BESA® Wiki - User contributions [en]

Supported Data Formats

2026-07-28T07:13:56Z

Harald:

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

BESA Research supports most major EEG and MEG file formats. Most file format readers are written by ourselves, others are supplied by the manufacturers.
This document gives an overview of all the data formats that can be imported in BESA Research 6.1 or higher. If your file format cannot be found in this list, please contact us via our support portal: [https://besagmbh.atlassian.net/servicedesk/customer/portals/ BESA support portal]

The readers are part of the product installations, and the latest readers are included in the product installations.

==Supported EEG data formats==

{| class="wikitable sortable"
! style="text-align: center; font-weight: bold;" | File Format / Manufacturer / Software
! style="text-align: center; font-weight: bold;" | File Extension
! style="text-align: center; font-weight: bold;" class="unsortable" | File Formats Version
! style="font-weight: bold;" class="unsortable" | Notes
|-
| Alpha-Trace (alpha-trace medical software)
| .alp
| tested up to v418-05
|
|-
| ASCII
| .avr .mul
|
| [http://wiki.besa.de/index.php?title=ASCII_File_Format ASCII File Format]
|-
| ATES *
|
|
|
|-
| BDF (BioSemi)
| .bdf
|
| [http://wiki.besa.de/index.php?title=Reading_BioSemi_data_with_BESA Reading BioSemi data]
|-
| Beekeeper64 (Telefactor)
| .eeg .dat
|
|
|-
| Bio-logic (Natus) *
| .eeg
|
|
|-
| BrainAmp / BrainVision (Brain Products)
| .eeg .vhdr
|
|
|-
| BrainLab (Schwarzer)
| .sig
|
|
|-
| BrainStar (Schwind Medizintechnik)
| .eeg
|
|
|-
| Cadwell *, ***
| .flex
| tested up to Arc API 2.1.106.0
| ARC API needs to be installed ***
|-
| Compumedics (ProFusion) *, **
| .sdy
| ProFusion EEG 4, 5
|
|-
| DCmes, PolyDC (MES)
| .dat
|
|
|-
| Deltamed (Natus, Coherence) *
| .eeg
|
|
|-
| Deltamed (Natus, Neurofile)
| .eeg
|
|
|-
| EBNeuro (Galileo) *, **
| .gnt .set
| Galileo.NT, Galileo.NET 3.5
| [http://wiki.besa.de/index.php?title=Reading_EBNeuro_Files Reading EBNeuro Files]
|-
| EDF (European Data Format)
| .edf
| EDF, EDF+
| [http://wiki.besa.de/index.php?title=Reading_EDF_Files Reading EDF Files]
|-
| EEProbe (ANT)
| .cnt
|
|
|-
| Electrical Geodesics, Inc. - Raw data format
| .raw .ses
|
| [http://wiki.besa.de/index.php?title=Reading_EGI_RAW_Files Reading EGI Raw Files]
|-
| Electrical Geodesics, Inc. - Metafile Format (EGI MFF) *
| .xml
| up to MFF v3
|
|-
| magstim EGI (Philips) MFF
| .mff
|
|
|-
| ERPSS *
|
|
|
|-
| g.Tec (Guger Technologies) *
| .hdf5
|
| requires BESA Research 7.0 or higher
|-
| Galileo (EBNeuro) *
| .nt
|
|
|-
| Generic Reader (any ASCII formats; see BESA Program Help)
| .avr .mul
|
|
|-
| Grass-Telefactor (Natus) *
| .ref
| up to Twin v3.1
|
|-
| InstEP *, ****
| .c .is .ia
| up to version 7.3 of the IWave Input/Output library
|
|-
| Konstanz file format *
| .raw .sum
|
|
|-
| ManScan interchange format (SAM) *
| .mbi
|
|
|-
| MED Dark Horse Neuro *
|
|
| requires BESA Research version 7.1.3.0 or higher
|-
| Medtronic *
| .wg1
|
|
|-
| MEF (Multiscale Electrophysiology File) *
| .xml
| MEF 2.0
| [http://wiki.besa.de/index.php?title=Reading_MEF_Files Reading MEF Files]
|-
| Micromed (Natus) *
| .trc
| Micromed System98 EEG file (version 3, 4, and 5)
| version 5 requires BESA Research version 7.1.3.0 or higher
|-
| Neuralynx *
| .ncs
|
| requires BESA Research version 7.0 or higher
|-
| NeurOne (Bittium, formerly known as Mega Electronics) *
| .xml
|
|
|-
| Neuronic *
|
|
|
|-
| NeuroScan
| .cnt .avg
| NeuroScan 3.x
| [http://wiki.besa.de/index.php?title=Reading_Neuroscan_Files Reading NeuroScan Files]]
|-
| NeuroScan Curry 7 *
| .rs3 .dap .dat .ce*
| Curry 6 and 7 files
| requires BESA Research version 7.0 or higher. See also [http://wiki.besa.de/index.php?title=Reading_Neuroscan_Files Reading NeuroScan Files]
|-
| NeuroScan Curry 8 *
| .dpa .cdt .ceo
| Curry 8 files
| requires BESA Research 7.1 or higher
|-
| NeuroScan Curry 9 *
| .dpo .cdt .ceo
| Curry 9 files
| requires BESA Research 7.1.3.0 or higher
|-
| NexStim
| .nxe
|
|
|-
| Nicolet (Natus) *
| .eeg
|
|
|-
| NicoletOne / Nervus (Natus) *
| .e .eeg
|
|
|-
| Nihon Kohden
| .eeg
| EEG-1100, EEG-1200, EEG-2100
|
|-
| Phoenix II (EMS) *
| s*.0 s*.1 …
|
|
|-
| Stellate Systems - Harmonie (Natus) *, **
| .sig
| Harmonie 5.2c, 5.4, 6.1, 6.2, 7a
|
|-
| Stellate Systems - Monitor (Natus) *, **
| .eeg
|
|
|-
| Vangard (LaMont Medical Inc.) *
| B****, no extension
|
|
|-
| XDF *
| .xdf
|
| requires BESA Research 7.1 or higher
|-
| Natus NeuroWorks (former XLTEK)
| .eeg .erd
| up to v. 9.3
| version 9.3 requires BESA Research version 7.1.3.0 or higher
|}

If files are in one of these formats, they can be read directly and conversion is not required.
BESA Research also has a new, flexible interface for importing ASCII files which can be used in conjunction with the ASCII export functions of your software.
Any EEG format can be converted to the compressed BESA binary format, ASCII format, EDF+ or simple binary format.

<nowiki>*</nowiki> Install this reader using "''Install Additional Readers.htm''" in the "''Utilities\Additional Readers\''" subfolder. 
<nowiki>**</nowiki> The EEG data format requires installation of the corresponding EEG system reader software or SDK. 
<nowiki>***</nowiki> The Cadwell reader requires the installation of the Cadwell Arc API. If this API is not already installed on your computer, please contact Cadwell directly to obtain it. The API must be installed in the suggested default path on your C: drive. 
<nowiki>****</nowiki> Please note that a valid license for the IWave library is required in order to be able to read InstEP files.

==Supported MEG data formats==

{| class="wikitable sortable"
! style="text-align: center; font-weight: bold;" | File Format / Manufacturer / Software
! style="text-align: center; font-weight: bold;" | File Extension
! style="text-align: center; font-weight: bold;" | File Formats Version
! style="font-weight: bold;" | Notes
|-
| ASCII
| .avr .mul
|
| [http://wiki.besa.de/index.php?title=ASCII_File_Format ASCII File Format]
|-
| BESA 2000 / FOCUS High Compression Format
| .foc .fsg
|
|
|-
| BTI
|
|
| special export program exp2BESAbin is required (Unix system)
|-
| Cerca Magnetics OPM *
| .fif
|
| requires BESA Research 7.1.3.0 or higher
|-
| CTF
| .meg4
|
|
|-
| Elekta Neuromag Functional Image File Format (FIFF)
| .fif
| FIFF v2.0
|
|-
| Ricoh **
| .con
|v3.0
|requires BESA Research 7.0 or higher
|-
| Yokogawa **
| .con .raw .ave .SQD
|up to version 2
|
|}
<nowiki>*</nowiki> Requires prior conversion to .fif using a proprietary script supplied by Cerca Magnetics. subfolder. 
<nowiki>**</nowiki> Install this reader using "''Install Additional Readers.htm''" in the "''Utilities\Additional Readers\''" subfolder.

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

Useful batches

2025-11-28T16:23:58Z

Harald:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = 7.1 or higher
}}

This page lists a number of useful batches that you can try yourself.

==Download the batch files==
Download and unzip the following files into your folder C:\Users\Public\Documents\BESA\Research_7_1\Scripts\Batch\ (you may need to replace ''C:\Users\Public\Documents\'' with the equivalent Public Documents folder on your computer).

Then move the file ''TenDipBlue.bsa'' to the folder C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes\ (you may need to replace ''C:\Users\Public\Documents\'' with the equivalent Public Documents folder on your computer).

[https://github.com/BESA-GmbH/BESA-Research-Batches/releases/latest/download/BesaResearch_Batches.zip Download batches]

==ECG correction==
===Batch name===
''ECGCorrection.bbat''

===What does it do?===
This batch is used for correcting ECG artifacts. It is particularly useful for MEG data. It should be called before creating an MEG source montage.

===How to use it===
Load a data set that contains an ECG channel, or a clear manifestation of the ECG artifact. Make sure that the channel label of this channel is visible at the left (if not, adjust the montage, or change displayed channel types using the buttons at the top right, until you can see it).
Run the batch. The batch will ask you to set a cursor on the peak of the signal, and mark the channel if possible. It will then mark a number of occurrences and use tag #2 to collect the average ECG signal. This will then be used as an artifact topography for an adaptive artifact correction with minimum distortion of signal of interest.

==Create an MEG source montage==
===Batch name===
''CreateMEGSourceMtg.bbat''

''CreateGRDSourceMtg.bbat''

===What does it do?===
This batch is used for creating an MEG source montage, taking an existing artifact correction for ECG artifacts into account. The batch creates a magnetometer-based [gradiometer-based] source montage with 29 montage channels. Each channel has two orientations. Thus, a maximum of 58 source waveforms will be displayed. The waveforms depict the signal originating from the brain region underlying the head position indicated by the channel label (e.g. F3L will be a brain region underneath the location of the F3 channel from the 10-10 nomenclature).

This batch will enable you to use the MEG review as described in the publications by Benicky et al. (2017)[https://www.sciencedirect.com/science/article/abs/pii/S1388245715007269] and Nenonen et al. (2022) [https://www.mdpi.com/2076-3425/12/1/105/review_report].

===How to use it===
It is recommended to first run ''ECGCorrection.bbat'', or create an ECG artifact topography manually. Then run the batch.
The batch ''CreateMEGSourceMtg'' creates a 29-channel source montage based on magnetometers or axial gradiometers. In case that planar gradiometers should be used, please use the batch ''CreateGRDSourceMtg.bbat''.
After finalization, the number of source waveforms displayed can be adjusted using the button “Opt” – either use Regional Source oriented, or Regional Source all.

==Moving dipole fit==
===Batch name===
MovingDipole11Dips_Minus20ToPeak.bbat

Additional file: TenDipBlue.bsa

===What does it do?===
This batch is intended to be used on epileptic spike averages. It performs a single dipole fit for each time point between 20 ms before the spike peak to the peak, in 2 ms steps. It displays the result in the 3D MRI view of the subject.

===How to use it===
As a pre-requisite, the associated solution file “TenDipBlue.bsa” needs to be copied to the folder “C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes”.

An averaged segment containing an epileptic spike should be loaded. It is assumed that the spike maximum lies at the zero latency point of the segment (indicated by a dotted line in the review display).

Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.

Run the batch and follow the instructions when prompted. The result is automatically saved in a solution file (file basename followed by “_MovDip_minus20_to_peak.bsa”).

==Dipole cluster fit==
===Batch name===
ClusterDipoleFit.bbat

===What does it do?===
For a number of segments of single events, the batch performs a dipole fit in each segment, and displays the result as a cluster in the 3D MRI view of the subject.

===How to use it===
As a prerequisite, you will need a segmented file that contains segments of single events of equal size. In order to get this, you can use the menu “''File / Export''”, then select “''Epochs around triggers''”, then press the button “''Triggers''” where you can define which trigger(s) to use (you can also use conditions that you defined in the ERP module).

The interval can be adjusted with the “Interval” button. The batch will expect at least 100 ms before and more than 100 ms after the event time point.
[[File:ExportMask.png]]

Run the export, and re-load the exported file.

Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.
Also, in case you have both MEG and EEG data in your file, select the general modality you want to fit (EEG or MEG) using the button at the top right of the review window.

Now, start the batch. You will be asked to supply the latency at which the fit should be performed. Then, all segments will be processed (up to a maximum of 50 segments).

==Create discrete solution from source image==
===Batch name===
CreateSourcesFromImageEEG.bbat
CreateSourcesFromImageMEG.bbat

===What does it do?===
After a source image has been computed, this batch (with EEG in the name for an EEG image, or with MEG in the name for an MEG image) will create a new discrete solution, add the sources from the maxima of the source image, and fit their orientation within the current fit interval.

===How to use it===
As a prerequisite, you will need to compute a source image in the Source Analysis window.
The batch should then be called directly from the BESA Source Analysis window, using the menu Fit / Run Batch.
It will ask for the number of maxima in the image, which you can read from the title bar of the 3D window. Then it will create the solution and ensure that orientations are fitted correctly.
[[File:2025_11_Sesame1.png]]
[[File:2025_11_Sesame2.png]]

[[Category:Batches]]

File:2025 11 Sesame2.png

2025-11-28T16:23:03Z

Harald: Batch creation of solution file

Batch creation of solution file

File:2025 11 Sesame1.png

2025-11-28T16:22:02Z

Harald: SESAME on MEG data

SESAME on MEG data

Useful batches

2025-11-28T15:50:09Z

Harald:

Main Page

2025-07-31T08:08:42Z

Harald:

Welcome to the BESA Wiki!

[[File:BESA_Logo.jpeg]]

This wiki is designed to help users with typical questions around using BESA to achieve their goals.

Topics are available for the following categories:

== Manual ==

* [[BESA Research Manual]]

== Videos ==

* [[Video tutorials]]

== FAQ ==

=== Licensing ===

* [[Licensing]]
* [[License session not freed|License session not freed (BESA MRI 64 bit version)]]

=== File Formats ===

<div style="column-count:2; -moz-column-count:2; -webkit-column-count:2">

* [[ASCII File Format]]
* [[Channel Definition File Formats]]
* [[Event File Format]]
* [[MEG Sensor Coordinate Files]]
* [[Supported Data Formats]]
* [[Paradigm File Format in BESA]]
* [[Importing Electrode Locations in Combined EEG/MEG Measurements with the Neuromag System]]
* [[BESA files extensions]]
* [[Talairach Transformation File]]
* [[Reading BioSemi data with BESA]]
* [[Using Net Station Data with BESA]]
* [[Importing Digitized Points Measured by Polhemus Fastrak]]

</div>

=== Data Review and Analysis ===

<div style="column-count:2; -moz-column-count:2; -webkit-column-count:2">

* [[Importing Digitized Coordinates]]
* [[Verify Electrode Coordinates]]
* [[Export Single Trial Data]]
* [[How to Average EEG channels]]
* [[Averaging Across EEG Datasets from Different Recording Systems]]
* [[Time Frequency Resolution In BESA]]
* [[Change Waveform Colours]]
* [[Best Strategy to Define a Multiple Source Model]]
* [[Export Dipole Moments of Fitted Sources]]
* [[Recommended Electrode Configurations]]
* [[Exporting Artifact-Corrected Data]]
* [[Create Triggers for Artifact-Rejected Epochs]]
* [[Inserting Triggers Relative to Existing Events]]
* [[Change or Exclude Erroneous Head Surface Point Locations]]
* [[Exporting Top Viewer Waveforms into other Graphics Software for Further Processing]]
* [[Seed dipole solutions from cortical images]]
* [[Pipeline for simultaneous EEG-fMRI recording]]
* [[The source space in individual FEM head models]]
* [[Export each gradiometer and magnetometer data separately]]
* [[Peak Finder explained]]
* [[Using BESA to correct blink and EKG artifacts in MEG data]]
* [[Filtering scope]]
* [[Enabling auto orientation for 3D topographic maps]]

</div>

=== MATLAB interface ===

* [[MATLAB_Interface#Configuration | How Do I Configure the Matlab Interface?]]
* [[MATLAB_Interface#Updating_the_MATLAB_Interface_after_MATLAB_Upgrade | Updating the Matlab Interface after Matlab Upgrade]]
* [[Exporting Data from Matlab to BESA Statistics]]
* [[Visualization with BESA Plot in FieldTrip]]

=== BESA MRI===

* [[Marking AC-PC Points in BESA MRI]]

=== BESA Statistics ===

* [[Cluster Alpha vs. Neighbor Distance]]
* [[How to Prepare Data for BESA Statistics]]
* [[Importing BESA Statistics Results into Excel]]
* [[Exporting Data from Matlab to BESA Statistics]]

=== BESA Connectivity ===

* [[How to Prepare Data for BESA Connectivity]]
* [[Export Connectivity Results]]
* [[How to Convert BESA Connectivity results for BESA Statistics]]

=== Operating systems ===

* [[Running BESA Research on the Mac]]

=== Troubleshooting ===

<div style="column-count:2; -moz-column-count:2; -webkit-column-count:2">

* [[MF Error 211| The internal error MF_211 (BESA MRI, BESA Statistics and BESA Connectivity)]]
* [[3D Graphics Display Issue Handling]]
* [[Batch Error Handling]]
* [[Error message: Failed to load library|Error message: Failed to load library during software installation]]
* [[License session not freed|License session not freed in BESA MRI 64 bit version]]
* [[Install And Update File Format Readers]]
* [[Issues related to the language setting of Windows]]
* [[Wrong characters in BESA software]]
* [[Blank white screen when capturing the 3D window of the source analysis window]]
* [[Error opening program or opening the file dialog box]]
* [[Problems with switching to individual head model]]
* [[Freezing issue when using the Chinese or Japanese keyboard setting]]

</div>

== BESA Recipes ==

<div style="column-count:2; -moz-column-count:2; -webkit-column-count:2">

* [[Control of BESA Research by external programs]]
* [[Correcting Volume Conductor Segmentations]]
* [[Exporting Data from Matlab to BESA Statistics]]
* [[Integration of Custom Template Head-Models]]
* [[Random Averaging]]
* [[Statistical Analysis for More than Two Levels]]
* [[Visualization with BESA Plot in FieldTrip]]
* [[Pipeline for simultaneous EEG-fMRI recording]]
* [[How to deal with TMS artifact in BESA Research]]
* [[Artifact correction with intracranial channels]]
* [[Export Data to Brainstorm]]
* [[Export Surface Images as the GIfTI File Format using MATLAB]]

</div>

== Did you know...? ==

<div style="column-count:2; -moz-column-count:2; -webkit-column-count:2">

* [[Moving Dipole Fit]]
* [[BESA Anonymizer]]
* [[Batch Processing]]
* [[Analyzing Electrocorticography Data]]
* [[Advanced Top Viewer Features]]
* [[Different beamformer types in the source analysis module]]

</div>

== All about batches ==

* [[BESA Research Batch Processing]]
* [[Useful batches]]

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

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

2025-07-30T08:09:28Z

Harald:

Useful batches

2025-07-28T14:32:19Z

Harald:

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = 7.1 or higher
}}

This page lists a number of useful batches that you can try yourself.
==ECG correction==
===Batch name===
''ECGCorrection.bbat''

===What does it do?===
This batch is used for correcting ECG artifacts. It is particularly useful for MEG data. It should be called before creating an MEG source montage.

===How to use it===
Load a data set that contains an ECG channel, or a clear manifestation of the ECG artifact. Make sure that the channel label of this channel is visible at the left (if not, adjust the montage, or change displayed channel types using the buttons at the top right, until you can see it).
Run the batch. The batch will ask you to set a cursor on the peak of the signal, and mark the channel if possible. It will then mark a number of occurrences and use tag #2 to collect the average ECG signal. This will then be used as an artifact topography for an adaptive artifact correction with minimum distortion of signal of interest.

==Create an MEG source montage==
===Batch name===
''CreateMEGSourceMtg.bbat''

''CreateGRDSourceMtg.bbat''

===What does it do?===
This batch is used for creating an MEG source montage, taking an existing artifact correction for ECG artifacts into account. The batch creates a magnetometer-based [gradiometer-based] source montage with 29 montage channels. Each channel has two orientations. Thus, a maximum of 58 source waveforms will be displayed. The waveforms depict the signal originating from the brain region underlying the head position indicated by the channel label (e.g. F3L will be a brain region underneath the location of the F3 channel from the 10-10 nomenclature).

This batch will enable you to use the MEG review as described in the publications by Benicky et al. (2017)[https://www.sciencedirect.com/science/article/abs/pii/S1388245715007269] and Nenonen et al. (2022) [https://www.mdpi.com/2076-3425/12/1/105/review_report].

===How to use it===
It is recommended to first run ''ECGCorrection.bbat'', or create an ECG artifact topography manually. Then run the batch.
The batch ''CreateMEGSourceMtg'' creates a 29-channel source montage based on magnetometers or axial gradiometers. In case that planar gradiometers should be used, please use the batch ''CreateGRDSourceMtg.bbat''.
After finalization, the number of source waveforms displayed can be adjusted using the button “Opt” – either use Regional Source oriented, or Regional Source all.

==Moving dipole fit==
===Batch name===
MovingDipole11Dips_Minus20ToPeak.bbat

Additional file: TenDipBlue.bsa

===What does it do?===
This batch is intended to be used on epileptic spike averages. It performs a single dipole fit for each time point between 20 ms before the spike peak to the peak, in 2 ms steps. It displays the result in the 3D MRI view of the subject.

===How to use it===
As a pre-requisite, the associated solution file “TenDipBlue.bsa” needs to be copied to the folder “C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes”.

An averaged segment containing an epileptic spike should be loaded. It is assumed that the spike maximum lies at the zero latency point of the segment (indicated by a dotted line in the review display).

Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.

Run the batch and follow the instructions when prompted. The result is automatically saved in a solution file (file basename followed by “_MovDip_minus20_to_peak.bsa”).

==Dipole cluster fit==
===Batch name===
ClusterDipoleFit.bbat

===What does it do?===
For a number of segments of single events, the batch performs a dipole fit in each segment, and displays the result as a cluster in the 3D MRI view of the subject.

===How to use it===
As a prerequisite, you will need a segmented file that contains segments of single events of equal size. In order to get this, you can use the menu “''File / Export''”, then select “''Epochs around triggers''”, then press the button “''Triggers''” where you can define which trigger(s) to use (you can also use conditions that you defined in the ERP module).

The interval can be adjusted with the “Interval” button. The batch will expect at least 100 ms before and more than 100 ms after the event time point.
[[File:ExportMask.png]]

Run the export, and re-load the exported file.

Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.

Now, start the batch. You will be asked to supply the latency at which the fit should be performed. Then, all segments will be processed (up to a maximum of 50 segments).

==Download the batch files==
Download and unzip the following files into your folder C:\Users\Public\Documents\BESA\Research_7_1\Scripts\Batch. Then move the file TenDipBlue.bsa to the folder C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes
[[File:Batches.zip]]

[[Category:Batches]]

Useful batches

2025-07-28T14:29:42Z

Harald:

This page lists a number of useful batches that you can try yourself.
==ECG correction==
===Batch name===
''ECGCorrection.bbat''

===What does it do?===
This batch is used for correcting ECG artifacts. It is particularly useful for MEG data. It should be called before creating an MEG source montage.

===How to use it===
Load a data set that contains an ECG channel, or a clear manifestation of the ECG artifact. Make sure that the channel label of this channel is visible at the left (if not, adjust the montage, or change displayed channel types using the buttons at the top right, until you can see it).
Run the batch. The batch will ask you to set a cursor on the peak of the signal, and mark the channel if possible. It will then mark a number of occurrences and use tag #2 to collect the average ECG signal. This will then be used as an artifact topography for an adaptive artifact correction with minimum distortion of signal of interest.

==Create an MEG source montage==
===Batch name===
''CreateMEGSourceMtg.bbat''

''CreateGRDSourceMtg.bbat''

===What does it do?===
This batch is used for creating an MEG source montage, taking an existing artifact correction for ECG artifacts into account. The batch creates a magnetometer-based [gradiometer-based] source montage with 29 montage channels. Each channel has two orientations. Thus, a maximum of 58 source waveforms will be displayed. The waveforms depict the signal originating from the brain region underlying the head position indicated by the channel label (e.g. F3L will be a brain region underneath the location of the F3 channel from the 10-10 nomenclature).

This batch will enable you to use the MEG review as described in the publications by Benicky et al. (2017)[https://www.sciencedirect.com/science/article/abs/pii/S1388245715007269] and Nenonen et al. (2022) [https://www.mdpi.com/2076-3425/12/1/105/review_report].

===How to use it===
It is recommended to first run ''ECGCorrection.bbat'', or create an ECG artifact topography manually. Then run the batch.
The batch ''CreateMEGSourceMtg'' creates a 29-channel source montage based on magnetometers or axial gradiometers. In case that planar gradiometers should be used, please use the batch ''CreateGRDSourceMtg.bbat''.
After finalization, the number of source waveforms displayed can be adjusted using the button “Opt” – either use Regional Source oriented, or Regional Source all.

==Moving dipole fit==
===Batch name===
MovingDipole11Dips_Minus20ToPeak.bbat

Additional file: TenDipBlue.bsa

===What does it do?===
This batch is intended to be used on epileptic spike averages. It performs a single dipole fit for each time point between 20 ms before the spike peak to the peak, in 2 ms steps. It displays the result in the 3D MRI view of the subject.

===How to use it===
As a pre-requisite, the associated solution file “TenDipBlue.bsa” needs to be copied to the folder “C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes”.

An averaged segment containing an epileptic spike should be loaded. It is assumed that the spike maximum lies at the zero latency point of the segment (indicated by a dotted line in the review display).

Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.

Run the batch and follow the instructions when prompted. The result is automatically saved in a solution file (file basename followed by “_MovDip_minus20_to_peak.bsa”).

==Dipole cluster fit==
===Batch name===
ClusterDipoleFit.bbat

===What does it do?===
For a number of segments of single events, the batch performs a dipole fit in each segment, and displays the result as a cluster in the 3D MRI view of the subject.

===How to use it===
As a prerequisite, you will need a segmented file that contains segments of single events of equal size. In order to get this, you can use the menu “''File / Export''”, then select “''Epochs around triggers''”, then press the button “''Triggers''” where you can define which trigger(s) to use (you can also use conditions that you defined in the ERP module).

The interval can be adjusted with the “Interval” button. The batch will expect at least 100 ms before and more than 100 ms after the event time point.
[[File:ExportMask.png]]

Run the export, and re-load the exported file.

Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.

Now, start the batch. You will be asked to supply the latency at which the fit should be performed. Then, all segments will be processed (up to a maximum of 50 segments).

==Download the batch files==
Download and unzip the following files into your folder C:\Users\Public\Documents\BESA\Research_7_1\Scripts\Batch. Then move the file TenDipBlue.bsa to the folder C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes
[[File:Batches.zip]]

Useful batches

2025-07-28T14:18:23Z

Harald:

This page lists a number of useful batches that you can try yourself.
==ECG correction==
===Batch name===
ECGCorrection.bbat

===What does it do?===
This batch is used for correcting ECG artifacts. It is particularly useful for MEG data. It should be called before creating an MEG source montage.

===How to use it===
Load a data set that contains an ECG channel, or a clear manifestation of the ECG artifact. Make sure that the channel label of this channel is visible at the left (if not, adjust the montage, or change displayed channel types using the buttons at the top right, until you can see it).
Run the batch. The batch will ask you to set a cursor on the peak of the signal, and mark the channel if possible. It will then mark a number of occurrences and use tag #2 to collect the average ECG signal. This will then be used as an artifact topography for an adaptive artifact correction with minimum distortion of signal of interest.

==Create an MEG source montage==
===Batch name===
CreateMEGSourceMtg.bbat

CreateGRDSourceMtg.bbat

===What does it do?===
This batch is used for creating an MEG source montage, taking an existing artifact correction for ECG artifacts into account. The batch creates a magnetometer-based [gradiometer-based] source montage with 29 montage channels. Each channel has two orientations. Thus, a maximum of 58 source waveforms will be displayed. The waveforms depict the signal originating from the brain region underlying the head position indicated by the channel label (e.g. F3L will be a brain region underneath the location of the F3 channel from the 10-10 nomenclature).

===How to use it===
It is recommended to first run ECGCorrection.bbat, or create an ECG artifact topography manually. Then run the batch.
The batch CreateMEGSourceMtg creates a 29-channel source montage based on magnetometers or axial gradiometers. In case that planar gradiometers should be used, please use the batch CreateGRDSourceMtg.bbat.
After finalization, the number of source waveforms displayed can be adjusted using the button “Opt” – either use Regional Source oriented, or Regional Source all.

==Moving dipole fit==
===Batch name===
MovingDipole11Dips_Minus20ToPeak.bbat
Additional file: TenDipBlue.bsa

===What does it do?===
This batch is intended to be used on epileptic spike averages. It performs a single dipole fit for each time point between 20 ms before the spike peak to the peak, in 2 ms steps. It displays the result in the 3D MRI view of the subject.

===How to use it===
As a pre-requisite, the associated solution file “TenDipBlue.bsa” needs to be copied to the folder “C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes”.
An averaged segment containing an epileptic spike should be loaded. It is assumed that the spike maximum lies at the zero latency point of the segment (indicated by a dotted line in the review display).
Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.
Run the batch and follow the instructions when prompted. The result is automatically saved in a solution file (file basename followed by “_MovDip_minus20_to_peak.bsa”).

==Dipole cluster fit==
===Batch name===
ClusterDipoleFit.bbat

===What does it do?===
For a number of segments of single events, the batch performs a dipole fit in each segment, and displays the result as a cluster in the 3D MRI view of the subject.

===How to use it===
As a prerequisite, you will need a segmented file that contains segments of single events of equal size. In order to get this, you can use the menu “File / Export”, then select “Epochs around triggers”, then press the button “Triggers” where you can define which trigger(s) to use (you can also use conditions that you defined in the ERP module).

The interval can be adjusted with the “Interval” button. The batch will expect at least 100 ms before and more than 100 ms after the event time point.
[[File:ExportMask.png]]

Run the export, and re-load the exported file.
Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.
Now, start the batch. You will be asked to supply the latency at which the fit should be performed. Then, all segments will be processed (up to a maximum of 50 segments).

==Download the batch files==
Download and unzip the following files into your folder C:\Users\Public\Documents\BESA\Research_7_1\Scripts\Batch. Then move the file TenDipBlue.bsa to the folder C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes
[[File:Batches.zip]]

File:Batches.zip

2025-07-28T14:11:52Z

Harald: A number of useful batches: Cluster Dipole Fit Create GRD Source Montage Create MAG Source Montage ECG Correction Moving Dipole Fit Additional solution file for moving dipole fit

A number of useful batches:
Cluster Dipole Fit
Create GRD Source Montage
Create MAG Source Montage
ECG Correction
Moving Dipole Fit
Additional solution file for moving dipole fit

File:ExportMask.png

2025-07-28T13:59:11Z

Harald:

Useful batches

2025-07-28T13:34:36Z

Harald: Created page with "This page lists a number of useful batches that you can try yourself. ==ECG correction== ===Batch name=== ECGCorrection.bbat ===What does it do?=== This batch is used for cor..."

This page lists a number of useful batches that you can try yourself.
==ECG correction==
===Batch name===
ECGCorrection.bbat

===What does it do?===
This batch is used for correcting ECG artifacts. It is particularly useful for MEG data. It should be called before creating an MEG source montage.

===How to use it===
Load a data set that contains an ECG channel, or a clear manifestation of the ECG artifact. Make sure that the channel label of this channel is visible at the left (if not, adjust the montage, or change displayed channel types using the buttons at the top right, until you can see it).
Run the batch. The batch will ask you to set a cursor on the peak of the signal, and mark the channel if possible. It will then mark a number of occurrences and use tag #2 to collect the average ECG signal. This will then be used as an artifact topography for an adaptive artifact correction with minimum distortion of signal of interest.

==Create an MEG source montage==
===Batch name===
CreateMEGSourceMtg.bbat
CreateGRDSourceMtg.bbat

===What does it do?===
This batch is used for creating an MEG source montage, taking an existing artifact correction for ECG artifacts into account. The batch creates a magnetometer-based [gradiometer-based] source montage with 29 montage channels. Each channel has two orientations. Thus, a maximum of 58 source waveforms will be displayed. The waveforms depict the signal originating from the brain region underlying the head position indicated by the channel label (e.g. F3L will be a brain region underneath the location of the F3 channel from the 10-10 nomenclature).

===How to use it===
It is recommended to first run ECGCorrection.bbat, or create an ECG artifact topography manually. Then run the batch.
The batch CreateMEGSourceMtg creates a 29-channel source montage based on magnetometers or axial gradiometers. In case that planar gradiometers should be used, please use the batch CreateGRDSourceMtg.bbat.
After finalization, the number of source waveforms displayed can be adjusted using the button “Opt” – either use Regional Source oriented, or Regional Source all.

==Moving dipole fit==
===Batch name===
MovingDipole11Dips_Minus20ToPeak.bbat
Additional file: TenDipBlue.bsa

===What does it do?===
This batch is intended to be used on epileptic spike averages. It performs a single dipole fit for each time point between 20 ms before the spike peak to the peak, in 2 ms steps. It displays the result in the 3D MRI view of the subject.

===How to use it===
As a pre-requisite, the associated solution file “TenDipBlue.bsa” needs to be copied to the folder “C:\Users\Public\Documents\BESA\Research_7_1\Scripts\ColorSchemes”.
An averaged segment containing an epileptic spike should be loaded. It is assumed that the spike maximum lies at the zero latency point of the segment (indicated by a dotted line in the review display).
Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.
Run the batch and follow the instructions when prompted. The result is automatically saved in a solution file (file basename followed by “_MovDip_minus20_to_peak.bsa”).

==Dipole cluster fit==
===Batch name===
ClusterDipoleFit.bbat

===What does it do?===
For a number of segments of single events, the batch performs a dipole fit in each segment, and displays the result as a cluster in the 3D MRI view of the subject.

===How to use it===
As a prerequisite, you will need a segmented file that contains segments of single events of equal size. In order to get this, you can use the menu “File / Export”, then select “Epochs around triggers”, then press the button “Triggers” where you can define which trigger(s) to use (you can also use conditions that you defined in the ERP module).

The interval can be adjusted with the “Interval” button. The batch will expect at least 100 ms before and more than 100 ms after the event time point.
Run the export, and re-load the exported file.
Before running the batch, check the filter settings: For epileptic spikes, we recommend setting a low cutoff of 3 Hz forward filter with 6dB, and a high cutoff of 35 Hz zero-phase with 24 dB.
Now, start the batch. You will be asked to supply the latency at which the fit should be performed. Then, all segments will be processed (up to a maximum of 50 segments).

The Initialization File: BESA.ini

2025-07-23T11:15:05Z

Harald:

{{BESAInfobox
|title = Module information
|module = BESA Research Basic or higher
|version = BESA Research 6.1 or higher; for [Neuromag] and [OPM] 7.1 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 x86 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.

=== Neuromag ===
Default settings provided for section [Neuromag]:

'''TriggerMultiplex=Off''' (set to '''On''' to enable reading of multiplexed trigger signals (see examples below)

'''MultiplexChannel=STI101''' (this is the channel label that is scanned for the large trigger first, then again for the small triggers. Will only be used if TriggerMultiplex=On is set)

'''MultiplexMinVoltageLargeTrigger=4000''' (set this to a different value if the large trigger value in a multiplexed trigger signals is smaller, or significantly higher. The value is used to distinguish between large and small trigger values in multiplexed trigger signals on one trigger channel. This key is only used if TriggerMultiplex=On is set)

Examples for a multiplexed trigger scenario:

[[File:Neuromag_Fig1.png]]

Here, small trigger signals are added to a large trigger signal. The two different trigger signal types can be disentangled upon trigger reading if the key '''TriggerMultiplex=On''' is set.

The below example has two trigger channels. One holds the multiplexed trigger signals, and the second one carries additional triggers. This can be distinguished correctly if the key '''TriggerMultiplex=On''' is set, and the key '''MultiplexChannel=<channel>''' holds the label of the trigger channel that has the multiplexed signal.

[[File:Neuromag_Fig2.png]]

In case that different triggers are encoded on two different channels, no additional setting is required. The below example will be read correctly even if no entries are made in section [Neuromag].

[[File:Neuromag_Fig3.png]]

=== 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.

=== OPM ===
[OPM]

OPMScale=5000

CercaSpatialProjection=On

'''OPMScale=5000''' Scale of OPM channels in [fT]. Typically OPM values will be approximately 10 times higher than magnetometers further away from the scalp. Default is '''5000'''.

'''CercaSpatialProjection=On''' Set CercaSpatialProjection=Off if you do not want to use a spatial projection to reduce the extra-cranial homogeneous magnetic field for data recorded with the Cerca Magnetics system. Default is '''On'''.

=== 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

2025-07-23T11:13:17Z

Harald: /* Reader-Specific Settings */

{{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 x86 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.

=== Neuromag ===
Default settings provided for section [Neuromag]:

'''TriggerMultiplex=Off''' (set to '''On''' to enable reading of multiplexed trigger signals (see examples below)

'''MultiplexChannel=STI101''' (this is the channel label that is scanned for the large trigger first, then again for the small triggers. Will only be used if TriggerMultiplex=On is set)

'''MultiplexMinVoltageLargeTrigger=4000''' (set this to a different value if the large trigger value in a multiplexed trigger signals is smaller, or significantly higher. The value is used to distinguish between large and small trigger values in multiplexed trigger signals on one trigger channel. This key is only used if TriggerMultiplex=On is set)

Examples for a multiplexed trigger scenario:

[[File:Neuromag_Fig1.png]]

Here, small trigger signals are added to a large trigger signal. The two different trigger signal types can be disentangled upon trigger reading if the key '''TriggerMultiplex=On''' is set.

The below example has two trigger channels. One holds the multiplexed trigger signals, and the second one carries additional triggers. This can be distinguished correctly if the key '''TriggerMultiplex=On''' is set, and the key '''MultiplexChannel=<channel>''' holds the label of the trigger channel that has the multiplexed signal.

[[File:Neuromag_Fig2.png]]

In case that different triggers are encoded on two different channels, no additional setting is required. The below example will be read correctly even if no entries are made in section [Neuromag].

[[File:Neuromag_Fig3.png]]

=== 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.

=== OPM ===
[OPM]

OPMScale=5000

CercaSpatialProjection=On

'''OPMScale=5000''' Scale of OPM channels in [fT]. Typically OPM values will be approximately 10 times higher than magnetometers further away from the scalp. Default is '''5000'''.

'''CercaSpatialProjection=On''' Set CercaSpatialProjection=Off if you do not want to use a spatial projection to reduce the extra-cranial homogeneous magnetic field for data recorded with the Cerca Magnetics system. Default is '''On'''.

=== 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}}

File:Neuromag Fig3.png

2025-07-23T11:10:03Z

Harald: Neuromag ini file settings Figure 3

Neuromag ini file settings Figure 3

File:Neuromag Fig2.png

2025-07-23T11:09:45Z

Harald: Neuromag ini file settings Figure 2

Neuromag ini file settings Figure 2

File:Neuromag Fig1.png

2025-07-23T11:08:15Z

2021-05-05T10:27:26Z

Harald: /* How to Start the Beamformer from the Time-Frequency Window */

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

== How to Start the Beamformer from the Time-Frequency Window ==

This chapter shows how to start the BESA Multiple Source Beamformer from the time-frequency window. The displayed screenshots are taken using the file '''BESA5/Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc''' (see BESA Tutorial 12: "''Tutorial on Time-frequency analysis, Connectivity analysis, and beamforming''" which you can download from our website https://www.besa.de).

The time-frequency beamformer is especially useful to image induced oscillatory activity in- or decrease. Induced activity cannot be observed in the averaged data, but shows up as enhanced averaged power in the TSE (Temporal-Spectral Evolution) plot.

In the time-frequency diagram of any channel, left-drag to mark a time-frequency region of interest, e.g. a region of power increase. When the left mouse button is released, select '''Image''' from the popup menu.

[[Image:Image001.gif]]

'''Note''': The current montage and the type of time-frequency plot currently displayed (TSE, amplitude/power, Coherence) does not affect the output of the beamformer image, because the image is always based on the complex single-trial spectral density of the original recording montage. The status of the 'subtract average signal' button is considered, however. This allows to image either evoked and induced activity or induced activity only.

The ''Image'' edit window is displayed. It allows for adjusting the time-frequency range of the target interval and for a re-definition of the baseline interval. If a control condition has been specified, you can choose to reference the power in the target time-frequency interval to the corresponding interval in the control condition instead of the baseline interval by checking '''Compare Conditions'''.

[[Image:Image002.gif]]

'''Note''': The text within the window emphasizes that it is recommended to use the same duration for the Baseline Interval and the Target Interval to obtain a reliable beamformer image. The reason is the dependence on the noise estimate on the number of trials that enter the covariance matrix computation. The same recommendation holds if two conditions are compared: It is recommended to define conditions such that they contain approximately the same number of trials. If the baseline interval defined in the Time-Frequency window (the red bar on the x-axis) is larger than the target time interval specified by the dragged rectangle, the baseline interval in the '''Image''' dialog window is automatically shortened to match the duration of the Target Interval. If for some reason these requirements cannot be met, it is recommended to compute a beamformer image with regularization. This is achieved by adjusting the SVD cutoff in the Source Analysis window using the menu entry '''Image/Settings'''.

Press the '''Go''' button to start the beamformer computation.

BESA Research now computes mean time-frequency covariance matrices for the target and the reference interval. The source analysis window opens with an enlarged 3D imaging display that compares the power in the target and the reference interval as computed with a bilateral beamformer. The result is superimposed onto the individual or standard MRI.

For more information on the multiple-source beamformer (MSBF), please refer to chapter '''[[Source_Analysis_3D_Imaging#Multiple_Source_Beamformer_.28MSBF.29|Source Analysis 3D imaging / Multiple Source Beamformer]]'''.

[[Image:Image003.gif]]

== How to Start DICS computation from the Time-Frequency Window ==

How to create DICS images you will find in the chapter '''[[Source_Analysis_3D_Imaging#Dynamic_Imaging_of_Coherent_Sources_.28DICS.29|Source Analysis / 3D Imaging / Dynamic Imaging of Coherent Sources (DICS)]]'''.

== How to Compute Time Lags between oscillations using Phase Diagrams ==

The phase diagram option is used to analyze phase differences between coherent channels. This can give an insight into a possible coupling of brain regions which may be necessary e.g. to integrate input from various specialized neurons to a common perception. However, the measured coupling is also influenced by volume conduction effects (scalp coherence) or the modeling parameters (source coherence).

If brain regions show oscillatory coupling in the same frequency range, the phase relationship should be constant over some time:

[[Image:Image005.gif]]

Since we cannot obtain an ideal frequency resolution using a time-frequency transform, any oscillation frequency is smeared out over several sampling frequencies in the transformed signal. If the delay between the two oscillations is constant, the phase shift between the signals rises linearly with the frequency. We can get a precise estimate of the delay if we use several neighboring frequencies for the calculation. Practically, you can achieve this by the following steps:

1. Enter '''coherence''' mode, either by '''double-clicking''' on the channel of interest, or by right-clicking on it and selecting coherence from the popup menu.

2. In a coherence plot, '''drag''' over an area of interest which comprises the time interval where the oscillation occurs and the relevant frequency range. The left-mouse popup menu appears (see the leftmost channel termed ACsL in the example below):

[[Image:Image006.gif]]

3. Select the menu entry '''View Phase Diagram'''. In all channels where coherence was shown previously, the plot changes to display the phase diagram. Inside the marked time-frequency region, the mean phase difference ϕi within the time window is calculated for each frequency νi, and the values are plotted. The phase is calculated from the cross-spectral matrices of the single trials. The error bars shown in the display are the standard deviations of the phase over the time.

The time lag is calculated from a regression fit to the values. The fitting procedure takes phase shifts of π into account, which can occur due to volume currents, or due to dipole orientations. First, a straight line is fitted to the data. Then, one of two different approaches are used to compute the time lag, depending on the characteristics of the values.
* If extrapolation of the line to ν = 0 Hz yields a phase difference of approximately 0 or approximately π, or if a zero crossing at the origin is within the error margins of the fit, the delay can be calculated directly from the data values. For each data value, the relationship ∆ti = ϕi / (2π νi) holds. The time lag is calculated as the weighted mean, where the weights are given by the individual errors of fi (the errors are given by the standard deviation over the time samples).
* If the regression line does not cross the origin, the gradient of the fit is used to calculate the time lag as ∆t = grad(f(ν)) / 2π

'''Note''': In both cases, any frequency only enters the calculation if the coherence value reaches or exceeds 70% of the current color map maximum for at least one time sample inside the selected time-frequency window. At least 3 valid values are required for the estimation. Channels with less than 3 valid values are not evaluated.

Phase values and fitted lines are only displayed for the channels where the above condition is satisfied. In the example below, the condition was only fulfilled for one channel (ACsL) due to the good separation of activities by the source montage. The calculated delay is displayed beside the channel label (in this case: 5 milliseconds).

[[Image:Image009.gif]]

To get back to coherence, '''right-click '''into the reference channel and select '''Coherence''' from the popup menu that appears.

== How to Compute a Probability Map ==

'''Statistical testing with one condition'''

This example uses the simulated data set in the file "'''Examples/Learn-by-Simulations/AC-Coherence/AC-Osc20.foc'''" (see also BESA Research Tutorial on source coherence on www.besa.de).

After the data file is loaded, start coherence analysis by
# selecting the montage "RC0" from the user montages (toolbar button "'''Usr'''")
# loading the paradigm (menu "''ERP/Open Paradigm''", select paradigm file "'''Auditory/AC_Osc.pdg'''")
# performing an artifact scan (paradigm tab "'''Artifact'''", press the "'''Scan'''..." button and adjust the amplitude threshold to about 135µV)
# starting analysis (paradigm tab "Coherence", press the "'''Go'''" button)

The progress bar runs through, and the temporal-spectral evolution (TSE) display is shown.

'''Statistics on TSE'''

In the TSE display, press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu that appears. Alternatively, select "''Statistics/Current Condition"'' from the menu. This starts the bootstrap test. The result looks somewhat like this:

[[Image:Image012.gif]]

''Example for p map of TSE, correction on p=0.05 level. Both significant synchronization and desynchronization is shown (red and blue colors; negative p values indicate desynchronization). The correction yields significant results only at the modelled time-frequency spots, with the exception of the frequency edges in channel PrM, FrR, and the occipital channels. The baseline interval is not tested.''

By default, the results are corrected for multiple testing, and only values with a significance of p < 0.05 after correction are kept. Correction can be switched off using statistics options (''Statistics/Options ''from the menu, or use the toolbar button [[Image:Image010.gif]] and select "''Options''" from the dropdown menu). This '''Options '''menu also enables correcting on the significance level p < 0.01. The text at the bottom left of the window indicates that a correction took place to find the significant sampling points, but the remaining p values were not corrected.

'''Statistics on Coherence and phase coherence'''

Double-click on a channel (e.g. ACsL) to display its coherence with the other channels. Then press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu (or select "''Statistics/Current'' ''Condition''" from the menu). This starts the permutation test, which is quite time-consuming. The result looks somewhat like this:

[[Image:Image013.gif]]

''Example for the p map of source coherence; correction on p=0.05 level. In all channels, alpha band coherence is significant. Furthermore, significant noise coherence can be observed in the proximate source channels, which only recedes where signal is present which is modelled by the reference channel. The oscillatory coupling between ACsL and ACsR is also significant.''

The same procedure applies for a phase coherence analysis. To switch to the p map for phase coherence, simply press the toolbar button [[Image:Image015.gif]] . If statistics mode is already active, the new p map will be computed automatically.

'''Statistical testing comparing conditions'''

This example uses the error-related negativity data set in the file ''''Examples/TFC-Error-Related''' '''Negativity/Correct+Error.foc'''' (see also BESA Research Tutorial on source coherence on [http://www.besa.de www.besa.de]).

After the data file is loaded, start coherence analysis by
# selecting the user montage "ERN9" from the user montages (toolbar button "'''Usr'''")
# Loading the paradigm (menu "'''ERP/Open Paradigm'''", select paradigm file "'''Cognitive/ERN.pdg'''")
# performing an artifact scan (paradigm tab "''Artifact''", press the "'''Scan'''..." button and adjust the amplitude and gradient thresholds to about 180 µV and 75 µV)
# select the conditions with error and correct response for analysis, triggered on the stimulus (tab "''Coherence''", select "''StErr''" as target condition, check the tick mark "''Use Control Condition''", and select "''StCor''" as control condition (see figure below). Press the "'''Go'''" button. The progress bar is displayed, followed by the temporal-spectral evolution (TSE) display for the target condition.

[[Image:Image017.gif]]

''Settings for comparing conditions in the time-frequency analysis.''

'''Statistics on TSE'''

Press the [[Image:Image018.gif]] toolbar button to see the difference between target and control condition.

Then press the toolbar button "" and select "''Compare Conditions''" from the dropdown menu that appears. Alternatively, select "''Statistics/Compare Conditions''" from the menu. This starts the permutation test. The result looks somewhat like this:

[[Image:Image019.gif]]

''Example of TSE p map when comparing conditions; correction on p=0.05 level. Both significant increase and decrease of TSE in target condition with respect to control condition is shown (red and blue colors; negative p values indicate decrease). The baseline interval is not tested.''

As in the case of one condition, the statistics options can be used to switch correction on or off, and to correct on two different significance levels.

'''Statistics on Coherence and phase coherence'''

Double-click on a channel (e.g. CgA) to display its coherence with the other channels. Then press the toolbar button [[Image:Image010.gif]] and select "''Current Condition''" from the dropdown menu (or select "''Statistics/Current Condition''" from the menu). This starts the permutation test, which is quite time-consuming. The result looks somewhat like this:

[[Image:Image021.gif]]

''Example for p-map of coherence comparing conditions; correction on p=0.05 level. The regions where coherence differs significantly between conditions are depicted in red. The main coherent regions are seen in channels CgP and TbR at low frequencies.''

Please note that the problems with noise coherence, which arise when testing within one condition, do not arise when comparing conditions. Computation is also much faster, since a different approach is used.

The same procedure applies for a phase coherence analysis. To switch to the p map for phase coherence, simply press the toolbar button [[Image:Image015.gif]] . If statistics mode is already active, the new p map will be computed automatically.

[[Category:Research Manual]]

{{BESAManualNav}}

Source Analysis Functions of the Window

2021-05-05T10:21:58Z

Harald:

{{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 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.
* 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

2021-05-05T10:21:33Z

Harald: /* 3D Window */

{{BESAInfobox
|title = Module information
|module = BESA Research Standard or higher
|version = 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 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.
* 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.

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