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REF: Split final boldref generation from BOLD-BOLD resampling, eliminate extra per-echo computation #2181

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merged 17 commits into from
Aug 18, 2020
Merged

REF: Split final boldref generation from BOLD-BOLD resampling, eliminate extra per-echo computation #2181

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abee610
Join bold masks and select first echo's mask for multi-echo data.
tsalo Jun 6, 2020
cd1925d
Fix and consolidate multi-echo-toggled connections.
tsalo Jun 6, 2020
559e11c
Merge remote-tracking branch 'poldracklab/master' into fix/meepi-aroma
tsalo Jun 9, 2020
a5e387d
Replace select_first with pop_file.
tsalo Jun 9, 2020
0b8a388
Merge branch 'master' into fix/meepi-aroma
tsalo Aug 15, 2020
d3d3dab
Add freesurfer check back in.
tsalo Aug 15, 2020
5d8fe48
Fix up merge.
tsalo Aug 15, 2020
211c298
Apply suggestions from code review
tsalo Aug 17, 2020
309a613
Move final boldref wf to init_func_preproc_wf.
tsalo Aug 17, 2020
80aa3b6
Fix the bugs.
tsalo Aug 17, 2020
0f8936a
Fix links.
tsalo Aug 17, 2020
9e5a689
Fix reference image link.
tsalo Aug 17, 2020
71226b9
Update fmriprep/workflows/bold/base.py
tsalo Aug 18, 2020
9d530ea
Update fmriprep/workflows/bold/base.py
tsalo Aug 18, 2020
3703963
Apply suggestions from code review
tsalo Aug 18, 2020
3e9d2cb
Update fmriprep/workflows/bold/base.py
tsalo Aug 18, 2020
7415cbb
Cleanup to minimize diff.
tsalo Aug 18, 2020
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113 changes: 65 additions & 48 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu

from niworkflows.utils.connections import pop_file, listify
from niworkflows.utils.connections import listify, pop_file
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from ...utils.meepi import combine_meepi_source
Expand Down Expand Up @@ -125,7 +125,7 @@ def init_func_preproc_wf(bold_file):
* :py:func:`~fmriprep.workflows.bold.t2s.init_bold_t2s_wf`
* :py:func:`~fmriprep.workflows.bold.registration.init_bold_t1_trans_wf`
* :py:func:`~fmriprep.workflows.bold.registration.init_bold_reg_wf`
* :py:func:`~fmriprep.workflows.bold.confounds.init_bold_confounds_wf`
* :py:func:`~fmriprep.workflows.bold.confounds.init_bold_confs_wf`
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* :py:func:`~fmriprep.workflows.bold.confounds.init_ica_aroma_wf`
* :py:func:`~fmriprep.workflows.bold.resampling.init_bold_std_trans_wf`
* :py:func:`~fmriprep.workflows.bold.resampling.init_bold_preproc_trans_wf`
Expand Down Expand Up @@ -307,13 +307,14 @@ def init_func_preproc_wf(bold_file):
])

# Generate a tentative boldref
bold_reference_wf = init_bold_reference_wf(
initial_boldref_wf = init_bold_reference_wf(
name='initial_boldref_wf',
omp_nthreads=omp_nthreads,
bold_file=bold_file,
sbref_files=sbref_files,
multiecho=multiecho,
)
bold_reference_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
initial_boldref_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans

# Top-level BOLD splitter
bold_split = pe.Node(FSLSplit(dimension='t'), name='bold_split',
Expand Down Expand Up @@ -365,17 +366,25 @@ def init_func_preproc_wf(bold_file):
)
bold_bold_trans_wf.inputs.inputnode.name_source = ref_file

# Generate a new BOLD reference
# This BOLD references *does not use* single-band reference images.
final_boldref_wf = init_bold_reference_wf(
name='final_boldref_wf',
omp_nthreads=omp_nthreads
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)
final_boldref_wf.__desc__ = None # Unset description to avoid second appearance

# SLICE-TIME CORRECTION (or bypass) #############################################
if run_stc is True: # bool('TooShort') == True, so check True explicitly
bold_stc_wf = init_bold_stc_wf(name='bold_stc_wf', metadata=metadata)
workflow.connect([
(bold_reference_wf, bold_stc_wf, [
(initial_boldref_wf, bold_stc_wf, [
('outputnode.skip_vols', 'inputnode.skip_vols')]),
(bold_stc_wf, boldbuffer, [('outputnode.stc_file', 'bold_file')]),
])
if not multiecho:
workflow.connect([
(bold_reference_wf, bold_stc_wf, [
(initial_boldref_wf, bold_stc_wf, [
('outputnode.bold_file', 'inputnode.bold_file')])])
else: # for meepi, iterate through stc_wf for all workflows
meepi_echos = boldbuffer.clone(name='meepi_echos')
Expand All @@ -385,7 +394,7 @@ def init_func_preproc_wf(bold_file):
elif not multiecho: # STC is too short or False
# bypass STC from original BOLD to the splitter through boldbuffer
workflow.connect([
(bold_reference_wf, boldbuffer, [('outputnode.bold_file', 'bold_file')])])
(initial_boldref_wf, boldbuffer, [('outputnode.bold_file', 'bold_file')])])
else:
# for meepi, iterate over all meepi echos to boldbuffer
boldbuffer.iterables = ('bold_file', bold_file)
Expand All @@ -404,10 +413,12 @@ def init_func_preproc_wf(bold_file):

inputnode.inputs.bold_file = ref_file # Replace reference w first echo

join_echos = pe.JoinNode(niu.IdentityInterface(fields=['bold_files']),
joinsource=('meepi_echos' if run_stc is True else 'boldbuffer'),
joinfield=['bold_files'],
name='join_echos')
join_echos = pe.JoinNode(
niu.IdentityInterface(fields=['bold_files', 'skullstripped_bold_files']),
joinsource=('meepi_echos' if run_stc is True else 'boldbuffer'),
joinfield=['bold_files'],
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name='join_echos'
)

# create optimal combination, adaptive T2* map
bold_t2s_wf = init_bold_t2s_wf(echo_times=tes,
Expand All @@ -422,10 +433,10 @@ def init_func_preproc_wf(bold_file):
# BOLD buffer has slice-time corrected if it was run, original otherwise
(boldbuffer, bold_split, [('bold_file', 'in_file')]),
# HMC
(bold_reference_wf, bold_hmc_wf, [
(initial_boldref_wf, bold_hmc_wf, [
('outputnode.raw_ref_image', 'inputnode.raw_ref_image'),
('outputnode.bold_file', 'inputnode.bold_file')]),
(bold_reference_wf, summary, [
(initial_boldref_wf, summary, [
('outputnode.algo_dummy_scans', 'algo_dummy_scans')]),
# EPI-T1 registration workflow
(inputnode, bold_reg_wf, [
Expand Down Expand Up @@ -456,7 +467,7 @@ def init_func_preproc_wf(bold_file):
# SDC (or pass-through workflow)
(t1w_brain, bold_sdc_wf, [
('out_file', 'inputnode.t1w_brain')]),
(bold_reference_wf, bold_sdc_wf, [
(initial_boldref_wf, bold_sdc_wf, [
('outputnode.ref_image', 'inputnode.epi_file'),
('outputnode.ref_image_brain', 'inputnode.epi_brain'),
('outputnode.bold_mask', 'inputnode.epi_mask')]),
Expand All @@ -477,11 +488,8 @@ def init_func_preproc_wf(bold_file):
('outputnode.rmsd_file', 'inputnode.rmsd_file')]),
(bold_reg_wf, bold_confounds_wf, [
('outputnode.itk_t1_to_bold', 'inputnode.t1_bold_xform')]),
(bold_reference_wf, bold_confounds_wf, [
(initial_boldref_wf, bold_confounds_wf, [
('outputnode.skip_vols', 'inputnode.skip_vols')]),
(bold_bold_trans_wf, bold_confounds_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask'),
]),
(bold_confounds_wf, outputnode, [
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('outputnode.confounds_file', 'confounds'),
]),
Expand All @@ -493,6 +501,8 @@ def init_func_preproc_wf(bold_file):
('out_files', 'inputnode.bold_file')]),
(bold_hmc_wf, bold_bold_trans_wf, [
('outputnode.xforms', 'inputnode.hmc_xforms')]),
(final_boldref_wf, bold_confounds_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask')]),
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# Summary
(outputnode, summary, [('confounds', 'confounds_file')]),
])
Expand All @@ -504,6 +514,8 @@ def init_func_preproc_wf(bold_file):
('bold_file', 'inputnode.source_file')]),
(bold_bold_trans_wf, bold_confounds_wf, [
('outputnode.bold', 'inputnode.bold')]),
(bold_bold_trans_wf, final_boldref_wf, [
('outputnode.bold', 'inputnode.bold_file')]),
(bold_split, bold_t1_trans_wf, [
('out_files', 'inputnode.bold_split')]),
(bold_hmc_wf, bold_t1_trans_wf, [
Expand All @@ -516,18 +528,22 @@ def init_func_preproc_wf(bold_file):
# update name source for optimal combination
(inputnode, func_derivatives_wf, [
(('bold_file', combine_meepi_source), 'inputnode.source_file')]),
(bold_bold_trans_wf, join_echos, [
('outputnode.bold', 'bold_files')]),
(join_echos, final_boldref_wf, [
('bold_files', 'inputnode.bold_file')]),
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(bold_bold_trans_wf, skullstrip_bold_wf, [
('outputnode.bold', 'inputnode.in_file')]),
(skullstrip_bold_wf, join_echos, [
('outputnode.skull_stripped_file', 'bold_files')]),
('outputnode.skull_stripped_file', 'skullstripped_bold_files')]),
(join_echos, bold_t2s_wf, [
('bold_files', 'inputnode.bold_file')]),
('skullstripped_bold_files', 'inputnode.bold_file')]),
(bold_t2s_wf, bold_confounds_wf, [
('outputnode.bold', 'inputnode.bold')]),
(bold_t2s_wf, split_opt_comb, [
('outputnode.bold', 'in_file')]),
(split_opt_comb, bold_t1_trans_wf, [
('out_files', 'inputnode.bold_split')]),
('out_files', 'inputnode.bold_split')])
])

# Already applied in bold_bold_trans_wf, which inputs to bold_t2s_wf
Expand All @@ -541,7 +557,7 @@ def init_func_preproc_wf(bold_file):
workflow.connect([
(inputnode, fmap_unwarp_report_wf, [
('t1w_dseg', 'inputnode.in_seg')]),
(bold_reference_wf, fmap_unwarp_report_wf, [
(initial_boldref_wf, fmap_unwarp_report_wf, [
('outputnode.ref_image', 'inputnode.in_pre')]),
(bold_reg_wf, fmap_unwarp_report_wf, [
('outputnode.itk_t1_to_bold', 'inputnode.in_xfm')]),
Expand Down Expand Up @@ -578,7 +594,7 @@ def init_func_preproc_wf(bold_file):
workflow.connect([
(inputnode, syn_unwarp_report_wf, [
('t1w_dseg', 'inputnode.in_seg')]),
(bold_reference_wf, syn_unwarp_report_wf, [
(initial_boldref_wf, syn_unwarp_report_wf, [
('outputnode.ref_image', 'inputnode.in_pre')]),
(bold_reg_wf, syn_unwarp_report_wf, [
('outputnode.itk_t1_to_bold', 'inputnode.in_xfm')]),
Expand Down Expand Up @@ -607,19 +623,19 @@ def init_func_preproc_wf(bold_file):
('outputnode.itk_bold_to_t1', 'transforms')]),
(bold_t1_trans_wf, boldmask_to_t1w, [
('outputnode.bold_mask_t1', 'reference_image')]),
(bold_bold_trans_wf, boldmask_to_t1w, [
('outputnode.bold_mask', 'input_image')]),
(boldmask_to_t1w, outputnode, [
('output_image', 'bold_mask_t1')]),
(final_boldref_wf, boldmask_to_t1w, [
('outputnode.bold_mask', 'input_image')])
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])

if nonstd_spaces.intersection(('func', 'run', 'bold', 'boldref', 'sbref')):
workflow.connect([
(bold_bold_trans_wf, outputnode, [
('outputnode.bold', 'bold_native')]),
(bold_bold_trans_wf, func_derivatives_wf, [
('outputnode.bold_ref', 'inputnode.bold_native_ref'),
(final_boldref_wf, func_derivatives_wf, [
('outputnode.ref_image', 'inputnode.bold_native_ref'),
('outputnode.bold_mask', 'inputnode.bold_mask_native')]),
(bold_bold_trans_wf if not multiecho else bold_t2s_wf, outputnode, [
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This seems to be a semantic change, not just a reorganization. Was this something we were doing wrong?

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Sorry, yes, I think it was wrong before, since it took the BOLD files from bold_bold_trans_wf for the native-space BOLD outputs.

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Looking through, I agree with this change. If I'm reading it right, a native BOLD space derivative for MEEPI will be the optimal combination, which seems appropriate.

('outputnode.bold', 'bold_native')])
])

if spaces.get_spaces(nonstandard=False, dim=(3,)):
Expand All @@ -640,26 +656,15 @@ def init_func_preproc_wf(bold_file):
('bold_file', 'inputnode.name_source'),
('t1w_aseg', 'inputnode.bold_aseg'),
('t1w_aparc', 'inputnode.bold_aparc')]),
(final_boldref_wf, bold_std_trans_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask')]),
(bold_reg_wf, bold_std_trans_wf, [
('outputnode.itk_bold_to_t1', 'inputnode.itk_bold_to_t1')]),
(bold_bold_trans_wf, bold_std_trans_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask')]),
(bold_std_trans_wf, outputnode, [('outputnode.bold_std', 'bold_std'),
('outputnode.bold_std_ref', 'bold_std_ref'),
('outputnode.bold_mask_std', 'bold_mask_std')]),
])

if freesurfer:
workflow.connect([
(bold_std_trans_wf, func_derivatives_wf, [
('outputnode.bold_aseg_std', 'inputnode.bold_aseg_std'),
('outputnode.bold_aparc_std', 'inputnode.bold_aparc_std'),
]),
(bold_std_trans_wf, outputnode, [
('outputnode.bold_aseg_std', 'bold_aseg_std'),
('outputnode.bold_aparc_std', 'bold_aparc_std')]),
])

if not multiecho:
workflow.connect([
(bold_split, bold_std_trans_wf, [
Expand All @@ -672,13 +677,24 @@ def init_func_preproc_wf(bold_file):
else:
workflow.connect([
(split_opt_comb, bold_std_trans_wf, [
('out_files', 'inputnode.bold_split')])
('out_files', 'inputnode.bold_split')]),
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])

# Already applied in bold_bold_trans_wf, which inputs to bold_t2s_wf
bold_std_trans_wf.inputs.inputnode.fieldwarp = 'identity'
bold_std_trans_wf.inputs.inputnode.hmc_xforms = 'identity'

if freesurfer:
workflow.connect([
(bold_std_trans_wf, func_derivatives_wf, [
('outputnode.bold_aseg_std', 'inputnode.bold_aseg_std'),
('outputnode.bold_aparc_std', 'inputnode.bold_aparc_std'),
]),
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(bold_std_trans_wf, outputnode, [
('outputnode.bold_aseg_std', 'bold_aseg_std'),
('outputnode.bold_aparc_std', 'bold_aparc_std')]),
])

# func_derivatives_wf internally parametrizes over snapshotted spaces.
workflow.connect([
(bold_std_trans_wf, func_derivatives_wf, [
Expand Down Expand Up @@ -721,7 +737,7 @@ def init_func_preproc_wf(bold_file):
('bold_file', 'inputnode.name_source')]),
(bold_hmc_wf, ica_aroma_wf, [
('outputnode.movpar_file', 'inputnode.movpar_file')]),
(bold_reference_wf, ica_aroma_wf, [
(initial_boldref_wf, ica_aroma_wf, [
('outputnode.skip_vols', 'inputnode.skip_vols')]),
(bold_confounds_wf, join, [
('outputnode.confounds_file', 'in_file')]),
Expand Down Expand Up @@ -815,15 +831,16 @@ def init_func_preproc_wf(bold_file):
('std2anat_xfm', 'inputnode.std2anat_xfm')]),
(bold_bold_trans_wf if not multiecho else bold_t2s_wf, carpetplot_wf, [
('outputnode.bold', 'inputnode.bold')]),
(bold_bold_trans_wf, carpetplot_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask')]),
(bold_reg_wf, carpetplot_wf, [
('outputnode.itk_t1_to_bold', 'inputnode.t1_bold_xform')]),
(final_boldref_wf, carpetplot_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask')]),
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])

workflow.connect([
(bold_confounds_wf, carpetplot_wf, [
('outputnode.confounds_file', 'inputnode.confounds_file')])
('outputnode.confounds_file', 'inputnode.confounds_file')
])
])

# REPORTING ############################################################
Expand All @@ -840,7 +857,7 @@ def init_func_preproc_wf(bold_file):

workflow.connect([
(summary, ds_report_summary, [('out_report', 'in_file')]),
(bold_reference_wf, ds_report_validation, [
(initial_boldref_wf, ds_report_validation, [
('outputnode.validation_report', 'in_file')]),
])

Expand Down
16 changes: 0 additions & 16 deletions fmriprep/workflows/bold/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -472,16 +472,9 @@ def init_bold_preproc_trans_wf(mem_gb, omp_nthreads,
-------
bold
BOLD series, resampled in native space, including all preprocessing
bold_mask
BOLD series mask calculated with the new time-series
bold_ref
BOLD reference image: an average-like 3D image of the time-series
bold_ref_brain
Same as ``bold_ref``, but once the brain mask has been applied

"""
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.func.util import init_bold_reference_wf
from niworkflows.interfaces.itk import MultiApplyTransforms
from niworkflows.interfaces.nilearn import Merge

Expand Down Expand Up @@ -515,10 +508,6 @@ def init_bold_preproc_trans_wf(mem_gb, omp_nthreads,

merge = pe.Node(Merge(compress=use_compression), name='merge', mem_gb=mem_gb * 3)

# Generate a new BOLD reference
bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
bold_reference_wf.__desc__ = None # Unset description to avoid second appearance

workflow.connect([
(inputnode, merge_xforms, [('fieldwarp', 'in1'),
('hmc_xforms', 'in2')]),
Expand All @@ -527,12 +516,7 @@ def init_bold_preproc_trans_wf(mem_gb, omp_nthreads,
(inputnode, merge, [('name_source', 'header_source')]),
(merge_xforms, bold_transform, [('out', 'transforms')]),
(bold_transform, merge, [('out_files', 'in_files')]),
(merge, bold_reference_wf, [('out_file', 'inputnode.bold_file')]),
(merge, outputnode, [('out_file', 'bold')]),
(bold_reference_wf, outputnode, [
('outputnode.ref_image', 'bold_ref'),
('outputnode.ref_image_brain', 'bold_ref_brain'),
('outputnode.bold_mask', 'bold_mask')]),
])

return workflow
Expand Down