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ENH: added 'hsvs' option to 5ttgen + mrtransform fix #3630

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Merged
merged 5 commits into from
Mar 17, 2024
Merged

ENH: added 'hsvs' option to 5ttgen + mrtransform fix #3630

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3afcd62
Update utils.py
teanijarv Feb 20, 2024
367776d
Update .zenodo.json
teanijarv Feb 20, 2024
c08e17b
Update utils.py
teanijarv Feb 20, 2024
eda6497
Fix generate5tt input
teanijarv Feb 28, 2024
7fc44fd
Remove the -inverse parameter position change
teanijarv Feb 28, 2024
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5 changes: 5 additions & 0 deletions .zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -911,6 +911,11 @@
"name": "Wu, Jianxiao",
"orcid": "0000-0002-4866-272X",
},
{
"affiliation": "Lund University",
"name": "Anijärv, Toomas Erik",
"orcid": "0000-0002-3650-4230",
},
],
"keywords": [
"neuroimaging",
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5 changes: 3 additions & 2 deletions nipype/interfaces/mrtrix3/utils.py
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Expand Up @@ -224,13 +224,14 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
"fsl",
"gif",
"freesurfer",
"hsvs",
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. :)

)
out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image")

Expand Down Expand Up @@ -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.

desc="Invert the specified transform before using it",
)
linear_transform = File(
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