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

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

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JailanOweda
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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 Fix #3653 and #3654 in the CAT12 Interface Fix nipy#3653 and nipy#3654 in the CAT12 Interface Sep 25, 2024
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codecov bot commented Oct 4, 2024 •
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Codecov Report

Attention: 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 29 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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effigies
effigies reviewed Oct 6, 2024
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nipype/interfaces/cat12/preprocess.py
@@ -239,33 +240,71 @@ class CAT12SegmentInputSpec(SPMCommandInputSpec):
neuromorphometrics = traits.Bool(
True,
field="output.ROImenu.atlases.neuromorphometrics",
usedefault=True,
# usedefault=True,
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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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Successfully merging this pull request may close these issues.

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