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BIAP3
Ongoing
DICOM files in particular have a lot of information in them that we might want to carry with the image. There are other image file types like Minc or Nrrd that have information we'd like to support but can't with standard nifti.
One obvious place to store this information is in a nifti header extension.
From adding nifti extensions:
- 0 = NIFTI_ECODE_IGNORE = unknown private format (not recommended!)
- 2 = NIFTI_ECODE_DICOM = DICOM format (i.e., attribute tags and values): http://medical.nema.org/
- 4 = NIFTI_ECODE_AFNI = AFNI header attributes: The format of the AFNI extension in the NIfTI-1.1 format is described at http://nifti.nimh.nih.gov/nifti-1/AFNIextension1/
- 6 = NIFTI_ECODE_COMMENT = comment: arbitrary non-NUL ASCII text, with no additional structure implied
- 8 = NIFTI_ECODE_XCEDE = XCEDE metadata: http://www.nbirn.net/Resources/Users/Applications/xcede/index.htm
- 10 = NIFTI_ECODE_JIMDIMINFO = Dimensional information for the JIM software (XML format); contact info is Dr Mark A Horsfield: mah5*AT*leicester.ac.uk.
- 12 = NIFTI_ECODE_WORKFLOW_FWDS = Fiswidget XML pipeline descriptions; documented at http://kraepelin.wpic.pitt.edu/~fissell/NIFTI_ECODE_WORKFLOW_FWDS/NIFTI_ECODE_WORKFLOW_FWDS.html ; contact info is Kate Fissell: fissell+*AT*pitt.edu.
Summary: we need probably need our own extension format
There is a DICOM type extension - code 2. This might be OK for DICOM but:
- We probably don't want to have to dump the entire DICOM header for every DICOM image. If we don't that means we have to edit the DICOM header, and
- The DICOM format is awful to work with, so it is not a pleasant prospect making a new DICOM header for images (like Minc) that aren't DICOM to start with.
- I (MB) can't find any evidence that it's being used in the wild.
- It's not completely clear what format the data should be in. See this nifti thread.
The AFNI extension format looks as if it is specific to AFNI.
The XCEDE format looks rather heavy. I'm (MB) trying to work out where the most current schema is. Candidates are bxh-xcede-tools and the xcede website. We'd need to validate the XML with the schema. It appears the python standard library doesn't support that so we'd need extra XML tools as a dependency.
JIM is closed source.
fiswidgets seems to have been quiet recently. The link for code 12 is dead, I had to go back to the http://www.archive.org to get an old copy and that didn't have the DTD or example links that we need to understand the format.
Gordon Kindlmann's NRRD format has gone through a few versions and has considerable use particularly by the 3D slicer team. I've tried to summarize the NRRD innovations not properly covered by nifti in nifti-nrrd.