File Formats

The following file formats are currently supported by SHIVA.

• Image volume files
  • Analyze(tm) (*.img, *.hdr): http://www.mayo.edu/bir/PDF/ANALYZE75.pdf
    Nifti header files are supported.
    SHIVA can also read GZIP compressed image files (*.img.gz).
    Big volume is supported for uncompressed image files with byte, short, and rgb formats only.
    Currently, SHIVA supports the following file types:
    • binary (1-bit, converted to byte format internally)
    • byte (8-bit)
    • short (16-bit, signed/unsigned)
    • rgb (24-bit)
    • float (32-bit, converted to short format internally)
  • Nifti (*.nii): http://nifti.nimh.nih.gov/nifti-1/
    SHIVA can only handle Nifti volumes with transformation matrix with scaling and shifting. Other transformations are treated as an identify matrix.
    SHIVA can also read GZIP compressed image files (*.nii.gz).
    
  • MINC (*.mnc): http://www.bic.mni.mcgill.ca/software/minc/prog_guide/
    SHIVA can also read GZIP compressed MINC files (*.mnc.gz). Currently, SHIVA supports the following file types:
    • byte (8-bit)
    • short (16-bit)
    • rgb (24-bit)
      
  • Biorad PIC (*.pic): http://rsb.info.nih.gov/ij/plugins/biorad.html
  • CIVM (*.headfile)
    Big volume is supported.
  • Bruker (reco, 2dseq): http://www.mrc-cbu.cam.ac.uk/Imaging/Common/brukerformat.shtml
  • TIFF with two variations
    • regular single layer.
    • ImageJ image stack (all frames are uncompressed).
• 3D files
  • Duff Surface (*.dfs)
  • Duff Curve (*.dfc)
  • LONI Triangle Model (*.tm)
  • LONI UCF (*.ucf)
  • Object File Format (*.off): http://shape.cs.princeton.edu/benchmark/documentation/off_format.html
    • Geomview Manual: http://www.geomview.org/docs/html/geomview_toc.html#TOC40
    • Binary Format (not supported by SHIVA): http://www.geomview.org/docs/html/geomview_33.html#SEC36
  • MNI OBJ files (*.obj): http://www.bic.mni.mcgill.ca/~david/FAQ/FAQ.html
    • Surface format: http://www.bic.mni.mcgill.ca/~david/FAQ/polygons_format.txt
    • Curve format: http://www.bic.mni.mcgill.ca/~david/FAQ/lines_format.txt
  • 3D atlas (*.atlas3d)
• Label/BrainGraph files
  • Label index file (*.lbl, *.txt)
  • XML BrainGraph file (*.bgx)
  • GML BrainGraph file (*.gml)
  • Integrated Label File (*.ilf)
• Misc files
  • Duff Keg (*.keg, *.atlas)