectome Project. In March 2018, the atlas consists of 246 structures labeled independently for each hemisphere. In BESA we provide the max probability map with labeling. Please visit the Brainnetome webpage to see more details related to the indicated brain regions (i.e. behavioral domains, paradigm classes and regions connectivity).

'''AAL''' 
Automated Anatomical Labeling atlas was created in 2002 by Tzourio-Mazoyer and collegues (2002). It is the mostly used atlas nowadays. The atlas is based on the averaged brain of one subject (young male) who was scanned 27 times. The atlas resolution is 1 mm isometric. The brain sulci were drawn manually on every 2mm slice and then brain regions were automatically assigned. The atlas consists of 116 regions which are asymmetrical between hemispheres. The atlas is implemented as in the [https://www.fil.ion.ucl.ac.uk/spm/ '''SPM12'''] toolbox.

'''Brodmann''' 
The Brodmann map was created by Brodmann (1909). The brain regions were differentiated by cytoarchitecture of each cortical area using the Nissi method of cell staining. The digitalization of the original Brodmann map was performed by Damasio and Damasio (1989). The digitalized atlas consists of 44 fields that are symmetric between hemispheres. BESA used the atlas implementation as in Chris Roden’s [https://people.cas.sc.edu/rorden/mricro/index.html '''MRICro'''] software.

'''AAL2015''' 
Automated Anatomical Labeling revision 2015. This is the updated AAL atlas. In comparison to the previous version (AAL) mainly the frontal lobe shows a higher degree of parcellation (Rolls, Joliot, and Tzourio-Mazoyer 2015). The atlas is implemented as in the [https://www.fil.ion.ucl.ac.uk/spm/ '''SPM12'''] toolbox.

'''Talairach''' 
Atlas was created in 1988 by Talairach and Tournoux (1988) and it is based on the post mortem brain slices of a 60 year old right handed European female. It was created by drawing and matching regions with the Brodmann map. The atlas is available at 5 tissue levels, however we used only the volumetric gyrus level as it is the most known in neuroscience and is the most appropriate for EEG. The atlas consists of 55 regions that are symmetric between hemispheres. The native resolution of the atlas was 0.43x0.43x2-5 mm. Please note that the poor resolution in Z direction is a direct consequence atlas definition, and since it is a post-mortem atlas it will not correctly match the brain template
(noticeable mainly on brain edges). The atlas digitalization was performed by Lancaster and colleagues (2000) resulting in a “golden standard” for neuroscience. The atlas was first implemented in a software called [http://www.talairach.org/daemon.html '''talairach daemon'''].

'''Yeo7 and Yeo17''' 
Yeo7 and Yeo17 are the resting state functional connectivity atlases created by Yeo et al. (2011). For atlas creation 1000 subjects, coregistered using surface-based alignment were used. Two versions of parcellation were used resulting for the 7 and 17 networks (Yeo7 and Yeo17 atlas respectively). In the original publication atlases for two different levels of brain structure coverage were prepared: neocortex and liberal. In BESA products, only one of them (liberal) is available. Note that in comparison to the other atlases, here networks are reflected, rather than the individual brain structures. These atlases are in line with [[BESA_Research_Montage_Editor#Standard_Source_Montage_-_Resting_State_Montages | Resting State Source Montages]].

'''Visualization modes'''

'''Just Labels''' 
Displayed are crosshair coordinates (Talairach or MNI), the currently used brain atlas and the region name where the crosshair is placed. No atlas overlay will be visible on the 3D image.

'''brainCOLOR''' 
All information is displayed as in “Just Labels” mode but also the atlas is visible as an overlay over the MRI. The coloring is performed using the algorithm introduced by Klein and colleagues (Klein et al. 2010). With this method of coloring the regions which are part of the same lobe are colored in a similar color but with different color shade. The shade is computed by the algorithm to make these regions visually differentiable from each other as much as possible.

'''Individual Color''' 
In this mode the native brain atlas color is used if provided by the authors of the brain atlas (i.e. Yeo7). Where this was not available BESA autogenerated colors for the atlas using an approach similar to political map coloring. This approach aims to differentiate most regions that are adjacent to each other and no presumptions on lobes is applied.

'''Contour''' 
Only region contours (borders between atlas regions) are drawn with blue color. This is the default mode in BESA Research.

'''References'''

* Brodmann, Korbinian. 1909. Vergleichende Lokalisationslehre Der Großhirnrinde. Leipzig: Barth. https://www.livivo.de/doc/437605.
* Damasio, Hanna, and Antonio R. Damasio. 1989. Lesion Analysis in Neuropsychology. Oxford University Press, USA.
* Fan, Lingzhong, Hai Li, Junjie Zhuo, Yu Zhang, Jiaojian Wang, Liangfu Chen, Zhengyi Yang, et al. 2016. “The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.” Cerebral Cortex 26 (8): 3508–26. https://doi.org/10.1093/cercor/bhw157.
* Klein, Arno, Andrew Worth, Jason Tourville, Bennett Landman, Tito Dal Canton, Satrajit S. Ghosh, and David Shattuck. 2010. “An Interactive Tool for Constructing Optimal Brain Colormaps.” https://mindboggle.info/braincolor/colormaps/index.html.
* Lancaster, Jack L., Marty G. Woldorff, Lawrence M. Parsons, Mario Liotti, Catarina S. Freitas, Lacy Rainey, Peter V. Kochunov, Dan Nickerson, Shawn A. Mikiten, and Peter T. Fox. 2000. “Automated Talairach Atlas Labels for Functional Brain Mapping.” Human Brain Mapping 10 (3): 120–131.
*Rolls, Edmund T., Marc Joliot, and Nathalie Tzourio-Mazoyer. 2015. “Implementation of a New Parcellation of the Orbitofrontal Cortex in the Automated Anatomical Labeling Atlas.” NeuroImage 122 (November): 1–5. https://doi.org/10.1016/j.neuroimage.2015.07.075.
* Talairach, J, and P Tournoux. 1988. Co-Planar Stereotaxic Atlas of the Human Brain. 3-Dimensional Proportional System: An Approach to Cerebral Imaging. Thieme.
*Thomas Yeo, B. T., F. M. Krienen, J. Sepulcre, M. R. Sabuncu, D. Lashkari, M. Hollinshead, J. L. Roffman, et al. 2011. “The Organization of the Human Cerebral Cortex Estimated by Intrinsic Functional Connectivity.” Journal of Neurophysiology 106 (3): 1125–65. https://doi.org/10.1152/jn.00338.2011.
* Tzourio-Mazoyer, N., B. Landeau, D. Papathanassiou, F. Crivello, O. Etard, N. Delcroix, B. Mazoyer, and M. Joliot. 2002. “Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain.” NeuroImage 15 (1): 273–89. https://doi.org/10.1006/nimg.2001.0978.

== Slice View ==
''This feature requires BESA Research 7.1 or higher.''

A convenient way to review MRI data and export it in graphical form is a multi-slice view. To enable multi-slice view press the toggle multiple view button until the slice view is shown in the 3D window.

[[Image:SliceView1.png|600px]]

In this view discrete sources, [[Source_Analysis_3D_Imaging#Overview | distributed sources]] and [[Source_Analysis_3D_Imaging#Brain Atlas| brain atlas]] can be also be overlayed. The display matrix can be adjusted by slice view controls that are available in the 3D Window tab of the Preferences Dialog Box. One of the following slicing direction can be selected: Transverse, Coronal, Sagittal by pressing the appropriate button in the 3D window toolbar.

By adjusting First slice and Last slice sliders, the span of the volume that will be displayed can be adjusted. The interval between slices can be adjusted by changing the Spacing slider value. The layout of slices will be automatically adjusted to fill the full space of the main window. All values in the sliders are given in mm.

'''Note''': The last slice value will be adjusted to the closest possible number matching the given first slice and spacing value. During multi-slice view the cursor is disabled and no
atlas information is provided.

== Glassbrain ==

[[Image:Glassbrain.png|600px]]

The glass brain can be enabled or disabled in one of the following ways:

*by pressing the button in the toolbar ,

*by using the shortcut SHIFT-G or

*by checking the checkbox in Preferences, 3D Display tab.

The transparency value of the glass brain can be adjusted in one of the following ways:

*by a slider/edit box in Preferences, 3D Display tab or

*by using the keyboard shortcut SHIFT-UP (to increase transparency by 10%) or SHIFT-DOWN (to decrease transparency by 10%).

Note that If a distributed solution is displayed together with the glass brain, a notification is displayed in the left bottom corner of 3D window to prevent misconception of the glass brain as a cortical image:

“Volume-based image only", which means that the results of distributed source analysis images are visualized only for the current MRI slice, and are not projected to the displayed surface.

{{BESAManualNav}}

Source Analysis 3D Imaging

2021-11-25T12:37:25Z

Dominik:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = BESA Research 6.1 or higher
}}


== Overview ==

BESA Research features a set of new functions that provide 3D images that are displayed superimposed to the individual subject's anatomy. This chapter introduces these different images and describe their properties and applications.

The 3D images can be divided into three categories:

'''Volume images:'''

* '''The Multiple Source Beamformer (MSBF)''' is a tool for imaging brain activity. It is applied in the time-domain or time-frequency domain. The beamformer technique in time-frequency domain can image not only evoked, but also induced activity, which is not visible in time-domain averages of the data.
* '''Dynamic Imaging of Coherent Sources (DICS)''' can find coherence between any two pairs of voxels in the brain or between an external source and brain voxels. DICS requires time-frequency-transformed data and can find coherence for evoked and induced activity.

The following imaging methods provide an image of brain activity based on a distributed multiple source model:
* '''CLARA''' is an iterative application of LORETA images, focusing the obtained 3D image in each iteration step.
* '''LAURA '''uses a spatial weighting function that has the form of a local autoregressive function.
* '''LORETA''' has the 3D Laplacian operator implemented as spatial weighting prior.
* '''sLORETA''' is an unweighted minimum norm that is standardized by the resolution matrix.
* '''swLORETA '''is equivalent to sLORETA, except for an additional depth weighting.
* '''SSLOFO '''is an iterative application of standardized minimum norm images with consecutive shrinkage of the source space.
* A '''User-defined volume image''' allows to experiment with the different imaging techniques. It is possible to specify user-defined parameters for the family of distributed source images to create a new imaging technique.
* Bayesian source imaging: '''SESAME''' uses a semi-automated Bayesian approach to estimate the number of dipoles along with their parameters.

'''Surface image:'''

* The '''Surface Minimum Norm Image'''. If no individual MRI is available, the minimum norm image is displayed on a standard brain surface and computed for standard source locations. If available, an individual brain surface is used to construct the distributed source model and to image the brain activity.
* '''Cortical LORETA'''. Unlike classical LORETA, cortical LORETA is not computed in a 3D volume, but on the cortical surface.
* '''Cortical CLARA'''. Unlike classical CLARA, cortical CLARA is not computed in a 3D volume, but on the cortical surface.

'''Discrete model probing:'''

These images do not visualize source activity. Rather, they visualize properties of the currently applied discrete source model:
* The '''Multiple Source Probe Scan (MSPS)''' is a tool for the validation of a discrete multiple source model.
* The '''Source Sensitivity image''' displays the sensitivity of a selected source in the current discrete source model and is therefore data independent.

== Multiple Source Beamformer (MSBF) in the Time-frequency Domain ==

 
'''Short mathematical introduction'''

The BESA beamformer is a modified version of the linearly constrained minimum variance vector beamformer in the time-frequency domain as described in [https://dx.doi.org/10.1073/pnas.98.2.694 Gross et al., "Dynamic imaging of coherent sources: Studying neural interactions in the human brain", PNAS 98, 694-699, 2001]. It allows to image evoked and induced oscillatory activity in a user-defined time-frequency range, where time is taken relative to a triggered event.

The computation is based on a transformation of each channel's single trial data from the time domain into the time-frequency domain. This transformation is performed by the BESA Research Source Coherence module and leads to the complex spectral density Si (f,t), where i is the channel index and f and t denote frequency and time, respectively. Complex cross spectral density matrices C are computed for each trial:

<math>\mathrm{C}_{ij}\left( f,t \right) = \mathrm{S}_{i}\left( f,t \right) \cdot \mathrm{S}_{j}^{*}\left( f,t \right)</math>


The output power P of the beamformer for a specific brain region at location r is then computed by the following equation:

<math>\mathrm{P}\left( r \right) = \operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{-1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{-1}</math>


Here, Cr-1 is the inverse of the SVD-regularized average of Cij(f,t) over trials and the time-frequency range of interest; L is the leadfield matrix of the model containing a regional source at target location r and, optionally, additional sources whose interference with the target source is to be minimized; tr'[] is the trace of the [3×3] (MEG:[2×2]) submatrix of the bracketed expression that corresponds to the source at target location r.

In BESA Research, the output power P(r) is normalized with the output power in a reference time-frequency interval Pref(r). A value q ist defined as follows:

<math> \mathrm{q}\left( r \right) =
\begin{cases}
\sqrt{\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}(r)}} - 1 = \sqrt{\frac{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{\text{ref},r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}} - 1, & \text{for }\mathrm{P}(r) \geq \mathrm{P}_{\text{ref}}(r) \\

1 - \sqrt{\frac{\mathrm{P}_{\text{ref}}\left( r \right)}{\mathrm{P}\left( r \right)}} = 1 - \sqrt{\frac{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{\text{ref},r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}{\operatorname{tr^{'}}\left\lbrack \mathrm{L}^{T}\left( r \right) \cdot \mathrm{C}_{r}^{- 1} \cdot \mathrm{L}\left( r \right) \right\rbrack^{- 1}}}, & \text{for }\mathrm{P}(r) < \mathrm{P}_{\text{ref}}(r)
\end{cases} </math>


Pref can be computed either from the corresponding frequency range in the baseline of the same condition (i.e. the beamformer images event-related power increase or decrease) or from the corresponding time-frequency range in a control condition (i.e. the beamformer images differences between two conditions). The beamformer image is constructed from values q(r) computed for all locations on a grid specified in the '''General Settings tab'''. For MEG data, the innermost grid points within a sphere of approx. 12% of the head diameter are assigned interpolated rather than calculated values).
q-values are shown in %, where where q[%] = q*100. Alternatively to the definition above, q can also be displayed in units of dB:

<math>\mathrm{q}\left\lbrack \text{dB} \right\rbrack = 10 \cdot \log_{10}\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}</math>


A beamformer operator is designed to pass signals from the brain region of interest r without attenuation, while minimizing interference from activity in all other brain regions. Traditional single-source beamformers are known to mislocalize sources if several brain regions have highly correlated activity. Therefore, the BESA beamformer extends the traditional single-source beamformer in order to implicitly suppress activity from possibly correlated brain regions. This is achieved by using a multiple source beamformer calculation that contains not only the leadfields of the source at the location of interest r, but also those of possibly interfering sources. As a default, BESA Research uses a bilateral beamformer, where specifically contributions from the homologue source in the opposite hemisphere are taken into account (the matrix L thus being of dimension N×6 for EEG and N×4 for MEG, respectively, where N is the number of sensors). This allows for imaging of highly correlated bilateral activity in the two hemispheres that commonly occurs during processing of external stimuli.

In addition, the beamformer computation can take into account possibly correlated sources at arbitrary locations that are specified in the current solution. This is achieved by adding their leadfield vectors to the matrix L in the equation above.

'''Applying the Beamformer'''

This chapter illustrates the usage of the BESA beamformer. The displayed figures are generated using the file ''''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''' (see BESA Tutorial 12: "''Time-frequency analysis, Connectivity analysis, and Beamforming''").

'''Starting the beamformer from the time-frequency window'''

The BESA beamformer is applied in the time-frequency domain and therefore requires the Source Coherence module to be enabled. The time-frequency beamformer is especially useful to image in- or decrease of induced oscillatory activity. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot. For instructions on how to initiate a beamformer computation in the time-frequency window, please refer to Chapter '''[[Source_Coherence_How_to...#How_to_Start_the_Beamformer_from_the_Time-Frequency_Window|How to Create Beamformer Images]]'''.

After the beamformer computation has been initiated in the time-frequency window, the source analysis window opens with an enlarged 3D image of the q-value computed with a '''bilateral beamformer'''. The result is superimposed onto the MR image assigned to the data set (individual or standard).

[[Image:SA 3Dimaging (5).gif]]

''Beamformer image after starting the computation in the Time-Frequency window. A bilateral pair of sources in the auditory cortex accounts for the highly correlated oscillatory induced activity. Only the bilateral beamformer manages to separate these activities; a traditional single-source beamformer would merge the two sources into one image maximum in the head center instead.''

'''Multiple source beamformer in the Source Analysis window'''

The 3D imaging display is part of the source analysis window. If you press the '''Restore''' button at the right end of the title bar of the 3D window, the window appears at the bottom right of the source analysis window. In the channel box, the averaged (evoked) data of the selected condition is shown. When a control condition was selected, its average is appended to the average of the target condition.

[[Image:SA 3Dimaging (6).gif]]

''Source Analysis window with beamformer image. The two sources have been added using the '''''Switch to''''' '''''Maximum''''' and '''''Add Source '''''toolbar buttons (see below). Source waveforms are computed from the displayed averaged data. Therefore, they do not represent the activity displayed in the beamformer image, which in this simulation example is induced (i.e. not phase-locked to the trigger)!''

When starting the beamformer from the time-frequency window, a bilateral beamformer scan is performed. In the source analysis window, the beamformer computation can be repeated taking into account possibly correlated sources that are specified in the current solution. Interfering activities generated by all sources in the current solution that are in the 'On' state are specifically suppressed ('''they enter the matrix L in the beamformer calculation''', see Chapter ''Short mathematical description'' above). The computation can be started from the '''Image''' menu or from the '''Image selector button''' dropdown menu. The '''Image''' menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window.

[[Image:SA 3Dimaging (7).gif]]

''Multiple source beamformer image calculated in the presence of a source in the left hemisphere. A '''single''' source scan has been performed. The source set in the current solution accounts for the left-hemispheric q-maximum in the data. Accordingly, the beamformer scan reveals only the as yet unmodeled additional activity in the right hemisphere (note the radiological convention in the 3D image display).''

The beamformer scan can be performed with a '''single''' or a '''bilateral''' source scan. The default scan type depends on the current solution:
* When the beamformer is started from the Time-Frequency window, the Source Analysis window opens with a new solution and a '''bilateral''' beamformer scan is performed.
* When the beamformer is started within the Source Analysis window, the default is
** a scan with a '''single''' source in addition to the sources in the current solution, if at least one source is active.
** a '''bilateral''' scan if no source in the current solution is active.

The default scan type is the multiple source beamformer. The non-default scan type can be enforced using the corresponding ''Volume Image / Beamformer'' entry in the '''Image''' menu.

'''Inserting Sources out of the Beamformer Image'''

The beamformer image can be used to add sources to the current solution. A simple double-click anywhere in the 2D- or 3D-view will generate a non-oriented regional source at the corresponding location. However, a better and easier way to create sources at image maxima and minima is to use the toolbar buttons '''Switch to Maximum''' [[Image:SA 3Dimaging (8).gif]] and '''Add Source''' [[Image:SA 3Dimaging (9).gif]].

Use the '''Switch to Maximum''' button to place the red crosshair of the 3D window onto a local image maximum or minimum. Hitting the '''Add Source''' button creates a regional source at the location of the crosshair and therefore ensures the exact placement of the source at the image extremum. Moreover, the '''Add Source''' button generates an oriented regional source. BESA Research automatically estimates the source orientation that contributes most to the power in the target time-frequency interval (or the reference time-frequency interval, if its power is larger than that in the target interval). The accuracy of this orientation estimate depends largely on the noise content of the data. The smaller the signal-to-noise ratio of the data, the lower is the accuracy of the orientation estimate. '''This feature allows to use the beamformer as a tool to create a source montage for source coherence analysis, where it is of advantage to work with oriented sources'''.

'''Notes:'''

* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image '''menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the''' Image''' menu.
* For scaling options, use the [[Image:SA 3Dimaging (10).gif]] and [[Image:SA 3Dimaging (11).gif]] '''Image Scale toolbar''' buttons.
* Parameters used for the beamformer calculations can be set in the '''Standard Volumes''' of the ''Image Settings dialog box.''

== Dynamic Imaging of Coherent Sources (DICS) ==

 
'''Short mathematical introduction'''

Dynamic Imaging of Coherent Sources (DICS) is a sophisticated method for imaging cortico-cortical coherence in the brain, or coherence between an external reference (e.g. EMG channel) and cortical structures. DICS can be applied to localize evoked as well as induced coherent cortical activity in a user-defined time-frequency range.

DICS was implemented in BESA closely following [https://dx.doi.org/10.1073/pnas.98.2.694 Gross et al., "Dynamic imaging of coherent sources: Studying neural interactions in the human brain", PNAS 98, 694-699, 2001].

The computation is based on a transformation of each channel's single trial data from the time domain into the frequency domain. This transformation is performed by the BESA Research Coherence module and results in the complex spectral density matrix that is used for constructing the spatial filter similar to beamforming.

DICS computation yields a 3-D image, each voxel being assigned a coherence value. Coherence values can be described as a neural activity index and do not have a unit. The neural activity index contrasts coherence in a target time-frequency bin with coherence of the same time-frequency bin in a baseline.

'''DICS for cortico-cortical coherence is computed as follows:'''

Let L(r) be the leadfield in voxel r in the brain and C the complex cross-spectral density matrix. The spatial filter W(r) for the voxel r in the head is defined as follows:

<math>W\left( r \right) = \left\lbrack L^{T}\left( r \right) \cdot C^{- 1} \cdot L\left( r \right) \right\rbrack^{- 1} \cdot L^{T}(r) \cdot C^{- 1}</math>


The cross-spectrum between two locations (voxels) r1 and r2 in the head are calculated with the following equation:

<math>C_{s}\left( r_{1},r_{2} \right) = W\left( r_{1} \right) \cdot C \cdot W^{*T}\left( r_{2} \right),</math>


where <nowiki>*T</nowiki> means the transposed complex conjugate of a matrix. The cross-spectral density can then be calculated from the cross spectrum as follows:

<math>c_{s}\left( r_{1},r_{2} \right) = \lambda_{1}\left\{ C_{s}\left( r_{1},r_{2} \right) \right\},</math>


where λ1{} indicates the largest singular value of the cross spectrum. Once the cross spectral density is estimated, the connectivity¹(CON) between the two brain regions r1 and r2 are calculated as follows:

<math>\text{CON}\left( r_{1},r_{2} \right) = \frac{c_{s}^{\text{sig}}\left( r_{1},r_{2} \right) - c_{s}^{\text{bl}}(r_{1},r_{2})}{c_{s}^{\text{sig}}\left( r_{1},r_{2} \right) + c_{s}^{\text{bl}}(r_{1},r_{2})},</math>


where cssig is the cross-spectral density for the signal of interest between the two brain regions r1 and r2, and csbl is the corresponding cross spectral density for the baseline or the control condition, respectively. In the case DICS is computed with a cortical reference, r1 is the reference region (voxel) and remains constant while r2 scans all the grid points within the brain sequentially. In that way, the connectivity between the reference brain region and all other brain regions is estimated. The value of CON(r1, r2) falls in the interval [-1 1]. If the cross-spectral density for the baseline is 0 the connectivity value will be 1. If the cross-spectral density for the signal is 0 the connectivity value will be -1.

¹ Here, the term connectivity is used rather than coherence, as strictly speaking the coherence equation is defined slightly differently. For simplicity reasons the rest of the tutorial uses the term coherence.

'''DICS for cortico-muscular coherence is computed as follows:'''

When using an external reference, the equation for coherence calculation is slightly different compared to the equation for cortico-cortical coherence. First of all, the cross-spectral density matrix is not only computed for the MEG/EEG channels, but the external reference channel is added. This resulting matrix is Call. In this case, the cross-spectral density between the reference signal and all other MEG/EEG channels is called cref. It is only one column of Call. Hence, the cross-spectrum in voxel r is calculated with the following equation:

<math>C_{s}\left( r \right) = W\left( r \right) \cdot c_{\text{ref}}</math>


and the corresponding cross-spectral density is calculated as the sum of squares of Cs:

<math>c_{s}\left( r \right) = \sum_{i = 1}^{n}{C_{s}\left( r \right)_{i}^{2}},</math>


where n is 2 for MEG and 3 for EEG. This equation can also be described as the squared Euclidean norm of the cross-spectrum:

<math>c_{s}\left( r \right) = \left\| C_{s} \right\|^{2},</math>


The power in voxel r is calculated as in the cortico-cortical case:

<math>p\left( r \right) = \lambda_{1}\left\{ C_{s}(r,r) \right\}.</math>


At last, coherence between the external reference and cortical activity is calculated with the equation:

<math>\text{CON}\left( r \right) = \frac{c_{s}(r)}{p\left( r \right) \cdot C_{\text{all}}(k,k)},</math>


where Call(k, k) is the (k,k)-th diagonal element of the matrix Call.

DICS is particularly useful, if coherence is to be calculated without an a-priory source model (in contrast to source coherence based on pre-defined source montages). However, the recommended analysis strategy for DICS is to use a brain source as a starting point for coherence calculation that is known to contribute to the EEG/MEG signal of interest. For example, one might first run a beamformer on the time-frequency range of interest and use the voxel with the strongest oscillatory activity as a starting point for DICS. The resulting coherence image will again lead to several maxima (ordered by magnitude), which in turn can serve as starting points for DICS calculation. This way, it is possible to detect even weak sources that show coherent activity in the given time-frequency range.

The other significant application for DICS is estimating coherence between an external source and voxels in the brain. For example, an external source can be muscle activity recoded by an electrode placed over the according peripheral region. This way, the direct relationship between muscle activity and brain activation can be measured.

'''Starting DICS computation from the Time-Frequency Window'''

DICS is particularly useful, if coherence in a user-defined time-frequency bin (evoked or induced) is to be calculated between any two brain regions or between an external reference and the brain. DICS runs only on time-frequency decomposed data, so time-frequency analysis needs to be run before starting DICS computation.

To start the DICS computation, left-drag a window over a selected time-frequency bin in the Time-Frequency Window. Right-click and select “Image”. A dialogue will open (see fig. 1) prompting you to specify time and frequency settings as well as the baseline period. It is recommended to use a baseline period of equal length as the data period of interest. Make sure to select “DICS” in the top row and press “'''Go'''”.

[[Image:SA 3Dimaging (21).gif|450px|thumb|c|none|Fig. 1: Time and frequency settings for DICS and MSBF]]

Next, a window will appear allowing you to specify the reference source for coherence calculation (see fig. 2). It is possible to select a channel (e.g. EMG) or a brain source. If a brain source is chosen and no source analysis was computed beforehand, the option “Use current cross-hair position” must be chosen. In case discrete source analysis was computed previously, the selected source can be chosen as the reference for DICS. Please note that DICS can be re-computed with any cross-hair or source position at a later stage.

[[Image:SA 3Dimaging (1).jpg|400px|thumb|c|none|Fig. 2: Possible options for choosing the reference]]

Confirming with “'''OK'''” will start computation of coherence between the selected channel/voxel and all other brain voxels. In case DICS is computed for a reference source in the brain, it can be advantageous to run a beamforming analysis in the selected time-frequency window first and use one of the beamforming maxima as reference for DICS. Fig. 3 shows an example for DICS calculation.

[[Image:SA 3Dimaging (22).gif|500px|thumb|c|none|Fig. 3: Coherence between left-hemispheric auditory areas and the selected voxel in the right auditory cortex.]]

Coherence values range between -1 and 1. If coherence in the signal is much larger than coherence in the baseline (control condition) then the DICS value is going to approach 1. Contrary, if coherence in the baseline is much larger than coherence in the signal, then the DICS value is going to approach -1. At last, if coherence in the signal is equal to coherence in the baseline, then the DICS value is 0.

In case DICS is to be re-computed with a different reference, simply mark the desired reference position by placing the cross-hair in the anatomical view and select “DICS” in the middle panel of the source analysis window (see Fig. 4). In case an external reference is to be selected, click on “DICS” in the middle panel to bring up the DICS dialogue (see. Fig. 2) and select the desired channel. Please note that DICS computation will only be available after running time-frequency analysis.

[[Image:SA 3Dimaging (23).gif|700px|thumb|c|none|Fig. 4: Integration of DICS in the Source Analysis window]]

== Multiple Source Beamformer (MSBF) in the Time Domain ==
''This feature requires BESA Research 7.0 or higher.''

'''Short mathematical introduction'''

Beamforming approach can be also applied in the time domain data. This approach was introduced as linearly constrained minimum variance (LCMV) beamformer (Van Veen et al., 1997). It allows to image evoked activity in a user-defined time range, where time is taken relative to a triggered event, and to estimate source waveforms using the calculated spatial weight at locations of interest. For an implementation of the beamformer in the time domain, data covariance matrices are required, while complex cross spectral density matrices are used for the beamformer approaches in the time-frequency domain as described in the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section.

The bilateral beamformer introduced in the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section is also implemented for the time-domain beamformer to take into account contributions from the homologue source in the opposite. This allows for imaging of highly correlated bilateral activity in the two hemispheres that commonly occurs during processing of external stimuli. In addition, the beamformer computation can take into account possibly correlated sources at arbitrary locations.

The beamformer spatial weight W(r) for the voxel r in the brain is defined as follows (Van Veen et al., 1997):

<math>\mathrm{W}(r) = [\mathrm{L}^T(r)\mathrm{C}^{-1}\mathrm{L}(r)]^{-1}\mathrm{L}^T(r)\mathrm{C}^{-1}</math>


where <math>\mathrm{C}^{-1}</math> is the inversed regularized average of covariance matrix over trials, '''L''' is the leadfield matrix of the model containing a regional source at target location r and optionally additional sources whose interference with the target source is to be minimized. The beamformer spatial weight '''W'''(r) can be applied to the measured data to estimate source waveform at a location r (beamformer virtual sensor):

<math>\mathrm{S}(r,t) = \mathrm{W}(r)\mathrm{M}(t)</math>


where '''S'''(r,t) represents the estimated source waveform and '''M'''(t) represents measured EEG or MEG signals. The output power P of the beamformer for a specific brain region at location r is computed by the following equation:

<math>\mathrm{P}(r) = \operatorname{tr^{'}}[\mathrm{W}(r) \cdot \mathrm{C} \cdot \mathrm{W}^T(r)]</math>


where tr’[ ] is the trace of the [3×3] (MEG: [2×2]) submatrix of the bracketed expression that corresponds to the source at target location r.

Beamformer can suppress noise sources that are correlated across sensors. However, uncorrelated noise will be amplified in a spatially non-uniform manner, with increasing distortion with increasing distance from the sensors (Van Veen et al., 1997; Sekihara et al., 2001). For this reason, estimated source power should be normalized by a noise power. In BESA Research, the output power P(r) is normalized with the output power in a baseline interval or with the output power of a uncorrelated noise: P(r) / Pref (r).

The time-domain beamformer image is constructed from values q(r) computed for all locations on a grid specified in the '''General Settings''' tab. A value q(r) is defined as described in
the ''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29_in_the_Time-frequency_Domain|Multiple Source Beamformer (MSBF) in the Time-frequency Domain]]'' section with data covariance matrices instead of cross-spectral density matrices.

'''Applying the Beamformer'''

This chapter illustrates the usage of the BESA beamformer in the time domain. The displayed figures are generated using the file ‘Examples/ERP-Auditory-Intensity/S1.cnt’.

'''''Starting the time-domain beamformer from the Average tab of the Paradigm dialog box'''''

The time-domain beamformer is needed data covariance matrices and therefore requires the ERP module to be enabled. After the beamformer computation has been initiated in the '''Average tab of the Paradigm dialog box''', the source analysis window opens with an enlarged 3D image of the q-value computed with a bilateral beamformer. The result is superimposed onto the MR image assigned to the data set (individual or standard).

[[File:MSBF4.png|500px|thumb|c|none|Beamformer image for auditory evoked data after starting the computation in the '''Average tab of the Paradigm dialog box'''. The bilateral beamformer manages to separate the activities in auditory areas, while a traditional single-source beamformer would merge the two sources into one image maximum in the head center instead.]]

'''''Multiple-source beamformer in the Source Analysis window'''''

The 3D imaging display is part of the source analysis window. In the Channel box, the averaged (evoked) data of the selected condition is shown. Selected covariance intervals in the ERP module can be checked in the Channel box. The red, gray, and blue rectangles indicate signal, baseline, and common interval, respectively.

[[File:MSBF55.png|700px|thumb|c|none|Source Analysis window with beamformer image. The two beamformer virtual sensors have been added using the Switch to Maximum and Add Source toolbar buttons (see below).
Source waveforms are computed using the beamformer spatial weights and the displayed averaged data (the noise normalized weights (5% noise) option was used to compute the beamformer image).]]

When starting the beamformer from the '''Average tab of the Paradigm dialog box''', the bilateral beamformer scan is performed. In the source analysis window, the beamformer computation can be repeated taking into account possibly correlated sources that are specified in the current solution. Interfering activities generated by all sources in the current solution that are in the 'On' state are specifically suppressed (they enter the leadfield matrix L in the beamformer calculation). The computation can be started from the '''Image''' menu or from the Image selector button [[File:MSBF_Button.png|22px|Image: 22 pixels]] dropdown menu. The Image menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window.

[[File:MSBF66.png|700px|thumb|c|none|Multiple-source beamformer image calculated in the presence of a source in the left hemisphere. A single-source scan has been performed instead of a bilateral beamforemr. The source set in the current solution accounts for the left-hemispheric q-maximum in the data. Accordingly, the beamformer scan reveals only the as yet unmodeled additional activity in the right hemisphere (note the radiological convention in the 3D image display). The source waveform of the beamformer virtual sensor in the left hemisphere is not shown since the location (blue square in the figure) is not considered for the multiple-source beamformer.]]

The beamformer scan can be performed with a single or a bilateral source scan. The default scan type depends on the current solution:

When the beamformer is started from the '''Average tab of the Paradigm dialog box''' the Source Analysis window opens with a new solution and a bilateral beamformer scan is performed.

When the beamformer is started within the Source Analysis window, the default is:
* a scan with a single source in addition to the sources in the current solution, if at least one source is active.
* a bilateral scan if no source in the current solution is active.
* a scan with a single source when scalar-type beamformer is selected in the '''beamformer option dialog box'''.

The default scan type is the multiple source beamformer. The non-default scan type can be enforced using the corresponding Volume Image / Beamformer entry in the Image main
menu or in the beamformer option dialog box (only for the time-domain beamformer).

'''Inserting Sources as Beamformer Virtual Sensor out of the Beamformer Image'''

This is similar to the inserting sources out of the beamformer image in Multiple Source Beamformer (MSBF) in the Time-frequency Domain section.

The beamformer image can be used to add beamformer virtual sensors to the current solution. A simple double-click anywhere in the 3D view (not in the 2D view) will generate a source at the corresponding location. A better and easier way to create sources at image maxima and minima is to use the toolbar buttons '''Switch to Maximum''' [[Image:SA 3Dimaging (8).gif]] and '''Add Source''' [[Image:SA 3Dimaging (9).gif]].

This feature allows to use the beamformer as a tool to create a source montage for '''source coherence''' analysis. A source montage file (*.mtg) for beamformer virtual sensors can
be saved using File \ Save Source Montage As… entry.

The time-domain beamformer image can be also used to add regional or dipole sources to the current solution. Press '''N''' key when there is no source in the current source array or there is more than one beamformer virtual sensor. To create a new source array for beamformer virtual sensor, press '''N''' key when there is more than one regional or dipole source in the current source array.

'''Notes'''

* You can hide or re-display the last computed image by selecting ''Hide Image'' entry in the '''Image''' menu.
* The current image can be exported to ASCII, ANALYZE, or BrainVoyager (*.vmp) format from the '''Image''' menu.
* For scaling options, use [[Image:SA 3Dimaging (10).gif]] and [[Image:SA 3Dimaging (11).gif]] '''Image Scale toolbar''' buttons.
* Parameters used for the beamformer calculations can be set in the '''Standard Volume tab of the Image Settings dialog box'''.
* Note that Model, Residual, Order, and Residual variance are not shown for the beamformer virtual sensor type sources.

'''References'''

* Sekihara, K., Nagarajan, S. S., Poeppel, D., Marantz, A., & Miyashita, Y. (2001). Reconstructing spatio-temporal activities of neural sources using an MEG vector beamformer technique. IEEE Transactions on Biomedical Engineering, 48(7), 760–771.

* Van Veen, B. D., Van Drongelen, W., Yuchtman, M., & Suzuki, A. (1997). Localization of brain electrical activity via linearly constrained minimum variance spatial filtering. IEEE Transactions on Biomedical Engineering, 44(9), 867–880

== CLARA ==

CLARA ('Classical LORETA Analysis Recursively Applied') is an iterative application of weighted LORETA images with a reduced source space in each iteration.

In an initialization step, a LORETA image is calculated. Then in each iteration the following steps are performed:

# The obtained image is spatially smoothed (this step is left out in the first iteration).
# All grid points with amplitudes below a threshold of 1% of the maximum activity are set to zero, thus being effectively eliminated from the source space in the following step.
# The resulting image defines a spatial weighting term (for each voxel the corresponding image amplitude).
# A LORETA image is computed with an additional spatial weighting term for each voxel as computed in step 3. By the default settings in BESA Research, the regularization values used in the iteration steps are slightly higher than that of the initialization LORETA image.

The procedure stops after 2 iterations, and the image computed in the last iteration is displayed. Please note that you can change all parameters by creating a user-defined volume image.

The advantage of CLARA over non-focusing distributed imaging methods is visualized by the figure below. Both images are computed from the N100 response in an auditory oddball experiment (file '''Oddball.fsg''' in subfolder ''fMRI+EEG-RT-Experiment'' of the ''Examples'' folder). The CLARA image is much more focal than the sLORETA image, making it easier to determine the location of the image maxima.

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (24).gif|thumb|350px|sLORETA image]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (25).gif|thumb|350px|CLARA image]] </li>
</ul></div>

'''Notes:'''

* Starting CLARA: CLARA can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]'' for important information on regularization of distributed inverses.

== LAURA ==

LAURA (Local Auto Regressive Average) belongs to the distributed inverse method of the family of weighted minimum norm methods ([https://doi.org/10.1023/A:1012944913650 Grave de Peralta Menendeza et al., "Noninvasive Localization of Electromagnetic Epileptic Activity. I. Method Descriptions and Simulations", BrainTopography 14(2), 131-137, 2001]). LAURA uses a spatial weighting function that includes depth weighting and that term has the form of a local autoregressive function.

The source activity is estimated by applying the general formula for a weighted minimum norm:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T}\left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings.''

In LAURA, V contains both a depth weighting term W and a representation of a local autoregressive function A. V is computed as:

<math>\mathrm{V} = \left( \mathrm{U}^{T} \cdot \mathrm{U} \right)^{-1}</math>


where

<math>\mathrm{U} = \left( \mathrm{W} \cdot \mathrm{A} \right) \otimes \mathrm{I}_{3}</math>


Here, <math>\otimes</math> denotes the Kronecker product. I3 is the [3×3] identity matrix. W is an [s×s] diagonal matrix (with s the number of source locations on the grid), where each diagonal element is the inverse of the maximum singular value of the corresponding regional source's leadfields. The formula for the diagonal components Aii and the off-diagonal components Aik are as follows:

<math>\mathrm{A}_{ii} = \frac{26}{\mathrm{N}_{i}}\sum_{k \subset V_{i}}^{}\frac{1}{\mathrm{d}_{ik}^{2}}</math>


<math>
\mathrm{A}_{ik} =
\begin{cases}
- 1/\operatorname{dist}\left( i,k \right)^{2}, & \text{if } k \subset V_{i} \\
0, & \text{otherwise}
\end{cases}
</math>


Here, Vi is the vicinity around grid point i that includes the 26 direct neighbors.

The LAURA image in BESA Research displays the norm of the 3 components of S at each location r. Using the menu function ''Image / Export Image As... ''you have the option to save this norm of S or alternatively all components separately to disk.

'''Notes:'''

* '''Grid spacing:''' Due to memory limitations, LAURA images require a grid spacing of 7 mm or more.
* '''Computation time:''' Computation speed during the first LAURA image calculation depends on the grid spacing (computation is faster with larger grid spacing). After the first computation of a LAURA image, a '''*.laura''' file is stored in the data folder, containing intermediate results of the LAURA inverse. This file is used during all subsequent LAURA image computations. Thereby, the time needed to obtain the image is substantially reduced.
* '''MEG:''' In the case of MEG data, an additional constraint is implemented in the LAURA algorithm that prevents solutions from containing radial source currents (compare Pascual-Marqui, ISBET Newsletter 1995, 22-29). In MEG, an additional source space regularization is necessary in the inverse matrix operation required compute V
* '''Starting LAURA:''' LAURA can be started from the''' Image''' menu or from the '''Image Selection''' button.
* '''Regularization:''' Please refer to Chapter'' “Regularization of distributed volume images” ''for important information on regularization of distributed inverses.

== LORETA ==

LORETA ("Low Resolution Electromagnetic Tomography") is a distributed inverse method of the family of ''weighted minimum norm'' methods. LORETA was suggested by R.D. Pascual-Marqui (International Journal of Psychophysiology. 1994, 18:49-65). LORETA is characterized by a smoothness constraint, represented by a discrete 3D Laplacian.

The source activity is estimated by applying the general formula for a weighted minimum norm:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T}\left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings.''

In LORETA, V contains both a depth weighting term and a representation of the 3D Laplacian matrix. V is computed as:

<math>\mathrm{V} = \left( \mathrm{U}^{T} \cdot \mathrm{U} \right)^{- 1}</math>


where

<math>\mathrm{U} = \left( \mathrm{W} \cdot \mathrm{A} \right) \otimes \mathrm{I}_{3}</math>


Here, <math>\otimes</math> denotes the Kronecker product. I3 is the [3x3] identity matrix. W is an [sxs] diagonal matrix (with s the number of source locations on the grid), where each diagonal element is the inverse of the maximum singular value of the corresponding regional source's leadfields. A contains the 3D Laplacian and is computed as

<math>\mathrm{A} = \mathrm{Y} - \mathrm{I}_{s}</math>


with Is the [sxs] identity matrix, where s is the number of sources (= three times the number of grid points) and

<math>\mathrm{Y} = \frac{1}{2}\left\{ \mathrm{I}_{s} + \left\lbrack \operatorname{diag}\left( \mathrm{Z} \cdot \left\lbrack 111 \ldots 1 \right\rbrack^{T} \right) \right\rbrack^{- 1} \right\} \cdot \mathrm{Z}</math>


where

<math>
\mathrm{Z}_{ik} =
\begin{cases}
1/6, & \text{if } \operatorname{dist}\left( i,k \right) = 1 \text{ grid point} \\
0, & \text{otherwise}
\end{cases}
</math>


The LORETA image in BESA Research displays the norm of the 3 components of S at each location r. Using the menu function ''Image / Export Image As... ''you have the option to save this norm of S or alternatively all components separately to disk.

'''Notes:'''
* '''Grid spacing:''' Due to memory limitations, LORETA images require a grid spacing of 5 mm or more.
* '''Computation time:''' Computation speed during the first LORETA image calculation depends on the grid spacing (computation is faster with larger grid spacing). After the first computation of a LORETA image, a '''<nowiki>*.loreta</nowiki>''' file is stored in the data folder, containing intermediate results of the LORETA inverse. This file is used during all subsequent LORETA image computations. Thereby, the time needed to obtain the image is substantially reduced.
* '''MEG''': In the case of MEG data, an additional constraint is implemented in the LORETA algorithm that prevents solutions from containing radial source currents (Pascual-Marqui, ISBET Newsletter 1995, 22-29). In MEG, an additional source space regularization is necessary in the inverse matrix operation required compute V.
* '''Starting LORETA:''' LORETA can be started from the''' Image''' menu or from the '''Image Selection '''button.
* '''Regularization:''' Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed source models.

== sLORETA ==

This distributed inverse method consists of a ''standardized, unweighted minimum norm''. The method was originally suggested by R.D. Pascual-Marqui (Methods & Findings in Experimental & Clinical Pharmacology 2002, 24D:5-12) Starting point is an unweighted minimum norm computation:

<math>\mathrm{S}_{\text{MN}}\left( t \right) = \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{L}^{T} \right)^{- 1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings''.

This minimum norm estimate is now standardized to produce the sLORETA activity at a certain brain location r:

<math>\mathrm{S}_{\text{sLORETA}, r} = \mathrm{R}_{rr}^{-1/2} \cdot \mathrm{S}_{\text{MN},r}</math>


SsMN,r is the [3x1] (MEG: [2x1]) minimum norm estimate of the 3 (MEG: 2) dipoles at location r. Rrr is the [3x3] (MEG: [2x2]) diagonal block of the resolution matrix R that corresponds to the source components at the target location r. The resolution matrix is defined as:

<math>\mathrm{R} = \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{L}^{T} + \lambda \cdot \mathrm{I} \right)^{-1} \cdot \mathrm{L}</math>


The sLORETA image in BESA Research displays the norm of SsLORETA, r at each location r. Using the menu function ''Image / Export Image As...'' you have the option to save this norm of SsLORETA, r or alternatively all components separately to disk.

'''Notes:'''

* sLORETA can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter [[#Regularization_of_distributed_volume_images|''Regularization of distributed volume images'']] for important information on regularization of distributed inverses.

== swLORETA ==

This distributed inverse method is a ''standardized, depth-weighted minimum norm'' (E. Palmero-Soler et al 2007 Phys. Med. Biol. 52 1783-1800). It differs from sLORETA only by an additional depth weighting.

Starting point is a depth-weighted minimum norm computation:

<math>\mathrm{S}_{\text{MN}}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. The term in parentheses is generally regularized. Regularization parameters can be specified in the ''Image Settings''.

V is the diagonal depth weighting matrix. For s grid locations, V is of dimension [3s x 3s] (MEG: [2s x 2s]). Each diagonal element of V is the inverse of the first singular value of the leadfield of the corresponding regional source. Hence, the first 3 (MEG: 2) diagonal elements equal the inverse of the largest eigenvalue of the leadfield matrix of regional source 1, and so on.

This minimum norm estimate is now standardized to produce the swLORETA activity at a certain brain location r:

<math>\mathrm{S}_{\text{swLORETA},r} = \mathrm{R}_{rr}^{-1/2} \cdot \mathrm{S}_{\text{MN},r}</math>


SsMN,r is the [3x1] (MEG: [2x1]) depth-weighted minimum norm estimate of the regional source at location r. Rrr is the [3x3] (MEG: [2x2]) diagonal block of the resolution matrix R that corresponds to the source components at the target location r. The resolution matrix is defined as:

<math>\mathrm{R} = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} + \lambda \cdot \mathrm{I} \right)^{-1} \cdot \mathrm{L}</math>


The swLORETA image in BESA Research displays the norm of SswLORETA, r at each location r. Using the menu function ''Image / Export Image As...'' you have the option to save this norm of SswLORETA, r or alternatively all components separately to disk.

'''Notes:'''

* sLORETA can be started from the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''Regularization of distributed volume images”'' for important information on regularization of distributed inverses.

== sSLOFO ==

SSLOFO (standardized shrinking LORETA-FOCUSS) is an iterative application of weighted distributed source images with a reduced source space in each iteration ([https://dx.doi.org/10.1109/TBME.2005.855720 Liu et al., "Standardized shrinking LORETA-FOCUSS (SSLOFO): a new algorithm for spatio-temporal EEG source reconstruction", IEEE Transactions on Biomedical Engineering 52(10), 1681-1691, 2005]).

In an initialization step, an [[#sLORETA | sLORETA]] image is calculated. Then in each iteration the following steps are performed:

# A weighted minimum norm solution is computed according to the formula <math display="inline">\mathrm{S} = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}</math> . Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D is the data at the time point under consideration. V is a diagonal spatial weighting matrix that is computed in the previous iteration step. In the first iteration, the elements of V contain the magnitudes of the initially computed LORETA image.
# Standardization of this weighted minimum norm image is performed with the resolution matrix as in [[#sLORETA | sLORETA]].
# The obtained standardized weighted minimum norm image is being smoothed to get Ssmooth.
# All voxels with amplitudes below a threshold of 1% of the maximum activity get a weight of zero in the next iteration step, thus being effectively eliminated from the source space in the next iteration step.
# For all other voxels, compute the elements of the spatial weighting matrix V to be used in the next iteration as follows: <math display="inline">\mathrm{V}_{ii,\text{next iteration}} = \frac{1}{\left\| \mathrm{L}_{i} \right\|} \cdot \mathrm{S}_{ii,\text{smooth}} \cdot \mathrm{V}_{ii,\text{current iteration}}</math>



The procedure stops after 3 iterations. Please note that you can change all parameters by creating a [[#User-Defined Volume Image | user-defined volume image]].

'''Notes:'''
* '''Starting sSLOFO''': sSLOFO can be started from the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''[[#Regularization of distributed volume images | Regularization of distributed volume images]]'' for important information on regularization of distributed inverses.

== User-Defined Volume Image ==

In addition to the predefined 3D imaging methods in BESA Research, it is possible to create user-defined imaging methods based on the general formula for distributed inverses:

<math>\mathrm{S}\left( t \right) = \mathrm{V} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{V} \cdot \mathrm{L}^{T} \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed source model with regional sources distributed on a regular cubic grid. D(t) is the data at time point t. Custom-defined parameters are:

* '''The spatial weighting matrix V''': This may include depth weighting, image weighting, or cross-voxel weighting with a 3D Laplacian (as in LORETA) or an autoregressive function (as in LAURA).
* '''Regularization''': The term in parentheses is generally regularized. Note that regularization has a strong effect on the obtained results. Please refer to chapter ''Regularization of Distributed Volume Images''for more information.
* '''Standardization''': Optionally, the result of the distributed inverse can be standardized with the resolution matrix (as in sLORETA).
* '''Iterations''': Inverse computations can be applied iteratively. Each iteration is weighted with the image obtained in the previous iteration.

All parameters for the user-defined volume image are specified in the User-Defined Volume Tab of the Image Settings dialog box. Please refer to chapter ''User-Defined Volume Tab'' for details.

'''Notes:'''

* Starting the user-defined volume image: the image calculation can be started from the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter ''Regularization of distributed volume images'' for important information on regularization of distributed inverses.

== Regularization of distributed volume images ==

Distributed source images require the inversion of a term of the form L V LT. This term is generally regularized before its inversion. In BESA Research, selection can be made between two different regularization approaches (parameters are defined in the ''Image Settings dialog box''):

* '''Tikhonov regularization''': In Tikhonov regularization, the term L V LT is inverted as (L V LT +λ I)-1. Here, l is the regularization constant, and I is the identity matrix.
** One way of determining the optimum regularization constant is by minimizing the ''generalized cross'' ''validation error'' (CVE).
** Alternatively, the regularization constant can be specified manually as a percentage of the trace of the matrix L V LT.
* '''TSVD''': In the truncated singular value decomposition (TSVD) approach, an SVD decomposition of L V LT is computed as  L V LT = U S UT, where the diagonal matrix S contains the singular values. All singular values smaller than the specified percentage of the maximum singular values are set to zero. The inverse is computed as U S-1 UT, where the diagonal elements of S-1 are the inverse of the corresponding non-zero diagonal elements of S.

Regularization has a critical effect on the obtained distributed source images. The results may differ completely with different choices of the regularization parameter (see examples below). Therefore, it is important to evaluate the generated image critically with respect to the regularization constant, and to keep in mind the uncertainties resulting from this fact when interpreting the results. The default setting in BESA Research is a TSVD regularization with a 0.03% threshold. However, this value might need to be adjusted to the specific data set at hand.

The following example illustrates the influence of the regularization parameter on the obtained images. The data used here is condition '''St-Cor of dataset Examples \ TFC-Error-Related-Negativity \ Correct+Error.fsg''' at 176 ms following the visual stimulus. Discrete dipole analysis reveals the main activity in the left and right lateral visual cortex at this latency.

[[File:SA 3Dimaging (42).gif|400px|thumb|c|none|Discrete source model at 176 ms: Main activity in the left and right lateral visual cortex, no visual midline activity.]]

LORETA images computed at this latency depend critically on the choice of the regularization constant. The following 3D images are created with TSVD regularization with SVD cutoffs of 0.1%, 0.005%, and 0.0001%, respectively. The volume grid size was 9 mm. The example demonstrates the dramatic effect of regularization and demonstrates the typical tradeoff between too strong regularization (leading to too smeared 3D images that tend to show blurred maxima) and too small regularization (resulting in too superficial 3D images with multiple maxima).

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (44).gif|thumb|350px|'''SVD cutoff 0.1%''': Regularization too strong. No separation between sources, mislocalization towards the middle of the brain.]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (43).gif|thumb|350px|'''SVD cutoff 0.005%''': Appropriate regularization. Separation of the bilateral activities. Location in agreement with the discrete multiple source model.]] </li>
<li style="display: inline-block;"> [[File:SA 3Dimaging (45).gif|thumb|350px|'''SVD cutoff 0.0001%''': Too small regularization. Mislocalization, too superficial 3D image. ]] </li>
</ul></div>

The automatic determination of the regularization constant using the CVE approach does not necessarily result in the optimum regularization parameter either. In this example, the unscaled CVE approach rather resembles the TSVD image with a cutoff of 0.0001%, i.e. regularization is too small. Therefore, it is advisable to compare different settings of the regularization parameter and make the final choice based on the above-mentioned considerations.

== Cortical LORETA ==

Cortical LORETA is principally the same technique as LORETA, however, Cortical LORETA is not computed in a 3D volume, but on the cortical surface.

The cortical reconstruction in BESA Research fed from BESA MRI is a closed 2D surface with no boundaries and a very close approximation of the actual cortical form. It consists of an irregular triangulated grid.

The Laplace operator that is used for identifying a smooth solution in a three-dimensional space is exchanged with a Laplace operator that runs on the two-dimensional cortical surface.

There is a wide variety of 2D Laplace operators with different characteristics. The general form of the discrete Laplace operator is

<math>\Delta f\left( p_{i} \right) = \frac{1}{d_{i}}\sum_{j \in N(i)}^{}{w_{ij}\left\lbrack f\left( p_{i} \right) - f\left( p_{j} \right) \right\rbrack},</math>


where '''pi''' is the '''i-th''' node of the triangular mesh, '''f(pi) '''is the value of a function f defined on the cortical mesh at the node '''pi''', '''wij''' is the weight for the connection between the nodes '''pi''' and '''pj''' and '''di''' is a normalization factor for the '''i-th''' row of the operator. Furthermore, '''N(i)''' is the set of indices corresponding to the direct (also called "1-ring") neighbors of '''pi'''.

BESA offers the choice of three Laplace operators with slightly different characteristics.

* '''Unweighted Graph Laplacian''': This is the simplest operator. It takes into account only the adjacency of the nodes and not the geometry of the mesh:

<math>
w_{ij} =
\begin{cases}
1, & \text{if } p_{i} \text{ and } p_{j} \text{ are connected by an edge} \\
0, & \text{otherwise}
\end{cases}
</math>

<math>d_{i} = 1</math>


[[Image:SA 3Dimaging (4).jpg |450px]]

* '''Weighted Graph Laplacian:''' This operator is similar to the unweighted graph Laplacian but with different weights for the different connections. The connections between nearby nodes get larger weights than the connections between farther nodes:

<math>w_{ij} = \frac{1}{\operatorname{dist}\left( p_{i},p_{j} \right)}</math>

<math>d_{i} = \sum_{j \in N(i)}^{} {\operatorname{dist}\left(p_{i}, p_{j} \right)}</math>


where '''dist''' ('''pi''' , '''pj''') is the distance between the nodes '''pi '''and '''pj'''.

[[Image:SA 3Dimaging (6).jpg|450px]]

* '''Geometric Laplacian with mixed area weights''': This operator takes into account the angles in the corresponding triangles into account as well as the area around the nodes in order to determine the connection weights:

<math>w_{ij} = \frac{\cot\left( \alpha_{ij} \right) + \cot\left( \beta_{ij} \right)}{2}</math>

<math>d_{i} = A_{\text{mixed}}</math>


where '''αij''' and '''βij''' denote the two angles opposite to the edge ('''i , j''') and '''Amixed '''is either the Voronoi area, or 1/2 of the triangle area or 1/4 of the triangle area depending on the type of the triangle.

[[Image:SA 3Dimaging (8).jpg|450px]]

'''Regularization and other parameters:'''

[[Image:CorticalLOR.png‎]]

* '''SVD cutoff''': The regularization for the inverse operator as a percent of the largest singular value.
* '''Depth weighting''': Turn depth weighting on or off.
* '''Laplacian type''': Selection of Laplacian operators (see above).

'''Notes:'''
* '''Starting Cortical LORETA''': Cortical LORETA can be started from the sub-menu '''Surface Image''' of the '''Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]''” for important information on regularization of distributed inverses.

'''References:'''

Please refer to ''Iordanov et al.: LORETA With Cortical Constraint: Choosing an Adequate Surface Laplacian Operator. Front Neurosci 12, Article 746, 2018'', for more information - full article available [https://www.frontiersin.org/articles/10.3389/fnins.2018.00746/full here].

== Cortical CLARA ==

Cortical CLARA is principally the same technique as CLARA, but Cortical CLARA is not computed in a 3D volume, but on the cortical surface. Instead of using a LORETA image as the basis for the iterative application, cortical CLARA uses cortical LORETA.

'''Regularization and other parameters:'''

[[Image:SA 3Dimaging (47).gif]]

* '''SVD cutoff''': The regularization for the inverse operator as a percent of the largest singular value.
* '''Depth weighting''': Turn depth weighting on or off.
* '''Laplacian type''': Selection of Laplacian operators (see Cortical LORETA).
* '''No of iterations''': Number of iterations for CLARA. The more iterations are used, the sparser becomes the solution.
* '''Automatic''': The algorithm tries to determine the number of iterations automatically. The goodness of fit (GOF) is calculated after every iteration and if there is a big jump in the GOF then the algorithm will stop. If no jumps appear during the calculations then CLARA iterates until the specified number of iterations is reached.
* '''Regularize iterations''': If one wants to use different regularization for the CLARA iterations than the value specified as "SVD cutoff", this option should be selected.
* '''Amount to clip from img (%)''': Cortical CLARA uses the solution from the previous iteration as an additional weighting matrix for the current iteration. That weighting matrix is constructed by cutting the "low" activity from the solution. This number specifies how much of the activity should be cut from the previous solution in order to construct the weighting matrix. This value is given as a percentage of the maximal activity. Default value is 10%.

'''Notes:'''

* '''Starting Cortical CLARA:''' Cortical CLARA can be started from the sub-menu '''Surface Image''' of the''' Image''' menu or from the '''Image Selection''' button.
* Please refer to Chapter “''[[Source_Analysis_3D_Imaging#Regularization_of_distributed_volume_images|Regularization of distributed volume images]]''” for important information on regularization of distributed inverses.

== Cortex Inflation ==

The inflated cortex is a smoothened version of the individual cortical surface with minimal metric distortions (Fischl, B. et al. (1999). Cortical Surface-Based Analysis: II: Inflation, Flattening, and a Surface-Based Coordinate System. ''NeuroImage'', 9(2), 195–207). Gyri and sulci are smoothened out. The original distances between each point on the cortex and its neighbors are, however, mostly preserved.

[[Image:SA 3Dimaging (48).gif]]

''Cortical LORETA map overlaid on top of the inflated cortical surface.''

A lighter gray color overlaid on top of the surface image indicates the location of a gyrus of the individual cortex surface, while a darker gray color indicates the location of a sulcus. The inflated cortical surface can be computed in '''BESA MRI 2.0'''. For more details please refer to the BESA MRI 2.0 help.

== Surface Minimum Norm Image ==

'''Introduction'''

The minimum norm approach is a common method to estimate a distributed electrical current image in the brain at each time sample (Hämäläinen & Ilmoniemi 1984). The source activities of a large number of regional sources are computed. The sources are evenly distributed using 1500 standard locations 10% and 30% below the smoothed standard brain surface (when using the standard MRI) or using between 3000-4000 locations on the individual brain surface defined by the gray-white-matter boundary.

Since the number of sources is much larger than the number of sensors in a minimum norm solution, the inverse problem is highly underdetermined and must be stabilized by a mathematical constraint, the minimum norm. Out of the many current distributions that can account for the recorded sensor data, the solution with the minimum L2 norm, i.e. the minimum total power of the current distribution is displayed in BESA Research.

First, the forward solution (leadfield matrix L) of all sources is calculated in the current head model. Then, the source activities S(t) of all source components are computed from the data matrix D(t) using an inverse regularized by the estimated noise covariance matrix:

<math>\mathrm{S}\left( t \right) = \mathrm{R} \cdot \mathrm{L}^{T} \cdot \left( \mathrm{L} \cdot \mathrm{R} \cdot \mathrm{L}^{T} + \mathrm{C}_N \right)^{-1} \cdot \mathrm{D}(t)</math>


Here, L is the leadfield matrix of the distributed regional source model, CN denotes the noise correlation matrix in sensor space, and R is a weighting matrix in source space. R and CN can be designed in different ways in order to optimize the minimum norm result. The total activity of each regional source is computed as the root mean square of the source activities S(t) of its 3 (MEG:2) components. This total source activity is transformed to a color-coded image of the brain surface. (When the standard brain is used, two sources are assigned to each surface location, located 10% and 30% below the surface, respectively. The color that is displayed on the standard brain surface is the larger of the two corresponding source activities.)

'''Weighting options'''

The minimum norm current imaging techniques of BESA Research provide different weighting strategies. Two weighting approaches are available: Depth weighting and spatio-temporal approaches.
* '''Depth weighting:''' Without depth weighting, deep sources appear very smeared in a minimum-norm reconstruction. With depth weighting, both deep and superficial sources produce a similar, more focal result. If this weighting method is selected, the leadfield of each regional source is scaled with the largest singular value of the SVD (singular value decomposition) of the source's leadfield.
* '''Spatio-temporal weighting''': Spatio-temporal weighting tries to assign large weight to sources that are assumed to be more likely to contribute to the recorded data.
** '''Subspace correlation after single source scan''': This method divides the signal into a signal and a noise subspace. The correlation of the leadfield of a regional source i with the signal subspace (pi) is computed to find out if the source location contributes to the measured data. The weighting matrix R becomes a diagonal matrix. Each of the three (MEG: 2) components of a regional source get the same weighting value pi2. This approach is based on the signal subspace correlation measure introduced by J.C. Mosher, R. M. Leahy (Recursive MUSIC: A Framework for EEG and MEG Source Localization, IEEE Trans. On Biomed. Eng. Vol. 45, No. 11, November 1998)
** '''Dale & Sereno 1993:''' In the approach of Dale and Sereno (J Cogn Neurosci, 1993, 5: 162-176) a signal subspace needs not be defined. The correlation pi of the leadfield of regional source i with the inverse of the data covariance matrix is computed along with the largest singular value λmax of the data covariance matrix. The weighting matrix R is a diagonal matrix with weights: [[Image:SA 3Dimaging (50).gif]]. Each of the three (MEG: 2) components of a regional source receives the same weighting value.

'''Noise regularization'''

Three methods to estimate the channel noise correlation matrix CN are provided by the program:
* '''Use baseline:''' Select this option to estimate the noise from the user-definable baseline. The signal is computed from the data at non-baseline latencies.
* '''Use 15% lowest values:''' The baseline activity is computed from the data at those 15% of all displayed latencies that have the lowest global field power. The signal is computed from all displayed latencies.
* '''Use the full baseline covariance matrix''': This option is only available if a previous beamformer image in the time-domain was calculated. In this case, it can be selected from the general image settings dialog tab. The baseline covariance interval is the one selected for the beamformer, and is indicated by a thin horizontal bar in the channel box.

In each case, the activity (noise or signal, respectively) is defined as root-mean-square across all respective latencies for each channel.

The noise covariance matrix CN is constructed as a diagonal matrix. The entries in the main diagonal are proportional to the noise activity of the individual channels (if selected) or are all equally proportional to the average noise activity over all channels. The noise covariance matrix CN is then scaled such that the ratio of the Frobenius norms of the weighted leadfield projector matrix (LRLT) and the noise covariance matrix CN equals the Signal-to-Noise ratio. This scaling can be multiplied by an additional factor (default=1) to sharpen (<1) or smoothen (>1) the minimum norm image.

'''Applying the Minimum Norm Image'''

The minimum-norm algorithm is started via the ''Surface minimum norm image dialog box'', which is opened from the''' Image''' menu, or by typing the shortcut '''Ctrl-M''': Please refer to Chapter ''“Surface'' ''Minimum Norm Tab”'' for more details.

As opposed to the other 3D images available from the '''Image '''menu, the surface minimum norm image is not computed on a volumetric grid, but rather for locations on the brain surface. Accordingly, the results of the minimum norm image are displayed superimposed to the brain surface mesh rather than to the volumetric MR image.

The figure below shows a minimum norm image computed from the file '''Examples\Epilepsy\Spikes\Spikes-Child4_EEG+MEG_averaged.fsg'''. The EEG spike peak was imaged using the individual brain surface of the subject. A baseline from -300 to -70 ms was used. Minimum norm was computed with depth weighting, Spatio-temporal weighting according to Dale & Sereno 1993 and individual noise weighting with a noise scale factor of 0.01. The minimum norm image reveals the location of the spike generator in the close vicinity of the frontal left-hemispheric lesion in this subject.

[[Image:SA 3Dimaging (51).gif]]

== Multiple Source Probe Scan (MSPS) ==

 
'''Introduction'''

The MSPS function provides a tool for the validation of a given solution. It is based on the following theoretical consideration: If the recorded EEG/MEG data has been modeled adequately, i.e. all active brain regions are represented by a source in the current solution, then any additional probe source added to the solution will not show any activity apart from noise. The only exception occurs if this probe source is placed in close vicinity to one of the sources in the current solution. In that case, the solution's source and the probe source will share the activity of the corresponding brain area. The MSPS applies these considerations by scanning the brain on a pre-defined grid with a regional probe added to the current solution. Grid extent and density can be specified in the Image settings. The power P of the probe source at location r in the signal interval is compared with the power of the probe source in a reference interval, defining a value q:

<math>\mathrm{q}\left( r \right) = \sqrt{\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}} - 1</math>


MSPS can be computed on time domain or time-frequency domain data:
* In the time domain, q(r) is computed from the source waveform of the probe source. Here, P(r) is the mean power of the probe source at location r in the marked latency range, and Pref(r) is the mean probe source power in the user-definable baseline interval.
* In the time-frequency domain, an MSPS image can be computed from the complex cross spectral density matrices. By applying the inverse operator for a source configuration consisting of the current solution and the probe source, the power of the probe source can be computed for the target interval [P(r)] and the reference time-frequency interval [Pref(r)]. In the resulting MSPS image, q-values are shown in %, where q[%] = q*100.

The inverse operator used to determine the probe source power uses different regularization constants for the probe source and the sources in the current solution. The regularization constant of the sources in the current solution can be specified in the Image settings (default 4%). The regularization constant of the probe source is internally set to 0%.

Alternatively to the definition above, q can also be displayed in units of dB:

<math>\mathrm{q}\left\lbrack \text{dB} \right\rbrack = 10 \cdot \log_{10}\frac{\mathrm{P}\left( r \right)}{\mathrm{P}_{\text{ref}}\left( r \right)}</math>


Values of q smaller than zero are not shown in the MSPS image.

According to the considerations above, an MSPS of a correct source model should optimally yield image maxima around the sources in the current solution only. If the MSPS image is blurred or shows maxima at locations different from the modeled sources, this indicates a non-sufficient or incorrect solution.

'''Applying the MSPS'''

This chapter illustrates the application of the Multiple Source Probe Scan. The figures are generated with data from file '''Examples/Epilepsy/Spikes/Rolandic-Spike-Child.fsg''' (-300 : +200 ms, filtered from 3 Hz [forward] to 40 Hz [zero-phase]).

'''Time domain versus time-frequency domain MSPS'''

The multiple source probe scan can be computed in the time domain or the time-frequency domain. The latter is possible only when time-frequency domain data is available for the current condition, i.e. if the condition has been created by starting a multiple source beamformer (MSBF) computation from the source coherence window. In this case, evoking the MSPS calculation from the '''Imaging '''button or from the '''Image''' menu will bring up the following dialog window that allows to choose between time- or time-frequency MSPS. If only time domain data is available, this dialog window will not appear and MSPS will be computed in the time domain.

[[Image:SA 3Dimaging (53).gif]]

For a time-frequency domain MSPS, the target and the reference time-frequency interval have been specified already in the Time-Frequency window (see Chapter "''How To Create Beamformer Images''"). For a time-domain MSPS, the target and the reference epoch have to be specified in the Source Analysis window as described below.

'''Time domain MSPS'''

The time-domain MSPS image displays the ratio of the power of a regional probe source in the signal and the baseline interval. The currently set baseline is indicated by a horizontal line in the upper left corner of the channel box.

[[Image:SA 3Dimaging (54).gif|thumb|c|none|330px|The black horizontal bar in the upper part of the channel box (here circled in red) indicates the baseline interval.]]

By default, BESA Research defines the pre-stimulus interval of the current data segment as baseline. The baseline should represent a latency range in which no event-related activity is present in the data. There are several possibilities to modify the baseline interval: by clicking on the horizontal line with the left mouse button or by using the corresponding entry in the '''Condition '''menu or '''Fit Interval''' popup menu.

Mark an interval to define the target epoch, i.e. the time-interval for which the current solution is to be tested. Start the MSPS by selecting it from the '''Image selection '''button or from the '''Image''' menu to start the probe source scan. The''' Image '''menu can be evoked either from the menu bar or by right-clicking anywhere in the source analysis window. The 3D window opens and displays the scan result.

<div><ul>
<li style="display: inline-block;"> [[Image:SA 3Dimaging (55).gif|thumb|c|none|650px|This figure shows the MSPS image applied on the three left-hemispheric sources in the solution ''''Rolandic-Spike-Child-RS2.bsa''''. The baseline is set from -300ms to -50 ms. The right-hemispheric sources have been switched off. The fit interval is set to the latency range of large overall activity in the data (-43 ms : 117 ms). A realistic FEM model appropriate for the subject's age (12 years, conductivity ratios (cr) 50) is applied. The MSPS image does not show maxima at the modeled source locations and rather shows a spread q-value distribution.]] </li>

<li style="display: inline-block;"> [[Image:SA 3Dimaging (56).gif|thumb|c|none|650px|The MSPS image for the same latency range when the right-hemispheric sources have been included. The MSPS image appears more focal and shows maxima around the modeled brain regions. This indicates the substantial improvement of the solution by adding the right-hemispheric sources that model the propagation of the epileptic spike from the left to the right hemisphere (note the radiological side convention in the 3D window).]] </li>
</ul></div>

'''Time-Resolved MSPS'''

If the MSPS has been computed on time domain data, the image can be shown separately for each latency in the selected interval. After the MSPS has been computed for the marked epoch, double-click anywhere within this epoch to display the ratio of the probe source magnitude at the selected latency and the mean probe source magnitude in the baseline. Scanning the latency range by moving the cursor (e.g. with the left and right arrow cursor keys) provides a time-resolved MSPS image.

Time-resolved MSPS images are not available if the MSPS has been computed on data in the time-frequency domain.

<div><ul>
<li style="display: inline-block;"> [[File:SA 3Dimaging (57).gif|thumb|450px|MSPS image of the spike peak activity at 0ms. The activity mainly occurs in the left hemisphere. This fact is illustrated by the source waveforms and confirmed in the MSPS image, which shows a focal maximum around the location of the red sources.]] </li>

<li style="display: inline-block;"> [[File:SA 3Dimaging (58).gif|thumb|450px|Around +27 ms, the spike has propagated to the right hemisphere. This becomes evident from the waveforms of the blue sources, which show a significant latency lag with respect to the first three sources, and from the MSPS image, which shows the maximum around blue sources at this latency.]] </li>
</ul></div>



'''Notes:'''

* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image''' menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the''' Image''' menu.
* For scaling options, please refer to the '''scaling buttons''' popup menu .
* Parameters used for the MSPS calculations can be set in the ''General Settings tab'' of the ''Image Settings dialog box.''

== Source Sensitivity ==

'''Introduction'''

The 'Source sensitivity' function displays the sensitivity of the selected source in the current source model to activity in other brain regions. Sensitivity is defined as the fraction of power at the scanned brain location that is mapped onto the selected source.

To compute the source sensitivity, unit brain activity is modeled at different locations (probe source) throughout the brain. To this data, the current source model is applied to compute the source waveforms SCM of all modeled sources:

<math>\mathrm{S}_{\text{CM}} = \mathrm{L}_{\text{CM}}^{-1} \cdot \mathrm{L}_{\text{PS}}</math>


Here LCM-1 is the regularized inverse operator for the current model, and LPS is the leadfield of the regional probe source (dimension [Nx3] for EEG and [Nx2] for MEG, respectively, where N is the number of sensors). The source amplitude SSS of the selected source in the model is a 3x3 (MEG: 2x2) sub-matrix of SCM (if the selected source is a regional source) or a 1x3-matrix (MEG: 1x2) (if the selected source is a dipole). The root mean square of the singular values of SCM is defined as the source sensitivity.

The 3D source sensitivity image displays this value for all locations on a grid specified under '''Image/Settings'''. Grid density can be specified in the Image Settings.

'''Applying the Source Sensitivity Image'''

The Source Sensitivity image is evoked from the '''Image''' menu or by pressing the corresponding hot key (default: '''V''').

This function is enabled only when a solution with an active selected source is present in the Source Analysis window. The source sensitivity image then displays the sensitivity of the selected source to activity in other brain regions.

[[Image:SA 3Dimaging (59).gif]]

''Source Sensitivity image for the selected frontal source (green) in model ''''''High_Intensity_3RS.bsa'''''' in folder 'Examples/ERP_Auditory_Intensity'. The data displayed is the '100dB' condition in file ''''''All_Subjects_cc.fsg''''''. The selected source is sensitive to activity in the frontal brain region (yellow/white), while it is not influenced by activity in the vicinity of the left and right auditory cortex areas, which are modeled by the red and blue source in the model (transparent/gray).''

'''Notes:'''

* The sensitivity image is independent of the recorded sensor signals. It only depends on the current source model, the sensor configuration, the head model, and the regularization constant.
* If the regularization constant is set to zero, each source has a sensitivity of 100% to activity around its own location. With increasing regularization, the spatial filter becomes less focused, and the sensitivity of a source to activity at its location decreases.
* You can hide or re-display the last computed image by selecting the corresponding entry in the '''Image''' menu.
* The current image can be exported to ASCII or BrainVoyager vmp-format from the '''Image''' menu.

== SESAME ==
''This feature requires BESA Research 7.0 or higher.''

'''SESAME''' (Sequential Semi-Analytic Monte-Carlo Estimation) is a Bayesian approach for estimating sources that uses Markov-Chain Monte-Carlo method for efficient computation of the probability distribution as described in Sommariva, S., & Sorrentino, A. "Sequential Monte Carlo samplers for semi-linear inverse problems and application to magnetoencephalography." Inverse Problems 30.11 (2014): 114020.

It allows to automatically estimate simultaneously the number of dipoles, their locations and time courses requiring virtually no user input. The algorithm is divided in two blocks:

* The first block consists of a Monte Carlo sampling algorithm that produces, with an adaptive number of iterations, a set of samples representing the posterior distribution for the number of dipoles and the dipole locations.
* The second block estimates the source time courses, given the number of dipoles and the dipole locations.

The Monte Carlo algorithm in the first block works by letting a set of weighted samples evolve with each iteration. At each iteration, the samples (a multi-dipole state) approximates the n-th element of a sequence of distributions p1, …, pN, that reaches the desired posterior distribution (pN = p(x|y)). The sequence is built as pN = p(x) p(y|x) α(n), such that α(1) = 0, α(N) = 1. The actual sequence of values of alpha is determined online. Dipole moments are estimated after the number of dipoles and the dipole locations have been estimated with the Monte Carlo procedure. This continues until a steady state is reached.

The SESAME image in BESA Research displays the final probability of source location along with an estimate for number of sources. Using the menu function '''Image / Export Image As...''' you have the option to save this SESAME image.

'''Notes:'''

*'''Grid spacing:''' Due to memory and computational limitations, it is recommended to use SESAME with a grid spacing of 5 mm or more.
*'''Fit Interval:''' SESAME requires a fit interval of more than 2 samples to start the computation.
*'''Computation time:''' Computation speed during SESAME calculation depends on the grid spacing (computation is faster with larger grid spacing) and number of channels.

== Brain Atlas ==
''This feature requires BESA Research 7.0 or higher.''

'''Introduction'''

Brain atlas is a priori data that can be applied over any discrete or distributed source image displayed in the 3D window. It is a reference value that strongly depends on the selected brain atlas and should not be used as medical reference since individual brains may differ from the brain atlas. The display settings can be adjusted in 3D Window Tab.

[[Image:BrainAtlas1.png|600px]]

'''Brain Atlases'''

In BESA Research the atlases listed below are provided. '''BESA is not the author of the atlases; please cite the appropriate publications if you use any of the atlases in your publication.'''

[http://atlas.brainnetome.org/bnatlas.html '''Brainnetome'''] 
This is one of the most modern brain probabilistic atlas where structural, functional, and connectivity information was used to perform cortical parcellation. It was introduce by Fan and colleagues (2016), and is still work in progress. The atlas was created using data from 40 healthy adults taking part in the Human Connectome Project. In March 2018, the atlas consists of 246 structures labeled independently for each hemisphere. In BESA we provide the max probability map with labeling. Please visit the Brainnetome webpage to see more details related to the indicated brain regions (i.e. behavioral domains, paradigm classes and regions connectivity).

'''AAL''' 
Automated Anatomical Labeling atlas was created in 2002 by Tzourio-Mazoyer and collegues (2002). It is the mostly used atlas nowadays. The atlas is based on the averaged brain of one subject (young male) who was scanned 27 times. The atlas resolution is 1 mm isometric. The brain sulci were drawn manually on every 2mm slice and then brain regions were automatically assigned. The atlas consists of 116 regions which are asymmetrical between hemispheres. The atlas is implemented as in the [https://www.fil.ion.ucl.ac.uk/spm/ '''SPM12'''] toolbox.

'''Brodmann''' 
The Brodmann map was created by Brodmann (1909). The brain regions were differentiated by cytoarchitecture of each cortical area using the Nissi method of cell staining. The digitalization of the original Brodmann map was performed by Damasio and Damasio (1989). The digitalized atlas consists of 44 fields that are symmetric between hemispheres. BESA used the atlas implementation as in Chris Roden’s [https://people.cas.sc.edu/rorden/mricro/index.html '''MRICro'''] software.

'''AAL2015''' 
Automated Anatomical Labeling revision 2015. This is the updated AAL atlas. In comparison to the previous version (AAL) mainly the frontal lobe shows a higher degree of parcellation (Rolls, Joliot, and Tzourio-Mazoyer 2015). The atlas is implemented as in the [https://www.fil.ion.ucl.ac.uk/spm/ '''SPM12'''] toolbox.

'''Talairach''' 
Atlas was created in 1988 by Talairach and Tournoux (1988) and it is based on the post mortem brain slices of a 60 year old right handed European female. It was created by drawing and matching regions with the Brodmann map. The atlas is available at 5 tissue levels, however we used only the volumetric gyrus level as it is the most known in neuroscience and is the most appropriate for EEG. The atlas consists of 55 regions that are symmetric between hemispheres. The native resolution of the atlas was 0.43x0.43x2-5 mm. Please note that the poor resolution in Z direction is a direct consequence atlas definition, and since it is a post-mortem atlas it will not correctly match the brain template
(noticeable mainly on brain edges). The atlas digitalization was performed by Lancaster and colleagues (2000) resulting in a “golden standard” for neuroscience. The atlas was first implemented in a software called [http://www.talairach.org/daemon.html '''talairach daemon'''].

'''Yeo7 and Yeo17''' 
Yeo7 and Yeo17 are the resting state functional connectivity atlases created by Yeo et al. (2011). For atlas creation 1000 subjects, coregistered using surface-based alignment were used. Two versions of parcellation were used resulting for the 7 and 17 networks (Yeo7 and Yeo17 atlas respectively). In the original publication atlases for two different levels of brain structure coverage were prepared: neocortex and liberal. In BESA products, only one of them (liberal) is available. Note that in comparison to the other atlases, here networks are reflected, rather than the individual brain structures. These atlases are in line with [[BESA_Research_Montage_Editor#Standard_Source_Montage_-_Resting_State_Montages | Resting State Source Montages]].

'''Visualization modes'''

'''Just Labels''' 
Displayed are crosshair coordinates (Talairach or MNI), the currently used brain atlas and the region name where the crosshair is placed. No atlas overlay will be visible on the 3D image.

'''brainCOLOR''' 
All information is displayed as in “Just Labels” mode but also the atlas is visible as an overlay over the MRI. The coloring is performed using the algorithm introduced by Klein and colleagues (Klein et al. 2010). With this method of coloring the regions which are part of the same lobe are colored in a similar color but with different color shade. The shade is computed by the algorithm to make these regions visually differentiable from each other as much as possible.

'''Individual Color''' 
In this mode the native brain atlas color is used if provided by the authors of the brain atlas (i.e. Yeo7). Where this was not available BESA autogenerated colors for the atlas using an approach similar to political map coloring. This approach aims to differentiate most regions that are adjacent to each other and no presumptions on lobes is applied.

'''Contour''' 
Only region contours (borders between atlas regions) are drawn with blue color. This is the default mode in BESA Research.

'''References'''

* Brodmann, Korbinian. 1909. Vergleichende Lokalisationslehre Der Großhirnrinde. Leipzig: Barth. https://www.livivo.de/doc/437605.
* Damasio, Hanna, and Antonio R. Damasio. 1989. Lesion Analysis in Neuropsychology. Oxford University Press, USA.
* Fan, Lingzhong, Hai Li, Junjie Zhuo, Yu Zhang, Jiaojian Wang, Liangfu Chen, Zhengyi Yang, et al. 2016. “The Human Brainnetome Atlas: A New Brain Atlas Based on Connectional Architecture.” Cerebral Cortex 26 (8): 3508–26. https://doi.org/10.1093/cercor/bhw157.
* Klein, Arno, Andrew Worth, Jason Tourville, Bennett Landman, Tito Dal Canton, Satrajit S. Ghosh, and David Shattuck. 2010. “An Interactive Tool for Constructing Optimal Brain Colormaps.” https://mindboggle.info/braincolor/colormaps/index.html.
* Lancaster, Jack L., Marty G. Woldorff, Lawrence M. Parsons, Mario Liotti, Catarina S. Freitas, Lacy Rainey, Peter V. Kochunov, Dan Nickerson, Shawn A. Mikiten, and Peter T. Fox. 2000. “Automated Talairach Atlas Labels for Functional Brain Mapping.” Human Brain Mapping 10 (3): 120–131.
*Rolls, Edmund T., Marc Joliot, and Nathalie Tzourio-Mazoyer. 2015. “Implementation of a New Parcellation of the Orbitofrontal Cortex in the Automated Anatomical Labeling Atlas.” NeuroImage 122 (November): 1–5. https://doi.org/10.1016/j.neuroimage.2015.07.075.
* Talairach, J, and P Tournoux. 1988. Co-Planar Stereotaxic Atlas of the Human Brain. 3-Dimensional Proportional System: An Approach to Cerebral Imaging. Thieme.
*Thomas Yeo, B. T., F. M. Krienen, J. Sepulcre, M. R. Sabuncu, D. Lashkari, M. Hollinshead, J. L. Roffman, et al. 2011. “The Organization of the Human Cerebral Cortex Estimated by Intrinsic Functional Connectivity.” Journal of Neurophysiology 106 (3): 1125–65. https://doi.org/10.1152/jn.00338.2011.
* Tzourio-Mazoyer, N., B. Landeau, D. Papathanassiou, F. Crivello, O. Etard, N. Delcroix, B. Mazoyer, and M. Joliot. 2002. “Automated Anatomical Labeling of Activations in SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject Brain.” NeuroImage 15 (1): 273–89. https://doi.org/10.1006/nimg.2001.0978.

== Slice View ==
''This feature requires BESA Research 7.1 or higher.''

A convenient way to review MRI data and export it in graphical form is a multi-slice view. To enable multi-slice view press the toggle multiple view button until the slice view is shown in the 3D window.

[[Image:SliceView1.png|600px]]

In this view discrete sources, [[Source_Analysis_3D_Imaging#Overview | distributed sources]] and [[Source_Analysis_3D_Imaging#Brain Atlas| brain atlas]] can be also be overlayed. The display matrix can be adjusted by slice view controls that are available in the 3D Window tab of the Preferences Dialog Box. One of the following slicing direction can be selected: Transverse, Coronal, Sagittal by pressing the appropriate button in the 3D window toolbar.

By adjusting First slice and Last slice sliders, the span of the volume that will be displayed can be adjusted. The interval between slices can be adjusted by changing the Spacing slider value. The layout of slices will be automatically adjusted to fill the full space of the main window. All values in the sliders are given in mm.

'''Note''': The last slice value will be adjusted to the closest possible number matching the given first slice and spacing value. During multi-slice view the cursor is disabled and no
atlas information is provided.

== Glassbrain ==

[[Image:Glassbrain.png|600px]]

The glass brain can be enabled or disabled in one of the following ways:

*by pressing the button in the toolbar ,

*by using the shortcut SHIFT-G or

*by checking the checkbox in Preferences, 3D Display tab.

The transparency value of the glass brain can be adjusted in one of the following ways:

*by a slider/edit box in Preferences, 3D Display tab or

by using the keyboard shortcut SHIFT-UP (to increase transparency by 10%) or SHIFT-DOWN (to decrease transparency by 10%).

Note that If a distributed solution is displayed together with the glass brain, a notification is displayed in the left bottom corner of 3D window to prevent misconception of the glass brain as a cortical image:

“Volume-based image only", which means that the results of distributed source analysis images are visualized only for the current MRI slice, and are not projected to the displayed surface.

{{BESAManualNav}}

File:Glassbrain.png

2021-11-25T12:30:23Z

Dominik: