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Add multi run support #26

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merged 5 commits into from
Nov 22, 2023
Merged

Add multi run support #26

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4bb6aba
adding ports to datasinks for multiruns and extra workflows with *run-*
bendhouseart Nov 21, 2023
9665c28
mostly behaving, registration file is still not differentiated betwee…
bendhouseart Nov 22, 2023
f53d403
renamed registration file tested good on inherited, each, first, and …
bendhouseart Nov 22, 2023
5bc4324
bump version, format with black
bendhouseart Nov 22, 2023
50d81f7
Update petdeface/petdeface.py
bendhouseart Nov 22, 2023
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25 changes: 19 additions & 6 deletions petdeface/petdeface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -303,16 +303,24 @@ def init_single_subject_wf(
ses_id = ""
pet_string = f"sub-{subject_id}"

pet_wf_name = f"pet_{pet_string}_wf"
# collect run info from pet file
try:
run_id = "_" + re.search("run-[^_|\/]*", str(pet_file)).group(0)
except AttributeError:
run_id = ""
pet_wf_name = f"pet_{pet_string}{run_id}_wf"
pet_wf = Workflow(name=pet_wf_name)

weighted_average = Node(
WeightedAverage(pet_file=pet_file), name="weighted_average"
)

coreg_pet_to_t1w = Node(
MRICoreg(reference_file=t1w_file), name="coreg_pet_to_t1w"
)
# rename registration file to something more descriptive than registration.lta
# we do this here to account for mulitple runs during the same session
mricoreg = MRICoreg(reference_file=t1w_file)
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mricoreg.inputs.out_lta_file = f"{pet_string}{run_id}_desc-pet2anat_pet.lta"

coreg_pet_to_t1w = Node(mricoreg, "coreg_pet_to_t1w")

deface_pet = Node(ApplyMideface(in_file=pet_file), name="deface_pet")

Expand All @@ -323,12 +331,17 @@ def init_single_subject_wf(
(
coreg_pet_to_t1w,
datasink,
[("out_lta_file", f"{pet_string.replace('_', '.')}.pet")],
[("out_lta_file", f"{pet_string.replace('_', '.')}.pet.@{run_id}")],
),
(
deface_pet,
datasink,
[("out_file", f"{pet_string.replace('_', '.')}.pet.@defaced")],
[
(
"out_file",
f"{pet_string.replace('_', '.')}.pet.@defaced{run_id}",
)
],
),
]
)
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2 changes: 1 addition & 1 deletion pyproject.toml
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@@ -1,6 +1,6 @@
[tool.poetry]
name = "petdeface"
version = "0.0.1"
version = "0.0.2"
description = "A nipype PET and MR defacing pipeline for BIDS datasets utilizing FreeSurfer's MiDeFace."
authors = ["Martin Nørgaard <martin.noergaard@nru.dk>", "Anthony Galassi <28850131+bendhouseart@users.noreply.github.com>", "Murat Bilgel <bilgelm@gmail.com>"]
license = "MIT"
Expand Down