Merge pull request #3095 from stilley2/FIX/betskull

Add skull_file output to fsl.BET interface

Author: effigies

nipype/interfaces/fsl/preprocess.py

@@ -129,6 +129,7 @@ class BETOutputSpec(TraitedSpec):
     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)")
+    skull_file = File(desc="path/name of skull file (if generated)")
 
 
 class BET(FSLCommand):
@@ -208,6 +209,10 @@ def _list_outputs(self):
             outputs["skull_mask_file"] = self._gen_fname(
                 outputs["out_file"], suffix="_skull_mask"
             )
+        if isdefined(self.inputs.skull) and self.inputs.skull:
+            outputs["skull_file"] = self._gen_fname(
+                outputs["out_file"], suffix="_skull"
+            )
         if isdefined(self.inputs.no_output) and self.inputs.no_output:
             outputs["out_file"] = Undefined
         return outputs

nipype/interfaces/fsl/tests/test_auto_BET.py

@@ -126,6 +126,7 @@ def test_BET_outputs():
         outskin_mesh_file=dict(extensions=None,),
         outskull_mask_file=dict(extensions=None,),
         outskull_mesh_file=dict(extensions=None,),
+        skull_file=dict(extensions=None,),
         skull_mask_file=dict(extensions=None,),
     )
     outputs = BET.output_spec()