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Update outputs.py
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@tsalo
tsalo committed Nov 16, 2023
1 parent cf48a13 commit a415c2f
Showing 1 changed file with 36 additions and 31 deletions.
67 changes: 36 additions & 31 deletions aslprep/workflows/asl/outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,6 +191,11 @@ def init_asl_derivatives_wf(
"goodvoxels_mask",
"surf_files",
"surf_refs",
# Freesurfer outputs
"asl_aseg_t1",
"asl_aseg_std",
"asl_aparc_t1",
"asl_aparc_std",
],
),
name="inputnode",
Expand Down Expand Up @@ -486,7 +491,7 @@ def init_asl_derivatives_wf(
# fmt:on

if freesurfer:
ds_bold_aseg_t1 = pe.Node(
ds_asl_aseg_t1 = pe.Node(
DerivativesDataSink(
base_directory=config.execution.aslprep_dir,
space="T1w",
Expand All @@ -495,11 +500,11 @@ def init_asl_derivatives_wf(
compress=True,
dismiss_entities=("echo",),
),
name="ds_bold_aseg_t1",
name="ds_asl_aseg_t1",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
ds_bold_aparc_t1 = pe.Node(
ds_asl_aparc_t1 = pe.Node(
DerivativesDataSink(
base_directory=config.execution.aslprep_dir,
space="T1w",
Expand All @@ -508,19 +513,19 @@ def init_asl_derivatives_wf(
compress=True,
dismiss_entities=("echo",),
),
name="ds_bold_aparc_t1",
name="ds_asl_aparc_t1",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
# fmt:off
workflow.connect([
(inputnode, ds_bold_aseg_t1, [
(inputnode, ds_asl_aseg_t1, [
("source_file", "source_file"),
("bold_aseg_t1", "in_file"),
("asl_aseg_t1", "in_file"),
]),
(inputnode, ds_bold_aparc_t1, [
(inputnode, ds_asl_aparc_t1, [
("source_file", "source_file"),
("bold_aparc_t1", "in_file"),
("asl_aparc_t1", "in_file"),
]),
])
# fmt:on
Expand Down Expand Up @@ -585,60 +590,60 @@ def init_asl_derivatives_wf(

if freesurfer:
select_fs_std = pe.Node(
KeySelect(fields=["bold_aseg_std", "bold_aparc_std", "template"]),
KeySelect(fields=["asl_aseg_std", "asl_aparc_std", "template"]),
name="select_fs_std",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
ds_bold_aseg_std = pe.Node(
ds_asl_aseg_std = pe.Node(
DerivativesDataSink(
base_directory=config.execution.aslprep_dir,
desc="aseg",
suffix="dseg",
compress=True,
dismiss_entities=("echo",),
),
name="ds_bold_aseg_std",
name="ds_asl_aseg_std",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
ds_bold_aparc_std = pe.Node(
ds_asl_aparc_std = pe.Node(
DerivativesDataSink(
base_directory=config.execution.aslprep_dir,
desc="aparcaseg",
suffix="dseg",
compress=True,
dismiss_entities=("echo",),
),
name="ds_bold_aparc_std",
name="ds_asl_aparc_std",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
# fmt:off
workflow.connect([
(spacesource, select_fs_std, [("uid", "key")]),
(inputnode, select_fs_std, [
("bold_aseg_std", "bold_aseg_std"),
("bold_aparc_std", "bold_aparc_std"),
("asl_aseg_std", "asl_aseg_std"),
("asl_aparc_std", "asl_aparc_std"),
("template", "template"),
("spatial_reference", "keys"),
]),
(select_fs_std, ds_bold_aseg_std, [("bold_aseg_std", "in_file")]),
(spacesource, ds_bold_aseg_std, [
(select_fs_std, ds_asl_aseg_std, [("asl_aseg_std", "in_file")]),
(spacesource, ds_asl_aseg_std, [
("space", "space"),
("cohort", "cohort"),
("resolution", "resolution"),
("density", "density"),
]),
(select_fs_std, ds_bold_aparc_std, [("bold_aparc_std", "in_file")]),
(spacesource, ds_bold_aparc_std, [
(select_fs_std, ds_asl_aparc_std, [("asl_aparc_std", "in_file")]),
(spacesource, ds_asl_aparc_std, [
("space", "space"),
("cohort", "cohort"),
("resolution", "resolution"),
("density", "density"),
]),
(inputnode, ds_bold_aseg_std, [("source_file", "source_file")]),
(inputnode, ds_bold_aparc_std, [("source_file", "source_file")])
(inputnode, ds_asl_aseg_std, [("source_file", "source_file")]),
(inputnode, ds_asl_aparc_std, [("source_file", "source_file")])
])
# fmt:on

Expand All @@ -662,14 +667,14 @@ def init_asl_derivatives_wf(
run_without_submitting=True,
)

ds_bold_surfs = pe.MapNode(
ds_asl_surfs = pe.MapNode(
DerivativesDataSink(
base_directory=config.execution.aslprep_dir,
extension=".func.gii",
TaskName=metadata.get("TaskName"),
),
iterfield=["in_file", "hemi"],
name="ds_bold_surfs",
name="ds_asl_surfs",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
Expand All @@ -680,12 +685,12 @@ def init_asl_derivatives_wf(
("surf_refs", "keys"),
]),
(select_fs_surf, name_surfs, [("surfaces", "in_file")]),
(inputnode, ds_bold_surfs, [("source_file", "source_file")]),
(select_fs_surf, ds_bold_surfs, [
(inputnode, ds_asl_surfs, [("source_file", "source_file")]),
(select_fs_surf, ds_asl_surfs, [
("surfaces", "in_file"),
("key", "space"),
]),
(name_surfs, ds_bold_surfs, [("hemi", "hemi")]),
(name_surfs, ds_asl_surfs, [("hemi", "hemi")]),
])
# fmt:on

Expand Down Expand Up @@ -715,22 +720,22 @@ def init_asl_derivatives_wf(

# CIFTI output
if cifti_output:
ds_bold_cifti = pe.Node(
ds_asl_cifti = pe.Node(
DerivativesDataSink(
base_directory=config.execution.aslprep_dir,
suffix="bold",
suffix="asl",
compress=False,
TaskName=metadata.get("TaskName"),
space="fsLR",
),
name="ds_bold_cifti",
name="ds_asl_cifti",
run_without_submitting=True,
mem_gb=config.DEFAULT_MEMORY_MIN_GB,
)
# fmt:off
workflow.connect([
(inputnode, ds_bold_cifti, [
("bold_cifti", "in_file"),
(inputnode, ds_asl_cifti, [
("asl_cifti", "in_file"),
("source_file", "source_file"),
("cifti_density", "density"),
(("cifti_metadata", _read_json), "meta_dict"),
Expand Down

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