ENH: added 'hsvs' option to 5ttgen + mrtransform fix #3630
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teanijarv
commented
Feb 20, 2024
•
teanijarv
commented
- added Hybrid Surface and Volume Segmentation ('hsvs') option to the 5TT image generation class
- removed the in_file existing requirement (exists=True -> exists=False) for 5ttgen because hsvs requires a directory not a file as input
- changed '-inverse' parameter location from 1 to 2 in mrtransform class (to make it possible to insert it in the command together with other parameters)
- Added 'hsvs' option for 5ttgen function
- Changed '-inverse' parameter location from 1 to 2 (otherwise cannot use together with -linear)
teanijarv
changed the title
nipype/interfaces/mrtrix3/utils.py
Outdated
| argstr="%s", | ||
| position=-3, | ||
| mandatory=True, | ||
| desc="tissue segmentation algorithm", | ||
| ) | ||
| in_file = File( | ||
| exists=True, argstr="%s", mandatory=True, position=-2, desc="input image" | ||
| exists=False, argstr="%s", mandatory=True, position=-2, desc="input image" |
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So it seems like you need either a file or a directory, not a missing file.
in_file = traits.Either(
File(exists=True),
Directory(exists=True),
argstr="%s", mandatory=True, position=-2, desc="input image / directory"
)
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Thanks! I added this solution now. :)
nipype/interfaces/mrtrix3/utils.py
Outdated
| @@ -822,7 +823,7 @@ class MRTransformInputSpec(MRTrix3BaseInputSpec): | |||
| ) | |||
| invert = traits.Bool( | |||
| argstr="-inverse", | |||
| position=1, | |||
| position=2, | |||
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This means -invert will appear after all of the things with position=1. Does it need to come last, before in_files/out_file?
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I removed the position change for now, but I just added this previously because if I wanted to use -inverse with some other parameter and they both had 'position=1' then only one would show up on the command. But it can also be fixed by just using inputs.args string.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #3630 +/- ##
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Coverage 63.15% 63.15%
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Files 308 308
Lines 40825 40825
Branches 5656 5656
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