diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index 1b4b5e3d15..6edb1399e9 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/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): diff --git a/nipype/workflows/smri/freesurfer/recon.py b/nipype/workflows/smri/freesurfer/recon.py index c9206812f3..b574314f35 100644 --- a/nipype/workflows/smri/freesurfer/recon.py +++ b/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: