RF: Convert recon_method none to Nonetype

Author: mgxd

nibabies/cli/parser.py

@@ -150,6 +150,11 @@ def _slice_time_ref(value, parser):
             raise parser.error(f'Slice time reference must be in range 0-1. Received {value}.')
         return value
 
+    def _str_none(val):
+        if not isinstance(val, str):
+            return val
+        return None if val.lower() == 'none' else val
+
     verstr = f'NiBabies v{config.environment.version}'
     currentv = Version(config.environment.version)
 
@@ -757,7 +762,8 @@ def _slice_time_ref(value, parser):
     )
     g_baby.add_argument(
         '--surface-recon-method',
-        choices=('auto', 'infantfs', 'freesurfer', 'mcribs', 'none'),
+        choices=('auto', 'infantfs', 'freesurfer', 'mcribs', None),
+        type=_str_none,
         default='auto',
         help='Method to use for surface reconstruction.',
     )

nibabies/workflows/base.py

@@ -108,8 +108,8 @@ def init_nibabies_wf(subworkflows_list):
     nibabies_wf.base_dir = config.execution.work_dir
 
     execution_spaces = init_execution_spaces()
-    freesurfer = config.workflow.surface_recon_method is not None
-    if freesurfer:
+    surface_recon = config.workflow.surface_recon_method is not None
+    if surface_recon:
         fsdir = pe.Node(
             BIDSFreeSurferDir(
                 derivatives=config.execution.output_dir,
@@ -157,7 +157,7 @@ def init_nibabies_wf(subworkflows_list):
         single_subject_wf.config['execution']['crashdump_dir'] = str(log_dir)
         for node in single_subject_wf._get_all_nodes():
             node.config = deepcopy(single_subject_wf.config)
-        if freesurfer:
+        if surface_recon:
             nibabies_wf.connect(fsdir, 'subjects_dir', single_subject_wf, 'inputnode.subjects_dir')
         else:
             nibabies_wf.add_nodes([single_subject_wf])