File formats

Alois Schlögl maintains a list of signal data formats mostly for EEG and other biomedical signals:

Neuroimaging volume data file formats

Table 27: Neuroimaging volume file formats. ECAT and Interfile information kindly provided by Frédéric Schoenahl. Not all information might be accurate.
Name Ext. Description Conversion software Reference
AFNI BRIK, HEAD Format with two files: binary BRIK data file and ACII HEAD header file. (Presumably) only used in AFNI. AFNI
ANALYZE img, hdr Format with two files: Binary img data file and binary hdr header file. There are different versions of ANALYZE files, see Mayo Clinic's information. Mayo Clinic's ANALYZE, NIH's ImageJ, Andrew Jankes' software,
ANALYZE (SPM) img, hdr, (mat) Variation of an ANALYZE file format (version 7) with offset and scale fields added. Widespread file format and used in SPM. SPM also uses an extra Matlab file to describe a 3D transformation. Andrew Jankes' software, Matthew Brett's ana4dto3d
Bruker .5X1 (?)   pvconv
COR (none and ``.info'') MGH-NMR COR format used in FreeSurfer. One file for each coronal slice. Prefix as converted by FreeSurfer is ``COR''. mri_convert program in FreeSurfer. ?
Curry (CDR) iso(???) Current density result from the Curry Program CdrSPM 1.0 from Seoul National University converts to SPM ANALYZE.
Descriptor des, dat File format used by RIC, San Antonio HIPG's AliceTM
DICOM   Extensive image data format. Different variants: DICOM3, DICOM2 (ACR-NEMA) NIH's ImageJ, The commercial dicomread.m and dicominfo.m from Matlab Image Processing toolbox (works both on Siemens and GE DICOM), MedX. SPM2, IDICON, DicomWorks. See also next row., Newsgroup: comp.protocols.dicom, David Clunie's Medical Image Format Site
DICOM SuperMosaic (?) IMA (?) Format used in Siemens Syngo (It is not clear -- for the author -- which subset of DICOM is used by Siemens and GE and is supported, more information is needed) volumestack from xmedcon (see, e.g.,, kulCONV, MRIcro, Pieter Vandemaele's dcmsmosaic.c, MySplitMosaic.m Newsgroup: comp.protocols.dicom.
ECAT .s .S .v .V .a .A .N Format by CTI/Siemens primarily for PET and SPECT able to store 2D/3D sinograms and volumes as well as bull-eyes. Filename extensions are lowercase for data, uppercase for database entry containing sinogram, volume, attenuation data, normalization data, respectively. `One file (datablock) per dataset, which contains a binary header with common fields in nuclear medicine (dose.. patient name..) + an image-type specific subheader, and the image data coded in function of the image-type'. cti2analyze (; (x)medcon (, version 6.4 of ECAT);
GE   General Electric scanner format Souheil Inati's GE2SPM ( Krish Singh's ge2spm ( in BrainTools
Interfile HDR, IMG (CRV, ROI, H01, I01, C01, R01) Format for nuclear medicine (SPECT) with a binary image file and an ASCII header (not the same header as ANALYZE though they have the same file extension) (x)medcon (; IDICON Interfile/DICOM Conversion Program, [Todd-Pokropek et al., 1992], Extension for PET
MINC mnc File format from MNI in Montreal. Related to NetCDF. Used in MNI's and Keith Worsley's software. 3D and 4D versions. EMMA, Andrew Jankes' ana2mnc|mnc2ana rotor/software/, Satrajit Ghosh's `MINC to Analyze',
NetCDF   General array data format
NIfTI-1 nii, hdr, img A standard by ``Neuroimaging Informatics Technology Initiative''. Extension of ANALYZE. Planned support in AFNI, FSL and SPM. [Cox et al., 2004],
PFF   ``The Pittsburgh File Format''. A file format used in Pittsburgh fMRI community
SDT sdt, spr Format used in Stimulate
Siemens IMA Internal format used by Siemens. Not DICOM format although it has the same file extension, see (SPM mailing 2002-04-18) (???) (x)medcon, visionToSPM

Simple File Format sfd, sfh Used at Hvidovre Hospital, Denmark sf_utils.tar.gz from Hvidovre Hospital.
VAPET (none) File format used in VA Medical center, PET imaging service, Minneapolis. Exists in a 3D and 4D version. Header information is in the beginning of the file in ASCII representation MRIWarp from the Technical University of Denmark
UNC s??? Multi-dimensional data format from University Of North Carolina. Used by BAMM, unc2mnc,
VISTA .v ? ? ?
XPrime   ? (File format known from Hvidovre Hospital) MRIWarp from the Technical University of Denmark

Table 13.1 displays some of the file formats for functional neuroimaging (volumes). See also Andrew Janke's list at as well as the list in connection with (x)medcon ( Chris Rorden has also a list of conversion software:

The ``Medical Image Format FAQ'' is available, e.g., at

SPM uses a specific prefixing scheme for processed files: A character is added in front of the filename: masked files (m), realign/reslice (r), spatial smoothing (s), spatial normalization (n), slice timing (a) and warped (w). MRIcro uses (l) for exported region of interests volume files.

NIfTI-1 is a new standard that is planned to be supported by Brain Voyager, AFNI, FSL and SPM [Cox et al., 2004]. It is based on ANALYZE.

Other file formats

The Protein Data Bank format is for atomic coordinate files with the extension .mod, see These can be read by molecular visualization programs, such as RasMol

Finn Årup Nielsen 2010-04-23