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conform with new style rules
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bpinsard committed Jan 15, 2024
1 parent 0767f70 commit 7826ef2
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Showing 2 changed files with 8 additions and 13 deletions.
5 changes: 2 additions & 3 deletions smriprep/cli/run.py
Original file line number Diff line number Diff line change
Expand Up @@ -215,11 +215,10 @@ def get_parser():
'(default: OUTPUT_DIR/freesurfer)',
)
g_fs.add_argument(
"--fs-reuse-base",
'--fs-reuse-base',
action='store_true',
dest='fs_reuse_base',
help='Reuse freesurfer base template'
'(from longitudinal preprocessing)',
help='Reuse freesurfer base template' '(from longitudinal preprocessing)',
)
g_fs.add_argument(
'--cifti-output',
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16 changes: 6 additions & 10 deletions smriprep/workflows/surfaces.py
Original file line number Diff line number Diff line change
Expand Up @@ -247,22 +247,21 @@ def init_surface_recon_wf(
)

if not fs_reuse_base:
recon_config = pe.Node(FSDetectInputs(hires_enabled=hires), name='recon_config')

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 = 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",
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")
skull_strip_extern = pe.Node(FSInjectBrainExtracted(), name='skull_strip_extern')

autorecon_resume_wf = init_autorecon_resume_wf(omp_nthreads=omp_nthreads)

Expand Down Expand Up @@ -303,10 +302,7 @@ def init_surface_recon_wf(
])
# fmt:on
else:
fs_base_inputs = autorecon1 = pe.Node(
nio.FreeSurferSource(),
name='fs_base_inputs'
)
fs_base_inputs = autorecon1 = pe.Node(nio.FreeSurferSource(), name='fs_base_inputs')

# fmt:off
workflow.connect([
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