[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 +1,42 @@
+# 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_files=dict(argstr='--combinesurfs %s',
+    mandatory=True,
+    position=1,
+    ),
+    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 +954,64 @@ 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_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_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_files.')
+
+
+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_files = ['lh.pial', 'rh.pial']
+    >>> mris.inputs.out_file = 'bh.pial'
+    >>> mris.cmdline  # doctest: +ALLOW_UNICODE
+    '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
+        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