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

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Merged
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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19 changes: 19 additions & 0 deletions fmriprep/utils/misc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,3 +11,22 @@ def check_deps(workflow):
for node in workflow._get_all_nodes()
if (hasattr(node.interface, '_cmd') and
which(node.interface._cmd.split()[0]) is None))


def select_first(in_files):
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@oesteban oesteban Jun 7, 2020

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Let's use niworkflows.utils.connections.pop_file instead (requires nipreps/niworkflows#408 to be merged)

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@tsalo tsalo Jun 7, 2020

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Do we want to use the first echo's brain mask, though? I am using it to fix the bug, but I don't know if it's the appropriate choice.

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@tsalo tsalo Jun 9, 2020

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I think we can also replace fmriprep.workflows.bold.resampling._first with pop_file as well.

"""
Select the first file from a list of filenames.
Used to grab the first echo's file when processing
multi-echo data through workflows that only accept
a single file.

Examples
--------
>>> select_first('some/file.nii.gz')
'some/file.nii.gz'
>>> select_first(['some/file1.nii.gz', 'some/file2.nii.gz'])
'some/file1.nii.gz'
"""
if isinstance(in_files, (list, tuple)):
return in_files[0]
return in_files
91 changes: 63 additions & 28 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
from nipype.interfaces import utility as niu

from ...utils.meepi import combine_meepi_source
from ...utils.misc import select_first

from ...interfaces import DerivativesDataSink
from ...interfaces.reports import FunctionalSummary
Expand Down Expand Up @@ -122,7 +123,7 @@ 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`
* :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 @@ -390,10 +391,11 @@ 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']),
join_echos = pe.JoinNode(niu.IdentityInterface(fields=['bold_files', 'bold_masks']),
joinsource=('meepi_echos' if run_stc is True else 'boldbuffer'),
joinfield=['bold_files'],
name='join_echos')
# join_echos2 = join_echos.clone(name='join_echos2')

# create optimal combination, adaptive T2* map
bold_t2s_wf = init_bold_t2s_wf(echo_times=tes,
Expand Down Expand Up @@ -474,9 +476,6 @@ def init_func_preproc_wf(bold_file):
('outputnode.itk_t1_to_bold', 'inputnode.t1_bold_xform')]),
(bold_reference_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, [
('outputnode.confounds_file', 'confounds'),
]),
Expand All @@ -501,6 +500,9 @@ def init_func_preproc_wf(bold_file):
('outputnode.bold', 'inputnode.bold')]),
(bold_split, bold_t1_trans_wf, [
('out_files', 'inputnode.bold_split')]),
(bold_bold_trans_wf, bold_confounds_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask'),
]),
])
else: # for meepi, create and use optimal combination
workflow.connect([
Expand All @@ -513,6 +515,11 @@ def init_func_preproc_wf(bold_file):
('outputnode.bold', 'inputnode.bold')]),
(bold_t2s_wf, bold_t1_trans_wf, [
('outputnode.bold', 'inputnode.bold_split')]),
(bold_bold_trans_wf, join_echos, [
('outputnode.bold_mask', 'bold_masks')]),
(join_echos, bold_confounds_wf, [
(('bold_masks', select_first), 'inputnode.bold_mask')
])
])

if fmaps:
Expand Down Expand Up @@ -588,20 +595,38 @@ 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')]),
])
if not multiecho:
workflow.connect([
(bold_bold_trans_wf, boldmask_to_t1w, [
('outputnode.bold_mask', 'input_image')]),
])
else:
workflow.connect([
(join_echos, boldmask_to_t1w, [
(('bold_masks', select_first), 'input_image')]),
])

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'),
('outputnode.bold_mask', 'inputnode.bold_mask_native')]),
('outputnode.bold_ref', 'inputnode.bold_native_ref')
]),
])
if not multiecho:
workflow.connect([
(bold_bold_trans_wf, func_derivatives_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask_native')]),
])
else:
workflow.connect([
(join_echos, func_derivatives_wf, [
(('bold_masks', select_first), 'inputnode.bold_mask_native')]),
])

if spaces.get_spaces(nonstandard=False, dim=(3,)):
# Apply transforms in 1 shot
Expand All @@ -626,39 +651,40 @@ def init_func_preproc_wf(bold_file):
('outputnode.xforms', 'inputnode.hmc_xforms')]),
(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_sdc_wf, bold_std_trans_wf, [
('outputnode.out_warp', 'inputnode.fieldwarp')]),
(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_bold_trans_wf, bold_std_trans_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask')]),
(bold_split, bold_std_trans_wf, [
('out_files', 'inputnode.bold_split')])
('out_files', 'inputnode.bold_split')]),
])
else:
split_opt_comb = bold_split.clone(name='split_opt_comb')
workflow.connect([
(join_echos, bold_std_trans_wf, [
(('bold_masks', select_first), 'inputnode.bold_mask')]),
(bold_t2s_wf, split_opt_comb, [
('outputnode.bold', 'in_file')]),
(split_opt_comb, bold_std_trans_wf, [
('out_files', 'inputnode.bold_split')
])
('out_files', 'inputnode.bold_split')]),
])

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')]),
])

# func_derivatives_wf internally parametrizes over snapshotted spaces.
Expand Down Expand Up @@ -798,15 +824,24 @@ 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')]),
])
if not multiecho:
workflow.connect([
(bold_bold_trans_wf, carpetplot_wf, [
('outputnode.bold_mask', 'inputnode.bold_mask')]),
])
else:
workflow.connect([
(join_echos, carpetplot_wf, [
(('bold_masks', select_first), 'inputnode.bold_mask')]),
])

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

# REPORTING ############################################################
Expand Down