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FIX: ME | Revise SDC compute graph #2610

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merged 10 commits into from
Oct 22, 2021
Merged

FIX: ME | Revise SDC compute graph #2610

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0ad307b
fix: ME | Revise SDC compute graph
oesteban Oct 20, 2021
d903174
fix: revise bad connection naming, clean up style
oesteban Oct 20, 2021
bc203a3
sty: cosmetic change to connection
oesteban Oct 20, 2021
a720d1a
fix: broken SE workflow path, PEP8 error
oesteban Oct 21, 2021
6ac3f81
fix: use joined fields when calculating final boldref
oesteban Oct 21, 2021
b67636b
FIX: Connect unwarped bold masks to join_echos
effigies Oct 21, 2021
e43a8fd
FIX: Connect up bold_t2s_wf.inputs.bold_mask unconditionally
effigies Oct 21, 2021
a7785d6
fix: revise @effigies' b67636b & e43a8fd
oesteban Oct 22, 2021
9eed5bc
fix: addressing joining issues in ME pathway
oesteban Oct 22, 2021
7fc382e
fix: missing formatting interpolation placement in interface input
oesteban Oct 22, 2021
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4 changes: 2 additions & 2 deletions fmriprep/interfaces/multiecho.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,8 @@ class T2SMapInputSpec(CommandLineInputSpec):
mandatory=True,
minlen=3,
desc='echo times')
mask_file = File(argstr='--mask',
mask_file = File(argstr='--mask %s',
position=3,
mandatory=False,
desc='mask file',
exists=True)
fittype = traits.Enum('curvefit', 'loglin',
Expand Down Expand Up @@ -95,6 +94,7 @@ class T2SMap(CommandLine):
>>> t2smap.cmdline # doctest: +ELLIPSIS
't2smap -d sub-01_run-01_echo-1_bold.nii.gz sub-01_run-01_echo-2_bold.nii.gz \
sub-01_run-01_echo-3_bold.nii.gz -e 13.0 27.0 43.0 --fittype curvefit'

"""
_cmd = 't2smap'
input_spec = T2SMapInputSpec
Expand Down
165 changes: 109 additions & 56 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -350,7 +350,10 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):

# BOLD buffer: an identity used as a pointer to either the original BOLD
# or the STC'ed one for further use.
boldbuffer = pe.Node(niu.IdentityInterface(fields=["bold_file"]), name="boldbuffer")
boldbuffer = pe.Node(niu.IdentityInterface(fields=["bold_file", "name_source"]),
name="boldbuffer")
if multiecho:
boldbuffer.synchronize = True
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I forget what this does. Can look it up when there's time, or if you want to say a quick word?

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Yup. Because boldbuffer now has two fields, and both are iterable, synchronize = True preempts the dot product of the values of the two iterable inputs.


summary = pe.Node(
FunctionalSummary(
Expand Down Expand Up @@ -482,22 +485,30 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
# fmt:on
else: # for meepi, iterate through stc_wf for all workflows
meepi_echos = boldbuffer.clone(name="meepi_echos")
meepi_echos.iterables = ("bold_file", bold_file)
meepi_echos.iterables = [
("bold_file", bold_file),
("name_source", bold_file),
]
# fmt:off
workflow.connect([
(meepi_echos, bold_stc_wf, [("bold_file", "inputnode.bold_file")]),
(meepi_echos, boldbuffer, [("name_source", "name_source")]),
])
# fmt:on
elif not multiecho: # STC is too short or False

# bypass STC from original BOLD in both SE and ME cases
elif not multiecho: # SE and skip-STC
# fmt:off
# bypass STC from original BOLD to the splitter through boldbuffer
workflow.connect([
(initial_boldref_wf, boldbuffer, [("outputnode.bold_file", "bold_file")]),
])
# fmt:on
else:
else: # ME and skip-STC
# for meepi, iterate over all meepi echos to boldbuffer
boldbuffer.iterables = ("bold_file", bold_file)
boldbuffer.iterables = [
("bold_file", bold_file),
("name_source", bold_file),
]

# MULTI-ECHO EPI DATA #############################################
if multiecho: # instantiate relevant interfaces, imports
Expand Down Expand Up @@ -637,12 +648,12 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
(inputnode, func_derivatives_wf, [
(("bold_file", combine_meepi_source), "inputnode.source_file"),
]),
(join_echos, bold_t2s_wf, [("bold_files", "inputnode.bold_file")]),
(join_echos, bold_t2s_wf, [
("bold_files", "inputnode.bold_file"),
]),
(bold_t2s_wf, split_opt_comb, [("outputnode.bold", "in_file")]),
(split_opt_comb, bold_t1_trans_wf, [("out_files", "inputnode.bold_split")]),
(bold_t2s_wf, bold_final, [
("outputnode.bold", "bold"),
]),
(bold_t2s_wf, bold_final, [("outputnode.bold", "bold")]),
])
# fmt:on

Expand Down Expand Up @@ -975,9 +986,11 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
use_fieldwarp=False,
name="bold_bold_trans_wf",
)
bold_bold_trans_wf.inputs.inputnode.name_source = ref_file
bold_bold_trans_wf.inputs.inputnode.fieldwarp = "identity"

if not multiecho:
bold_bold_trans_wf.inputs.inputnode.name_source = ref_file

# fmt:off
workflow.connect([
# Connect bold_bold_trans_wf
Expand All @@ -986,37 +999,33 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
("outputnode.xforms", "inputnode.hmc_xforms"),
]),
])
# fmt:on

# fmt:off
workflow.connect(
[
(bold_bold_trans_wf, final_boldref_wf, [
("outputnode.bold", "inputnode.bold_file"),
]),
(bold_bold_trans_wf, bold_final, [
("outputnode.bold", "bold"),
]),
] if not multiecho
else [
(bold_bold_trans_wf, join_echos, [
("outputnode.bold", "bold_files"),
]),
(join_echos, final_boldref_wf, [("bold_files", "inputnode.bold_file")]),
# use reference image mask used by bold_bold_trans_wf
(bold_bold_trans_wf, bold_t2s_wf, [
(("outputnode.bold_mask", pop_file), "inputnode.bold_mask"),
]),
]
)
workflow.connect([
(bold_bold_trans_wf, bold_final, [("outputnode.bold", "bold")]),
(bold_bold_trans_wf, final_boldref_wf, [
("outputnode.bold", "inputnode.bold_file"),
]),
] if not multiecho else [
(initial_boldref_wf, bold_t2s_wf, [
("outputnode.bold_mask", "inputnode.bold_mask"),
]),
(boldbuffer, bold_bold_trans_wf, [
("name_source", "inputnode.name_source"),
]),
(bold_bold_trans_wf, join_echos, [
("outputnode.bold", "bold_files"),
]),
(join_echos, final_boldref_wf, [
("bold_files", "inputnode.bold_file"),
]),
])
# fmt:on
return workflow

from niworkflows.interfaces.reportlets.registration import (
SimpleBeforeAfterRPT as SimpleBeforeAfter,
)
from niworkflows.interfaces.utility import KeySelect
from sdcflows.utils.misc import front as _pop
from sdcflows.workflows.apply.registration import init_coeff2epi_wf
from sdcflows.workflows.apply.correction import init_unwarp_wf

Expand Down Expand Up @@ -1087,41 +1096,85 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
("outputnode.xforms", "inputnode.hmc_xforms")]),
(initial_boldref_wf, sdc_report, [
("outputnode.ref_image", "before")]),
(unwarp_wf, final_boldref_wf, [
("outputnode.corrected_ref", "inputnode.bold_file"),
]),
(bold_split, unwarp_wf, [
("out_files", "inputnode.distorted")]),
(final_boldref_wf, sdc_report, [
("outputnode.ref_image", "after"),
("outputnode.bold_mask", "wm_seg")]),
(inputnode, ds_report_sdc, [("bold_file", "source_file")]),
(sdc_report, ds_report_sdc, [("out_report", "in_file")]),
# remaining workflow connections
(unwarp_wf, bold_std_trans_wf, [
# TEMPORARY: For the moment we can't use frame-wise fieldmaps
(("outputnode.fieldwarp", _pop), "inputnode.fieldwarp"),
]),
(unwarp_wf, bold_final, [("outputnode.corrected", "bold")]),
(unwarp_wf, bold_t1_trans_wf, [
# TEMPORARY: For the moment we can't use frame-wise fieldmaps
(("outputnode.fieldwarp", _pop), "inputnode.fieldwarp"),
]),

])
# fmt:on

if not multiecho:
# fmt:off
workflow.connect([
(bold_split, unwarp_wf, [
("out_files", "inputnode.distorted")]),
])
# fmt:on
else:
# fmt:off
workflow.connect([
(split_opt_comb, unwarp_wf, [
("out_files", "inputnode.distorted")])
(unwarp_wf, bold_final, [("outputnode.corrected", "bold")]),
# remaining workflow connections
(unwarp_wf, final_boldref_wf, [
("outputnode.corrected", "inputnode.bold_file"),
]),
(unwarp_wf, bold_t1_trans_wf, [
# TEMPORARY: For the moment we can't use frame-wise fieldmaps
(("outputnode.fieldwarp", pop_file), "inputnode.fieldwarp"),
]),
(unwarp_wf, bold_std_trans_wf, [
# TEMPORARY: For the moment we can't use frame-wise fieldmaps
(("outputnode.fieldwarp", pop_file), "inputnode.fieldwarp"),
]),
])
# fmt:on
return workflow

# Finalize connections if ME-EPI
join_sdc_echos = pe.JoinNode(
niu.IdentityInterface(
fields=[
"fieldmap",
"fieldwarp",
"corrected",
"corrected_ref",
"corrected_mask",
]
),
joinsource=("meepi_echos" if run_stc is True else "boldbuffer"),
joinfield=["bold_files"],
name="join_sdc_echos",
)

def _dpop(list_of_lists):
return list_of_lists[0][0]

# fmt:off
workflow.connect([
(unwarp_wf, join_echos, [
("outputnode.corrected", "bold_files"),
]),
(unwarp_wf, join_sdc_echos, [
("outputnode.fieldmap", "fieldmap"),
("outputnode.fieldwarp", "fieldwarp"),
("outputnode.corrected", "corrected"),
("outputnode.corrected_ref", "corrected_ref"),
("outputnode.corrected_mask", "corrected_mask"),
]),
# remaining workflow connections
(join_sdc_echos, final_boldref_wf, [
("corrected", "inputnode.bold_file"),
]),
(join_sdc_echos, bold_t2s_wf, [
("corrected_mask", "inputnode.bold_mask"),
]),
(join_sdc_echos, bold_t1_trans_wf, [
# TEMPORARY: For the moment we can't use frame-wise fieldmaps
(("fieldwarp", _dpop), "inputnode.fieldwarp"),
]),
(join_sdc_echos, bold_std_trans_wf, [
# TEMPORARY: For the moment we can't use frame-wise fieldmaps
(("fieldwarp", _dpop), "inputnode.fieldwarp"),
]),
])
# fmt:on

return workflow

Expand Down