wip: add a flag to reuse freesurfer as is, for longitudinal base case

Author: bpinsard

fmriprep/cli/parser.py

@@ -635,6 +635,12 @@ def _slice_time_ref(value, parser):
         dest='run_reconall',
         help='Disable FreeSurfer surface preprocessing.',
     )
+    g_fs.add_argument(
+        "--fs-reuse-base",
+        action="store_true",
+        dest="fs_reuse_base",
+        help="Reuse freesurfer base template (from longitudinal preprocessing)",
+    )
 
     g_carbon = parser.add_argument_group('Options for carbon usage tracking')
     g_carbon.add_argument(

fmriprep/config.py

@@ -561,6 +561,8 @@ class workflow(_Config):
     """Run *fieldmap-less* susceptibility-derived distortions estimation."""
     hires = None
     """Run FreeSurfer ``recon-all`` with the ``-hires`` flag."""
+    fs_reuse_base = None
+    """Adjust pipeline to reuse base template of existing longitudinal freesurfer"""
     ignore = None
     """Ignore particular steps for *fMRIPrep*."""
     level = None

fmriprep/workflows/base.py

@@ -321,6 +321,7 @@ def init_single_subject_wf(subject_id: str):
         output_dir=fmriprep_dir,
         freesurfer=config.workflow.run_reconall,
         hires=config.workflow.hires,
+        fs_reuse_base=config.workflow.fs_reuse_base,
         longitudinal=config.workflow.longitudinal,
         msm_sulc=msm_sulc,
         t1w=subject_data['t1w'],