def hmc_mcflirt(settings, name='fMRI_HMC_mcflirt'):
"""
An :abbr:`HMC (head motion correction)` for functional scans
using FSL MCFLIRT
.. workflow::
from mriqc.workflows.functional import hmc_mcflirt
wf = hmc_mcflirt({'biggest_file_size_gb': 1})
"""
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['in_file', 'fd_radius', 'start_idx', 'stop_idx']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=['out_file', 'out_fd']),
name='outputnode')
gen_ref = pe.Node(nwr.EstimateReferenceImage(mc_method="AFNI"),
name="gen_ref")
mcflirt = pe.Node(fsl.MCFLIRT(save_plots=True, interpolation='sinc'),
name='MCFLIRT',
mem_gb=settings['biggest_file_size_gb'] * 2.5)
fdnode = pe.Node(nac.FramewiseDisplacement(normalize=False,
parameter_source="FSL"),
name='ComputeFD')
workflow.connect([
(inputnode, gen_ref, [('in_file', 'in_file')]),
(gen_ref, mcflirt, [('ref_image', 'ref_file')]),
(inputnode, mcflirt, [('in_file', 'in_file')]),
(inputnode, fdnode, [('fd_radius', 'radius')]),
(mcflirt, fdnode, [('par_file', 'in_file')]),
(mcflirt, outputnode, [('out_file', 'out_file')]),
(fdnode, outputnode, [('out_file', 'out_fd')]),
])
return workflow
def hmc_afni(settings,
name='fMRI_HMC_afni',
st_correct=False,
despike=False,
deoblique=False,
start_idx=None,
stop_idx=None):
"""
A :abbr:`HMC (head motion correction)` workflow for
functional scans
.. workflow::
from mriqc.workflows.functional import hmc_afni
wf = hmc_afni({'biggest_file_size_gb': 1})
"""
biggest_file_gb = settings.get("biggest_file_size_gb", 1)
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['in_file', 'fd_radius', 'start_idx', 'stop_idx']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=['out_file', 'out_fd']),
name='outputnode')
if (start_idx is not None) or (stop_idx is not None):
drop_trs = pe.Node(afni.Calc(expr='a', outputtype='NIFTI_GZ'),
name='drop_trs')
workflow.connect([
(inputnode, drop_trs, [('in_file', 'in_file_a'),
('start_idx', 'start_idx'),
('stop_idx', 'stop_idx')]),
])
else:
drop_trs = pe.Node(niu.IdentityInterface(fields=['out_file']),
name='drop_trs')
workflow.connect([
(inputnode, drop_trs, [('in_file', 'out_file')]),
])
gen_ref = pe.Node(nwr.EstimateReferenceImage(mc_method="AFNI"),
name="gen_ref")
# calculate hmc parameters
hmc = pe.Node(afni.Volreg(args='-Fourier -twopass',
zpad=4,
outputtype='NIFTI_GZ'),
name='motion_correct',
mem_gb=biggest_file_gb * 2.5)
# Compute the frame-wise displacement
fdnode = pe.Node(nac.FramewiseDisplacement(normalize=False,
parameter_source="AFNI"),
name='ComputeFD')
workflow.connect([
(inputnode, fdnode, [('fd_radius', 'radius')]),
(gen_ref, hmc, [('ref_image', 'basefile')]),
(hmc, outputnode, [('out_file', 'out_file')]),
(hmc, fdnode, [('oned_file', 'in_file')]),
(fdnode, outputnode, [('out_file', 'out_fd')]),
])
# Slice timing correction, despiking, and deoblique
st_corr = pe.Node(afni.TShift(outputtype='NIFTI_GZ'), name='TimeShifts')
deoblique_node = pe.Node(afni.Refit(deoblique=True), name='deoblique')
despike_node = pe.Node(afni.Despike(outputtype='NIFTI_GZ'), name='despike')
if st_correct and despike and deoblique:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, despike_node, [('out_file', 'in_file')]),
(despike_node, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct and despike:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, despike_node, [('out_file', 'in_file')]),
(despike_node, gen_ref, [('out_file', 'in_file')]),
(despike_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct and deoblique:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, gen_ref, [('out_file', 'in_file')]),
(st_corr, hmc, [('out_file', 'in_file')]),
])
elif despike and deoblique:
workflow.connect([
(drop_trs, despike_node, [('out_file', 'in_file')]),
(despike_node, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif despike:
workflow.connect([
(drop_trs, despike_node, [('out_file', 'in_file')]),
(despike_node, gen_ref, [('out_file', 'in_file')]),
(despike_node, hmc, [('out_file', 'in_file')]),
])
elif deoblique:
workflow.connect([
(drop_trs, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
else:
workflow.connect([
(drop_trs, gen_ref, [('out_file', 'in_file')]),
(drop_trs, hmc, [('out_file', 'in_file')]),
])
return workflow