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BrainVoyager Analysis Predictor Tool (Stand Alone, Multi-Platform)

Developed by Jurriaan Born

Functionality

BVA-PT (previously BVA-HT) is a free tool, developed as an adaptation of a utility that the author wrote when he was working on fMRI data with BrainVoyagerâ„¢. It provides easy to use processing of design matrix files (.rtc and .sdm files), which contain predictors (regressors) for general linear model (GLM) analyses with BrainVoyagerâ„¢. 

At this time, the tool offers an easy to use interface to create empty (a.k.a. "dummy coded") predictors for use in multi-subject GLM.

Furthermore, the tool can now also create predictors to model the effects of habituation during an fMRI scan session. Three types of models are supported to start with: linear decrease, sigmoidal and non-linear decrease. See the program manual which is included in the downloads for more details. 

Finally, the program can read in motion correction estimates (that are created in the fmr-preprocessing) remove linear trend, z-transform and filter the data with a high pass and/or low pass filter.

All procedures can be performed on single files, or on multiple files that are recognized by a name pattern.

Downloads
The tool is available as a package including documentation from here (Updated Version 1.5.2, February 25th 2011):

System requirements
Windows system:

  • Windows 2000 or later (2000/XP/Vista)

Linux system (test system was Ubuntu 8.10, 32bit)

  • x86-based Linux distributions with GTK+ 2.8 (or higher)
  • libc-2.3 (or higher)
  • libstdc++.so.6

Macintosh system

  • Intel or PowerPC Macintosh with Mac OS X 10.2 or later

Version history
1.5.2 Minor update

  • Added wildcard search using "*" to indicate any variable field in the multi-file dialogs
  • Added [?] buttons to the filter settings in the relevant dialogs, which opens a window that allows for easy definition of the correct filter setting, using either frequency, cycles, or filter width
  • Changed the allowable filter settings to maximum 20 points in time course
  • Added R squared value to matrix correlation and matrix GLM
  • Minor corrections such as replacing remaining "BVA-HT" with the correct "BVA-PT"
  • The multiple file habituation addition routine would process any file with a matching file name patteren, leading to unexpected, additional gibberish files. This has been fixed. Only files with the same number of predictors are now processed.
    - The correct update URL is implemented and will now be updated along with the update information.

1.5.1 Minor update

  • If SDM files contained numbers in scientific notation, this would lead to unexpected outcomes. This has been corrected now.
  • Corrected auto update function to suppress the message window if the software is up to date.
  • If a SDM/RTC file is double clicked (when associated with the program), a click on a button will open the doubleclicked file in the chosen function.
  • The number of predictors in the design matrix file reported one to few. Now the correct number is shown.
  • When analyzing a design matrix with identical or almost identical predictors, this would lead to multiple singularity warning messages popping up. This is now fixed

1.5 Major update

  • Included a function to make predictors that model habituation as a linear, sigmoid or nonlinear function
  • In previous versions exception errors would occur trying to overwrite a file that was open. This was corrected
  • Improved the SDM output format to match the original BVQX format more closely to avoid future problems
  • Added a correlation function with display to test each predictor separately against all other predictors
  • Added export function for the correlation analysis
  • Improved the open file dialog in the MacOS version
  • Added file drop support - suitable files can be dropped directly on the buttons of the main screen
  • The SDM dummy code routine was corrected: now confound predictors are omitted from dummy coding.
  • The programs automatically checks for updates once every week
  • A preference file is used to store a few settings such as paths to the last accessed location for saving/opening files. (This will be much more extensive in the future
  • Fixed multiple multiple minor issues

1.2.1

  • Corrected SDM dummy code routine: files that contained a constant were not dummy coded, due to an incorrect file check

1.2

  • Corrected a bug in the SDM output file routine. Now the colors of the predictors are correctly included in the dummy coded output files.
  • Added an experimental predictor analysis, that uses a GLM to determine the correlation between multiple predictors
  • Added a "check for updates function" and a menu "check for updates" in the help menu
  • 1.1 Major update. Support for SDM matrix files has been added. Additionally, files can now be searched through up to 10 folder levels (to be used with great care!)

1.0.1 Minor update.

  • Fixed bug in dealing with long file names when performing actions on multiple files. Corrected description of filter to read 'Points in time course (TR)' instead of 'Cycles in time course'. This is a more correct description since the program's filter window has a width of n times TR, where the user specifies n.

1.0b first release

Known Issues
The linux version may not react to the quit button correctly. This is a suspected problem caused by an error in writing the preferences file. While it is annoying, it is harmless. (6 May 2009)