How to use smriprep - 10 common examples

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', {}),
)

from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1, hires=True)

from smriprep.workflows.anatomical import init_anat_template_wf
wf = init_anat_template_wf(
    longitudinal=False, omp_nthreads=1, num_t1w=1)

from smriprep.workflows.surfaces import init_gifti_surface_wf
wf = init_gifti_surface_wf()

from smriprep.workflows.surfaces import init_segs_to_native_wf
wf = init_segs_to_native_wf()

def git_versions_from_keywords(keywords, tag_prefix, verbose):
    """Get version information from git keywords."""
    if not keywords:
        raise NotThisMethod("no keywords at all, weird")
    date = keywords.get("date")
    if date is not None:
        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
        # -like" string, which we must then edit to make compliant), because
        # it's been around since git-1.5.3, and it's too difficult to
        # discover which version we're using, or to work around using an
        # older one.
        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
    refnames = keywords["refnames"].strip()
    if refnames.startswith("$Format"):
        if verbose:
            print("keywords are unexpanded, not using")
        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
    refs = set([r.strip() for r in refnames.strip("()").split(",")])
    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of

if not keywords:
        raise NotThisMethod("no keywords at all, weird")
    date = keywords.get("date")
    if date is not None:
        # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
        # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
        # -like" string, which we must then edit to make compliant), because
        # it's been around since git-1.5.3, and it's too difficult to
        # discover which version we're using, or to work around using an
        # older one.
        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
    refnames = keywords["refnames"].strip()
    if refnames.startswith("$Format"):
        if verbose:
            print("keywords are unexpanded, not using")
        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
    refs = set([r.strip() for r in refnames.strip("()").split(",")])
    # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
    # just "foo-1.0". If we see a "tag: " prefix, prefer those.
    TAG = "tag: "
    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
    if not tags:
        # Either we're using git < 1.8.3, or there really are no tags. We use
        # a heuristic: assume all version tags have a digit. The old git %d
        # expansion behaves like git log --decorate=short and strips out the
        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
        # between branches and tags. By ignoring refnames without digits, we
        # filter out many common branch names like "release" and
        # "stabilization", as well as "HEAD" and "master".
        tags = set([r for r in refs if re.search(r'\d', r)])
        if verbose:
            print("discarding '%s', no digits" % ",".join(refs - tags))

from niworkflows.utils.misc import _copy_any
            dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
            _copy_any(dseg_tsv,
                      str(Path(output_dir) / 'smriprep' / 'desc-aseg_dseg.tsv'))
            _copy_any(dseg_tsv,
                      str(Path(output_dir) / 'smriprep' / 'desc-aparcaseg_dseg.tsv'))
        logger.log(25, 'sMRIPrep finished without errors')
    finally:
        from niworkflows.reports import generate_reports
        from ..utils.bids import write_derivative_description

        logger.log(25, 'Writing reports for participants: %s', ', '.join(subject_list))
        # Generate reports phase
        errno += generate_reports(subject_list, output_dir, run_uuid,
                                  packagename='smriprep')
        write_derivative_description(bids_dir, str(Path(output_dir) / 'smriprep'))
    sys.exit(int(errno > 0))

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']),
)

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']),
)