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Merged
merged 4 commits into from
May 16, 2025
Merged

Support ushort for the mgh/mgz reader #1415

merged 4 commits into from
May 16, 2025

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bthyreau
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Hi,

nibabel currently crashes when loading an mgh/mgz file of type unsigned short.
As an consequence, recent FreeSurfer 7.4/8 clinical pipelines (that uses nibabel) now crashes on uint16 input MRIs (of any format, e.g nifti1) with an unfriendly python traceback, because it can't read back the mgz it just converted its input to.

I noted a bit of conflicting opinion on whether ushort should be supported for the MGH/MGZ file format.

  • Nibabel's freesurfer explicitly (e.g test_mghformat.py:bad_dtype_mgh) forbids it for new object creation. And ANTs ITK-based tools refuse both to read and to write ushort mgz.
  • But on the other hand, Freesurfer's own "mri_info" fully handle it, as so do other tools. In particular "mri_convert" obviously too (though not for explicit cast, ie. the -odt option!) considering FreeSurfer itself may create such ushort mgz out of well-supported regular ushort nifti files - without user's easily actionable workaround.

Therefore, officially supported or not, i suggest there is little drawback in nibabel not crashing when loading such ushort mgz.
The attached one-liner do that.

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codecov bot commented May 14, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.34%. Comparing base (db4c859) to head (643f7a1).
Report is 5 commits behind head on master.

Additional details and impacted files 
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##           master    #1415   +/-   ##
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  Coverage   95.34%   95.34%           
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  Files         209      209           
  Lines       29777    29777           
  Branches     3357     3357           
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  Hits        28390    28390           
  Misses        948      948           
  Partials      439      439

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@effigies
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Thanks! I agree, if FreeSurfer creates it, we should be able to read it.

Do you have a link to FreeSurfer source that we can cross-reference? If we add it in a comment, it will make it easier to look up in the future, if they add more dtypes (however unlikely that may be).

@effigies
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Looks like:

I guess I would follow the load_mgh.m fields, since others don't seem to be used.

@bthyreau
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Thanks for the quick reply and fixing my botched commit. Indeed, it seems that FreeSurfer introduced the USHORT into mgz only in 2021, in freesurfer/freesurfer@b82c3a8, which may explain why it is not consistently mentionned everywhere.
I agree with you that supporting only the 5 types is probably the best for now, as the other types defined in mri.h are rarely used, if at all.

effigies
effigies reviewed May 15, 2025
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Adding a comment so we can find these links again easily. Can you remove the now-failing test, or select another unsupported datatype (like float16)?

@bthyreau
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Thanks a lot. I updated the comment in the code.
To update the failure-case test, i picked float64 (double) that is popular with FSL Nifti, yet poorly supported by FreeSurfer in general and fully unsupported by its mgz format

@effigies effigies merged commit e0ae56a into nipy:master May 16, 2025
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@bthyreau @effigies