diff --git a/smriprep/workflows/surfaces.py b/smriprep/workflows/surfaces.py index 3c0552653d..12e78c501a 100644 --- a/smriprep/workflows/surfaces.py +++ b/smriprep/workflows/surfaces.py @@ -248,7 +248,6 @@ def init_surface_recon_wf( ) if not fs_no_resume: - # fmt:off workflow.connect([ # Configuration (inputnode, recon_config, [('t1w', 't1w_list'), @@ -282,15 +281,16 @@ def init_surface_recon_wf( ('outputnode.subjects_dir', 'base_directory'), ('outputnode.subject_id', 'container'), ]), - ]) - # fmt:on + ]) # fmt:skip else: + # Pretend to be the autorecon1 node so fsnative2t1w_xfm gets run ASAP fs_base_inputs = autorecon1 = pe.Node(nio.FreeSurferSource(), name='fs_base_inputs') - # fmt:off workflow.connect([ - (inputnode, fs_base_inputs, [('subjects_dir', 'subjects_dir'), - ('subject_id', 'subject_id')]), + (inputnode, fs_base_inputs, [ + ('subjects_dir', 'subjects_dir'), + ('subject_id', 'subject_id'), + ]), # Generate mid-thickness surfaces (inputnode, get_surfaces, [ ('subjects_dir', 'subjects_dir'), @@ -300,10 +300,8 @@ def init_surface_recon_wf( ('subjects_dir', 'base_directory'), ('subject_id', 'container'), ]), - ]) - # fmt:on + ]) # fmt:skip - # fmt:off workflow.connect([ (get_surfaces, midthickness, [ ('white', 'in_file'),