Merge pull request nipy#1894 from effigies/fssource_refine

satra · web-flow · commit c6d24b87d097 · 2017-03-22T18:09:08.000-04:00
Split over-eager globs in FreeSurferSource
diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py
@@ -124,17 +124,25 @@ def test_ReconAll_outputs():
     aparc_stats=dict(altkey='aparc',
     loc='stats',
     ),
+    area_pial=dict(altkey='area.pial',
+    loc='surf',
+    ),
     aseg=dict(loc='mri',
     ),
     aseg_stats=dict(altkey='aseg',
     loc='stats',
     ),
+    avg_curv=dict(loc='surf',
+    ),
     brain=dict(loc='mri',
     ),
     brainmask=dict(loc='mri',
     ),
     curv=dict(loc='surf',
     ),
+    curv_pial=dict(altkey='curv.pial',
+    loc='surf',
+    ),
     curv_stats=dict(altkey='curv',
     loc='stats',
     ),
@@ -145,6 +153,8 @@ def test_ReconAll_outputs():
     ),
     inflated=dict(loc='surf',
     ),
+    jacobian_white=dict(loc='surf',
+    ),
     label=dict(altkey='*label',
     loc='label',
     ),
diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py
@@ -1478,7 +1478,7 @@ class FSSourceInputSpec(BaseInterfaceInputSpec):
     subjects_dir = Directory(mandatory=True,
                              desc='Freesurfer subjects directory.')
     subject_id = Str(mandatory=True,
-                            desc='Subject name for whom to retrieve data')
+                     desc='Subject name for whom to retrieve data')
     hemi = traits.Enum('both', 'lh', 'rh', usedefault=True,
                        desc='Selects hemisphere specific outputs')
 
@@ -1487,8 +1487,8 @@ class FSSourceOutputSpec(TraitedSpec):
     T1 = File(
         exists=True, desc='Intensity normalized whole-head volume', loc='mri')
     aseg = File(
-        exists=True, desc='Volumetric map of regions from automatic segmentation',
-        loc='mri')
+        exists=True, loc='mri',
+        desc='Volumetric map of regions from automatic segmentation')
     brain = File(
         exists=True, desc='Intensity normalized brain-only volume', loc='mri')
     brainmask = File(
@@ -1507,16 +1507,27 @@ class FSSourceOutputSpec(TraitedSpec):
         loc='mri', altkey='*ribbon')
     wm = File(exists=True, desc='Segmented white-matter volume', loc='mri')
     wmparc = File(
-        exists=True, desc='Aparc parcellation projected into subcortical white matter',
-        loc='mri')
+        exists=True, loc='mri',
+        desc='Aparc parcellation projected into subcortical white matter')
     curv = OutputMultiPath(File(exists=True), desc='Maps of surface curvature',
                            loc='surf')
+    avg_curv = OutputMultiPath(
+        File(exists=True), desc='Average atlas curvature, sampled to subject',
+        loc='surf')
     inflated = OutputMultiPath(
         File(exists=True), desc='Inflated surface meshes',
         loc='surf')
     pial = OutputMultiPath(
         File(exists=True), desc='Gray matter/pia mater surface meshes',
         loc='surf')
+    area_pial = OutputMultiPath(
+        File(exists=True),
+        desc='Mean area of triangles each vertex on the pial surface is '
+        'associated with',
+        loc='surf', altkey='area.pial')
+    curv_pial = OutputMultiPath(
+        File(exists=True), desc='Curvature of pial surface',
+        loc='surf', altkey='curv.pial')
     smoothwm = OutputMultiPath(File(exists=True), loc='surf',
                                desc='Smoothed original surface meshes')
     sphere = OutputMultiPath(
@@ -1531,6 +1542,10 @@ class FSSourceOutputSpec(TraitedSpec):
     white = OutputMultiPath(
         File(exists=True), desc='White/gray matter surface meshes',
         loc='surf')
+    jacobian_white = OutputMultiPath(
+        File(exists=True),
+        desc='Distortion required to register to spherical atlas',
+        loc='surf')
     label = OutputMultiPath(
         File(exists=True), desc='Volume and surface label files',
         loc='label', altkey='*label')
@@ -1590,12 +1605,17 @@ def _get_files(self, path, key, dirval, altkey=None):
         elif dirval == 'stats':
             globsuffix = '.stats'
         globprefix = ''
-        if key == 'ribbon' or dirval in ['surf', 'label', 'stats']:
+        if dirval in ('surf', 'label', 'stats'):
+            if self.inputs.hemi != 'both':
+                globprefix = self.inputs.hemi + '.'
+            else:
+                globprefix = '?h.'
+        elif key == 'ribbon':
             if self.inputs.hemi != 'both':
                 globprefix = self.inputs.hemi + '.'
             else:
                 globprefix = '*'
-        if key == 'aseg_stats' or key == 'wmparc_stats':
+        elif key in ('aseg_stats', 'wmparc_stats'):
             globprefix = ''
         keydir = os.path.join(path, dirval)
         if altkey:
diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py
@@ -39,17 +39,25 @@ def test_FreeSurferSource_outputs():
     aparc_stats=dict(altkey='aparc',
     loc='stats',
     ),
+    area_pial=dict(altkey='area.pial',
+    loc='surf',
+    ),
     aseg=dict(loc='mri',
     ),
     aseg_stats=dict(altkey='aseg',
     loc='stats',
     ),
+    avg_curv=dict(loc='surf',
+    ),
     brain=dict(loc='mri',
     ),
     brainmask=dict(loc='mri',
     ),
     curv=dict(loc='surf',
     ),
+    curv_pial=dict(altkey='curv.pial',
+    loc='surf',
+    ),
     curv_stats=dict(altkey='curv',
     loc='stats',
     ),
@@ -60,6 +68,8 @@ def test_FreeSurferSource_outputs():
     ),
     inflated=dict(loc='surf',
     ),
+    jacobian_white=dict(loc='surf',
+    ),
     label=dict(altkey='*label',
     loc='label',
     ),
