def build_core_nodes(self):
"""Build and connect the core nodes of the pipelines.
"""
import nipype.interfaces.fsl as fsl
import nipype.interfaces.utility as nutil
import nipype.pipeline.engine as npe
import clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_utils as utils
import clinica.pipelines.dwi_preprocessing_using_t1.dwi_preprocessing_using_t1_workflows as workflows
from clinica.utils.dwi import prepare_reference_b0
from clinica.workflows.dwi_preprocessing import (
ecc_pipeline,
hmc_pipeline,
remove_bias,
)
# Nodes creation
# ==============
# Prepare b0 image for further corrections
prepare_b0 = npe.Node(name="PrepareB0", interface=nutil.Function(
input_names=['in_dwi', 'in_bval', 'in_bvec', 'low_bval'],
output_names=['out_reference_b0', 'out_b0_dwi_merge',
'out_updated_bval', 'out_updated_bvec'],
function=prepare_reference_b0))
prepare_b0.inputs.low_bval = self.parameters['low_bval']
# Mask b0 for computations purposes
mask_b0_pre = npe.Node(fsl.BET(frac=0.3, mask=True, robust=True),
name='PreMaskB0')
# Head-motion correction
hmc = hmc_pipeline(name='HeadMotionCorrection')
# Eddy-currents correction
ecc = ecc_pipeline(name='EddyCurrentCorrection')
# Susceptibility distortion correction using T1w image
sdc = workflows.susceptibility_distortion_correction_using_t1(
name='SusceptibilityDistortionCorrection')
# Remove bias correction
bias = remove_bias(name='RemoveBias')
# Apply all corrections
aac = workflows.apply_all_corrections_using_ants(
name='ApplyAllCorrections')
print_begin_message = npe.Node(
interface=nutil.Function(
input_names=['in_bids_or_caps_file'],
function=utils.print_begin_pipeline),
name='Write-Begin_Message')
print_end_message = npe.Node(
interface=nutil.Function(
input_names=['in_bids_or_caps_file', 'final_file'],
function=utils.print_end_pipeline),
name='Write-End_Message')
# Connection
# ==========
self.connect([
# Print begin message
(self.input_node, print_begin_message, [('dwi', 'in_bids_or_caps_file')]), # noqa
# Preliminary step (possible computation of a mean b0):
(self.input_node, prepare_b0, [('dwi', 'in_dwi'), # noqa
('bval', 'in_bval'), # noqa
('bvec', 'in_bvec')]), # noqa
# Mask b0 before corrections
(prepare_b0, mask_b0_pre, [('out_reference_b0', 'in_file')]), # noqa
# Head-motion correction
(prepare_b0, hmc, [('out_b0_dwi_merge', 'inputnode.in_file'), # noqa
('out_updated_bval', 'inputnode.in_bval'), # noqa
('out_updated_bvec', 'inputnode.in_bvec')]), # noqa
(mask_b0_pre, hmc, [('mask_file', 'inputnode.in_mask')]), # noqa
# Eddy-current correction
(hmc, ecc, [('outputnode.out_xfms', 'inputnode.in_xfms')]), # noqa
(prepare_b0, ecc, [('out_b0_dwi_merge', 'inputnode.in_file')]), # noqa
(prepare_b0, ecc, [('out_updated_bval', 'inputnode.in_bval')]), # noqa
(mask_b0_pre, ecc, [('mask_file', 'inputnode.in_mask')]), # noqa
# Magnetic susceptibility correction
(self.input_node, sdc, [('T1w', 'inputnode.in_t1')]), # noqa
(ecc, sdc, [('outputnode.out_file', 'inputnode.in_dwi')]), # noqa
(hmc, sdc, [('outputnode.out_bvec', 'inputnode.in_bvec')]), # noqa
# Apply all corrections
(prepare_b0, aac, [('out_b0_dwi_merge', 'inputnode.in_dwi')]), # noqa
(hmc, aac, [('outputnode.out_xfms', 'inputnode.in_hmc')]), # noqa
(ecc, aac, [('outputnode.out_xfms', 'inputnode.in_ecc')]), # noqa
(sdc, aac, [('outputnode.out_warp', 'inputnode.in_sdc_syb')]), # noqa
(self.input_node, aac, [('T1w', 'inputnode.in_t1')]), # noqa
# Bias correction
(aac, bias, [('outputnode.out_file', 'inputnode.in_file')]),
# Outputnode:
(bias, self.output_node, [('outputnode.out_file', 'preproc_dwi')]), # noqa
(sdc, self.output_node, [('outputnode.out_bvec', 'preproc_bvec')]), # noqa
(prepare_b0, self.output_node, [('out_updated_bval', 'preproc_bval')]), # noqa
(bias, self.output_node, [('outputnode.b0_mask', 'b0_mask')]), # noqa
# Print end message
(self.input_node, print_end_message, [('dwi', 'in_bids_or_caps_file')]), # noqa
(bias, print_end_message, [('outputnode.out_file', 'final_file')]), # noqa
])
def build_core_nodes(self):
"""Build and connect the core nodes of the pipeline.
"""
import nipype.interfaces.utility as nutil
import nipype.pipeline.engine as npe
import nipype.interfaces.fsl as fsl
from nipype.workflows.dmri.fsl.utils import apply_all_corrections
from clinica.utils.dwi import prepare_reference_b0
from clinica.workflows.dwi_preprocessing import ecc_pipeline
from clinica.workflows.dwi_preprocessing import hmc_pipeline
from clinica.workflows.dwi_preprocessing import remove_bias
import clinica.pipelines.dwi_preprocessing_using_phasediff_fieldmap.dwi_preprocessing_using_phasediff_fieldmap_workflows as workflows
# Nodes creation
# ==============
# Prepare b0 image for further corrections
prepare_b0 = npe.Node(
name="PrepareB0",
interface=nutil.Function(
input_names=['in_dwi', 'in_bval', 'in_bvec', 'low_bval'],
output_names=[
'out_reference_b0', 'out_b0_dwi_merge', 'out_updated_bval',
'out_updated_bvec'
],
function=prepare_reference_b0))
prepare_b0.inputs.low_bval = self.parameters['low_bval']
# Mask b0 for computations purposes
mask_b0_pre = npe.Node(fsl.BET(frac=0.3, mask=True, robust=True),
name='PreMaskB0')
# Head-motion correction
hmc = hmc_pipeline(name='HeadMotionCorrection')
# Eddy-currents correction
ecc = ecc_pipeline(name='EddyCurrentCorrection')
# Susceptibility distortion correction using fmap
sdc = workflows.susceptibility_distortion_correction_using_phasediff_fmap(
register_fmap_on_b0=True,
name='SusceptibilityDistortionCorrection')
# Apply all corrections
unwarp = apply_all_corrections(name='ApplyAllCorrections')
# Remove bias correction
bias = remove_bias(name='RemoveBias')
#
# Connection
# ==========
self.connect([
# Preliminary step (possible computation of a mean b0)
(
self.input_node,
prepare_b0,
[
('dwi', 'in_dwi'), # noqa
('bval', 'in_bval'), # noqa
('bvec', 'in_bvec')
]), # noqa
# Mask b0 before corrections
(prepare_b0, mask_b0_pre, [('out_reference_b0', 'in_file')]
), # noqa
# Head-motion correction
(
prepare_b0,
hmc,
[
('out_b0_dwi_merge', 'inputnode.in_file'), # noqa
('out_updated_bval', 'inputnode.in_bval'), # noqa
('out_updated_bvec', 'inputnode.in_bvec')
]), # noqa
(mask_b0_pre, hmc, [('mask_file', 'inputnode.in_mask')]), # noqa
# Eddy-current correction
(hmc, ecc, [('outputnode.out_xfms', 'inputnode.in_xfms')]), # noqa
(prepare_b0, ecc, [('out_b0_dwi_merge', 'inputnode.in_file')
]), # noqa
(prepare_b0, ecc, [('out_updated_bval', 'inputnode.in_bval')
]), # noqa
(mask_b0_pre, ecc, [('mask_file', 'inputnode.in_mask')]), # noqa
# Magnetic susceptibility correction
(ecc, sdc, [('outputnode.out_file', 'inputnode.in_dwi')]), # noqa
(mask_b0_pre, sdc, [('mask_file', 'inputnode.in_mask')]), # noqa
(self.input_node, sdc, [('fmap_phasediff',
'inputnode.in_fmap_phasediff')]), # noqa
(self.input_node, sdc, [('fmap_magnitude',
'inputnode.in_fmap_magnitude')]), # noqa
(self.input_node, sdc, [('delta_echo_time',
'inputnode.delta_echo_time')]), # noqa
(self.input_node, sdc, [
('effective_echo_spacing', 'inputnode.effective_echo_spacing')
]), # noqa
(self.input_node, sdc, [('phase_encoding_direction',
'inputnode.phase_encoding_direction')
]), # noqa
# Apply all corrections
(prepare_b0, unwarp, [('out_b0_dwi_merge', 'inputnode.in_dwi')]
), # noqa
(hmc, unwarp, [('outputnode.out_xfms', 'inputnode.in_hmc')
]), # noqa
(ecc, unwarp, [('outputnode.out_xfms', 'inputnode.in_ecc')
]), # noqa
(sdc, unwarp, [('outputnode.out_warp', 'inputnode.in_sdc')
]), # noqa
# Bias correction
(unwarp, bias, [('outputnode.out_file', 'inputnode.in_file')]),
# Outputnode
(bias, self.output_node, [('outputnode.out_file', 'preproc_dwi')]
), # noqa
(hmc, self.output_node, [('outputnode.out_bvec', 'preproc_bvec')
]), # noqa
(prepare_b0, self.output_node, [('out_updated_bval',
'preproc_bval')]), # noqa
(bias, self.output_node, [('outputnode.b0_mask', 'b0_mask')]
) # noqa
])