Add a --fs-reuse-base option to reuse existing freesurfer outputs from a longitudinal pipeline

fmriprep/cli/parser.py

@@ -585,6 +585,12 @@ 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

@@ -542,6 +542,8 @@ 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

@@ -297,6 +297,7 @@ def init_single_subject_wf(subject_id: str):
         output_dir=str(config.execution.output_dir),
         freesurfer=config.workflow.run_reconall,
         hires=config.workflow.hires,
+        fs_reuse_base=config.workflow.fs_reuse_base,
         longitudinal=config.workflow.longitudinal,
         msm_sulc=config.workflow.run_msmsulc,
         t1w=subject_data['t1w'],