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The information in this chapter about the file formats of BrainVoyager QX is intended for advanced users who want to combine custom-made software (written, for example, in Python or Matlab) with BrainVoyager QX. Using the information provided here, you are able to use the data produced at various processing stages in BrainVoyager for your own programs, i.e. you can read BrainVoyager QX data files and do additional processing. You can also do custom processing (e.g. motion correction, statistics) and then save your data back into BrainVoyager file formats, which allows to do further processing and visualization in BrainVoyager QX. Note that all binary files in BrainVoyager QX are stored in Little Endian byte order, even on systems with Big Endian ordering. Systems with different byte ordering are handled transparently to the user in BrainVoyager QX. Having the same byte order on all platforms allows to move binary data files without problems across computer systems.

Important Note. BrainVoyager QX provides a Plugin interface, which is the recommended way for integrating custom computational routines with BrainVoyager QX. The plugin interface provides direct access to data structures in memory as well as commands to load and save core file formats. The level of provided "services" allows developers to focus on those new routines they are really interested in. Matlab programmers can use the BVQXtools to easily read, process and write BrainVoyager data files.

The following file types are described in this chapter:

Core Project Files

  • FMR files - Functional projects
  • DMR files - Diffusion-weighted projects
  • AMR files - Anatomical or functional inplane data
  • VMR files - High-resolution 3D anatomical projects
  • SRF files - Surface (mesh) representations, typically of reconstructed head skin and (morphed) cortical hemispheres

Functional and Diffusion-Weighted Data Files

  • STC files - Functional data belonging to an FMR project file
  • DWI files - Diffusion-weighted data belonging to a DMR project file
  • VTC files - Functional data transformed in a 3D reference space, e.g.Talairach space
  • VDW files - Diffusion-weighted data transformed in a 3D reference space
  • MTC files - Mesh time course files

Analysis Result Files

  • GLM files - Result of statistical GLM analysis for FMR-STC, VMR-VTC and SRF-MTC projects
  • AVA files - Result of ANCOVA analysis for VMR-VTC and SRF-MTC projects

(Statistical) Map Files

  • MAP files - Slice-based files containing real values, e.g. from statistical tests
  • VMP files - 3D map files containing float values, e.g. from statistical tests (in "native" (e.g. VTC) resolution)
  • ICA files - Independent component analysis file: special VMP file with some extra information
  • AR-VMP files - 3D map files containing float values, e.g. from statistical tests (in anatomical (VMR) resolution)
  • SMP files - Surface-based statistical files containing real values, e.g. from statistical tests
  • PMP files - Spherical map (coordinates-based)

Region-Of-Interest Files

  • VOI files - Files containing a description of a set of volumes-of-interest (VOIs)
  • VOM files - Files containing native resolution volumes-of-interest and optionally associated map data
  • POI files - Files containing a description of a set of patches-of-interest (POIs)
  • RTC files - Files containing time course data of regions-of-interest

Spatial Transformation Files

  • POS files - Slice positioning information files
  • TRF files - Description of affine spatial transformations, typically rigid body transformations
  • TAL files - Talairach coordinates, including AC, PC and cerebral border points
  • LOG files - Log file created during interpolation or transformation
  • SSM files - Sphere to sphere vertex mapping

Experimental Design and Auxiliary Files

  • PRT files - Protocol files describing experimental conditions
  • SDM files - Contains the design matrix for time courses
  • MDM files - Design matrix for group studies
  • AVG files - Event related averaging (time course coordinates)
  • DAT files - Event related averaging actual data
  • MSK files - Mask file used to limit the amount of voxels in a statistical analysis
  • CTR files - Contrast files for predictor selection

Visualization Files

  • VWP files - Visualization settings in the surface module (viewpoint etc.)
  • FBR files - Fiber coordinates, e.g. from DTI data analysis

Misceallaneous Files

  • V16 files - High-resolution 3D anatomical files like VMR files but intensity values have 2 bytes
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