Merge pull request #1972 from effigies/enh/graymid

ENH: Find graymid/midthickness surfs

Author: chrisgorgo

nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py

@@ -151,6 +151,9 @@ def test_ReconAll_outputs():
     ),
     filled=dict(loc='mri',
     ),
+    graymid=dict(altkey=['graymid', 'midthickness'],
+    loc='surf',
+    ),
     inflated=dict(loc='surf',
     ),
     jacobian_white=dict(loc='surf',

nipype/interfaces/io.py

@@ -1546,6 +1546,9 @@ class FSSourceOutputSpec(TraitedSpec):
         File(exists=True),
         desc='Distortion required to register to spherical atlas',
         loc='surf')
+    graymid = OutputMultiPath(
+        File(exists=True), desc='Graymid/midthickness surface meshes',
+        loc='surf', altkey=['graymid', 'midthickness'])
     label = OutputMultiPath(
         File(exists=True), desc='Volume and surface label files',
         loc='label', altkey='*label')
@@ -1617,12 +1620,12 @@ def _get_files(self, path, key, dirval, altkey=None):
                 globprefix = '*'
         elif key in ('aseg_stats', 'wmparc_stats'):
             globprefix = ''
-        keydir = os.path.join(path, dirval)
-        if altkey:
-            key = altkey
-        globpattern = os.path.join(
-            keydir, ''.join((globprefix, key, globsuffix)))
-        return [os.path.abspath(f) for f in glob.glob(globpattern)]
+        keys = filename_to_list(altkey) if altkey else [key]
+        globfmt = os.path.join(path, dirval,
+                               ''.join((globprefix, '{}', globsuffix)))
+        return [os.path.abspath(f)
+                for key in keys
+                for f in glob.glob(globfmt.format(key))]
 
     def _list_outputs(self):
         subjects_dir = self.inputs.subjects_dir

nipype/interfaces/tests/test_auto_FreeSurferSource.py

@@ -66,6 +66,9 @@ def test_FreeSurferSource_outputs():
     ),
     filled=dict(loc='mri',
     ),
+    graymid=dict(altkey=['graymid', 'midthickness'],
+    loc='surf',
+    ),
     inflated=dict(loc='surf',
     ),
     jacobian_white=dict(loc='surf',