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raamana opened this issue Feb 15, 2018 · 4 comments
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List of all image/surface/data formats readable by Nibabel #596

raamana opened this issue Feb 15, 2018 · 4 comments

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@raamana
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raamana commented Feb 15, 2018

Did someone compile a list of all formats that can be read by Nibabel? Also writable list would be helpful too, as part of docs.

We can get a sense of this via API docs, but we could make it easier for a novice eye:
http://nipy.org/nibabel/api.html

From what I can tell, this seems to be the list:

  • Nifti
  • MGH/Freesurfer
  • MINC
  • Analyze
  • DICOM
  • PAR/REC
  • ECAT
  • TrackVis
  • Streamlines
  • gifti

So a small table with different columns noting whether nibabel can read or write it, and what versions etc might be helpful, it one doesn't exist already. Listing what is not supported, and what is coming up soon (like BRIK/HEAD) would be useful too.

@raamana
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raamana commented Feb 15, 2018

Never mind, its right on the home page:
"This package provides read +/- write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write FreeSurfer geometry, annotation and morphometry files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI."

I think it might be helpful to add it to manual/docs for sake of completeness.

@raamana raamana closed this as completed Feb 15, 2018
@satra
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satra commented Feb 15, 2018

it should also say CIFTI2 if it doesn't state it.

@raamana
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raamana commented Feb 15, 2018

No, it doesn't seem to be mentioned, but I didn't look thoroughly enough.

@effigies
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I believe it's missing. It should probably also be promoted in the file formats list.

effigies pushed a commit to effigies/nibabel that referenced this issue Feb 19, 2018
MRG: fix nipy#596 First point of `LazyTractogram` is not saved

With this PR, we now assume tractogram objects can be iterated over only once at saving time.

This PR fixes issue nipy#586.
Thanks to @nilgoyette for providing the missing unit test and part of the solution
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