Change inputs to MRICombine and add explanation for out_file renaming.

Author: tsalo

nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py

@@ -12,14 +12,10 @@ def test_MRIsCombine_inputs():
  ignore_exception=dict(nohash=True,
  usedefault=True,
  ),
- in_file1=dict(argstr='--combinesurfs %s',
+ in_files=dict(argstr='--combinesurfs %s',
  mandatory=True,
  position=1,
  ),
- in_file2=dict(argstr='%s',
- mandatory=True,
- position=2,
- ),
  out_file=dict(argstr='%s',
  genfile=True,
  mandatory=True,

nipype/interfaces/freesurfer/utils.py

@@ -958,24 +958,20 @@ class MRIsCombineInputSpec(FSTraitedSpec):
  """
  Uses Freesurfer's mris_convert to combine two surface files into one.
  """
- in_file1 = File(exists=True, mandatory=True, position=1,
- argstr='--combinesurfs %s',
- desc='File to be combined with in_file2')
- in_file2 = File(exists=True, mandatory=True, position=2,
- argstr='%s',
- desc='File to be combined with in_file1')
+ in_files = traits.List(File(Exists=True), maxlen=2, minlen=2,
+ mandatory=True, position=1, argstr='--combinesurfs %s',
+ desc='Two surfaces to be combined.')
  out_file = File(argstr='%s', position=-1, genfile=True,
  mandatory=True,
- desc='Output filename. Combined surfaces from in_file1 and '
- 'in_file2.')
+ desc='Output filename. Combined surfaces from in_files.')
 
 
 class MRIsCombineOutputSpec(TraitedSpec):
  """
  Uses Freesurfer's mris_convert to combine two surface files into one.
  """
  out_file = File(exists=True, desc='Output filename. Combined surfaces from '
- 'in_file1 and in_file2.')
+ 'in_files.')
 
 
 class MRIsCombine(FSCommand):
@@ -990,18 +986,23 @@ class MRIsCombine(FSCommand):
 
  >>> import nipype.interfaces.freesurfer as fs
  >>> mris = fs.MRIsCombine()
- >>> mris.inputs.in_file1 = 'lh.pial'
- >>> mris.inputs.in_file2 = 'rh.pial'
- >>> mris.inputs.out_file = 'out.stl'
+ >>> mris.inputs.in_files = ['lh.pial', 'rh.pial']
+ >>> mris.inputs.out_file = 'bh.pial'
  >>> mris.cmdline # doctest: +ALLOW_UNICODE
- 'mris_convert --combinesurfs lh.pial rh.pial out.stl'
+ 'mris_convert --combinesurfs lh.pial rh.pial bh.pial'
  >>> mris.run() # doctest: +SKIP
  """
  _cmd = 'mris_convert'
  input_spec = MRIsCombineInputSpec
  output_spec = MRIsCombineOutputSpec
 
  def _list_outputs(self):
+ """
+ If the output file is not specified starting with 'lh.' or 'rh.',
+ FreeSurfer prepends 'lh.' to the filename. It never adds 'rh.', even if
+ both input files are from the right hemisphere. Output out_file must be
+ adjusted to accommodate this.
+ """
  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