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ENH: Update PETsurfer interface #3602

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merged 9 commits into from
Mar 20, 2024
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mnoergaard
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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

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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@mnoergaard
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Thank you, @effigies!

@bendhouseart
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Oh wow! Thanks @effigies

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3 participants