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Give this a try.
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@tsalo
tsalo committed Nov 9, 2023
1 parent 219fa3a commit 7f8df8f
Showing 1 changed file with 54 additions and 49 deletions.
103 changes: 54 additions & 49 deletions aslprep/workflows/asl/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -211,6 +211,39 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
processing_target = select_processing_target(aslcontext=run_data["aslcontext"])
m0type = metadata["M0Type"]

# Determine which CBF outputs to expect
cbf_derivs = ["mean_cbf"]
mean_cbf_derivs = ["mean_cbf"]

if is_multi_pld:
cbf_derivs += ["att"]
else:
cbf_derivs += ["cbf_ts"]

if scorescrub:
cbf_derivs += [
"cbf_ts_score",
"mean_cbf_score",
"mean_cbf_scrub",
]
mean_cbf_derivs += [
"mean_cbf_score",
"mean_cbf_scrub",
]

if basil:
cbf_derivs += [
"mean_cbf_basil",
"mean_cbf_gm_basil",
"mean_cbf_wm_basil",
"att_basil",
]
# We don't want mean_cbf_wm_basil for this list.
mean_cbf_derivs += [
"mean_cbf_basil",
"mean_cbf_gm_basil",
]

if has_fieldmap:
from sdcflows import fieldmaps as fm

Expand Down Expand Up @@ -264,6 +297,13 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
"surfaces",
"morphometrics",
"sphere_reg_fsLR",
# Field map stuff
"fmap",
"fmap_ref",
"fmap_coeff",
"fmap_mask",
"fmap_id",
"sdc_method",
],
),
name="inputnode",
Expand Down Expand Up @@ -359,43 +399,6 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
name="outputnode",
)

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

if is_multi_pld:
cbf_derivs += ["att"]
else:
cbf_derivs += ["cbf_ts"]

if scorescrub:
cbf_derivs += [
"cbf_ts_score",
"mean_cbf_score",
"mean_cbf_scrub",
]
mean_cbf_derivs += [
"mean_cbf_score",
"mean_cbf_scrub",
]

if basil:
cbf_derivs += [
"mean_cbf_basil",
"mean_cbf_gm_basil",
"mean_cbf_wm_basil",
"att_basil",
]
# We don't want mean_cbf_wm_basil for this list.
mean_cbf_derivs += [
"mean_cbf_basil",
"mean_cbf_gm_basil",
]

if sbref_file is not None:
from niworkflows.interfaces.header import ValidateImage

val_sbref = pe.Node(ValidateImage(in_file=sbref_file), name="val_sbref")

# Generate a brain-masked version of the t1w
t1w_brain = pe.Node(ApplyMask(), name="t1w_brain")

Expand Down Expand Up @@ -519,6 +522,7 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
# Generate a tentative aslref from the most appropriate available image type in the ASL file
initial_aslref_wf = init_asl_reference_wf(
aslcontext=run_data["aslcontext"],
sbref_files=[sbref_file],
name="initial_aslref_wf",
)
initial_aslref_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_vols
Expand All @@ -529,9 +533,6 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
])
# fmt:on

if sbref_file is not None:
workflow.connect([(val_sbref, initial_aslref_wf, [("out_file", "inputnode.sbref_file")])])

# Drop volumes in the ASL file that won't be used
# (e.g., precalculated CBF volumes if control-label pairs are available).
reduce_asl_file = pe.Node(
Expand Down Expand Up @@ -594,6 +595,10 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
]),
(t1w_brain, asl_reg_wf, [("out_file", "inputnode.t1w_brain")]),
(asl_reg_wf, summary, [("outputnode.fallback", "fallback")]),
(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 @@ -670,10 +675,6 @@ 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, outputnode, [
("outputnode.itk_t1_to_bold", "anat_to_aslref_xfm"),
("outputnode.itk_bold_to_t1", "aslref_to_anat_xfm"),
]),
])
# fmt:on

Expand All @@ -700,7 +701,10 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
# fmt:off
workflow.connect([
(initial_aslref_wf, final_aslref_wf, [("outputnode.skip_vols", "inputnode.dummy_scans")]),
(final_aslref_wf, asl_final, [("outputnode.ref_image", "aslref")]),
(final_aslref_wf, asl_final, [
("outputnode.ref_image", "aslref"),
("outputnode.asl_mask", "mask"),
]),
])
# fmt:on

Expand All @@ -714,7 +718,8 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
workflow.connect([
(inputnode, refine_mask, [("t1w_mask", "t1w_mask")]),
(asl_reg_wf, refine_mask, [("outputnode.itk_t1_to_bold", "transforms")]),
(refine_mask, asl_final, [("out_mask", "mask")]),
# the below is circular since asl_reg_wf gets output from asl_final
# (refine_mask, asl_final, [("out_mask", "mask")]),
])
# fmt:on

Expand Down Expand Up @@ -797,7 +802,7 @@ def init_asl_preproc_wf(asl_file, has_fieldmap=False):
workflow.connect([
(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")]),
(compute_cbf_wf, cbf_to_t1w, [(f"outputnode.{cbf_deriv}", "input_image")]),
(cbf_to_t1w, outputnode, [("output_image", f"{cbf_deriv}_t1")]),
])
# fmt:on
Expand Down Expand Up @@ -1138,8 +1143,8 @@ def _last(inlist):
(inputnode, asl_asl_trans_wf, [("name_source", "inputnode.name_source")]),
(asl_split, asl_asl_trans_wf, [("out_files", "inputnode.bold_file")]),
(asl_hmc_wf, asl_asl_trans_wf, [("outputnode.xforms", "inputnode.hmc_xforms")]),
(asl_asl_trans_wf, asl_final, [("outputnode.bold", "bold")]),
(asl_asl_trans_wf, final_aslref_wf, [("outputnode.bold", "inputnode.bold_file")]),
(asl_asl_trans_wf, asl_final, [("outputnode.bold", "asl")]),
(asl_asl_trans_wf, final_aslref_wf, [("outputnode.bold", "inputnode.asl_file")]),
])
# fmt:on

Expand Down

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