fix rebase/merge messups, docstrings

Author: bpinsard

smriprep/cli/run.py

@@ -218,9 +218,8 @@ def get_parser():
         '--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)!",
+        help='EXPERT: Import pre-computed FreeSurfer reconstruction without resuming. '
+        'The user is responsible for ensuring that all necessary files are present.',
     )
     g_fs.add_argument(
         '--cifti-output',

smriprep/workflows/anatomical.py

@@ -186,8 +186,8 @@ def init_anat_preproc_wf(
         run-to-run replicability when used with --omp-nthreads 1
         (default: ``False``).
     fs_no_resume : bool
-        use precomputed freesurfer without attempting to resume
-        (eg. for longitudinal base or fastsurfer)
+        EXPERT: Import pre-computed FreeSurfer reconstruction without resuming.
+        The user is responsible for ensuring that all necessary files are present.
         (default: ``False``).
 
     Inputs

smriprep/workflows/surfaces.py

@@ -248,24 +248,6 @@ def init_surface_recon_wf(
     )
 
     if not fs_no_resume:
-        recon_config = pe.Node(FSDetectInputs(hires_enabled=hires), name='recon_config')
-
-        fov_check = pe.Node(niu.Function(function=_check_cw256), name='fov_check')
-        fov_check.inputs.default_flags = ['-noskullstrip', '-noT2pial', '-noFLAIRpial']
-
-        autorecon1 = pe.Node(
-            ReconAll(directive='autorecon1', openmp=omp_nthreads),
-            name='autorecon1',
-            n_procs=omp_nthreads,
-            mem_gb=5,
-        )
-        autorecon1.interface._can_resume = False
-        autorecon1.interface._always_run = True
-
-        skull_strip_extern = pe.Node(FSInjectBrainExtracted(), name='skull_strip_extern')
-
-        autorecon_resume_wf = init_autorecon_resume_wf(omp_nthreads=omp_nthreads)
-
         # fmt:off
         workflow.connect([
             # Configuration