Bv2D_3DDataPreprocessing

The Bv2D_3DDataPreprocessing gui generates a perl script to perform a series of commands in BrainVoyager. The 2D Preprocessing portion of the gui generates commands for Slice Scan Time Correction, Spatial Smoothing and Temporal Smoothing. The 3D Preprocessing portion of the gui has not yet been implemented.
For more information, see the BrainVoyager documentation on scripting.
BrainVoyager homepage

Invocation

java Bv2D_3DDataPreprocessing

This starts the Java interpreter and runs the Bv2D_3DDataPreprocessing application. The following file needs to be installed in the PERL_PATH (a FisProperty) directory for this application to work: on Windows: perl.exe

Bv2D_3DDataPreprocessing window

2D Data Preprocessing
2D Preprocessing is done on FMR files.
- Input
  The name of the input FMR file(s) or directory.
- Output
  The output FMR and STC files will be put in the directory containing the input files. As in BrainVoyager, the output filenames will be constructed as the input file name (without the suffix) followed by sections separated by a "_". These sections indicate which preprocessing steps were used.
  - FMR file prefix
    Optional prefix name to use in output FMR files.
  - STC file prefix
    Optional prefix name to use in output FMR files.
- Options
  - Spatial data smoothing
    Spatial smoothing is done with a 3D gaussian kernel. The width of the kernel (FWHM) is specified in millimeters. Smoothing is done in the frequency domain, which is faster for large (>15mm) kernels than for small kernels. However, for single subject analysis in BrainVoyager, use of large kernels is not recommended. For single subjects, a kernel of 4mm is recommended.
    - Low pass filter -
  - Temporal data smoothing
    - High pass filter
    - Low pass filter
  - Slice scan time correction
    - Inter slice time
    - Slice sampling type
  - TR
    The time interval between successive measurements of the same slice
  - Number of Volumes
    The number of time points
3D Data Preprocessing
Not yet implemented.
Scripting
- Script output directory/file - the name of the output Perl script file.
- Append to script file - when selected, if a script file of the same name exists, the newly generated script will be appended to it.
- Run script - if this option is not selected, the script file will be generated but not run.