ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming

fmriprep/cli/parser.py

@@ -635,6 +635,14 @@ def _slice_time_ref(value, parser):
         dest='run_reconall',
         help='Disable FreeSurfer surface preprocessing.',
     )
+    g_fs.add_argument(
+        '--fs-no-resume',
+        action='store_true',
+        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')
     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_no_resume = 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_no_resume=config.workflow.fs_no_resume,
         longitudinal=config.workflow.longitudinal,
         msm_sulc=msm_sulc,
         t1w=subject_data['t1w'],

pyproject.toml

@@ -33,7 +33,7 @@ dependencies = [
     "pybids >= 0.15.2",
     "requests",
     "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
-    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
+    "smriprep @ git+https://github.com/nipreps/smriprep.git@refs/pull/393/merge",
     "tedana >= 23.0.2",
     "templateflow >= 23.0.0",
     "toml",