Absolute paths for out_file

Author: Erik Ziegler

nipype/interfaces/freesurfer/utils.py

@@ -878,7 +878,7 @@ class MRIMarchingCubes(FSCommand):
 
  def _list_outputs(self):
  outputs = self.output_spec().get()
- outputs['surface'] = os.path.abspath(self._gen_outfilename())
+ outputs['surface'] = self._gen_outfilename()
  return outputs
 
  def _gen_filename(self, name):
@@ -889,10 +889,10 @@ def _gen_filename(self, name):
 
  def _gen_outfilename(self):
  if isdefined(self.inputs.out_file):
- return self.inputs.out_file
+ return os.path.abspath(self.inputs.out_file)
  else:
  _, name, ext = split_filename(self.inputs.in_file)
- return name + ext + '_' + str(self.inputs.label_value)
+ return os.path.abspath(name + ext + '_' + str(self.inputs.label_value))
 
 class SmoothTessellationInputSpec(FSTraitedSpec):
  """
@@ -946,7 +946,7 @@ class SmoothTessellation(FSCommand):
 
  def _list_outputs(self):
  outputs = self.output_spec().get()
- outputs['surface'] = os.path.abspath(self._gen_outfilename())
+ outputs['surface'] = self._gen_outfilename()
  return outputs
 
  def _gen_filename(self, name):
@@ -957,8 +957,8 @@ def _gen_filename(self, name):
 
  def _gen_outfilename(self):
  if isdefined(self.inputs.out_file):
- return self.inputs.out_file
+ return os.path.abspath(self.inputs.out_file)
  else:
  _, name, ext = split_filename(self.inputs.in_file)
- return name + '_smoothed' + ext
+ return os.path.abspath(name + '_smoothed' + ext)