Difference between revisions of "How to Prepare Data for BESA Connectivity"

Revision as of 13:22, 5 May 2021

Note and general remarks

This article applies to data that are prepared using BESA Research. It is also possible to read data prepared by other programs. For the requirements, please refer to the BESA Connectivity manual, the chapter on "Loading data that were created in other software" and the chapter "File formats".

BESA Connectivity needs the following data:

1. A file containing the binary data matrix. All epochs in the data file need to have the same length, the same stimulus position, the same baseline interval, and the same channel configuration.
2. A header file in ASCII format.
3. A channel description file in ASCII format. Two types of files are supported: elp files and bsa files.

File format descriptions

Header file format

The header file is a standard ASCII file. It contains the following lines:

Channel configuration file format

The channel description file is an ASCII file. Two types of files are supported: .elp files and .bsa files.

ELP file format

Elp files describe surface channel coordinates using spherical coordinates (theta, phi). It contains one line for each channel in the data file. Each line contains the following entries:

BSA file format

Bsa files describe source channel data. They have a header section for format version and readability, followed by one line for each source channel.

The coordinate system is defined by a sphere with unit dimensions, which is fitted to the coordinates of sensors on the head. In the absence of co-registration information with individual MRI data, the axes are defined by reference points on the head known as fiducials. The reference points are normally the nasion (NAS), the left preauricular point (LPA), and the right preauricular point (RPA). The direction of the x axis is defined by the line joining LPA and RPA, positive towards RPA. The direction of the y axis is defined by the line through NAS that is perpendicular to the x axis (positive towards NAS). The z axis is perpendicular to the x and y axes, and goes up out of the upper part of the head (e.g. Cz). On average, the center of the unit sphere is about 4 cm above the origin of the head coordinate system.

Binary data matrix file format

The binary data matrix is saved in float format and contains <Number of epochs> * <Number of samples per epoch> * <Number of channels> values. These are stored in the following order:

• Slowest index: epochs
• Next index: samples
• Fastest index: channels

This is the so-called multiplexed file format. The default extension for this header file is: *.dat

Export data using BESA Research

Please follow the steps in the BESA Research 7.0 tutorial, chapter 13 - Time Frequency and Connectivity Analysis: Link

Batch export data using BESA Research

BESA Research provides batch processing multiple files to export data for BESA Connectivity. This will simplify and speed up your analysis if you need to apply the same data preparation steps for a large number of files.

This section will provide the batch that is required to export the data epochs and will also explain additional steps that need to be performed to load the exported data sets into BESA Connectivity.

BESA Research Batch

The batch commands required to export all epochs around trigger #1 is displayed below. The first step is to set the specific montage in which all epochs should be exported. Then, the default epoch length needs to be set. In this example, epochs range from -500ms to 2000ms. However, preceding and succeeding padding intervals of 2000ms are required to avoid edge effects during time-frequency transformation. Therefore, the resulting default epoch is set to -2500ms to 4000ms. After this, trigger #1 is selected and epochs are exported to C:\Users\<USERNAME>\Documents\BESA\Research_7_0\Export\Batch Export\. Finally, the batch will also export the channel configuration file (*.elp) in case of sensor data. In case of source data, the corresponding source configuration file (*.bsa) that was used to create the respective source montage needs to be copied to the output folder manually!

Please note: adjust the <USERNAME> placeholder or the export path according to your needs.

; Set montage
MAINMontage(DMN with Noise Sources, Wait if invalid, GlobalMontage)
; Set epoch length. Note: add 2000ms padding ad start & end
EditDefaultEpoch(-2500.000,4000.000)
;
; Export epochs for trigger #1
TriggerSelect(1)
MAINExport(%basename%-export-T1, C:\Users\<USERNAME>\Documents\BESA\Research_7_0\Export\Batch Export\, Epochs, SimpleBin, Current, FiltOff, NoResample, Replace, -, , WholeFile)
;
; Export channel configuration file
MAINMarkBlock(Rawdata,-,1)
MAINExport(%basename%-export-T1, C:\Users\<USERNAME>\Documents\BESA\Research_7_0\Export\Batch Export\, Segment, ASCmul, Original, FiltOff, NoResample, Replace, -, , WholeFile)

This batch can be downloaded from the following link and loaded in the Batch tab of the Batch Processing module:Download link.

Additional Steps

In order to be able to import the saved data sets into BESA Connectivity, there are a few changes that need to be made to the exported *.generic file(s).

When opening the *.generic file with a text editor you will realize that the format slightly differs from the file format description above. the following images compare the exported file (left) and the adjusted file that can be imported into BESA Connectivity (right).

Please adjust or add the following sections to the *.generic file:

• File format version: set to V1.1
• Add lines for baselineStart, baselineEnd and epochLength. Note: the time stamps do not include the padding intervals!
• Add the line to specify the padding interval of 2000ms.
• Add the specification of the condition name.
• Add one line per channel/source and specify the its label and unit.

Save the file after performing the changes.

If you are working with source data, make sure that the corresponding source configuration file (*.bsa) has the same basename as the *.generic file. Otherwise, BESA Connectivity will not be able to load the file.

Now the exported data sets are ready to be loaded into BESA Connectivity!

Export data using Matlab

We provide several Matlab routines for exporting the required data files from Matlab to BESA Connectivity. The scripts can be downloaded from the following website: MATLAB Scripts.

The following script can be used as an example to generate and export data from MATLAB to BESA Connectivity: Matlab to BESA Connectivity It shows how to define required parameters, generates example sine waves and calls the export function besa_save2Connectivity to store the simulated example data to disc. It will store the file containing the binary data matrix, as well as the header file and channel description file in ASCII format.

The script can be easily adopted to export your trial data do BESA Connectivity for time-frequency and connectivity analysis!

Examples

Minimal examples for data files that can be imported in BESA Connectivity can be downloaded here.

1. EEG data: this data set contains 25 trials (trial length: -400ms to 1200ms) of scalp data with 27 electrodes at a sampling rate of 320 samples/second.

   Download link.

   

2. Source data: this data set contains 33 trials (trial length: -400ms to 1200ms) of source data with 19 dipoles at a sampling rate of 320 samples/second.

   Download link.