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Alois Schlögl maintains a list of signal data formats mostly for EEG and other biomedical signals: http://www-dpmi.tu-graz.ac.at/~schloegl/matlab/eeg/.
| 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 | http://afni.nimh.nih.gov/afni/afni_faq.shtml#BRIKformat http://afni.nimh.nih.gov/afni/docREADME/README.attributes |
| 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 http://www.mrc-cbu.cam.ac.uk/Imaging/ana4dto3d.html | http://www.fil.ion.ucl.ac.uk/spm/distrib.html#AzeFmt |
| Bruker | .5X1 (?) | pvconv http://pvconv.sourceforge.net/ | http://www.mrc-cbu.cam.ac.uk/Imaging/Common/brukerformat.shtml | |
| 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 | http://ric.uthscsa.edu/projects/chsn/des.html |
| 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. | http://medical.nema.org/dicom.html, 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., http://xmedcon.sourceforge.net/faq/stack.html, 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 (ftp://dormeur.topo.ucl.ac.be/pub/ecat/); (x)medcon (http://xmedcon.sourceforge.net/, version 6.4 of ECAT); | |
| GE | General Electric scanner format | Souheil Inati's GE2SPM (http://dbic.dartmouth.edu/~inati/tools/ge2spm.php). Krish Singh's ge2spm (http://www.aston.ac.uk/lhs/staff/singhkd/mri3dX/mri3dX_download.html) 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 (http://xmedcon.sourceforge.net/); IDICON Interfile/DICOM Conversion Program http://www.inf.u-szeged.hu/~idicon/shortdoc.html | http://www.keston.com/Interfile/, [Todd-Pokropek et al., 1992], Extension for PET http://www.irsl.org/~kris/petinterfile.html |
| 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 http://www.cmr.uq.edu.au/ rotor/software/, Satrajit Ghosh's `MINC to Analyze' http://www.cns.bu.edu/~satra/software.php | http://www.bic.mni.mcgill.ca/software/minc/minc.html, http://poldracklab.psych.ucla.edu/spm/minc_spm.html |
| NetCDF | General array data format | http://www.unidata.ucar.edu/packages/netcdf/index.html | ||
| NIfTI-1 | nii, hdr, img | A standard by ``Neuroimaging Informatics Technology Initiative''. Extension of ANALYZE. Planned support in AFNI, FSL and SPM. | http://nifti.nimh.nih.gov/dfwg/src/ | [Cox et al., 2004], http://nifti.nimh.nih.gov/dfwg/ |
| PFF | ``The Pittsburgh File Format''. A file format used in Pittsburgh fMRI community | http://lib.stat.cmu.edu/~fiasco/overview/pff_intro.html | ||
| SDT | sdt, spr | Format used in Stimulate | http://www.cmrr.umn.edu/stimulate/stimUsersGuide/node57.html | |
| 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
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| Simple File Format | sfd, sfh | Used at Hvidovre Hospital, Denmark | sf_utils.tar.gz from Hvidovre Hospital. | http://www.drcmr.dk/software/index.html |
| 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 | http://www-bmu.psychiatry.cam.ac.uk/BAMM/FBAMM/FILEFORMAT/unc.html, unc2mnc, http://www.cmr.uq.edu.au/~rotor/software/ | |
| VISTA | .v | ? | ? | ? http://www.cs.ubc.ca/nest/lci/vista/vista.html |
| 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 http://www.cmr.uq.edu.au/~rotor/minc/ as well as the list in connection with (x)medcon (http://xmedcon.sourceforge.net/docs/content.html). Chris Rorden has also a list of conversion software: http://www.psychology.nottingham.ac.uk/staff/cr1/mricro.html#otherconv.
The ``Medical Image Format FAQ'' is available, e.g., at http://www.cs.uu.nl/wais/html/na-dir/medical-image-faq/.html.
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.
The Protein Data Bank format is for atomic coordinate files with the extension .mod, see http://www.umass.edu/microbio/rasmol/pdb.htm. These can be read by molecular visualization programs, such as RasMol
Finn Årup Nielsen 2010-04-23