[ENH] Add MRIsCombine to FreeSurfer utils.

nipype/interfaces/freesurfer/__init__.py

@@ -21,7 +21,7 @@
  MRIFill, MRIsInflate, Sphere, FixTopology, EulerNumber,
  RemoveIntersection, MakeSurfaces, Curvature, CurvatureStats,
  Jacobian, MRIsCalc, VolumeMask, ParcellationStats, Contrast,
- RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand)
+ RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand, MRIsCombine)
 from .longitudinal import (RobustTemplate, FuseSegmentations)
 from .registration import (MPRtoMNI305, RegisterAVItoTalairach, EMRegister, Register,
  Paint)

nipype/interfaces/freesurfer/tests/test_auto_MRIsCombine.py

@@ -0,0 +1,46 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import MRIsCombine
+
+
+def test_MRIsCombine_inputs():
+ input_map = dict(args=dict(argstr='%s',
+ ),
+ environ=dict(nohash=True,
+ usedefault=True,
+ ),
+ ignore_exception=dict(nohash=True,
+ usedefault=True,
+ ),
+ in_file1=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,
+ position=-1,
+ ),
+ subjects_dir=dict(),
+ terminal_output=dict(nohash=True,
+ ),
+ )
+ inputs = MRIsCombine.input_spec()
+
+ for key, metadata in list(input_map.items()):
+ for metakey, value in list(metadata.items()):
+ assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_MRIsCombine_outputs():
+ output_map = dict(out_file=dict(),
+ )
+ outputs = MRIsCombine.output_spec()
+
+ for key, metadata in list(output_map.items()):
+ for metakey, value in list(metadata.items()):
+ assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/freesurfer/utils.py

@@ -954,6 +954,63 @@ def _gen_outfilename(self):
  return name + ext + "_converted." + self.inputs.out_datatype
 
 
+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')
+ out_file = File(argstr='%s', position=-1, genfile=True,
+ mandatory=True,
+ desc='Output filename. Combined surfaces from in_file1 and '
+ 'in_file2.')
+
+
+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.')
+
+
+class MRIsCombine(FSCommand):
+ """
+ Uses Freesurfer's mris_convert to combine two surface files into one.
+
+ For complete details, see the `mris_convert Documentation.
+ <https://surfer.nmr.mgh.harvard.edu/fswiki/mris_convert>`_
+
+ Example
+ -------
+
+ >>> 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.cmdline # doctest: +ALLOW_UNICODE
+ '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
+
+ return outputs
+
+
 class MRITessellateInputSpec(FSTraitedSpec):
  """
  Uses Freesurfer's mri_tessellate to create surfaces by tessellating a given input volume