BVQX scripts
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Scripts
For information about scripting in BrainVoyager QX, please see the BrainVoyager QX scripting documentation page.
Scripting news
In BrainVoyager QX 2.1, the underlying scripting module has changed due to changes in Qt. The BrainVoyager functions are the same, the editor and GUI functionality has changed. Read more about it and find example scripts on the BrainVoyager support page: http://support.brainvoyager.com/.
In BrainVoyager QX 1.9.10 are now 3 interpolation methods available: "The motion correction commands "CorrectMotionEx" and "CorrectMotionTargetVolumeInOtherRunEx" always used trilinear interpolation in previous versions. The third parameter "InterpolationMethod" allows now to specify the same interpolation methods as used in the GUI; value "1" (or "0") is interpreted as trilinear interpolation, value "2" is interpreted as "trilinear-sinc" (trilinear interpolation for detection of motion parameters, sinc interpolation for final transformation) and value "3" is interpreted as "sinc-sinc" (sinc interpolation is used for detection and transformation)." (from Release Notes v1.10).
Note on BrainVoyager QX 1.9: the scripting projects are not compatible to 1.8. The recommended option is to export the scripts from 1.8 script projects via the Script Editor's File > Export Script... function, create a new script project in QX 1.9 and then import the scripts in this new script project.
QSA scripts and projects released with BrainVoyager QX
(by Rainer Goebel)
- Script project released with BrainVoyager QX 1.9
- Script project released with BrainVoyager QX 1.6
- Script I released with BrainVoyager QX 1.3 on creating a stimulation protocol (*.prt) and creating VTCs.
- Script II released with BrainVoyager QX 1.3 on creating a design matrix and computing GLMs.
- Script released with BrainVoyager QX 1.2
- Example script to create VMR/FMR/AMR projects
- Preprocessing example functions
- Help functions
Other QSA scripts
(by Hester Breman)
Importing experimental data
- eprimer (v0.3): Tool for importing E-Prime Log files (*.txt) to BrainVoyager stimulation protocol (*.prt). This is a BrainVoyager script project that can be directly used when installed as current project.
- Manual (v0.4) for eprimer v0.3 (*.pdf).
Note: In case the BVQXLog tab shows empty lines when importing via eprimer, please read the following. The cause is a text mark-up problem. The solution for importing the *.txt log file from E-Prime is to copy-paste the logtext to a mark-up free text/programming editor (like Code::Blocks, see http://www.codeblocks.org/), save in a different extension and import the 'mark-up free' text with eprimer.
- For importing Presentation log files, the protocolgenerator plugin is available at the plugins page.
Wizards (batch processing)
- Wizard for multiple 4D data sets (v0.6): Wizard for processing 4D data: batch processing for functional (FMR, VTC) and diffusion weighted images (DMR, VDW). Only for BrainVoyager QX 1.10.4 (or higher)! To prevent naming problems, please put each functional run in a different subfolder.
- Here is the Manual for wizard v0.6 (*.pdf). Version 0.5 of the manual for wizard v0.6: added description of creating DMR and VDW files (Latest update: 24-Dec-08).
- Wizard for multiple functional data sets (v0.5). Wizard v0.5 to process multiple functional data sets (create and preprocess FMRs, create VTCs) all in one go. The idea is to first enter all parameters for the processing options that have been selected (via the dialog shown below), then select the files once and run all processing steps for all projects. This version has been created in BrainVoyager QX 1.10.2. Changes:
- changed VTC naming scheme to _NATIVE, _ACPC and _TAL
- finished the "Rename DICOM in multiple directories" function
- added the Trilinear/SINC interpolation option for motion correction that became available in BrainVoyager QX 1.10
- the target for intra-session alignment is now first motion corrected, before other runs are aligned to this target. (Latest update: 11-Okt-08).
- And here is the Manual for wizard v0.5 (*.pdf). Version 0.3 of the manual for wizard v0.5: added description of possible file selection procedure(s) (Latest update: 30-Apr-08).
- The User's guide (for wizard v0.3 and v0.4) shows the dialogs of each function. Please update to this version when using an older batch processing project, thanks.
- Version for BVQX 1.8: version 0.4 for BVQX 1.8.
- Wizard to compute GLMs via batches (version 0.1 for QX 1.8). The simple
manual (for version 0.1) demonstrates the dialogs of the functionality.
- Functions in a script to select multiple subdirectories via the user interface.
- Create multiple VMR projects via this script with user interface (no modification in script needed).
- In this document the dialogs of the script are shown.
The newer script project including VMR transformations (isovoxel, autosag) is to be used with QX 1.9.
- Script to create a number of VTCs in VMR, AC-PC or TAL space All input via a user interface, so script does not need to be modified before use.
- Script to create quickly 3 VTCs in Talairach space with regular or extended bounding box. Load script in script project, and run (no modifications in script needed).
- Rename DICOM files in multiple directories Little function and demonstration to rename DICOM files in multiple directories.
Scripts for use with Diffusion Weighted data
by Pim
- Script for bypassing the create project wizard CreateCustomDMR
- Documentation The_createCustomDMR_script.pdf
- Obsolete Script to create a DMR project from the 'Scripts' menu (after incorporation in a script project): functions_bvqx19_create_dmr_project.qs
Sample scripts
Please note that if the QX version is not mentioned, the script might be for an older BrainVoyager QX version.
- Functions to print information about a project or stimulation protocol to the BrainVoyager QX Log tab: projectinfo.qs.
- Script to create a DMR project from the 'Scripts' menu (after incorporation in a script project): functions_bvqx19_create_dmr_project.qs
- Create design matrix interactively: script and description
- QSA script to create a text file with filenames of a certain extension in a directory
- Sample script project for BVQX 1.3
- Script to create contrasts
- Simple script for creating a VMR project via a dialog
- Script to manipulate viewpoint settings in the surface window
- Example script to work with files and directories
- Script showing how to capture input from dialogs
- Script project with simple functions showing how to show information to the user or retrieve user input via message boxes and f.e. file dialogs. As separate scripts.
