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BrainVoyager Available Tools Available Plugins batchprocessingwizard for 4d data

batchprocessingwizard for 4d data


To process multiple 4-dimensional files, the batchprocessingwizard can be used. Download v1.9.5 beta for BrainVoyager 22.4, which includes starting from NIfTI instead of DICOM, v1.9.4 for BrainVoyager 22.2 and higher; for coregistration, argument 2 is temporarily set to 'use FMR' (instead of using AMR), v1.9.3 (for BrainVoyager 22; lightly tested), v1.9.2 (for BrainVoyager 21.4 and higher) v1.9.1 (11-01-18, fixed cancel button for selecting files) for BrainVoyager 20.4 or higher. With this version, one can start at FMR creation and end with MTC creation in one process. Manual for batchprocessingwizard v1.9 in PDF.

batchprocessingwizard v19 globaloptions

1. Install and activate: place *.js/*.ui files in /Documents/BVExtensions/Scripts/. Start BrainVoyager. Go to BrainVoyager menu > Scripts > Edit and Run Scripts... The batchprocessingwizard dialog will appear.

2. Specify options: First specify the options on the ‘Global options’ tab. The parameters for each option that has been checked, need to be specified on the following tabs. Unlike in the BrainVoyager interface, no values are read from the *.dcm input files, so the scan parameters like size of the image, number of volumes, etc, need to be specified manually. Also, there are no default settings, so if one would like to use default settings for temporal filtering for example, it might be good to obtain those from BrainVoyager or the BrainVoyager documentation.

3. File selection: The names of the input files can be specified either via selecting all files manually, or by specifying the required files in a text file.
For the creation of FMR or DMR projects, it is possible to edit the resulting file name by clicking the box ‘Edit future filenames’ on the ‘Source files’ tab before the files are selected. In that case, the names of the selected files will appear on the `Rename’ tab. Example: Say the original file is: “/MyExperiment/data-0001.dcm”, then the batchprocessingwizard will automatically create the name “/MyExperiment/data-0001.fmr”; it is possible to change this to something else, also in another folder if required, for example: “/MyExperiment/subfolder/subj1.fmr”.
All subjects can be processed in one go, except in case of intra-session alignment, where the target run needs to be created and preprocessed first (because the batchprocessingwizard will ask for a target *.fmr to be used for intra-session alignment). After that, all other runs from the different subjects can be processed in one go. Supporting files, like structural/anatomical files (*.vmr), anatomical transformation files (*_ACPC.trf or *_MNI.trf) and surface files (*.srf) need to have been created in advance, if used. The functional transformation files (*_IA.trf and *_FA.trf) will be created during the coregistration, which can be performed by the batchprocessingwizard.
4. Run the batchprocessing: If all options and files have been selected, click ‘Start’.

Batch files (*.txt) are automatically produced when running the batchprocessingwizard. So if the procedure needs to be repeated for some reason, on tab "Source files" one can select the option "Read file" and load this text file. The format of batch files has changed: example for TAL, example for MNI space. Any text before the separator ':' does not mattter and is just included for clarity. For entry "7 ACPC.trf", can be written "7 MNI.trf" if the VTC is supposed to be created in MNI space. The filename is supposed to appear on the right hand side of the ':', except if this file will be created in the process or when this step is skipped; in those cases, please write 'none' on the right hand side. So in the example below, the fmr, IA.trf, FA.trf, vtc and mtc entries are `none', because they will be created by batchprocessingwizard and the names will be known during the creation process. The fmr ISA entry is empty, so apparently there will be no intra-session motion correction. Anatomical (VMR), a target file for intra session motion correction ("3 fmr ISA") and surface files (SRF) need to have been created in advance (if used) and mentioned on this batch file.

batchprocessingwizard v19 batch file example

Note 07-11-22: Non-mosaic FMRs are now (BrainVoyager 22.4 and before) also in float format, so can be created via the batchprocessingwizard if needed for fieldmap creation. Non-mosaic FMRs are in integer format in BV20.6 (not suitable for anatabacus); therefore, in BrainVoyager 20.6, non-mosaic float-based FMRs (for example fieldmaps) need to be created manually instead of via this wizard/scripting.

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