change option name to --fs-no-resume

Author: bpinsard

.circleci/config.yml

@@ -545,10 +545,10 @@ jobs:
           path: /tmp/ds005/derivatives
           destination: fasttrack
       - run:
-          name: Check fs-reuse-base using existing freesufer output
+          name: Check fs-no-resume using existing freesufer output
           no_output_timeout: 5m
           command: |
-            bash /tmp/src/smriprep/.circleci/ds005_run.sh --fs-reuse-base
+            bash /tmp/src/smriprep/.circleci/ds005_run.sh --fs-no-resume
       - run:
           name: Clean working directory
           when: on_fail
@@ -558,10 +558,10 @@ jobs:
                 -exec sh -c 'rm -f {}; touch {}' \;
       - store_artifacts:
           path: /tmp/ds005/work
-          destination: fs_reuse_base
+          destination: fs_no_resume
       - store_artifacts:
           path: /tmp/ds005/derivatives
-          destination: fs_reuse_base
+          destination: fs_no_resume
   ds054:
     <<: *machine_defaults
     environment:

smriprep/cli/run.py

@@ -215,10 +215,12 @@ def get_parser():
         '(default: OUTPUT_DIR/freesurfer)',
     )
     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_fs.add_argument(
         '--cifti-output',
@@ -613,7 +615,7 @@ def build_workflow(opts, retval):
         freesurfer=opts.run_reconall,
         fs_subjects_dir=opts.fs_subjects_dir,
         hires=opts.hires,
-        fs_reuse_base=opts.fs_reuse_base,
+        fs_no_resume=opts.fs_no_resume,
         layout=layout,
         longitudinal=opts.longitudinal,
         low_mem=opts.low_mem,

smriprep/workflows/anatomical.py

@@ -111,7 +111,7 @@ def init_anat_preproc_wf(
     cifti_output: ty.Literal['91k', '170k', False] = False,
     name: str = 'anat_preproc_wf',
     skull_strip_fixed_seed: bool = False,
-    fs_reuse_base: bool = False,
+    fs_no_resume: bool = False,
 ):
     """
     Stage the anatomical preprocessing steps of *sMRIPrep*.
@@ -184,7 +184,7 @@ def init_anat_preproc_wf(
         Do not use a random seed for skull-stripping - will ensure
         run-to-run replicability when used with --omp-nthreads 1
         (default: ``False``).
-    fs_reuse_base : bool
+    fs_no_resume : bool
         Adjust pipeline to reuse base template
         of an existing longitudinal freesurfer output
         (default: ``False``).
@@ -280,7 +280,7 @@ def init_anat_preproc_wf(
         sloppy=sloppy,
         omp_nthreads=omp_nthreads,
         skull_strip_fixed_seed=skull_strip_fixed_seed,
-        fs_reuse_base=fs_reuse_base,
+        fs_no_resume=fs_no_resume,
     )
     template_iterator_wf = init_template_iterator_wf(spaces=spaces)
     ds_std_volumes_wf = init_ds_anat_volumes_wf(
@@ -464,7 +464,7 @@ def init_anat_fit_wf(
     sloppy: bool = False,
     name='anat_fit_wf',
     skull_strip_fixed_seed: bool = False,
-    fs_reuse_base: bool = False,
+    fs_no_resume: bool = False,
 ):
     """
     Stage the anatomical preprocessing steps of *sMRIPrep*.
@@ -1047,7 +1047,7 @@ def init_anat_fit_wf(
         name='surface_recon_wf',
         omp_nthreads=omp_nthreads,
         hires=hires,
-        fs_reuse_base=fs_reuse_base,
+        fs_no_resume=fs_no_resume,
         precomputed=precomputed,
     )
     if t2w or flair:

smriprep/workflows/base.py

@@ -46,7 +46,7 @@ def init_smriprep_wf(
     freesurfer,
     fs_subjects_dir,
     hires,
-    fs_reuse_base,
+    fs_no_resume,
     layout,
     longitudinal,
     low_mem,
@@ -89,7 +89,7 @@ def init_smriprep_wf(
                 freesurfer=True,
                 fs_subjects_dir=None,
                 hires=True,
-                fs_reuse_base=False,
+                fs_no_resume=False,
                 layout=BIDSLayout('.'),
                 longitudinal=False,
                 low_mem=False,
@@ -180,7 +180,7 @@ def init_smriprep_wf(
             freesurfer=freesurfer,
             derivatives=derivatives,
             hires=hires,
-            fs_reuse_base=fs_reuse_base,
+            fs_no_resume=fs_no_resume,
             layout=layout,
             longitudinal=longitudinal,
             low_mem=low_mem,
@@ -217,7 +217,7 @@ def init_single_subject_wf(
     derivatives,
     freesurfer,
     hires,
-    fs_reuse_base,
+    fs_no_resume,
     layout,
     longitudinal,
     low_mem,
@@ -262,7 +262,7 @@ def init_single_subject_wf(
                 freesurfer=True,
                 derivatives=[],
                 hires=True,
-                fs_reuse_base=False,
+                fs_no_resume=False,
                 layout=BIDSLayout('.'),
                 longitudinal=False,
                 low_mem=False,
@@ -291,7 +291,7 @@ def init_single_subject_wf(
         Enable FreeSurfer surface reconstruction (may increase runtime)
     hires : :obj:`bool`
         Enable sub-millimeter preprocessing in FreeSurfer
-    fs_reuse_base : bool
+    fs_no_resume : bool
         Adjust pipeline to reuse base template
         of an existing longitudinal freesurfer output
     layout : BIDSLayout object
@@ -426,7 +426,7 @@ def init_single_subject_wf(
         precomputed=deriv_cache,
         freesurfer=freesurfer,
         hires=hires,
-        fs_reuse_base=fs_reuse_base,
+        fs_no_resume=fs_no_resume,
         longitudinal=longitudinal,
         msm_sulc=msm_sulc,
         name='anat_preproc_wf',

smriprep/workflows/surfaces.py

@@ -64,7 +64,7 @@ def init_surface_recon_wf(
     *,
     omp_nthreads: int,
     hires: bool,
-    fs_reuse_base: bool,
+    fs_no_resume: bool,
     precomputed: dict,
     name='surface_recon_wf',
 ):
@@ -133,7 +133,7 @@ def init_surface_recon_wf(
             wf = init_surface_recon_wf(
                 omp_nthreads=1,
                 hires=True,
-                fs_reuse_base=False,
+                fs_no_resume=False,
                 precomputed={})
 
     Parameters
@@ -142,7 +142,7 @@ def init_surface_recon_wf(
         Maximum number of threads an individual process may use
     hires : bool
         Enable sub-millimeter preprocessing in FreeSurfer
-    fs_reuse_base : bool
+    fs_no_resume : bool
         Adjust pipeline to reuse base template
         of an existing longitudinal freesurfer output
 
@@ -246,7 +246,7 @@ def init_surface_recon_wf(
         name='sync',
     )
 
-    if not fs_reuse_base:
+    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')