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How to use the smriprep.workflows.anatomical.init_anat_preproc_wf function in smriprep

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github poldracklab / smriprep / doc_test_2 / _sources / smriprep-workflows-1.py View on Github external
from collections import OrderedDict
from smriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
    bids_root='.',
    freesurfer=True,
    hires=True,
    longitudinal=False,
    num_t1w=1,
    omp_nthreads=1,
    output_dir='.',
    output_spaces=OrderedDict([
        ('MNI152NLin2009cAsym', {}), ('fsaverage5', {})]),
    reportlets_dir='.',
    skull_strip_template=('MNI152NLin2009cAsym', {}),
)
github poldracklab / smriprep / 0.5.1 / api / smriprep-workflows-anatomical-1.py View on Github external
from niworkflows.utils.spaces import SpatialReferences, Reference
from smriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
    bids_root='.',
    freesurfer=True,
    hires=True,
    longitudinal=False,
    t1w=['t1w.nii.gz'],
    omp_nthreads=1,
    output_dir='.',
    skull_strip_mode='force',
    skull_strip_template=Reference('OASIS30ANTs'),
    spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
)
github poldracklab / smriprep / rel_0.4.1 / api / smriprep-workflows-anatomical-1.py View on Github external
from niworkflows.utils.spaces import SpatialReferences, Reference
from smriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
    bids_root='.',
    freesurfer=True,
    hires=True,
    longitudinal=False,
    t1w=['t1w.nii.gz'],
    omp_nthreads=1,
    output_dir='.',
    reportlets_dir='.',
    skull_strip_mode='force',
    skull_strip_template=Reference('OASIS30ANTs'),
    spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
)
github nipreps / dmriprep / dmriprep / workflows / base.py View on Github external
about = pe.Node(AboutSummary(version=__version__,
                                 command=' '.join(sys.argv)),
                    name='about', run_without_submitting=True)

    ds_report_summary = pe.Node(
        DerivativesDataSink(base_directory=reportlets_dir,
                            desc='summary', keep_dtype=True),
        name='ds_report_summary', run_without_submitting=True)

    ds_report_about = pe.Node(
        DerivativesDataSink(base_directory=reportlets_dir,
                            desc='about', keep_dtype=True),
        name='ds_report_about', run_without_submitting=True)

    # Preprocessing of T1w (includes registration to MNI)
    anat_preproc_wf = init_anat_preproc_wf(
        bids_root=layout.root,
        debug=debug,
        freesurfer=freesurfer,
        hires=hires,
        longitudinal=longitudinal,
        name="anat_preproc_wf",
        num_t1w=len(subject_data['t1w']),
        omp_nthreads=omp_nthreads,
        output_dir=output_dir,
        output_spaces=std_spaces,
        reportlets_dir=reportlets_dir,
        skull_strip_fixed_seed=skull_strip_fixed_seed,
        skull_strip_template=skull_strip_template,
    )

    workflow.connect([
github poldracklab / smriprep / api / smriprep-workflows-anatomical-1.py View on Github external
from niworkflows.utils.spaces import SpatialReferences, Reference
from smriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
    bids_root='.',
    freesurfer=True,
    hires=True,
    longitudinal=False,
    t1w=['t1w.nii.gz'],
    omp_nthreads=1,
    output_dir='.',
    skull_strip_mode='force',
    skull_strip_template=Reference('OASIS30ANTs'),
    spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
)
github poldracklab / smriprep / smriprep / workflows / base.py View on Github external
about = pe.Node(AboutSummary(version=__version__,
                                 command=' '.join(sys.argv)),
                    name='about', run_without_submitting=True)

    ds_report_summary = pe.Node(
        DerivativesDataSink(base_directory=output_dir, dismiss_entities=("session",),
                            desc='summary', datatype="figures"),
        name='ds_report_summary', run_without_submitting=True)

    ds_report_about = pe.Node(
        DerivativesDataSink(base_directory=output_dir, dismiss_entities=("session",),
                            desc='about', datatype="figures"),
        name='ds_report_about', run_without_submitting=True)

    # Preprocessing of T1w (includes registration to MNI)
    anat_preproc_wf = init_anat_preproc_wf(
        bids_root=layout.root,
        debug=debug,
        existing_derivatives=deriv_cache,
        freesurfer=freesurfer,
        hires=hires,
        longitudinal=longitudinal,
        name="anat_preproc_wf",
        t1w=subject_data['t1w'],
        omp_nthreads=omp_nthreads,
        output_dir=output_dir,
        skull_strip_fixed_seed=skull_strip_fixed_seed,
        skull_strip_mode=skull_strip_mode,
        skull_strip_template=skull_strip_template,
        spaces=spaces,
    )
github poldracklab / smriprep / 0.5.3 / api / smriprep-workflows-anatomical-1.py View on Github external
from niworkflows.utils.spaces import SpatialReferences, Reference
from smriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
    bids_root='.',
    freesurfer=True,
    hires=True,
    longitudinal=False,
    t1w=['t1w.nii.gz'],
    omp_nthreads=1,
    output_dir='.',
    skull_strip_mode='force',
    skull_strip_template=Reference('OASIS30ANTs'),
    spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
)
github poldracklab / smriprep / 0.6.0rc1 / api / smriprep-workflows-anatomical-1.py View on Github external
from niworkflows.utils.spaces import SpatialReferences, Reference
from smriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
    bids_root='.',
    freesurfer=True,
    hires=True,
    longitudinal=False,
    t1w=['t1w.nii.gz'],
    omp_nthreads=1,
    output_dir='.',
    skull_strip_mode='force',
    skull_strip_template=Reference('OASIS30ANTs'),
    spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
)
github poldracklab / smriprep / master / api / smriprep-workflows-1.py View on Github external
from collections import OrderedDict
from smriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
    bids_root='.',
    freesurfer=True,
    hires=True,
    longitudinal=False,
    num_t1w=1,
    omp_nthreads=1,
    output_dir='.',
    output_spaces=OrderedDict([
        ('MNI152NLin2009cAsym', {}), ('fsaverage5', {})]),
    reportlets_dir='.',
    skull_strip_template=('MNI152NLin2009cAsym', {}),
)
github poldracklab / smriprep / 0.4.1-1 / api / smriprep-workflows-anatomical-1.py View on Github external
from niworkflows.utils.spaces import SpatialReferences, Reference
from smriprep.workflows.anatomical import init_anat_preproc_wf
wf = init_anat_preproc_wf(
    bids_root='.',
    freesurfer=True,
    hires=True,
    longitudinal=False,
    t1w=['t1w.nii.gz'],
    omp_nthreads=1,
    output_dir='.',
    skull_strip_mode='force',
    skull_strip_template=Reference('OASIS30ANTs'),
    spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
)

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Structural MRI Preprocessing Pipelines

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