feat: Add --fs-legacy-id flag

fmriprep/cli/parser.py

@@ -657,6 +657,14 @@ def _fallback_trt(value, parser):
         help='Path to existing FreeSurfer subjects directory to reuse. '
         '(default: OUTPUT_DIR/freesurfer)',
     )
+    g_fs.add_argument(
+        '--fs-legacy-id',
+        action=BooleanOptionalAction,
+        default=False,
+        help='Use BIDS subject IDs as FreeSurfer subject IDs, for compatibility with '
+        'reusing FreeSurfer reconstructions generated by older versions of fMRIPrep. '
+        'This option is incompatible with `--subject-anatomical-reference sessionwise`.',
+    )
     g_fs.add_argument(
         '--submm-recon',
         action=BooleanOptionalAction,

fmriprep/config.py

@@ -591,6 +591,8 @@ class workflow(_Config):
     """Run FreeSurfer ``recon-all`` with the ``-hires`` flag."""
     fs_no_resume = None
     """Adjust pipeline to reuse base template of existing longitudinal freesurfer"""
+    fs_legacy_id = False
+    """Use BIDS subject IDs as FreeSurfer subject IDs."""
     ignore = None
     """Ignore particular steps for *fMRIPrep*."""
     force = None

fmriprep/workflows/base.py

@@ -410,6 +410,17 @@ def init_single_subject_wf(
         (about, ds_report_about, [('out_report', 'in_file')]),
     ])  # fmt:skip
 
+    if config.workflow.fs_legacy_id:
+        config.loggers.workflow.info(f'Using legacy FreeSurfer subject ID: sub-{subject_id}')
+        if (
+            config.workflow.subject_anatomical_reference == 'sessionwise'
+            and session_id is not None
+        ):
+            msg = 'Session-wise anatomical reference is incompatible with legacy FreeSurfer subject IDs.'
+            config.loggers.workflow.error(msg)
+            raise RuntimeError(msg)
+        workflow.disconnect(bids_info, create_fs_id, [('session', 'session_id')])
+
     # Set up the template iterator once, if used
     template_iterator_wf = None
     select_MNI2009c_xfm = None