How to use the smriprep.workflows.surfaces.init_surface_recon_wf function in smriprep

To help you get started, we’ve selected a few smriprep examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github poldracklab / smriprep / doc_test_2 / _sources / smriprep-workflows-16.py View on Github external
from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1, hires=True)
github poldracklab / smriprep / api / smriprep-workflows-surfaces-4.py View on Github external
from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1, hires=True)
github poldracklab / smriprep / master / api / smriprep-workflows-surfaces-7.py View on Github external
from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1, hires=True)
github poldracklab / smriprep / smriprep / workflows / anatomical.py View on Github external
(fast2bids, outputnode, [('out', 't1w_tpms')]),
        ])
        return workflow

    # Map FS' aseg labels onto three-tissue segmentation
    lut_t1w_dseg.inputs.lut = _aseg_to_three()
    split_seg = pe.Node(niu.Function(function=_split_segments),
                        name='split_seg')

    # check for older IsRunning files and remove accordingly
    fs_isrunning = pe.Node(niu.Function(function=_fs_isRunning),
                           overwrite=True, name='fs_isrunning')
    fs_isrunning.inputs.logger = LOGGER

    # 5. Surface reconstruction (--fs-no-reconall not set)
    surface_recon_wf = init_surface_recon_wf(name='surface_recon_wf',
                                             omp_nthreads=omp_nthreads, hires=hires)
    applyrefined = pe.Node(fsl.ApplyMask(), name='applyrefined')
    workflow.connect([
        (inputnode, fs_isrunning, [
            ('subjects_dir', 'subjects_dir'),
            ('subject_id', 'subject_id')]),
        (inputnode, surface_recon_wf, [
            ('t2w', 'inputnode.t2w'),
            ('flair', 'inputnode.flair'),
            ('subject_id', 'inputnode.subject_id')]),
        (fs_isrunning, surface_recon_wf, [('out', 'inputnode.subjects_dir')]),
        (anat_validate, surface_recon_wf, [('out_file', 'inputnode.t1w')]),
        (brain_extraction_wf, surface_recon_wf, [
            (('outputnode.out_file', _pop), 'inputnode.skullstripped_t1'),
            ('outputnode.out_segm', 'inputnode.ants_segs'),
            (('outputnode.bias_corrected', _pop), 'inputnode.corrected_t1')]),
github poldracklab / smriprep / master / api / smriprep-workflows-surfaces-4.py View on Github external
from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1, hires=True)
github poldracklab / smriprep / 0.4.0rc1 / api / smriprep-workflows-surfaces-4.py View on Github external
from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1, hires=True)