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ENH: Update PETsurfer interface #3602

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effigies merged 9 commits into nipy:master from mnoergaard:update_petsurfer
Mar 20, 2024
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@mnoergaard mnoergaard commented Sep 8, 2023

Summary

This PR updates the PETsurfer interface in nipype to be in line with the FreeSurfer implementation and closes issue #3601.

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

  1. Update description of GTMPVC interface (before it was a duplicate of the GTMSEG interface)
  2. Add extra outputs to the GTMPVC interface
  3. Update kinetic modeling naming schemes to be in line with actual implementation. MRTM has been updated to MRTM1 as this definition is more correct (also the flag used in FreeSurfer). Furthermore, LoganRef has been renamed to Logan, as it is the Logan modeling (https://www.pmod.com/files/download/v31/doc/pkin/2329.htm) and NOT the Logan reference modeling (https://doc.pmod.com/pkin/pmclass_lib_pmkin_models_pklogannoninvasivev2.html) that is currently implemented in FreeSurfer.
  4. Two extra PET-specific arguments (bp-clip-neg and bp-clip-max) have been added to the mri_glmfit interface. These have been a part of FreeSurfer since v. 7.2.0

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codecov bot commented Sep 8, 2023 •
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Codecov Report

Attention: Patch coverage is 72.22222% with 5 lines in your changes are missing coverage. Please review.

Project coverage is 63.14%. Comparing base (d2f4953) to head (6b7bda4).

Files Patch % Lines
nipype/interfaces/freesurfer/petsurfer.py 68.75% 5 Missing ⚠️
Additional details and impacted files 
@@ Coverage Diff @@
## master #3602 +/- ##
==========================================
- Coverage 63.14% 63.14% -0.01% 
==========================================
 Files 308 308 
 Lines 40824 40836 +12 
 Branches 5655 5655 
==========================================
+ Hits 25780 25787 +7 
- Misses 14031 14036 +5 
 Partials 1013 1013

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@effigies effigies merged commit 1b5793a into nipy:master Mar 20, 2024
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Thank you, @effigies!

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Oh wow! Thanks @effigies

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@effigies effigies effigies approved these changes

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