How to use the smriprep.workflows.base.init_smriprep_wf function in smriprep

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github poldracklab / smriprep / _sources / smriprep-workflows-7.py View on Github external
import os
from collections import OrderedDict
from bids import BIDSLayout
os.environ['FREESURFER_HOME'] = os.getcwd()
from smriprep.workflows.base import init_smriprep_wf
wf = init_smriprep_wf(
    debug=False,
    freesurfer=True,
    hires=True,
    layout=BIDSLayout('.', validate=False),
    longitudinal=False,
    low_mem=False,
    omp_nthreads=1,
    output_dir='.',
    output_spaces=OrderedDict([('MNI152NLin2009cAsym', {}),
                               ('fsaverage5', {})]),
    run_uuid='testrun',
    skull_strip_fixed_seed=False,
    skull_strip_template=('OASIS30ANTs', {}),
    subject_list=['smripreptest'],
    work_dir='.',
)
github poldracklab / smriprep / master / api / smriprep-workflows-base-2.py View on Github external
import os
from collections import namedtuple
BIDSLayout = namedtuple('BIDSLayout', ['root'])
os.environ['FREESURFER_HOME'] = os.getcwd()
from smriprep.workflows.base import init_smriprep_wf
from niworkflows.utils.spaces import SpatialReferences, Reference
wf = init_smriprep_wf(
    debug=False,
    fast_track=False,
    freesurfer=True,
    fs_subjects_dir=None,
    hires=True,
    layout=BIDSLayout('.'),
    longitudinal=False,
    low_mem=False,
    omp_nthreads=1,
    output_dir='.',
    run_uuid='testrun',
    skull_strip_fixed_seed=False,
    skull_strip_mode='force',
    skull_strip_template=Reference('OASIS30ANTs'),
    spaces=SpatialReferences(spaces=['MNI152NLin2009cAsym', 'fsaverage5']),
    subject_list=['smripreptest'],
github poldracklab / smriprep / smriprep / cli / run.py View on Github external
if opts.run_uuid is not None:
            run_uuid = opts.run_uuid
        retval['return_code'] = generate_reports(subject_list, str(output_dir), run_uuid,
                                                 packagename="smriprep")
        return retval

    logger.log(25, INIT_MSG(
        version=__version__,
        bids_dir=bids_dir,
        subject_list=subject_list,
        uuid=run_uuid,
        spaces=opts.output_spaces)
    )

    # Build main workflow
    retval['workflow'] = init_smriprep_wf(
        debug=opts.sloppy,
        fast_track=opts.fast_track,
        freesurfer=opts.run_reconall,
        fs_subjects_dir=opts.fs_subjects_dir,
        hires=opts.hires,
        layout=layout,
        longitudinal=opts.longitudinal,
        low_mem=opts.low_mem,
        omp_nthreads=omp_nthreads,
        output_dir=str(output_dir),
        run_uuid=run_uuid,
        skull_strip_fixed_seed=opts.skull_strip_fixed_seed,
        skull_strip_mode=opts.skull_strip_mode,
        skull_strip_template=opts.skull_strip_template[0],
        spaces=opts.output_spaces,
        subject_list=subject_list,