feat: Deprecate --force-syn for --force syn-sdc

Author: effigies

fmriprep/cli/parser.py

@@ -50,6 +50,7 @@ def _build_parser(**kwargs):
         'bold2t1w_dof': ('--bold2anat-dof', '24.2.0'),
         'force_bbr': ('--force bbr', '26.0.0'),
         'force_no_bbr': ('--force no-bbr', '26.0.0'),
+        'force_syn': ('--force syn-sdc', '26.0.0'),
     }
 
     class DeprecatedAction(Action):
@@ -346,7 +347,7 @@ def _slice_time_ref(value, parser):
         action='store',
         nargs='+',
         default=[],
-        choices=['bbr', 'no-bbr'],
+        choices=['bbr', 'no-bbr', 'syn-sdc'],
         help='Force selected processing choices, overriding automatic selections '
         '(a space delimited list)',
     )
@@ -632,10 +633,9 @@ def _slice_time_ref(value, parser):
     )
     g_syn.add_argument(
         '--force-syn',
-        action='store_true',
+        action=DeprecatedAction,
         default=False,
-        help='EXPERIMENTAL/TEMPORARY: Use SyN correction in addition to '
-        'fieldmap correction, if available',
+        help='Deprecated - use `--force syn-sdc` instead.',
     )
 
     # FreeSurfer options

fmriprep/workflows/base.py

@@ -557,7 +557,7 @@ def init_single_subject_wf(subject_id: str):
         bold_data=bold_runs,
         ignore_fieldmaps='fieldmaps' in config.workflow.ignore,
         use_syn=config.workflow.use_syn_sdc,
-        force_syn=config.workflow.force_syn,
+        force_syn='syn-sdc' in config.workflow.force,
         filters=config.execution.get().get('bids_filters', {}).get('fmap'),
     )
 

fmriprep/workflows/tests/test_base.py

@@ -114,7 +114,6 @@ def _make_params(
     run_msmsulc: bool = True,
     skull_strip_t1w: str = 'auto',
     use_syn_sdc: str | bool = False,
-    force_syn: bool = False,
     freesurfer: bool = True,
     ignore: list[str] = None,
     force: list[str] = None,
@@ -136,7 +135,6 @@ def _make_params(
         run_msmsulc,
         skull_strip_t1w,
         use_syn_sdc,
-        force_syn,
         freesurfer,
         ignore,
         force,
@@ -157,7 +155,6 @@ def _make_params(
         'run_msmsulc',
         'skull_strip_t1w',
         'use_syn_sdc',
-        'force_syn',
         'freesurfer',
         'ignore',
         'force',
@@ -182,7 +179,7 @@ def _make_params(
         _make_params(cifti_output='91k', run_msmsulc=False),
         _make_params(skull_strip_t1w='force'),
         _make_params(skull_strip_t1w='skip'),
-        _make_params(use_syn_sdc='warn', force_syn=True, ignore=['fieldmaps']),
+        _make_params(use_syn_sdc='warn', ignore=['fieldmaps'], force=['syn-sdc']),
         _make_params(freesurfer=False),
         _make_params(freesurfer=False, force=['bbr']),
         _make_params(freesurfer=False, force=['no-bbr']),
@@ -208,7 +205,6 @@ def test_init_fmriprep_wf(
     run_msmsulc: bool,
     skull_strip_t1w: str,
     use_syn_sdc: str | bool,
-    force_syn: bool,
     freesurfer: bool,
     ignore: list[str],
     force: list[str],