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Fix nipy#3653 and nipy#3654 in the CAT12 Interface #3683

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JailanOweda wants to merge 4 commits into nipy:master
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@JailanOweda JailanOweda commented Sep 25, 2024

Summary

Fixes nipy#3653 and nipy#3654.

List of changes proposed in this PR (pull-request)

  • Added input trait for the option of no surface measures (noROI) in the CAT12 Segment function.
  • Added missing input traits (that were added to the Matlab GUI but not updated in Nipype's CAT12 Interface) for the templates used for surface measures (e.g. thalamus, thalamic_nuclei).
  • Added option to process compressed nifti files (.nii.gz) like the latest GUI version allows.
  • Corrected if statement for saving ROI and ROIs (surface measure) files.

@JailanOweda JailanOweda changed the title (削除) Fix #3653 and #3654 in the CAT12 Interface (削除ここまで) (追記) Fix nipy#3653 and nipy#3654 in the CAT12 Interface (追記ここまで) Sep 25, 2024
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codecov bot commented Oct 4, 2024
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Codecov Report

❌ Patch coverage is 26.31579% with 14 lines in your changes missing coverage. Please review.
✅ Project coverage is 70.54%. Comparing base (83e3903) to head (6afc8b5).
⚠️ Report is 166 commits behind head on master.

Files with missing lines Patch % Lines
nipype/interfaces/cat12/preprocess.py 26.31% 14 Missing ⚠️
Additional details and impacted files
@@ Coverage Diff @@
## master #3683 +/- ##
==========================================
- Coverage 70.89% 70.54% -0.36% 
==========================================
 Files 1277 1277 
 Lines 59212 59223 +11 
 Branches 9799 9804 +5 
==========================================
- Hits 41980 41779 -201 
- Misses 16066 16292 +226 
+ Partials 1166 1152 -14 

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@@ -239,33 +240,71 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
neuromorphometrics = traits.Bool(
True,
field="output.ROImenu.atlases.neuromorphometrics",
usedefault=True,
# usedefault=True,
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@effigies effigies Oct 6, 2024

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We can't change the interface like this. The reason to have defaults expliciltly added is so that when tools change their defaults, old workflows that depended on those defaults would continue using the old settings.

If the changes are this extensive, new interfaces will be needed.

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As noted before, any changes must be backwards compatible. If this cannot be done in the current interface, a new interface must be written.

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Successfully merging this pull request may close these issues.

nipype.interfaces.cat12.preprocess.CAT12Segment does not accept compressed .nii.gz files

AltStyle によって変換されたページ (->オリジナル) /