Merge pull request #1429 from akeshavan/applymask

Applymask

Author: satra

nipype/interfaces/freesurfer/utils.py

@@ -527,11 +527,6 @@ class ApplyMask(FSCommand):
     input_spec = ApplyMaskInputSpec
     output_spec = ApplyMaskOutputSpec
 
-    def _list_outputs(self):
-        outputs = self._outputs().get()
-        outputs["out_file"] = os.path.abspath(self.inputs.out_file)
-        return outputs
-
 
 class SurfaceSnapshotsInputSpec(FSTraitedSpec):
 

nipype/workflows/smri/freesurfer/recon.py

@@ -82,7 +82,7 @@ def link_masks(subjects_dir, subject_id):
 def create_reconall_workflow(name="ReconAll", plugin_args=None,
                              recoding_file=None):
     """Creates the ReconAll workflow in nipype.
-    
+
     Example
     -------
     >>> from nipype.workflows.smri.freesurfer import create_skullstripped_recon_flow
@@ -200,7 +200,7 @@ def checkarg(arg, default):
               'lookup_table',
               'wm_lookup_table',
               'awk_file']
-    
+
     config_node = pe.Node(niu.Function(params,
                                        params,
                                        setconfig),
@@ -509,7 +509,7 @@ def completemethod(datasinked_files, subject_id):
     reconall.connect([(datasink, completion, [('out_file', 'datasinked_files')]),
                       (inputspec, completion, [('subject_id', 'subject_id')]),
                       (completion, postds_outputspec, [('subject_id', 'subject_id')])])
-                                      
+
 
     #### Workflow additions go here
     if recoding_file: