From 719a71f1536bcaae9ee686f4e635d4cb1446281e Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 26 Sep 2024 16:41:37 -0400
Subject: [PATCH] FIX: Add none option when selecting surface recon method,
 deprecated ambiguous options

---
 nibabies/cli/parser.py     | 14 ++++++++------
 nibabies/workflows/base.py |  8 +++++---
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/nibabies/cli/parser.py b/nibabies/cli/parser.py
index 60c63910..b2b6a8a5 100644
--- a/nibabies/cli/parser.py
+++ b/nibabies/cli/parser.py
@@ -28,6 +28,8 @@ def _build_parser():
         # parser attribute name: (replacement flag, version slated to be removed in)
         'bold2t1w_init': ('--bold2anat-init', '24.2.0'),
         'bold2t1w_dof': ('--bold2anat-dof', '24.2.0'),
+        'force_reconall': ('--surface-recon-method freesurfer', '24.2.0'),
+        'fs_no_reconall': ('--surface-recon-method none', '24.2.0'),
     }
 
     class DeprecatedAction(Action):
@@ -597,9 +599,9 @@ def _slice_time_ref(value, parser):
     )
     g_surfs_xor.add_argument(
         '--fs-no-reconall',
-        action='store_false',
+        action=DeprecatedAction,
         dest='run_reconall',
-        help='disable FreeSurfer surface preprocessing.',
+        help='Deprecated - use `--surface-recon-method none` instead.',
     )
 
     g_other = parser.add_argument_group('Other options')
@@ -728,14 +730,14 @@ def _slice_time_ref(value, parser):
     g_baby.add_argument(
         '--force-reconall',
         default=False,
-        action='store_true',
-        help='Force traditional FreeSurfer surface reconstruction.',
+        action=DeprecatedAction,
+        help='Deprecated - use `--surface-recon-method freesurfer` instead.',
     )
     g_baby.add_argument(
         '--surface-recon-method',
-        choices=('infantfs', 'freesurfer', 'mcribs', 'auto'),
+        choices=('auto', 'infantfs', 'freesurfer', 'mcribs', 'none'),
         default='auto',
-        help='Method to use for surface reconstruction',
+        help='Method to use for surface reconstruction.',
     )
     g_baby.add_argument(
         '--reference-anat',
diff --git a/nibabies/workflows/base.py b/nibabies/workflows/base.py
index 1b85624c..8c851e53 100644
--- a/nibabies/workflows/base.py
+++ b/nibabies/workflows/base.py
@@ -351,9 +351,11 @@ def init_single_subject_wf(
                 f'Requested to use {requested_anat} as anatomical reference but none available'
             )
     elif (reference_anat := requested_anat) is None:  # Both available with no preference
-        reference_anat = 'T2w' if any(
-            (recon_method == 'none' and age <= AUTO_T2W_MAX_AGE, recon_method == 'mcribs')
-        ) else 'T1w'
+        reference_anat = (
+            'T2w'
+            if any((recon_method == 'none' and age <= AUTO_T2W_MAX_AGE, recon_method == 'mcribs'))
+            else 'T1w'
+        )
 
     anat = reference_anat.lower()  # To be used for workflow connections