ENH: Add mris_expand interface

Author: effigies

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)
+                    RelabelHypointensities, Aparc2Aseg, Apas2Aseg, MRIsExpand)
 from .longitudinal import (RobustTemplate, FuseSegmentations)
 from .registration import (MPRtoMNI305, RegisterAVItoTalairach, EMRegister, Register,
                            Paint)

nipype/interfaces/freesurfer/tests/test_auto_MRIsExpand.py

@@ -0,0 +1,47 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import MRIsExpand
+
+
+def test_MRIsExpand_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    distance=dict(argstr='%g',
+    mandatory=True,
+    position=-2,
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='%s',
+    mandatory=True,
+    position=-3,
+    ),
+    out_file=dict(name_source='in_file',
+    name_template='%s_expanded',
+    position=-1,
+    ),
+    subjects_dir=dict(),
+    terminal_output=dict(nohash=True,
+    ),
+    thickness=dict(argstr='-thickness',
+    ),
+    )
+    inputs = MRIsExpand.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_MRIsExpand_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = MRIsExpand.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

@@ -2906,3 +2906,41 @@ def _list_outputs(self):
         outputs = self._outputs().get()
         outputs["out_file"] = os.path.abspath(self.inputs.out_file)
         return outputs
+
+
+class MRIsExpandInputSpec(FSTraitedSpec):
+    in_file = File(
+        exists=True, mandatory=True, argstr='%s', position=-3,
+        desc='Surface to expand')
+    distance = traits.Float(
+        mandatory=True, argstr='%g', position=-2,
+        desc='Distance in mm or fraction of cortical thickness')
+    out_file = File(
+        name_template='%s_expanded', name_source='in_file', position=-1,
+        desc='Output surface file')
+    thickness = traits.Bool(
+        argstr='-thickness',
+        desc='Expand by fraction of cortical thickness, not mm')
+
+
+class MRIsExpandOutputSpec(TraitedSpec):
+    out_file = File(desc='Output surface file')
+
+
+class MRIsExpand(FSCommand):
+    """
+    Expands a surface (typically ?h.white) outwards while maintaining
+    smoothness and self-intersection constraints.
+
+    Examples
+    ========
+    >>> from nipype.interfaces.freesurfer import MRIsExpand
+    >>> mris_expand = MRIsExpand(thickness=True, distance=0.5)
+    >>> mris_expand.inputs.in_file = 'lh.white'
+    >>> mris_expand.inputs.out_file = 'lh.graymid'
+    >>> mris_expand.cmdline # doctest: +ALLOW_UNICODE
+    'mris_expand -thickness lh.white 0.5 lh.graymid'
+    """
+    _cmd = 'mris_expand'
+    input_spec = MRIsExpandInputSpec
+    output_spec = MRIsExpandOutputSpec