How to use the smriprep.workflows.norm.init_anat_norm_wf function in smriprep

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github poldracklab / smriprep / 0.4.1-1 / api / smriprep-workflows-norm-1.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
github poldracklab / smriprep / 0.4.0rc1 / api / smriprep-workflows-norm-1.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
github poldracklab / smriprep / smriprep / workflows / anatomical.py View on Github external
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')]),
github poldracklab / smriprep / 0.4.2 / api / smriprep-workflows-norm-1.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
github poldracklab / smriprep / ci_doc_deploy / api / smriprep-workflows-norm-2.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=[('MNI152NLin2009cAsym', {}), ('MNI152NLin6Asym', {})],
)
github poldracklab / smriprep / api / smriprep-workflows-norm-2.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=[('MNI152NLin2009cAsym', {}), ('MNI152NLin6Asym', {})],
)
github poldracklab / smriprep / 0.4.0rc4 / api / smriprep-workflows-norm-1.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
github poldracklab / smriprep / 0.4.0rc5 / api / smriprep-workflows-norm-1.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
github poldracklab / smriprep / api / smriprep-workflows-norm-1.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)
github poldracklab / smriprep / 0.4.0rc3 / api / smriprep-workflows-norm-1.py View on Github external
from smriprep.workflows.norm import init_anat_norm_wf
wf = init_anat_norm_wf(
    debug=False,
    omp_nthreads=1,
    templates=['MNI152NLin2009cAsym', 'MNI152NLin6Asym'],
)