Merge pull request #462 from moloney/bet-surface-output

ENH: Provide access to all relevant BET outputs when "surfaces" option u...

Author: chrisgorgo

nipype/interfaces/fsl/preprocess.py

@@ -89,13 +89,28 @@ class BETInputSpec(FSLCommandInputSpec):
 
 
 class BETOutputSpec(TraitedSpec):
-    out_file = File(desc="path/name of skullstripped file")
+    out_file = File(
+        desc="path/name of skullstripped file (if generated)")
     mask_file = File(
         desc="path/name of binary brain mask (if generated)")
     outline_file = File(
         desc="path/name of outline file (if generated)")
     meshfile = File(
         desc="path/name of vtk mesh file (if generated)")
+    inskull_mask_file = File(
+        desc="path/name of inskull mask (if generated)")
+    inskull_mesh_file = File(
+        desc="path/name of inskull mesh outline (if generated)")
+    outskull_mask_file = File(
+        desc="path/name of outskull mask (if generated)")
+    outskull_mesh_file = File(
+        desc="path/name of outskull mesh outline (if generated)")
+    outskin_mask_file = File(
+        desc="path/name of outskin mask (if generated)")
+    outskin_mesh_file = File(
+        desc="path/name of outskin mesh outline (if generated)")
+    skull_mask_file = File(
+        desc="path/name of skull mask (if generated)")
 
 
 class BET(FSLCommand):
@@ -138,7 +153,8 @@ def _gen_outfilename(self):
     def _list_outputs(self):
         outputs = self.output_spec().get()
         outputs['out_file'] = self._gen_outfilename()
-        if isdefined(self.inputs.mesh) and self.inputs.mesh:
+        if ((isdefined(self.inputs.mesh) and self.inputs.mesh) or 
+                (isdefined(self.inputs.surfaces) and self.inputs.surfaces)):
             outputs['meshfile'] = self._gen_fname(outputs['out_file'],
                                                suffix='_mesh.vtk',
                                                change_ext=False)
@@ -150,6 +166,21 @@ def _list_outputs(self):
         if isdefined(self.inputs.outline) and self.inputs.outline:
             outputs['outline_file'] = self._gen_fname(outputs['out_file'],
                                                suffix='_overlay')
+        if isdefined(self.inputs.surfaces) and self.inputs.surfaces:
+            outputs['inskull_mask_file'] = self._gen_fname(outputs['out_file'],
+                                               suffix='_inskull_mask')
+            outputs['inskull_mesh_file'] = self._gen_fname(outputs['out_file'],
+                                               suffix='_inskull_mesh')
+            outputs['outskull_mask_file'] = self._gen_fname(outputs['out_file'],
+                                               suffix='_outskull_mask')
+            outputs['outskull_mesh_file'] = self._gen_fname(outputs['out_file'],
+                                               suffix='_outskull_mesh')
+            outputs['outskin_mask_file'] = self._gen_fname(outputs['out_file'],
+                                               suffix='_outskin_mask')
+            outputs['outskin_mesh_file'] = self._gen_fname(outputs['out_file'],
+                                               suffix='_outskin_mesh')
+            outputs['skull_mask_file'] = self._gen_fname(outputs['out_file'],
+                                               suffix='_skull_mask')
         if isdefined(self.inputs.no_output) and self.inputs.no_output:
             outputs['out_file'] = Undefined
         return outputs

nipype/interfaces/fsl/tests/test_preprocess.py

@@ -78,6 +78,7 @@ def func():
         'center':             ('-c 54 75 80', [54, 75, 80]),
         'threshold':          ('-t', True),
         'mesh':               ('-e', True),
+        'surfaces':           ('-A', True)
         #'verbose':            ('-v', True),
         #'flags':              ('--i-made-this-up', '--i-made-this-up'),
             }