BESA® Wiki - User contributions [en]

Main Page

2016-07-07T12:31:04Z

Todor: /* Matlab interface */

=Welcome to the BESA Wiki!=

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

== FAQ ==

=== Licensing ===

[[Licensing]]

=== File Formats ===

[[Channel Definition File Formats]]

[[Event File Format]]

[[MEG Sensor Coordinate Files]]

[[Supported Data Formats]]

[[Paradigm File Format in BESA]]

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

=== Data Review and Analysis ===

[[Importing Digitized Coordinates]]

[[Verify Electrode Coordinates]]

[[Export Single Trial Data]]

[[How to Average EEG channels]]

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

[[Time Frequency Resolution In BESA]]

[[Change Waveform Colours]]

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

[[Export Dipole Moments of Fitted Sources]]

[[Recommended Electrode Configurations]]

[[Exporting Artifact-Corrected Data]]

[[Create Triggers for Artifact-Rejected Epochs]]

[[Inserting Triggers Relative to Existing Events]]

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

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

=== Matlab interface ===

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

[[Updating the Matlab Interface after Matlab Upgrade]]

[[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]]

[[Importing BESA Statistics Results into Excel]]

=== Trouble shooting ===

[[MF Error 211]]

[[3D Graphics Display Issue Handling]]

== BESA recipes ==

[[Control of BESA Research by external programs]]

[[Correcting Volume Conductor Segmentations]]

[[Random Averaging]]

[[Statistical Analysis for More than Two Levels]]

[[Exporting Data from Matlab to BESA Statistics]]

[[Visualization with BESA Plot in FieldTrip]]

== Did you know...? ==

[[Moving Dipole Fit]]

[[BESA Anonymizer]]

[[Batch Processing]]

[[Analyzing Electrocorticography Data]]

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

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

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

Main Page

2016-07-07T12:30:45Z

Todor: /* BESA recipes */

=Welcome to the BESA Wiki!=

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

== FAQ ==

=== Licensing ===

[[Licensing]]

=== File Formats ===

[[Channel Definition File Formats]]

[[Event File Format]]

[[MEG Sensor Coordinate Files]]

[[Supported Data Formats]]

[[Paradigm File Format in BESA]]

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

=== Data Review and Analysis ===

[[Importing Digitized Coordinates]]

[[Verify Electrode Coordinates]]

[[Export Single Trial Data]]

[[How to Average EEG channels]]

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

[[Time Frequency Resolution In BESA]]

[[Change Waveform Colours]]

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

[[Export Dipole Moments of Fitted Sources]]

[[Recommended Electrode Configurations]]

[[Exporting Artifact-Corrected Data]]

[[Create Triggers for Artifact-Rejected Epochs]]

[[Inserting Triggers Relative to Existing Events]]

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

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

=== Matlab interface ===

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

[[Updating the Matlab Interface after Matlab Upgrade]]

[[Visualization with BESA Plot in FieldTrip]]

=== BESA MRI===

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

=== BESA Statistics ===

[[Cluster Alpha vs. Neighbor Distance]]

[[Importing BESA Statistics Results into Excel]]

=== Trouble shooting ===

[[MF Error 211]]

[[3D Graphics Display Issue Handling]]

== BESA recipes ==

[[Control of BESA Research by external programs]]

[[Correcting Volume Conductor Segmentations]]

[[Random Averaging]]

[[Statistical Analysis for More than Two Levels]]

[[Exporting Data from Matlab to BESA Statistics]]

[[Visualization with BESA Plot in FieldTrip]]

== Did you know...? ==

[[Moving Dipole Fit]]

[[BESA Anonymizer]]

[[Batch Processing]]

[[Analyzing Electrocorticography Data]]

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

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

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

Main Page

2016-07-07T12:30:23Z

Todor: /* Matlab interface */

=Welcome to the BESA Wiki!=

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

== FAQ ==

=== Licensing ===

[[Licensing]]

=== File Formats ===

[[Channel Definition File Formats]]

[[Event File Format]]

[[MEG Sensor Coordinate Files]]

[[Supported Data Formats]]

[[Paradigm File Format in BESA]]

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

=== Data Review and Analysis ===

[[Importing Digitized Coordinates]]

[[Verify Electrode Coordinates]]

[[Export Single Trial Data]]

[[How to Average EEG channels]]

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

[[Time Frequency Resolution In BESA]]

[[Change Waveform Colours]]

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

[[Export Dipole Moments of Fitted Sources]]

[[Recommended Electrode Configurations]]

[[Exporting Artifact-Corrected Data]]

[[Create Triggers for Artifact-Rejected Epochs]]

[[Inserting Triggers Relative to Existing Events]]

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

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

=== Matlab interface ===

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

[[Updating the Matlab Interface after Matlab Upgrade]]

[[Visualization with BESA Plot in FieldTrip]]

=== BESA MRI===

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

=== BESA Statistics ===

[[Cluster Alpha vs. Neighbor Distance]]

[[Importing BESA Statistics Results into Excel]]

=== Trouble shooting ===

[[MF Error 211]]

[[3D Graphics Display Issue Handling]]

== BESA recipes ==

[[Control of BESA Research by external programs]]

[[Correcting Volume Conductor Segmentations]]

[[Random Averaging]]

[[Statistical Analysis for More than Two Levels]]

[[Exporting Data from Matlab to BESA Statistics]]

== Did you know...? ==

[[Moving Dipole Fit]]

[[BESA Anonymizer]]

[[Batch Processing]]

[[Analyzing Electrocorticography Data]]

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

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

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

Visualization with BESA Plot in FieldTrip

2016-07-07T12:27:09Z

Todor:

{{BESAInfobox
|title = Module information
|module = BESA Plot
|version = 1.1 or higher
}}

[http://www.besa.de/downloads/besa-plot/ BESA Plot] is a free tool created by [https://www.psychologie.uni-konstanz.de/forschung/clinicalpsychology/mitarbeiter/mitarbeiter-detailseite/berg-patrick-22/7347/7149/ Patrick Berg] ([http://www.besa.de/ BESA GmbH]) for visualization of MEEG data. Initially it was meant to be complementary visualization tool to [http://www.besa.de/products/besa-research/besa-research-overview/ BESA Research], however, it could be used in more general context. In this document we demonstrate the possibility of using BESA Plot as a visualization tool in the [https://www.mathworks.com/ Matlab] based open source package for MEEG data analysis [http://www.fieldtriptoolbox.org/ FieldTrip].

Since BESA Plot can be started with command line arguments, it can be called directly from Matlab and the required input parameters (e.g. data file, settings and plotting modalities) can be committed as such arguments. There are four files necessary for starting BESA Plot from Matlab and visualizing the corresponding data: 1) a data file (e.g. test1.avr), 2) a file containing the channel labels and coordinates (e.g. test1.elp), 3) a control file containing the plotting commands for BESA Plot (e.g. test1.bpctrl) and 4) a dataset file containing general information about the data file (e.g. test1.avr.dataset). These files should be generated dynamically in Matlab in order to be able to plot the Matlab data in BESA Plot.

== Generating the data file ==
First of all we need the data which are going to be saved as an avr-file. This is usually a Matlab structure generated in FieldTrip with the function <tt>ft_timelockanalysis</tt>. Its general form is something like this:
<tt>
avg: [147x271 double]
var: [147x271 double]
time: [1x271 double]
dof: [147x271 double]
label: {147x1 cell}
dimord: 'chan_time'
grad: [1x1 struct]
cfg: [1x1 struct]

</tt>
In order to create a data file from that structure one needs the function <tt>besa_save2Avr</tt> which can be found in the FieldTrip installation in the folder <tt>external\besa</tt> or can be downloaded directly from [ftp://h1772544.stratoserver.net/public/Matlab/MATLAB2BESA.zip BESA’s ftp-server]. Just unpack the archive and add the path to the Matlab path (e.g. <tt>addpath(‘D:\Path\to\MATLAB2BESA’)</tt>).
Use the function like this:
<source lang="matlab">
status = besa_save2Avr(cfg.datapath, DataFile, data_matrix, ...
time_samples, channel_labels, data_scale_factor, time_scale_factor);
</source>

== Generating the channel file (*.elp) ==
This file contains the channel type, the channel labels and the spherical coordinates of the channels. It can be created using the function <tt>besa_save2Elp</tt> again from the package <tt>MATLAB2BESA</tt>. Use the function like this:
<source lang="matlab">
status = besa_save2Elp(cfg.datapath, ElpFile, ...
SphericalCoords, channel_labels, channel_type);
</source>
== Creating the BESA Plot control file ==
This is the actual plotting script. It follows the syntax of a scripting language defined in BESA Plot. For more details about the scripting language please refer to the program help. For this file format there is no writer function, since it can contain different scripts for different visualization scenarios. One possible script for plotting two dipoles in a schematic head could look like this:
<source lang="matlab">
set color=black
set size=16
set dipole number=1 xloc=0.65 yloc=0.16 zloc=0.29 xori=0.15 yori=-0.73 zori=-0.67 color=blue length=0.1 diameter=0.05
set dipole number=2 xloc=-0.65 yloc=0.16 zloc=0.29 xori=-0.17 yori=-0.57 zori=-0.81 color=blue length=0.1 diameter=0.05
head width=35 height=40 viewpoint=top brain=on x=20.0 y=75.0
head width=35 height=40 viewpoint=back brain=on x=20.0 y=30.0
head width=35 height=40 viewpoint=left brain=on x=77.0 y=77.0
set dataset=1
set mapuV=18
set mapcolor negative=blue positive=red electrode=none
set mapsize=35
set maptype=amplitude
set maplambda=1E-5
set mapviewpoint=top
set maprange maximumuV=461 minimumuV=-419 zerouV=0.0 contours=on
map latency=110.6 end=150.4 step=20 mean=on label=on x=77.0 y=30.0
</source>
The result after running the script is shown in Figure 1.
[[File:DipoleFitResults.png|thumb|500px|Figure 1 Dipole fitting results visualized with BESA Plot]]
[[File:AverageResults.png|thumb|500px|Figure 2 Visualization of sensor level data with BESA Plot]]
== Creating the dataset file ==
The dataset file contains basic information about the data in the data file. It is not essential for the visualization process, however, if it is missing, the program asks the user additional questions about the settings before generating the image. The dataset file can be created with the function <tt>besa_save2Dataset</tt> which also in the package <tt>MATLAB2BESA</tt>. Use the function like this:
<source lang="matlab">
status = besa_save2Dataset(DatasetPath, DataFile, ...
ElpFile, ControlFile, NumChannels, NumTimeSamples, ...
SamplingInterval, FirstTimeSample);
</source>
== Starting BESA Plot with command line arguments ==
After the generation of the input files one can start BESA Plot with these files as input in order to visualize data. The syntax of the call is:

<tt>BesaPlot <data_file_name> <control_file_name></tt>

'''Example:'''

<source lang="dos">
start /b cmd /c "C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"
M:\QM\BesaPlot\erf1.avr M:\QM\BesaPlot\erf1.bpctrl
</source>
Please note that <tt>start /b cmd /c</tt> is used to start the program in background.
== Predefined plotting functions for data from FieldTrip ==
There are two functions available in the package <tt>MATLAB2BESA</tt> (and also in FieldTrip in the folder <tt>external\besa</tt>) which can be used to plot directly data from FieldTrip with BESA Plot. These functions are <tt>besa_plotFtSensorLevelMaps</tt> and <tt>besa_plotFtDipoleResults</tt>. The first one can be used to plot sensor level MEEG data generated by <tt>ft_timelockanalysis</tt> and the second one for dipole fit data resulted from <tt>ft_dipolefitting</tt>. The image gained with the function <tt>besa_plotFtSensorLevelMaps</tt> is shown in Figure 2 and the one generated with the function <tt>ft_dipolefitting</tt> is shown in Figure 1.
The functions can be called like this:
<source lang="matlab">
cfg = [];
cfg.badchannels = 1; % number of bad channels
cfg.latency = [0.000 0.250]; % interval of interest in seconds
cfg.timestep = 0.020; % time interval between two plots
% path to BESA Plot
cfg.besaplot = '"C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"';
cfg.filebasename = 'erf1'; % basename for the generated files
% folder where to save the generated files
cfg.datapath = 'D:\Data\BesaPlot';

status = besa_plotFtSensorLevelMaps(cfg, data_avg);
</source>
and
<source lang="matlab">
cfg = [];
cfg.badchannels = 1; % number of bad channels
cfg.besaplot = '"C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"'; % path to BESA Plot
cfg.filebasename = 'megdatafile'; % basename for the generated files
cfg.datapath = 'D:\Data\BesaPlot'; % folder where to save the generated files

status = besa_plotFtDipoleResults(cfg, data_avg, dipole_source);
</source>
Please note that there are two possible ways to customize the plots:
# Change the section '''Write the control file''' in the plotting functions <tt>besa_plotFtSensorLevelMaps</tt> and <tt>besa_plotFtDipoleResults</tt>.
# After the plots were created use BESA Plot to change the images.
For more information about which visualization possibilities are available in BESA Plot please read the program help or check the [http://www.besa.de/downloads/besa-plot/ feature list].

[[Category:BESA Plot, Matlab]]

Visualization with BESA Plot in FieldTrip

2016-07-07T12:23:11Z

Todor: /* Predefined plotting functions for data from FieldTrip */

[http://www.besa.de/downloads/besa-plot/ BESA Plot] is a free tool created by [https://www.psychologie.uni-konstanz.de/forschung/clinicalpsychology/mitarbeiter/mitarbeiter-detailseite/berg-patrick-22/7347/7149/ Patrick Berg] ([http://www.besa.de/ BESA GmbH]) for visualization of MEEG data. Initially it was meant to be complementary visualization tool to [http://www.besa.de/products/besa-research/besa-research-overview/ BESA Research], however, it could be used in more general context. In this document we demonstrate the possibility of using BESA Plot as a visualization tool in the [https://www.mathworks.com/ Matlab] based open source package for MEEG data analysis [http://www.fieldtriptoolbox.org/ FieldTrip].

Since BESA Plot can be started with command line arguments, it can be called directly from Matlab and the required input parameters (e.g. data file, settings and plotting modalities) can be committed as such arguments. There are four files necessary for starting BESA Plot from Matlab and visualizing the corresponding data: 1) a data file (e.g. test1.avr), 2) a file containing the channel labels and coordinates (e.g. test1.elp), 3) a control file containing the plotting commands for BESA Plot (e.g. test1.bpctrl) and 4) a dataset file containing general information about the data file (e.g. test1.avr.dataset). These files should be generated dynamically in Matlab in order to be able to plot the Matlab data in BESA Plot.

== Generating the data file ==
First of all we need the data which are going to be saved as an avr-file. This is usually a Matlab structure generated in FieldTrip with the function <tt>ft_timelockanalysis</tt>. Its general form is something like this:
<tt>
avg: [147x271 double]
var: [147x271 double]
time: [1x271 double]
dof: [147x271 double]
label: {147x1 cell}
dimord: 'chan_time'
grad: [1x1 struct]
cfg: [1x1 struct]

</tt>
In order to create a data file from that structure one needs the function <tt>besa_save2Avr</tt> which can be found in the FieldTrip installation in the folder <tt>external\besa</tt> or can be downloaded directly from [ftp://h1772544.stratoserver.net/public/Matlab/MATLAB2BESA.zip BESA’s ftp-server]. Just unpack the archive and add the path to the Matlab path (e.g. <tt>addpath(‘D:\Path\to\MATLAB2BESA’)</tt>).
Use the function like this:
<source lang="matlab">
status = besa_save2Avr(cfg.datapath, DataFile, data_matrix, ...
time_samples, channel_labels, data_scale_factor, time_scale_factor);
</source>

== Generating the channel file (*.elp) ==
This file contains the channel type, the channel labels and the spherical coordinates of the channels. It can be created using the function <tt>besa_save2Elp</tt> again from the package <tt>MATLAB2BESA</tt>. Use the function like this:
<source lang="matlab">
status = besa_save2Elp(cfg.datapath, ElpFile, ...
SphericalCoords, channel_labels, channel_type);
</source>
== Creating the BESA Plot control file ==
This is the actual plotting script. It follows the syntax of a scripting language defined in BESA Plot. For more details about the scripting language please refer to the program help. For this file format there is no writer function, since it can contain different scripts for different visualization scenarios. One possible script for plotting two dipoles in a schematic head could look like this:
<source lang="matlab">
set color=black
set size=16
set dipole number=1 xloc=0.65 yloc=0.16 zloc=0.29 xori=0.15 yori=-0.73 zori=-0.67 color=blue length=0.1 diameter=0.05
set dipole number=2 xloc=-0.65 yloc=0.16 zloc=0.29 xori=-0.17 yori=-0.57 zori=-0.81 color=blue length=0.1 diameter=0.05
head width=35 height=40 viewpoint=top brain=on x=20.0 y=75.0
head width=35 height=40 viewpoint=back brain=on x=20.0 y=30.0
head width=35 height=40 viewpoint=left brain=on x=77.0 y=77.0
set dataset=1
set mapuV=18
set mapcolor negative=blue positive=red electrode=none
set mapsize=35
set maptype=amplitude
set maplambda=1E-5
set mapviewpoint=top
set maprange maximumuV=461 minimumuV=-419 zerouV=0.0 contours=on
map latency=110.6 end=150.4 step=20 mean=on label=on x=77.0 y=30.0
</source>
The result after running the script is shown in Figure 1.
[[File:DipoleFitResults.png|thumb|500px|Figure 1 Dipole fitting results visualized with BESA Plot]]
[[File:AverageResults.png|thumb|500px|Figure 2 Visualization of sensor level data with BESA Plot]]
== Creating the dataset file ==
The dataset file contains basic information about the data in the data file. It is not essential for the visualization process, however, if it is missing, the program asks the user additional questions about the settings before generating the image. The dataset file can be created with the function <tt>besa_save2Dataset</tt> which also in the package <tt>MATLAB2BESA</tt>. Use the function like this:
<source lang="matlab">
status = besa_save2Dataset(DatasetPath, DataFile, ...
ElpFile, ControlFile, NumChannels, NumTimeSamples, ...
SamplingInterval, FirstTimeSample);
</source>
== Starting BESA Plot with command line arguments ==
After the generation of the input files one can start BESA Plot with these files as input in order to visualize data. The syntax of the call is:

<tt>BesaPlot <data_file_name> <control_file_name></tt>

'''Example:'''

<source lang="dos">
start /b cmd /c "C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"
M:\QM\BesaPlot\erf1.avr M:\QM\BesaPlot\erf1.bpctrl
</source>
Please note that <tt>start /b cmd /c</tt> is used to start the program in background.
== Predefined plotting functions for data from FieldTrip ==
There are two functions available in the package <tt>MATLAB2BESA</tt> (and also in FieldTrip in the folder <tt>external\besa</tt>) which can be used to plot directly data from FieldTrip with BESA Plot. These functions are <tt>besa_plotFtSensorLevelMaps</tt> and <tt>besa_plotFtDipoleResults</tt>. The first one can be used to plot sensor level MEEG data generated by <tt>ft_timelockanalysis</tt> and the second one for dipole fit data resulted from <tt>ft_dipolefitting</tt>. The image gained with the function <tt>besa_plotFtSensorLevelMaps</tt> is shown in Figure 2 and the one generated with the function <tt>ft_dipolefitting</tt> is shown in Figure 1.
The functions can be called like this:
<source lang="matlab">
cfg = [];
cfg.badchannels = 1; % number of bad channels
cfg.latency = [0.000 0.250]; % interval of interest in seconds
cfg.timestep = 0.020; % time interval between two plots
% path to BESA Plot
cfg.besaplot = '"C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"';
cfg.filebasename = 'erf1'; % basename for the generated files
% folder where to save the generated files
cfg.datapath = 'D:\Data\BesaPlot';

status = besa_plotFtSensorLevelMaps(cfg, data_avg);
</source>
and
<source lang="matlab">
cfg = [];
cfg.badchannels = 1; % number of bad channels
cfg.besaplot = '"C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"'; % path to BESA Plot
cfg.filebasename = 'megdatafile'; % basename for the generated files
cfg.datapath = 'D:\Data\BesaPlot'; % folder where to save the generated files

status = besa_plotFtDipoleResults(cfg, data_avg, dipole_source);
</source>
Please note that there are two possible ways to customize the plots:
# Change the section '''Write the control file''' in the plotting functions <tt>besa_plotFtSensorLevelMaps</tt> and <tt>besa_plotFtDipoleResults</tt>.
# After the plots were created use BESA Plot to change the images.
For more information about which visualization possibilities are available in BESA Plot please read the program help or check the [http://www.besa.de/downloads/besa-plot/ feature list].

Visualization with BESA Plot in FieldTrip

2016-07-07T12:22:46Z

Todor: /* Predefined plotting functions for data from FieldTrip */

[http://www.besa.de/downloads/besa-plot/ BESA Plot] is a free tool created by [https://www.psychologie.uni-konstanz.de/forschung/clinicalpsychology/mitarbeiter/mitarbeiter-detailseite/berg-patrick-22/7347/7149/ Patrick Berg] ([http://www.besa.de/ BESA GmbH]) for visualization of MEEG data. Initially it was meant to be complementary visualization tool to [http://www.besa.de/products/besa-research/besa-research-overview/ BESA Research], however, it could be used in more general context. In this document we demonstrate the possibility of using BESA Plot as a visualization tool in the [https://www.mathworks.com/ Matlab] based open source package for MEEG data analysis [http://www.fieldtriptoolbox.org/ FieldTrip].

Since BESA Plot can be started with command line arguments, it can be called directly from Matlab and the required input parameters (e.g. data file, settings and plotting modalities) can be committed as such arguments. There are four files necessary for starting BESA Plot from Matlab and visualizing the corresponding data: 1) a data file (e.g. test1.avr), 2) a file containing the channel labels and coordinates (e.g. test1.elp), 3) a control file containing the plotting commands for BESA Plot (e.g. test1.bpctrl) and 4) a dataset file containing general information about the data file (e.g. test1.avr.dataset). These files should be generated dynamically in Matlab in order to be able to plot the Matlab data in BESA Plot.

== Generating the data file ==
First of all we need the data which are going to be saved as an avr-file. This is usually a Matlab structure generated in FieldTrip with the function <tt>ft_timelockanalysis</tt>. Its general form is something like this:
<tt>
avg: [147x271 double]
var: [147x271 double]
time: [1x271 double]
dof: [147x271 double]
label: {147x1 cell}
dimord: 'chan_time'
grad: [1x1 struct]
cfg: [1x1 struct]

</tt>
In order to create a data file from that structure one needs the function <tt>besa_save2Avr</tt> which can be found in the FieldTrip installation in the folder <tt>external\besa</tt> or can be downloaded directly from [ftp://h1772544.stratoserver.net/public/Matlab/MATLAB2BESA.zip BESA’s ftp-server]. Just unpack the archive and add the path to the Matlab path (e.g. <tt>addpath(‘D:\Path\to\MATLAB2BESA’)</tt>).
Use the function like this:
<source lang="matlab">
status = besa_save2Avr(cfg.datapath, DataFile, data_matrix, ...
time_samples, channel_labels, data_scale_factor, time_scale_factor);
</source>

== Generating the channel file (*.elp) ==
This file contains the channel type, the channel labels and the spherical coordinates of the channels. It can be created using the function <tt>besa_save2Elp</tt> again from the package <tt>MATLAB2BESA</tt>. Use the function like this:
<source lang="matlab">
status = besa_save2Elp(cfg.datapath, ElpFile, ...
SphericalCoords, channel_labels, channel_type);
</source>
== Creating the BESA Plot control file ==
This is the actual plotting script. It follows the syntax of a scripting language defined in BESA Plot. For more details about the scripting language please refer to the program help. For this file format there is no writer function, since it can contain different scripts for different visualization scenarios. One possible script for plotting two dipoles in a schematic head could look like this:
<source lang="matlab">
set color=black
set size=16
set dipole number=1 xloc=0.65 yloc=0.16 zloc=0.29 xori=0.15 yori=-0.73 zori=-0.67 color=blue length=0.1 diameter=0.05
set dipole number=2 xloc=-0.65 yloc=0.16 zloc=0.29 xori=-0.17 yori=-0.57 zori=-0.81 color=blue length=0.1 diameter=0.05
head width=35 height=40 viewpoint=top brain=on x=20.0 y=75.0
head width=35 height=40 viewpoint=back brain=on x=20.0 y=30.0
head width=35 height=40 viewpoint=left brain=on x=77.0 y=77.0
set dataset=1
set mapuV=18
set mapcolor negative=blue positive=red electrode=none
set mapsize=35
set maptype=amplitude
set maplambda=1E-5
set mapviewpoint=top
set maprange maximumuV=461 minimumuV=-419 zerouV=0.0 contours=on
map latency=110.6 end=150.4 step=20 mean=on label=on x=77.0 y=30.0
</source>
The result after running the script is shown in Figure 1.
[[File:DipoleFitResults.png|thumb|500px|Figure 1 Dipole fitting results visualized with BESA Plot]]
[[File:AverageResults.png|thumb|500px|Figure 2 Visualization of sensor level data with BESA Plot]]
== Creating the dataset file ==
The dataset file contains basic information about the data in the data file. It is not essential for the visualization process, however, if it is missing, the program asks the user additional questions about the settings before generating the image. The dataset file can be created with the function <tt>besa_save2Dataset</tt> which also in the package <tt>MATLAB2BESA</tt>. Use the function like this:
<source lang="matlab">
status = besa_save2Dataset(DatasetPath, DataFile, ...
ElpFile, ControlFile, NumChannels, NumTimeSamples, ...
SamplingInterval, FirstTimeSample);
</source>
== Starting BESA Plot with command line arguments ==
After the generation of the input files one can start BESA Plot with these files as input in order to visualize data. The syntax of the call is:

<tt>BesaPlot <data_file_name> <control_file_name></tt>

'''Example:'''

<source lang="dos">
start /b cmd /c "C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"
M:\QM\BesaPlot\erf1.avr M:\QM\BesaPlot\erf1.bpctrl
</source>
Please note that <tt>start /b cmd /c</tt> is used to start the program in background.
== Predefined plotting functions for data from FieldTrip ==
There are two functions available in the package <tt>MATLAB2BESA</tt> (and also in FieldTrip in the folder <tt>external\besa</tt>) which can be used to plot directly data from FieldTrip with BESA Plot. These functions are <tt>besa_plotFtSensorLevelMaps</tt> and <tt>besa_plotFtDipoleResults</tt>. The first one can be used to plot sensor level MEEG data generated by <tt>ft_timelockanalysis</tt> and the second one for dipole fit data resulted from <tt>ft_dipolefitting</tt>. The image gained with the function <tt>besa_plotFtSensorLevelMaps</tt> is shown in Figure 2 and the one generated with the function <tt>ft_dipolefitting</tt> is shown in Figure 1.
The functions can be called like this:
<source lang="matlab">
cfg = [];
cfg.badchannels = 1; % number of bad channels
cfg.latency = [0.000 0.250]; % interval of interest in seconds
cfg.timestep = 0.020; % time interval between two plots
% path to BESA Plot
cfg.besaplot = '"C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"';
cfg.filebasename = 'erf1'; % basename for the generated files
% folder where to save the generated files
cfg.datapath = 'D:\Data\BesaPlot';

status = besa_plotFtSensorLevelMaps(cfg, data_avg);
</source>
and
<source lang="matlab">
cfg = [];
cfg.badchannels = 1; % number of bad channels
cfg.besaplot = '"C:\Program Files (x86)\BESA\Plot\BesaPlot.exe"'; % path to BESA Plot
cfg.filebasename = 'megdatafile'; % basename for the generated files
cfg.datapath = 'D:\Data\BesaPlot'; % folder where to save the generated files

status = besa_plotFtDipoleResults(cfg, data_avg, dipole_source);
</source>
Please note that there are two possible ways to customize the plots:
# Change the section '''Write the control file''' in the plotting functions <tt>besa_plotFtSensorLevelMaps</tt> and <tt>besa_plotFtDipoleResults</tt>.
## After the plots were created use BESA Plot to change the images.
For more information about which visualization possibilities are available in BESA Plot please read the program help or check the [http://www.besa.de/downloads/besa-plot/ feature list].

Visualization with BESA Plot in FieldTrip

2016-07-07T12:18:41Z

Visualization with BESA Plot in FieldTrip

2016-07-07T12:08:16Z

Todor:

Visualization with BESA Plot in FieldTrip

2016-07-07T12:06:45Z

Todor:

Visualization with BESA Plot in FieldTrip

2016-07-07T12:04:38Z

Todor: /* Creating the BESA Plot control file */

Visualization with BESA Plot in FieldTrip

2016-07-07T12:03:02Z

Todor: /* Creating the BESA Plot control file */

File:AverageResults.png

2016-07-07T12:00:32Z

Todor: Visualization of sensor level data with BESA Plot

Visualization of sensor level data with BESA Plot

File:DipoleFitResults.png

2016-07-07T11:59:15Z

2016-05-12T13:29:53Z

Todor: Microsoft Excel Data tab, From Text button

Microsoft Excel Data tab, From Text button

File:MicrosoftExcelDataTab.png

2016-05-12T13:29:01Z

Todor: Microsoft Excel Data tab

Microsoft Excel Data tab

Importing BESA Statistics Results into Excel

2016-05-12T13:27:44Z

Todor:

In BESA Statistics there are two options for exporting results: summary results and detailed results. In both cases the results are exported as ascii files in comma-separated values (CSV) format. For the values which are stored in the files a dot (.) is used as a decimal separator and no symbol is used as a thousands separator. This can causes problems when importing the data into Microsoft Excel and the settings in Excel are different than the assumed for the values, e.g. the decimal separator is a comma (,) and the thousands separator is a dot (.). This is the case, for example, in Germany.

In order to make sure that the results are imported correctly into Excel one has to follow the next procedure.

1) Open Excel and select the <tt>Data</tt> tab

2) Click on the icon <tt>From Text</tt> and select the corresponding CSV-file.

3) The <tt>Text Import Wizard</tt> opens. In the first step choose the option <tt>Delimited</tt> and click <tt>Next</tt>.

4) In the second step choose as a delimiter <tt>Semicolon</tt> and click next.

5) In the third step click on <tt>Advanced...</tt> and in the <tt>Advanced Text Import Settings</tt> dialog select a dot (.) as a decimal separator and empty character as a thousands separator.

6) Click <tt>OK</tt> and then on <tt>Finish</tt> to complete the <tt>Text Import Wizard</tt>. The data should be imported correctly now.