def all_fmb_pipeline(name='hmc_sdc_ecc', fugue_params=dict(smooth3d=2.0)):
"""
Builds a pipeline including three artifact corrections: head-motion
correction (HMC), susceptibility-derived distortion correction (SDC),
and Eddy currents-derived distortion correction (ECC).
The displacement fields from each kind of distortions are combined. Thus,
only one interpolation occurs between input data and result.
.. warning:: this workflow rotates the gradients table (*b*-vectors)
[Leemans09]_.
Examples
--------
>>> from nipype.workflows.dmri.fsl.artifacts import all_fmb_pipeline
>>> allcorr = all_fmb_pipeline()
>>> allcorr.inputs.inputnode.in_file = 'epi.nii'
>>> allcorr.inputs.inputnode.in_bval = 'diffusion.bval'
>>> allcorr.inputs.inputnode.in_bvec = 'diffusion.bvec'
>>> allcorr.inputs.inputnode.bmap_mag = 'magnitude.nii'
>>> allcorr.inputs.inputnode.bmap_pha = 'phase.nii'
>>> allcorr.inputs.inputnode.epi_param = 'epi_param.txt'
>>> allcorr.run() # doctest: +SKIP
"""
inputnode = pe.Node(niu.IdentityInterface(
fields=['in_file', 'in_bvec', 'in_bval', 'bmap_pha', 'bmap_mag',
'epi_param']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_file', 'out_mask', 'out_bvec']), name='outputnode')
list_b0 = pe.Node(niu.Function(
input_names=['in_bval'], output_names=['out_idx'],
function=b0_indices), name='B0indices')
avg_b0_0 = pe.Node(niu.Function(
input_names=['in_file', 'index'], output_names=['out_file'],
function=time_avg), name='b0_avg_pre')
avg_b0_1 = pe.Node(niu.Function(
input_names=['in_file', 'index'], output_names=['out_file'],
function=time_avg), name='b0_avg_post')
bet_dwi0 = pe.Node(fsl.BET(frac=0.3, mask=True, robust=True),
name='bet_dwi_pre')
bet_dwi1 = pe.Node(fsl.BET(frac=0.3, mask=True, robust=True),
name='bet_dwi_post')
hmc = hmc_pipeline()
sdc = sdc_fmb(fugue_params=fugue_params)
ecc = ecc_pipeline()
unwarp = apply_all_corrections()
wf = pe.Workflow(name=name)
wf.connect([
(inputnode, hmc, [('in_file', 'inputnode.in_file'),
('in_bvec', 'inputnode.in_bvec'),
('in_bval', 'inputnode.in_bval')]),
(inputnode, list_b0, [('in_bval', 'in_bval')]),
(inputnode, avg_b0_0, [('in_file', 'in_file')]),
(list_b0, avg_b0_0, [('out_idx', 'index')]),
(avg_b0_0, bet_dwi0, [('out_file', 'in_file')]),
(bet_dwi0, hmc, [('mask_file', 'inputnode.in_mask')]),
(hmc, sdc, [
('outputnode.out_file', 'inputnode.in_file')]),
(bet_dwi0, sdc, [('mask_file', 'inputnode.in_mask')]),
(inputnode, sdc, [('bmap_pha', 'inputnode.bmap_pha'),
('bmap_mag', 'inputnode.bmap_mag'),
('epi_param', 'inputnode.settings')]),
(list_b0, sdc, [('out_idx', 'inputnode.in_ref')]),
(hmc, ecc, [
('outputnode.out_xfms', 'inputnode.in_xfms')]),
(inputnode, ecc, [('in_file', 'inputnode.in_file'),
('in_bval', 'inputnode.in_bval')]),
(bet_dwi0, ecc, [('mask_file', 'inputnode.in_mask')]),
(ecc, avg_b0_1, [('outputnode.out_file', 'in_file')]),
(list_b0, avg_b0_1, [('out_idx', 'index')]),
(avg_b0_1, bet_dwi1, [('out_file', 'in_file')]),
(inputnode, unwarp, [('in_file', 'inputnode.in_dwi')]),
(hmc, unwarp, [('outputnode.out_xfms', 'inputnode.in_hmc')]),
(ecc, unwarp, [('outputnode.out_xfms', 'inputnode.in_ecc')]),
(sdc, unwarp, [('outputnode.out_warp', 'inputnode.in_sdc')]),
(hmc, outputnode, [('outputnode.out_bvec', 'out_bvec')]),
(unwarp, outputnode, [('outputnode.out_file', 'out_file')]),
(bet_dwi1, outputnode, [('mask_file', 'out_mask')])
])
return wf
def all_peb_pipeline(name='hmc_sdc_ecc',
epi_params=dict(echospacing=0.77e-3,
acc_factor=3,
enc_dir='y-',
epi_factor=1),
altepi_params=dict(echospacing=0.77e-3,
acc_factor=3,
enc_dir='y',
epi_factor=1)):
"""
Builds a pipeline including three artifact corrections: head-motion
correction (HMC), susceptibility-derived distortion correction (SDC),
and Eddy currents-derived distortion correction (ECC).
.. warning:: this workflow rotates the gradients table (*b*-vectors)
[Leemans09]_.
Examples
--------
>>> from nipype.workflows.dmri.fsl.artifacts import all_peb_pipeline
>>> allcorr = all_peb_pipeline()
>>> allcorr.inputs.inputnode.in_file = 'epi.nii'
>>> allcorr.inputs.inputnode.alt_file = 'epi_rev.nii'
>>> allcorr.inputs.inputnode.in_bval = 'diffusion.bval'
>>> allcorr.inputs.inputnode.in_bvec = 'diffusion.bvec'
>>> allcorr.run() # doctest: +SKIP
"""
inputnode = pe.Node(niu.IdentityInterface(
fields=['in_file', 'in_bvec', 'in_bval', 'alt_file']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_file', 'out_mask', 'out_bvec']), name='outputnode')
avg_b0_0 = pe.Node(niu.Function(
input_names=['in_dwi', 'in_bval'], output_names=['out_file'],
function=b0_average), name='b0_avg_pre')
avg_b0_1 = pe.Node(niu.Function(
input_names=['in_dwi', 'in_bval'], output_names=['out_file'],
function=b0_average), name='b0_avg_post')
bet_dwi0 = pe.Node(fsl.BET(frac=0.3, mask=True, robust=True),
name='bet_dwi_pre')
bet_dwi1 = pe.Node(fsl.BET(frac=0.3, mask=True, robust=True),
name='bet_dwi_post')
hmc = hmc_pipeline()
sdc = sdc_peb(epi_params=epi_params, altepi_params=altepi_params)
ecc = ecc_pipeline()
unwarp = apply_all_corrections()
wf = pe.Workflow(name=name)
wf.connect([
(inputnode, hmc, [('in_file', 'inputnode.in_file'),
('in_bvec', 'inputnode.in_bvec'),
('in_bval', 'inputnode.in_bval')]),
(inputnode, avg_b0_0, [('in_file', 'in_dwi'),
('in_bval', 'in_bval')]),
(avg_b0_0, bet_dwi0, [('out_file', 'in_file')]),
(bet_dwi0, hmc, [('mask_file', 'inputnode.in_mask')]),
(hmc, sdc, [
('outputnode.out_file', 'inputnode.in_file')]),
(bet_dwi0, sdc, [('mask_file', 'inputnode.in_mask')]),
(inputnode, sdc, [('in_bval', 'inputnode.in_bval'),
('alt_file', 'inputnode.alt_file')]),
(inputnode, ecc, [('in_file', 'inputnode.in_file'),
('in_bval', 'inputnode.in_bval')]),
(bet_dwi0, ecc, [('mask_file', 'inputnode.in_mask')]),
(hmc, ecc, [
('outputnode.out_xfms', 'inputnode.in_xfms')]),
(ecc, avg_b0_1, [('outputnode.out_file', 'in_dwi')]),
(inputnode, avg_b0_1, [('in_bval', 'in_bval')]),
(avg_b0_1, bet_dwi1, [('out_file', 'in_file')]),
(inputnode, unwarp, [('in_file', 'inputnode.in_dwi')]),
(hmc, unwarp, [('outputnode.out_xfms', 'inputnode.in_hmc')]),
(ecc, unwarp, [('outputnode.out_xfms', 'inputnode.in_ecc')]),
(sdc, unwarp, [('outputnode.out_warp', 'inputnode.in_sdc')]),
(hmc, outputnode, [('outputnode.out_bvec', 'out_bvec')]),
(unwarp, outputnode, [('outputnode.out_file', 'out_file')]),
(bet_dwi1, outputnode, [('mask_file', 'out_mask')])
])
return wf