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Update base.py
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@tsalo
tsalo committed Nov 9, 2023
1 parent c48f67a commit 219fa3a
Showing 1 changed file with 188 additions and 36 deletions.
224 changes: 188 additions & 36 deletions aslprep/workflows/asl/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -274,6 +274,91 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
inputnode.inputs.m0scan = run_data["m0scan"]
inputnode.inputs.m0scan_metadata = run_data["m0scan_metadata"]

outputnode = pe.Node(
niu.IdentityInterface(
fields=[
"template",
"spatial_reference",
"qc_file",
# Preprocessed ASL files
"asl_native",
"asl_t1",
"asl_std",
"asl_cifti",
"aslref_native",
"aslref_t1",
"aslref_std",
"asl_mask_native",
"asl_mask_t1",
"asl_mask_std",
# Transforms
"hmc_xforms",
"aslref_to_anat_xfm",
"anat_to_aslref_xfm",
# Standard CBF outputs
"cbf_ts_native",
"cbf_ts_t1",
"cbf_ts_std",
"cbf_ts_cifti",
"mean_cbf_native",
"mean_cbf_t1",
"mean_cbf_std",
"mean_cbf_cifti",
"att_native",
"att_t1",
"att_std",
"att_cifti",
# SCORE/SCRUB outputs
"cbf_ts_score_native",
"cbf_ts_score_t1",
"cbf_ts_score_std",
"cbf_ts_score_cifti",
"mean_cbf_score_native",
"mean_cbf_score_t1",
"mean_cbf_score_std",
"mean_cbf_score_cifti",
"mean_cbf_scrub_native",
"mean_cbf_scrub_t1",
"mean_cbf_scrub_std",
"mean_cbf_scrub_cifti",
# BASIL outputs
"mean_cbf_basil_native",
"mean_cbf_basil_t1",
"mean_cbf_basil_std",
"mean_cbf_basil_cifti",
"mean_cbf_gm_basil_native",
"mean_cbf_gm_basil_t1",
"mean_cbf_gm_basil_std",
"mean_cbf_gm_basil_cifti",
"mean_cbf_wm_basil_native",
"mean_cbf_wm_basil_t1",
"mean_cbf_wm_basil_std",
"mean_cbf_wm_basil_cifti",
"att_basil_native",
"att_basil_t1",
"att_basil_std",
"att_basil_cifti",
# Parcellated CBF outputs
"atlas_names",
"mean_cbf_parcellated",
"mean_cbf_score_parcellated",
"mean_cbf_scrub_parcellated",
"mean_cbf_basil_parcellated",
"mean_cbf_gm_basil_parcellated",
# Non-GE outputs
"confounds",
"confounds_metadata",
# CIFTI-related outputs
"cifti_metadata",
"cifti_density",
"goodvoxels_mask",
"surfaces",
"surf_refs",
],
),
name="outputnode",
)

cbf_derivs = ["mean_cbf"]
mean_cbf_derivs = ["mean_cbf"]

Expand Down Expand Up @@ -352,10 +437,78 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
asl_derivatives_wf.inputs.inputnode.cifti_density = config.workflow.cifti_output
# fmt:off
workflow.connect([
(inputnode, asl_derivatives_wf, [
("asl_file", "inputnode.source_file"),
(inputnode, asl_derivatives_wf, [("asl_file", "inputnode.source_file")]),
(outputnode, asl_derivatives_wf, [
("template", "inputnode.template"),
("spatial_reference", "inputnode.spatial_reference"),
("qc_file", "inputnode.qc_file"),
("asl_native", "inputnode.asl_native"),
("asl_t1", "inputnode.asl_t1"),
("asl_std", "inputnode.asl_std"),
("asl_cifti", "inputnode.asl_cifti"),
("aslref_native", "inputnode.aslref_native"),
("aslref_t1", "inputnode.aslref_t1"),
("aslref_std", "inputnode.aslref_std"),
("asl_mask_native", "inputnode.asl_mask_native"),
("asl_mask_t1", "inputnode.asl_mask_t1"),
("asl_mask_std", "inputnode.asl_mask_std"),
("hmc_xforms", "inputnode.hmc_xforms"),
("aslref_to_anat_xfm", "inputnode.aslref_to_anat_xfm"),
("anat_to_aslref_xfm", "inputnode.anat_to_aslref_xfm"),
("cbf_ts_native", "inputnode.cbf_ts_native"),
("cbf_ts_t1", "inputnode.cbf_ts_t1"),
("cbf_ts_std", "inputnode.cbf_ts_std"),
("cbf_ts_cifti", "inputnode.cbf_ts_cifti"),
("mean_cbf_native", "inputnode.mean_cbf_native"),
("mean_cbf_t1", "inputnode.mean_cbf_t1"),
("mean_cbf_std", "inputnode.mean_cbf_std"),
("mean_cbf_cifti", "inputnode.mean_cbf_cifti"),
("att_native", "inputnode.att_native"),
("att_t1", "inputnode.att_t1"),
("att_std", "inputnode.att_std"),
("att_cifti", "inputnode.att_cifti"),
("cbf_ts_score_native", "inputnode.cbf_ts_score_native"),
("cbf_ts_score_t1", "inputnode.cbf_ts_score_t1"),
("cbf_ts_score_std", "inputnode.cbf_ts_score_std"),
("cbf_ts_score_cifti", "inputnode.cbf_ts_score_cifti"),
("mean_cbf_score_native", "inputnode.mean_cbf_score_native"),
("mean_cbf_score_t1", "inputnode.mean_cbf_score_t1"),
("mean_cbf_score_std", "inputnode.mean_cbf_score_std"),
("mean_cbf_score_cifti", "inputnode.mean_cbf_score_cifti"),
("mean_cbf_scrub_native", "inputnode.mean_cbf_scrub_native"),
("mean_cbf_scrub_t1", "inputnode.mean_cbf_scrub_t1"),
("mean_cbf_scrub_std", "inputnode.mean_cbf_scrub_std"),
("mean_cbf_scrub_cifti", "inputnode.mean_cbf_scrub_cifti"),
("mean_cbf_basil_native", "inputnode.mean_cbf_basil_native"),
("mean_cbf_basil_t1", "inputnode.mean_cbf_basil_t1"),
("mean_cbf_basil_std", "inputnode.mean_cbf_basil_std"),
("mean_cbf_basil_cifti", "inputnode.mean_cbf_basil_cifti"),
("mean_cbf_gm_basil_native", "inputnode.mean_cbf_gm_basil_native"),
("mean_cbf_gm_basil_t1", "inputnode.mean_cbf_gm_basil_t1"),
("mean_cbf_gm_basil_std", "inputnode.mean_cbf_gm_basil_std"),
("mean_cbf_gm_basil_cifti", "inputnode.mean_cbf_gm_basil_cifti"),
("mean_cbf_wm_basil_native", "inputnode.mean_cbf_wm_basil_native"),
("mean_cbf_wm_basil_t1", "inputnode.mean_cbf_wm_basil_t1"),
("mean_cbf_wm_basil_std", "inputnode.mean_cbf_wm_basil_std"),
("mean_cbf_wm_basil_cifti", "inputnode.mean_cbf_wm_basil_cifti"),
("att_basil_native", "inputnode.att_basil_native"),
("att_basil_t1", "inputnode.att_basil_t1"),
("att_basil_std", "inputnode.att_basil_std"),
("att_basil_cifti", "inputnode.att_basil_cifti"),
("atlas_names", "inputnode.atlas_names"),
("mean_cbf_parcellated", "inputnode.mean_cbf_parcellated"),
("mean_cbf_score_parcellated", "inputnode.mean_cbf_score_parcellated"),
("mean_cbf_scrub_parcellated", "inputnode.mean_cbf_scrub_parcellated"),
("mean_cbf_basil_parcellated", "inputnode.mean_cbf_basil_parcellated"),
("mean_cbf_gm_basil_parcellated", "inputnode.mean_cbf_gm_basil_parcellated"),
("confounds", "inputnode.confounds"),
("confounds_metadata", "inputnode.confounds_metadata"),
("cifti_metadata", "inputnode.cifti_metadata"),
("cifti_density", "inputnode.cifti_density"),
("goodvoxels_mask", "inputnode.goodvoxels_mask"),
("surfaces", "inputnode.surf_files"),
]),
("surf_refs", "inputnode.surf_refs"),
])
])
# fmt:on

Expand Down Expand Up @@ -484,9 +637,9 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
("outputnode.itk_t1_to_bold", "inputnode.anat_to_aslref_xfm"),
]),
(initial_aslref_wf, asl_confounds_wf, [("outputnode.skip_vols", "inputnode.skip_vols")]),
(asl_confounds_wf, asl_derivatives_wf, [
("outputnode.confounds_file", "inputnode.confounds"),
("outputnode.confounds_metadata", "inputnode.confounds_metadata"),
(asl_confounds_wf, outputnode, [
("outputnode.confounds_file", "confounds"),
("outputnode.confounds_metadata", "confounds_metadata"),
]),
(asl_confounds_wf, summary, [("outputnode.confounds_file", "confounds_file")]),
])
Expand Down Expand Up @@ -517,9 +670,9 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
("outputnode.itk_t1_to_bold", "inputnode.anat_to_aslref_xfm"),
("outputnode.itk_bold_to_t1", "inputnode.aslref_to_anat_xfm"),
]),
(asl_reg_wf, asl_derivatives_wf, [
("outputnode.itk_t1_to_bold", "inputnode.anat_to_aslref_xfm"),
("outputnode.itk_bold_to_t1", "inputnode.aslref_to_anat_xfm"),
(asl_reg_wf, outputnode, [
("outputnode.itk_t1_to_bold", "anat_to_aslref_xfm"),
("outputnode.itk_bold_to_t1", "aslref_to_anat_xfm"),
]),
])
# fmt:on
Expand Down Expand Up @@ -587,7 +740,7 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
(asl_confounds_wf, compute_cbf_qc_wf, [
("outputnode.confounds_file", "inputnode.confounds_file"),
]),
(compute_cbf_qc_wf, asl_derivatives_wf, [("outputnode.qc_file", "inputnode.qc_file")]),
(compute_cbf_qc_wf, outputnode, [("outputnode.qc_file", "qc_file")]),
(compute_cbf_qc_wf, summary, [("outputnode.qc_file", "qc_file")]),
])
# fmt:on
Expand Down Expand Up @@ -645,7 +798,7 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
(asl_reg_wf, cbf_to_t1w, [("outputnode.itk_bold_to_t1", "transforms")]),
(asl_t1_trans_wf, cbf_to_t1w, [("outputnode.bold_mask_t1", "reference_image")]),
(asl_final, cbf_to_t1w, [(cbf_deriv, "input_image")]),
(cbf_to_t1w, asl_derivatives_wf, [("output_image", f"inputnode.{cbf_deriv}_t1")]),
(cbf_to_t1w, outputnode, [("output_image", f"{cbf_deriv}_t1")]),
])
# fmt:on

Expand All @@ -665,9 +818,7 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
("outputnode.bold_t1", "inputnode.asl_file"),
("outputnode.bold_mask_t1", "inputnode.asl_mask"),
]),
(asl_t1_reference_wf, asl_derivatives_wf, [
("outputnode.ref_image", "inputnode.aslref_t1"),
]),
(asl_t1_reference_wf, outputnode, [("outputnode.ref_image", "aslref_t1")]),
])
# fmt:on

Expand Down Expand Up @@ -707,9 +858,9 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
if freesurfer:
# fmt:off
workflow.connect([
(asl_std_trans_wf, asl_derivatives_wf, [
("outputnode.asl_aseg_std", "inputnode.asl_aseg_std"),
("outputnode.asl_aparc_std", "inputnode.asl_aparc_std"),
(asl_std_trans_wf, outputnode, [
("outputnode.asl_aseg_std", "asl_aseg_std"),
("outputnode.asl_aparc_std", "asl_aparc_std"),
]),
])
# fmt:on
Expand All @@ -724,21 +875,21 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
# func_derivatives_wf internally parametrizes over snapshotted spaces.
# fmt:off
workflow.connect([
(asl_std_trans_wf, asl_derivatives_wf, [
("outputnode.template", "inputnode.template"),
("outputnode.spatial_reference", "inputnode.spatial_reference"),
("outputnode.asl_std", "inputnode.asl_std"),
("outputnode.aslref_std", "inputnode.aslref_std"),
("outputnode.asl_mask_std", "inputnode.asl_mask_std"),
(asl_std_trans_wf, outputnode, [
("outputnode.template", "template"),
("outputnode.spatial_reference", "spatial_reference"),
("outputnode.asl_std", "asl_std"),
("outputnode.aslref_std", "aslref_std"),
("outputnode.asl_mask_std", "asl_mask_std"),
]),
])
# fmt:on

for cbf_deriv in cbf_derivs:
# fmt:off
workflow.connect([
(asl_std_trans_wf, asl_derivatives_wf, [
(f"outputnode.{cbf_deriv}_std", f"inputnode.{cbf_deriv}_std"),
(asl_std_trans_wf, outputnode, [
(f"outputnode.{cbf_deriv}_std", f"{cbf_deriv}_std"),
]),
])
# fmt:on
Expand All @@ -761,7 +912,10 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
("t1w2fsnative_xfm", "inputnode.t1w2fsnative_xfm"),
]),
(asl_t1_trans_wf, asl_surf_wf, [("outputnode.asl_t1", "inputnode.source_file")]),
(asl_surf_wf, asl_derivatives_wf, [("outputnode.target", "inputnode.surf_refs")]),
(asl_surf_wf, outputnode, [
("outputnode.surfaces", "surfaces"),
("outputnode.target", "surf_refs"),
]),
])
# fmt:on

Expand All @@ -784,8 +938,8 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
(asl_t1_trans_wf, asl_fsLR_resampling_wf, [
("outputnode.asl_t1", "inputnode.bold_file"),
]),
(asl_fsLR_resampling_wf, asl_derivatives_wf, [
("outputnode.goodvoxels_mask", "inputnode.goodvoxels_mask"),
(asl_fsLR_resampling_wf, outputnode, [
("outputnode.goodvoxels_mask", "goodvoxels_mask"),
]),
])
# fmt:on
Expand All @@ -804,9 +958,9 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
(asl_fsLR_resampling_wf, asl_grayords_wf, [
("outputnode.asl_fsLR", "inputnode.bold_fsLR"),
]),
(asl_grayords_wf, asl_derivatives_wf, [
("outputnode.cifti_bold", "inputnode.asl_cifti"),
("outputnode.cifti_metadata", "inputnode.cifti_metadata"),
(asl_grayords_wf, outputnode, [
("outputnode.cifti_bold", "asl_cifti"),
("outputnode.cifti_metadata", "cifti_metadata"),
]),
])
# fmt:on
Expand Down Expand Up @@ -912,9 +1066,7 @@ def _last(inlist):
(asl_reg_wf, parcellate_cbf_wf, [
("outputnode.itk_t1_to_bold", "inputnode.anat_to_aslref_xfm"),
]),
(parcellate_cbf_wf, asl_derivatives_wf, [
("outputnode.atlas_names", "inputnode.atlas_names"),
]),
(parcellate_cbf_wf, outputnode, [("outputnode.atlas_names", "atlas_names")]),
])
# fmt:on

Expand All @@ -924,8 +1076,8 @@ def _last(inlist):
(compute_cbf_wf, parcellate_cbf_wf, [
(f"outputnode.{cbf_deriv}", f"inputnode.{cbf_deriv}"),
]),
(parcellate_cbf_wf, asl_derivatives_wf, [
(f"outputnode.{cbf_deriv}_parcellated", f"inputnode.{cbf_deriv}_parcellated"),
(parcellate_cbf_wf, outputnode, [
(f"outputnode.{cbf_deriv}_parcellated", f"{cbf_deriv}_parcellated"),
]),
])
# fmt:on
Expand Down

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