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RF: Update workflow to use sdcflows@master unwarp_wf #3075

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RF: Update workflow to use sdcflows@master unwarp_wf #3075

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29 changes: 18 additions & 11 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1064,6 +1064,14 @@ def _last(inlist):
)
unwarp_wf.inputs.inputnode.metadata = metadata

unwarp_ref_wf = init_unwarp_wf(
free_mem=config.environment.free_mem,
debug="fieldmaps" in config.execution.debug,
omp_nthreads=config.nipype.omp_nthreads,
name="unwarp_ref_wf",
)
unwarp_ref_wf.inputs.inputnode.metadata = metadata

output_select = pe.Node(
KeySelect(fields=["fmap", "fmap_ref", "fmap_coeff", "fmap_mask", "sdc_method"]),
name="output_select",
Expand Down Expand Up @@ -1114,17 +1122,19 @@ def _last(inlist):
(initial_boldref_wf, coeff2epi_wf, [
("outputnode.ref_image", "inputnode.target_ref"),
("outputnode.bold_mask", "inputnode.target_mask")]),
(initial_boldref_wf, unwarp_wf, [
("outputnode.ref_image", "inputnode.distorted_ref"),
]),
(coeff2epi_wf, unwarp_wf, [
("outputnode.fmap_coeff", "inputnode.fmap_coeff")]),
(coeff2epi_wf, unwarp_ref_wf, [
("outputnode.fmap_coeff", "inputnode.fmap_coeff")]),
(bold_hmc_wf, unwarp_wf, [
("outputnode.xforms", "inputnode.hmc_xforms")]),
(initial_boldref_wf, sdc_report, [
("outputnode.ref_image", "before")]),
(bold_split, unwarp_wf, [
("out_files", "inputnode.distorted")]),
(initial_boldref_wf, unwarp_ref_wf, [
("outputnode.ref_image", "inputnode.distorted"),
]),
(final_boldref_wf, sdc_report, [
("outputnode.ref_image", "after"),
("outputnode.bold_mask", "wm_seg")]),
Expand Down Expand Up @@ -1187,7 +1197,7 @@ def _last(inlist):
]),
(inputnode, ds_report_sdc_coreg, [("bold_file", "source_file")]),
(sdc_coreg_report, ds_report_sdc_coreg, [("out_report", "in_file")]),
(unwarp_wf, fmap_report, [(("outputnode.fieldmap", pop_file), "fieldmap")]),
(unwarp_ref_wf, fmap_report, [(("outputnode.fieldmap", pop_file), "fieldmap")]),
(coeff2epi_wf, fmap_report, [
("coregister.inverse_warped_image", "reference"),
]),
Expand All @@ -1208,13 +1218,13 @@ def _last(inlist):
(unwarp_wf, final_boldref_wf, [
("outputnode.corrected", "inputnode.bold_file"),
]),
(unwarp_wf, bold_t1_trans_wf, [
(unwarp_ref_wf, bold_t1_trans_wf, [
# TEMPORARY: For the moment we can't use frame-wise fieldmaps
(("outputnode.fieldwarp_ref", pop_file), "inputnode.fieldwarp"),
(("outputnode.fieldwarp", pop_file), "inputnode.fieldwarp"),
]),
(unwarp_wf, bold_std_trans_wf, [
(unwarp_ref_wf, bold_std_trans_wf, [
# TEMPORARY: For the moment we can't use frame-wise fieldmaps
(("outputnode.fieldwarp_ref", pop_file), "inputnode.fieldwarp"),
(("outputnode.fieldwarp", pop_file), "inputnode.fieldwarp"),
]),
])
# fmt:on
Expand All @@ -1227,7 +1237,6 @@ def _last(inlist):
"fieldmap",
"fieldwarp",
"corrected",
"corrected_ref",
"corrected_mask",
]
),
Expand All @@ -1236,7 +1245,6 @@ def _last(inlist):
"fieldmap",
"fieldwarp",
"corrected",
"corrected_ref",
"corrected_mask",
],
name="join_sdc_echos",
Expand All @@ -1254,7 +1262,6 @@ def _dpop(list_of_lists):
("outputnode.fieldmap", "fieldmap"),
("outputnode.fieldwarp", "fieldwarp"),
("outputnode.corrected", "corrected"),
("outputnode.corrected_ref", "corrected_ref"),
("outputnode.corrected_mask", "corrected_mask"),
]),
# remaining workflow connections
Expand Down