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batchprocessingwizard for 4d data




To process multiple 4-dimensional files, the batchprocessingwizard can be used. Download 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’.

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


Non-mosaic FMRs will still be in integer format in BV20.6 (not suitable for anatabacus) Float-based FMRs need to be created manually instead of via this wizard/scripting.

Note 27-09-16: a new version (1.8.3), with a fix for VTCs not being preprocessed in certain cases, is still being tested. Apologies for any inconvenience. Please note that creating non-mosaic FMRs and DMRs now works in BrainVoyager 20.2 (not in BV20.0), but not via scripting, hence not via this wizard.
Batch processing wizard v1.8  for Mac/Win/Linux (script only)
Description: this version contains the following change:
- Load *.uff file
Download: v1.8 (*.js/*.ui only, place in Documents/BVQXExtensions/Scripts, start via BrainVoyager QX Menu > Scripts > Edit > Run).
Latest update: 01-07-15
Batch processing wizard v1.7 beta2 for Mac/Win/Linux (script only still)
Description: this version contains the following change:
- A new tab (see picture below) which makes it possible to edit the filenames (please note: the extension '.fmr' needs to be added to the name)
Download: v1.7 beta (*.js/*.ui only, place in Documents/BVQXExtensions/Scripts, start via BrainVoyager QX Menu > Scripts > Edit > Run); please note: needs more testing, therefore still beta.
Latest update: 04-06-15
editfilenames small
Batch processing wizard v1.6 beta2 for Mac/Win/Linux (script only now)
Description: this version contains the following changes:
- Create FMR/DMR dialog: 3 instead of 2 decimals for manually specifying the pixelsize
- Create FMR/DMR dialog: files without extensions are now also allowed (for example for Bruker files) -> still being tested
- Preprocessing: Added mean intensity adjustment (MIA); see elsewhere on support site for more information
- Selecting source files: the number of selected files is indicated in the BrainVoyager QX Log tab
- Added slice scan time correction for multi-band EPI
Download: v1.6 beta (*.js/*.ui only, place in Documents/BVQXExtensions/Scripts, start via BrainVoyager QX Menu > Scripts > Edit > Run); please note: needs more testing, therefore still beta.
Latest update: 29-01-15
Batch processing wizard v1.5 for Windows 64-bit, Mac OS 10.6.8
This version supports the user-defined file format (*.uff) and the order of spatial smoothing and temporal filtering is reversed so that it has the same order as the BrainVoyager user interface. (The *.uff file should be saved in the BrainVoyager program directory.)
Added: 27-04-2014.
Batch processing wizard v1.4 for BrainVoyager QX 2.4.1 or higher: for Mac OS X, Windows 64-bit, Windows 32-bit, Windows 8, Linux 64-bit. In this version it is possible to determine VTC bounding box size numerically. Latest update: 17-07-2012.
Manual for v1.4: PDF Added: 11-07-2012.
Batch processing wizard v1.3 for BrainVoyager QX 2.4.1: for Mac OS X, Windows 32-bit*, Windows 64-bit, Linux 64-bit*. This version includes FMR temporal high-pass filtering with the "GLM approach". Latest update: 26-03-2012.
* Compiled only, not tested.
09-07-12: Fixed script for MTC creation (filenaming used same name, so just 1 file was produded): batchprocessingwizard_v13.js (zipped). Please replace with current file in /Documents/BVQXExtensions/Plugins/ (also because of creating VTC files, the variable to create bounding boxes with coordinate values had to be set for all reference spaces).
Batch processing wizard v1.2 for BrainVoyager QX 2.3 and higher: for Mac OS X, Windows 64-bit, Windows 32-bit, Linux 64-bit. With this version it is also possible to create multiple VTC or VDW files, to preprocess VTC files or to create multiple MTC files. Latest update: 21-12-2011
Manual for v1.2: PDF Added: 14-03-2012.