rename option to --fs-no-resume

Author: bpinsard

fmriprep/cli/parser.py

@@ -636,10 +636,12 @@ def _slice_time_ref(value, parser):
         help='Disable FreeSurfer surface preprocessing.',
     )
     g_fs.add_argument(
-        "--fs-reuse-base",
+        "--fs-no-resume",
         action="store_true",
-        dest="fs_reuse_base",
-        help="Reuse freesurfer base template (from longitudinal preprocessing)",
+        dest="fs_no_resume",
+        help="Import precomputed freesurfer without resuming "
+        "(longitudinal or fastsurfer data) "
+        "!expert option (you know what you're doing)!",
     )
 
     g_carbon = parser.add_argument_group('Options for carbon usage tracking')

fmriprep/config.py

@@ -561,7 +561,7 @@ class workflow(_Config):
     """Run *fieldmap-less* susceptibility-derived distortions estimation."""
     hires = None
     """Run FreeSurfer ``recon-all`` with the ``-hires`` flag."""
-    fs_reuse_base = None
+    fs_no_resume = None
     """Adjust pipeline to reuse base template of existing longitudinal freesurfer"""
     ignore = None
     """Ignore particular steps for *fMRIPrep*."""

fmriprep/workflows/base.py

@@ -321,7 +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,
+        fs_no_resume=config.workflow.fs_no_resume,
         longitudinal=config.workflow.longitudinal,
         msm_sulc=msm_sulc,
         t1w=subject_data['t1w'],