Source code for dmriprep.workflows.fieldmap.fmap

#!/usr/bin/env python

from nipype.pipeline import engine as pe
from nipype.interfaces import fsl, utility as niu


def init_fmap_wf(bet_mag):

    wf = pe.Workflow(name='fmap_prep_wf')

    inputnode = pe.Node(
        niu.IdentityInterface(fields=['fieldmap', 'magnitude', 'b0_stripped']),
        name='inputnode',
    )

    outputnode = pe.Node(
        niu.IdentityInterface(fields=['out_fmap']), name='outputnode'
    )

    rad_to_hz = pe.Node(
        fsl.BinaryMaths(operation='div', operand_value=6.28), name='radToHz'
    )

    mag_bet = pe.Node(fsl.BET(frac=bet_mag, mask=True, robust=True), name='mag_bet')

    mag_flirt = pe.Node(fsl.FLIRT(dof=6), name='magFlirt')

    fmap_flirt = pe.Node(fsl.FLIRT(apply_xfm=True), name='fmapFlirt')

    wf.connect(
        [
            (inputnode, rad_to_hz, [('fieldmap', 'in_file')]),
            (inputnode, mag_bet, [('magnitude', 'in_file')]),
            (mag_bet, mag_flirt, [('out_file', 'in_file')]),
            (inputnode, mag_flirt, [('b0_stripped', 'reference')]),
            (rad_to_hz, fmap_flirt, [('out_file', 'in_file')]),
            (inputnode, fmap_flirt, [('b0_stripped', 'reference')]),
            (mag_flirt, fmap_flirt, [('out_matrix_file', 'in_matrix_file')]),
            (fmap_flirt, outputnode, [('out_file', 'out_fmap')]),
        ]
    )

    return wf