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from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
if skull_strip_mode in (True, 'skip'):
brain_extraction_wf = init_n4_only_wf(
omp_nthreads=omp_nthreads,
atropos_use_random_seed=not skull_strip_fixed_seed,
)
else:
brain_extraction_wf = init_brain_extraction_wf(
in_template=skull_strip_template.space,
template_spec=skull_strip_template.spec,
atropos_use_random_seed=not skull_strip_fixed_seed,
omp_nthreads=omp_nthreads,
normalization_quality='precise' if not debug else 'testing')
# 4. Spatial normalization
anat_norm_wf = init_anat_norm_wf(
debug=debug,
omp_nthreads=omp_nthreads,
templates=spaces.get_spaces(nonstandard=False, dim=(3,)),
)
workflow.connect([
# Step 1.
(inputnode, anat_template_wf, [('t1w', 'inputnode.t1w')]),
(anat_template_wf, anat_validate, [
('outputnode.t1w_ref', 'in_file')]),
(anat_validate, brain_extraction_wf, [
('out_file', 'inputnode.in_files')]),
(brain_extraction_wf, outputnode, [
(('outputnode.bias_corrected', _pop), 't1w_preproc')]),
(anat_template_wf, outputnode, [
('outputnode.t1w_realign_xfm', 't1w_ref_xfms')]),
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=[('MNI152NLin2009cAsym', {}), ('MNI152NLin6Asym', {})],
)
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=[('MNI152NLin2009cAsym', {}), ('MNI152NLin6Asym', {})],
)
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
debug=False,
omp_nthreads=1,
templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)