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FIX: Feed *NiTransforms* with LTAs of type RAS2RAS #2444

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Jul 16, 2021
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FIX: Feed *NiTransforms* with LTAs of type RAS2RAS #2444

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FIX: Feed *NiTransforms* with LTAs of type RAS2RAS
oesteban Jul 15, 2021
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oesteban Jul 15, 2021
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68 changes: 37 additions & 31 deletions fmriprep/workflows/bold/registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -439,6 +439,7 @@ def init_bbreg_wf(use_bbr, bold2t1w_dof, bold2t1w_init, omp_nthreads, name='bbre
Boolean indicating whether BBR was rejected (mri_coreg registration returned)

"""
from nipype.interfaces.base.traits_extension import Undefined
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
# See https://github.com/poldracklab/fmriprep/issues/768
from niworkflows.interfaces.freesurfer import (
Expand Down Expand Up @@ -479,41 +480,61 @@ def init_bbreg_wf(use_bbr, bold2t1w_dof, bold2t1w_init, omp_nthreads, name='bbre
LOGGER.warning("Initializing BBR with header; affine fallback disabled")
use_bbr = True

# Define both nodes, but only connect conditionally
mri_coreg = pe.Node(
MRICoregRPT(dof=bold2t1w_dof, sep=[4], ftol=0.0001, linmintol=0.01,
generate_report=not use_bbr),
name='mri_coreg', n_procs=omp_nthreads, mem_gb=5)

bbregister = pe.Node(
BBRegisterRPT(
dof=bold2t1w_dof,
contrast_type='t2',
registered_file=True,
out_lta_file=True,
generate_report=True
),
name='bbregister', mem_gb=12
)
if bold2t1w_init == "header":
bbregister.inputs.init = "header"

transforms = pe.Node(niu.Merge(1 if bold2t1w_init == "header" else 2),
run_without_submitting=True, name='transforms')
lta_ras2ras = pe.MapNode(LTAConvert(out_lta=True), iterfield=['in_lta'],
name='lta_ras2ras', mem_gb=2)
select_transform = pe.Node(niu.Select(), run_without_submitting=True, name='select_transform')
merge_ltas = pe.Node(niu.Merge(2), name='merge_ltas', run_without_submitting=True)
concat_xfm = pe.Node(ConcatenateXFMs(inverse=True), name='concat_xfm')

workflow.connect([
# Output ITK transforms
(inputnode, merge_ltas, [('fsnative2t1w_xfm', 'in2')]),
# Wire up the co-registration alternatives
(bbregister, transforms, [('out_lta_file', 'in1')]),
(transforms, lta_ras2ras, [('out', 'in_lta')]),
(lta_ras2ras, select_transform, [('out_lta', 'inlist')]),
(select_transform, merge_ltas, [('out', 'in1')]),
(merge_ltas, concat_xfm, [('out', 'in_xfms')]),
(concat_xfm, outputnode, [('out_xfm', 'itk_bold_to_t1')]),
(concat_xfm, outputnode, [('out_inv', 'itk_t1_to_bold')]),
])

# Define both nodes, but only connect conditionally
mri_coreg = pe.Node(
MRICoregRPT(dof=bold2t1w_dof, sep=[4], ftol=0.0001, linmintol=0.01,
generate_report=not use_bbr),
name='mri_coreg', n_procs=omp_nthreads, mem_gb=5)

bbregister = pe.Node(
BBRegisterRPT(dof=bold2t1w_dof, contrast_type='t2', registered_file=True,
out_lta_file=True, generate_report=True),
name='bbregister', mem_gb=12)

# Use mri_coreg
# Do not initialize with header, use mri_coreg
if bold2t1w_init == "register":
workflow.connect([
(inputnode, mri_coreg, [('subjects_dir', 'subjects_dir'),
('subject_id', 'subject_id'),
('in_file', 'source_file')]),
(mri_coreg, bbregister, [('out_lta_file', 'init_reg_file')]),
(mri_coreg, transforms, [('out_lta_file', 'in2')]),
])

# Short-circuit workflow building, use initial registration
if use_bbr is False:
select_transform.inputs.index = 1
workflow.connect([
(mri_coreg, outputnode, [('out_report', 'out_report')]),
(mri_coreg, merge_ltas, [('out_lta_file', 'in1')])])
])
outputnode.inputs.fallback = True

return workflow
Expand All @@ -525,43 +546,28 @@ def init_bbreg_wf(use_bbr, bold2t1w_dof, bold2t1w_init, omp_nthreads, name='bbre
('in_file', 'source_file')]),
])

if bold2t1w_init == "header":
bbregister.inputs.init = "header"
else:
workflow.connect([(mri_coreg, bbregister, [('out_lta_file', 'init_reg_file')])])

# Short-circuit workflow building, use boundary-based registration
if use_bbr is True:
select_transform.inputs.index = 0
workflow.connect([
(bbregister, outputnode, [('out_report', 'out_report')]),
(bbregister, merge_ltas, [('out_lta_file', 'in1')])])
])
outputnode.inputs.fallback = False

return workflow

# Only reach this point if bold2t1w_init is "register" and use_bbr is None

transforms = pe.Node(niu.Merge(2), run_without_submitting=True, name='transforms')
reports = pe.Node(niu.Merge(2), run_without_submitting=True, name='reports')

lta_ras2ras = pe.MapNode(LTAConvert(out_lta=True), iterfield=['in_lta'],
name='lta_ras2ras', mem_gb=2)
compare_transforms = pe.Node(niu.Function(function=compare_xforms), name='compare_transforms')

select_transform = pe.Node(niu.Select(), run_without_submitting=True, name='select_transform')
select_report = pe.Node(niu.Select(), run_without_submitting=True, name='select_report')

workflow.connect([
(bbregister, transforms, [('out_lta_file', 'in1')]),
(mri_coreg, transforms, [('out_lta_file', 'in2')]),
# Normalize LTA transforms to RAS2RAS (inputs are VOX2VOX) and compare
(transforms, lta_ras2ras, [('out', 'in_lta')]),
(lta_ras2ras, compare_transforms, [('out_lta', 'lta_list')]),
(compare_transforms, outputnode, [('out', 'fallback')]),
# Select output transform
(transforms, select_transform, [('out', 'inlist')]),
(compare_transforms, select_transform, [('out', 'index')]),
(select_transform, merge_ltas, [('out', 'in1')]),
# Select output report
(bbregister, reports, [('out_report', 'in1')]),
(mri_coreg, reports, [('out_report', 'in2')]),
Expand Down