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[ENH] Add MRIsCombine to FreeSurfer utils. #1948

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Merged
merged 15 commits into from
Apr 19, 2017
Merged

[ENH] Add MRIsCombine to FreeSurfer utils. #1948

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39348e8
Merge remote-tracking branch 'nipy/master'
tsalo Apr 9, 2017
50f47c2
Add MRIsCombine.
tsalo Apr 9, 2017
7f38790
Add to init.
tsalo Apr 9, 2017
e2b23d2
Add _list_outputs to MRIsCombine.
tsalo Apr 9, 2017
8fe4cf5
Fix mistake with _list_outputs.
tsalo Apr 9, 2017
2914140
Adjust naming in _list_outputs.
tsalo Apr 9, 2017
01cea35
Another adjustment.
tsalo Apr 9, 2017
36fd9c1
Fix MRIsCombine doctest and add necessary test file.
tsalo Apr 9, 2017
e9a5bb8
Merge remote-tracking branch 'nipy/master' into mriscombine
tsalo Apr 10, 2017
a7bafda
Change inputs to MRICombine and add explanation for out_file renaming.
tsalo Apr 10, 2017
6c0071c
Merge remote-tracking branch 'nipy/master' into mriscombine
tsalo Apr 12, 2017
9ca230f
Merge remote-tracking branch 'nipy/master' into mriscombine
tsalo Apr 17, 2017
5f4d402
Add FSSurfaceCommand and change MRIsCombine setup.
tsalo Apr 17, 2017
0a72b4e
Make requested changes.
tsalo Apr 18, 2017
7c3125d
Remove unnecessary use of in_file in freesurfer/utils/MRIsCombine.
tsalo Apr 18, 2017
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Fix MRIsCombine doctest and add necessary test file.
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@tsalo
tsalo committed Apr 9, 2017
commit 36fd9c18ed19ad10380be46cff38b7c4325989f2
10 changes: 5 additions & 5 deletions nipype/interfaces/freesurfer/utils.py
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Expand Up @@ -989,25 +989,25 @@ class MRIsCombine(FSCommand):
-------

>>> import nipype.interfaces.freesurfer as fs
>>> mris = fs.MRIsConvert()
>>> mris = fs.MRIsCombine()
>>> mris.inputs.in_file1 = 'lh.pial'
>>> mris.inputs.in_file2 = 'rh.pial'
>>> mris.inputs.out_file = 'bh.pial'
>>> mris.inputs.out_file = 'out.stl'
>>> mris.cmdline # doctest: +ALLOW_UNICODE
'mris_convert --combine_surfs lh.pial rh.pial bh.pial'
'mris_convert --combinesurfs lh.pial rh.pial out.stl'
>>> mris.run() # doctest: +SKIP
"""
_cmd = 'mris_convert'
input_spec = MRIsCombineInputSpec
output_spec = MRIsCombineOutputSpec

def _list_outputs(self):
outputs = self.output_spec().get()
if any(self.inputs.out_file.startswith(pre) for pre in ['lh.', 'rh.']):
outputs['out_file'] = self.inputs.out_file
else:
outputs['out_file'] = 'lh.' + self.inputs.out_file
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@effigies effigies Apr 10, 2017

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For your doctest example, you're going to get lh.out.stl. Is that what mris_convert produces? And if so, is that the same whether you pass lh.pial or rh.pial as in_file1?
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@tsalo tsalo Apr 10, 2017

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From what I've seen:

  • mris_convert --combinesurfs lh.pial rh.pial out.stl creates lh.out.stl
  • mris_convert --combinesurfs rh.pial lh.pial out.stl creates lh.out.stl
  • mris_convert --combinesurfs rh.pial rh.smoothwm out.stl creates lh.out.stl
  • mris_convert --combinesurfs lh.pial rh.pial rh.out.stl creates rh.out.stl

So it doesn't seem to matter what order you pass in the files or even if both files are from the right hemisphere. As long as the output file doesn't start with lh. or rh., it will prepend lh. to the output filename.
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@effigies effigies Apr 10, 2017

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Haha. That's awful. Can you add a short comment explaining that this is a FreeSurfer behavior you're accommodating?
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@tsalo tsalo Apr 10, 2017

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Added an explanation to the docstring for _list_outputs in a7bafda. Should be clear now.

return outputs


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Empty file added nipype/testing/data/rh.pial
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