How to Prepare Data for BESA Connectivity - Revision history

Jaehyun: /* Export data using Matlab */

2021-08-27T11:03:39Z

‎Export data using Matlab

Mateusz at 19:48, 5 May 2021

2021-05-05T19:48:08Z

Robert: /* Export data using Matlab */

2021-05-05T12:32:33Z

‎Export data using Matlab

Robert at 12:23, 5 May 2021

2021-05-05T12:23:02Z

Robert: /* Export data using BESA Research */

2021-05-05T12:22:18Z

‎Export data using BESA Research

Robert at 11:08, 2 February 2021

2021-02-02T11:08:06Z

Mateusz at 14:29, 18 October 2019

2019-10-18T14:29:28Z

Robert at 12:46, 13 February 2019

2019-02-13T12:46:14Z

Robert: /* Export data using Matlab */

2018-11-15T14:36:52Z

‎Export data using Matlab

Robert: /* Export data using Matlab */

2018-06-11T13:40:22Z

‎Export data using Matlab

@@ Line 265: / Line 265: @@
 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: [http://www.besa.de/downloads/matlab/ MATLAB Scripts].
-The ''Matlab_to_BESAConnectivity.m'' script (download available here: [https://www.besa.de/wp-content/uploads/2020/10/BESAConnectivityScripts.zip BESA Connectivity Scripts]) can be used as an example to generate and export data from MATLAB to BESA Connectivity.
+The <code>Matlab_to_BESAConnectivity.m</code> script (download available here: [https://github.com/BESA-GmbH/BESA-MATLAB-Scripts/releases/latest/download/BesaConnectivityScripts.zip BESA Connectivity Scripts]) can be used as an example to generate and export data from MATLAB to BESA Connectivity.
-It shows how to define required parameters, generates example sine waves and calls the export function ''besa_save2Connectivity'' (included in: [https://www.besa.de/wp-content/uploads/2020/10/MATLAB2BESA.zip MATLAB to BESA Export functions]) 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.
+It shows how to define required parameters, generates example sine waves and calls the export function <code>besa_save2Connectivity</code> (included in: [https://github.com/BESA-GmbH/BESA-MATLAB-Scripts/releases/latest/download/MATLAB2BESA.zip MATLAB2BESA]) 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!

@@ Line 11: / Line 11: @@
 # 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.
 # A header file in ASCII format.
-# A channel description file in ASCII format. Two types of files are supported: elp files and bsa files.
+# A channel description file in ASCII format. Two types of files are supported: [[#ELP file format|elp]] files and [[BSA file format|bsa]] files.
 == File format descriptions ==
@@ Line 194: / Line 194: @@
 |}
-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.
+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 [[Integration with MRI and fMRI|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 ===
@@ Line 206: / Line 206: @@
 == Export data using BESA Research ==
-Please follow the steps in the BESA Research 7.0 tutorial, chapter 13 - Time Frequency and Connectivity Analysis: [https://www.besa.de/wp-content/uploads/2021/04/BESA-Research-7.1-Tutorial.pdf Link]
+Please follow the steps in the BESA Research 7.1 tutorial, chapter 12 - Time-frequency Analysis, Connectivity Analysis and Beamforming: [https://www.besa.de/wp-content/uploads/2021/04/BESA-Research-7.1-Tutorial.pdf 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.
@@ Line 216: / Line 217: @@
 ==== 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!
+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_1\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.
@@ Line 228: / Line 229: @@
 ; 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)
+MAINExport(%basename%-export-T1, C:\Users\<USERNAME>\Documents\BESA\Research_7_1\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)
+MAINExport(%basename%-export-T1, C:\Users\<USERNAME>\Documents\BESA\Research_7_1\Export\Batch Export\, Segment, ASCmul, Original, FiltOff, NoResample, Replace, -, , WholeFile)
 </source >

@@ Line 264: / Line 264: @@
 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: [http://www.besa.de/downloads/matlab/ MATLAB Scripts].
-The following script can be used as an example to generate and export data from MATLAB to BESA Connectivity: [ftp://h1772544.stratoserver.net/public/Matlab/BESA_Utilities/BESAConnectivityScripts/Matlab_to_BESAConnectivity.m Matlab to BESA Connectivity]
+The ''Matlab_to_BESAConnectivity.m'' script (download available here: [https://www.besa.de/wp-content/uploads/2020/10/BESAConnectivityScripts.zip BESA Connectivity Scripts]) can be used as an example to generate and export data from 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.
+It shows how to define required parameters, generates example sine waves and calls the export function ''besa_save2Connectivity'' (included in: [https://www.besa.de/wp-content/uploads/2020/10/MATLAB2BESA.zip MATLAB to BESA Export functions]) 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!

@@ Line 1: / Line 1: @@
 {{BESAInfobox
 |title = Module information
-|module = BESA Research Basic or higher,
+|module = BESA Research Basic or higher<br/>BESA Connectivity
-BESA Connectivity
+|version = BESA Research 7.0 or higher<br/>BESA Connectivity 1.0 or higher
-|version = 7.0 or higher (BR), 1.0 or higher (BC)
 }}

@@ Line 207: / Line 207: @@
 == Export data using BESA Research ==
-Please follow the steps in the BESA Research 7.0 tutorial, chapter 13 - Time Frequency and Connectivity Analysis: [ftp://h1772544.stratoserver.net/public/Connectivity/Tutorial%20-%20BESA%20Connectivity%20%5B2018-04-17%5D.pdf Link]
+Please follow the steps in the BESA Research 7.0 tutorial, chapter 13 - Time Frequency and Connectivity Analysis: [https://www.besa.de/wp-content/uploads/2021/04/BESA-Research-7.1-Tutorial.pdf Link]
 == Batch export data using BESA Research ==

@@ Line 279: / Line 279: @@
 --><p>[[Media:BESA_Connectivity_Source_data.zip|Download link.]]</p><!--
 --><p>[[File:BESA_Connectivity_Set_Parameters_Source_Data.png|400px]][[File:BESA_Connectivity_Run_Analysis_Source_Data_iCoh.png|400px|alt text]]</p>
 [[Category:Connectivity]] [[Category:Time-Frequency]]

← Older revision		Revision as of 12:46, 13 February 2019
Line 208:		Line 208:

	Please follow the steps in the BESA Research 7.0 tutorial, chapter 13 - Time Frequency and Connectivity Analysis: [ftp://h1772544.stratoserver.net/public/Connectivity/Tutorial%20-%20BESA%20Connectivity%20%5B2018-04-17%5D.pdf Link]		Please follow the steps in the BESA Research 7.0 tutorial, chapter 13 - Time Frequency and Connectivity Analysis: [ftp://h1772544.stratoserver.net/public/Connectivity/Tutorial%20-%20BESA%20Connectivity%20%5B2018-04-17%5D.pdf 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.
		+
		+	<source lang="dos">
		+	; 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)
		+	</source >
		+
		+	This batch can be downloaded from the following link and loaded in the ''Batch'' tab of the ''Batch Processing'' module:[[Media:Batch_Export_for_BESA_Connectivity.bbat\|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).
		+
		+	<!--
		+	--><p>[[File:Generic_File_Unchanged.png\|150px\|top]][[File:Generic File Modified.png\|150px\|alt text]]</p>
		+
		+
		+	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 ==		== Export data using Matlab ==

@@ Line 213: / Line 213: @@
 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: [http://www.besa.de/downloads/matlab/ MATLAB Scripts].
-The following script can be used as an example to generate and export data from MATLAB to BESA Connectivity: [ftp://h1772544.stratoserver.net/public/Matlab/Matlab2Connectivity/Matlab_to_BESAConnectivity.m Matlab to BESA Connectivity]
+The following script can be used as an example to generate and export data from MATLAB to BESA Connectivity: [ftp://h1772544.stratoserver.net/public/Matlab/BESAConnectivityScripts/Matlab_to_BESAConnectivity.m 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.

@@ Line 215: / Line 215: @@
 The following script can be used as an example to generate and export data from MATLAB to BESA Connectivity: [ftp://h1772544.stratoserver.net/public/Matlab/Matlab2Connectivity/Matlab_to_BESAConnectivity.m 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!
 == Examples ==