Biomedical imaging file formats

  • Digital Imaging and Communications in Medicine (DICOM) (.dcm)
  • Neuroimaging Informatics Technology Initiative (NIfTI)
    • .nii – single-file (combined data and meta-data) style
      • .nii.gz – gzip-compressed, used transparently by some software, notably the FMRIB Software Library (FSL)
      • .gii – single-file (combined data and meta-data) style; NIfTI offspring for brain surface data
    • .img,.hdr – dual-file (separate data and meta-data, respectively) style
  • AFNI data, meta-data (.BRIK,.HEAD)
  • Massachusetts General Hospital imaging format, used by the FreeSurfer brain analysis package
    • .MGH – uncompressed
    • .MGZ – zip-compressed
  • Analyze data, meta-data (.img,.hdr)
  • Signed Differential Mapping (SDM) brain maps and/or distributions (.sdm)
  • Medical Imaging NetCDF (MINC) format, previously based on NetCDF; since version 2.0, based on HDF5 (.mnc)

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