BrainVoyager QX Scripts

This page contains scripts written for BVQX. Please write me (Chris Asplund) with any questions or comments about using the scripts. That said, I'm primarily an FSL user now, so my BV knowledge is becoming increasingly dated. Nicely enough, the BV folk have finally produced some decent batch scripts, which can be found here.

The individual scripts are:

• RAWToFMRs.qs - Performs batch creation of FMRs and correctly sets the TR, voxel resolution, and slice gap (PAR files have problems with these values). Last updated: 23 June 2008.
• FMRsToPreprocessedFMRs.qs - Performs batch preprocessing on sets of FMRs. Like RAWToFMRs.qs, this script correctly sets the TR, voxel resolution, and slice gap. Last updated: 23 June 2008.
• CreateVTCs.qs - Creates VTC files from the necessary precursor files. Last updated: 23 June 2008.
• FMRsToPreprocessedFMRs_MC2nd.qs - Performs the same function as FMRsToPreprocessedFMRs.qs, but switches the order of motion correction and slice timing correction. BVQX v1.5 and earlier applied motion correction first, but the newer versions apply slice timing correction first by default. Last updated: 18 April 2008.

Additional information about using each script is provided in the comments in the script files themselves. I claim that the GUI for each script is pretty good - as good as QSA will allow, anyway - so use should be fairly simple. Although no modifications of the script files are necessary, you may find it useful to change the default values for the important parameters so that you do not have to do so in the GUI. The relevant variables are found under the heading "//Variable defaults", which is found at the beginning of each script.

Each script now creates a log file of the form shortscriptname_YYYY-MM-DD_hh-mm-ss.txt, where the time indicates the log file's creation. The file, which is created in the first target directory chosen, lists the relevant parameters, the files affected, and the status of the batch. The log file is helpfully updated during script execution.

Please do write me with questions, especially if something is particularly opaque.

You can download the scripts in a convenient .QSA file. Important: Choose v4-3 for BV 1.9 and later. There were QT script function call changes with this BV release.

• RAWtoVTCs_v4-1.qsa
• RAWtoVTCs_v4-3.qsa

Importing and using the scripts

Importing the .qsa file - Open BrainVoyager QX and choose "Edit Scripts..." from the "Scripts" menu. From the "File" menu of the Script Editor, select "Load Script Project" and then select the relevant .qsa file. Once the .qsa file has been chosen, the scripts in the script project will be visible in the Script Editor, and the main BrainVoyager window's "Scripts" menu will list the names of these imported scripts.

Executing a script - Execution of a script is simple: just select the script from the "Scripts" menu. Each script has a full GUI so that no parameters need be set in the script file itself.