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

Author: bpinsard

fmriprep/cli/parser.py

@@ -574,6 +574,12 @@ 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

@@ -533,6 +533,8 @@ 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*."""
     longitudinal = False

fmriprep/workflows/base.py

@@ -310,6 +310,7 @@ def init_single_subject_wf(subject_id: str):
         existing_derivatives=anat_derivatives,
         freesurfer=config.workflow.run_reconall,
         hires=config.workflow.hires,
+        fs_reuse_base=config.workflow.fs_reuse_base,
         longitudinal=config.workflow.longitudinal,
         omp_nthreads=config.nipype.omp_nthreads,
         output_dir=fmriprep_dir,