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rename option to --fs-no-resume
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bpinsard committed Mar 14, 2024
1 parent 674bbf1 commit e8b2534
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Showing 3 changed files with 7 additions and 5 deletions.
8 changes: 5 additions & 3 deletions fmriprep/cli/parser.py
Original file line number Diff line number Diff line change
Expand Up @@ -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')
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2 changes: 1 addition & 1 deletion fmriprep/config.py
Original file line number Diff line number Diff line change
Expand Up @@ -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*."""
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2 changes: 1 addition & 1 deletion fmriprep/workflows/base.py
Original file line number Diff line number Diff line change
Expand Up @@ -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'],
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