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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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72 changes: 28 additions & 44 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -488,14 +488,15 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
(meepi_echos, bold_stc_wf, [("bold_file", "inputnode.bold_file")]),
])
# 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)

Expand Down Expand Up @@ -640,9 +641,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
(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 @@ -985,30 +984,22 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
(bold_hmc_wf, bold_bold_trans_wf, [
("outputnode.xforms", "inputnode.hmc_xforms"),
]),
(bold_bold_trans_wf, final_boldref_wf, [
("outputnode.bold", "inputnode.bold_file"),
]),
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])
# 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")]),
] if not multiecho else [
(bold_bold_trans_wf, join_echos, [("outputnode.bold", "bold_files")]),
# 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"),
]),
])
# fmt:on
return workflow

Expand Down Expand Up @@ -1087,6 +1078,8 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
("outputnode.xforms", "inputnode.hmc_xforms")]),
(initial_boldref_wf, sdc_report, [
("outputnode.ref_image", "before")]),
(bold_split, unwarp_wf, [
("out_files", "inputnode.distorted")]),
(unwarp_wf, final_boldref_wf, [
("outputnode.corrected_ref", "inputnode.bold_file"),
]),
Expand All @@ -1096,32 +1089,23 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
(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, [
(unwarp_wf, bold_t1_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, [
(unwarp_wf, bold_std_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")])
])
# fmt:on
# Connect corrected ouputs depending on whether it is SE or ME
workflow.connect([
(unwarp_wf, bold_final, [("outputnode.corrected", "bold")]),
] if not multiecho else [
(unwarp_wf, join_echos, [("outputnode.corrected", "bold_files")]),
])
# fmt:on

return workflow

Expand Down