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Template inject Lflip vs R #310

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merged 4 commits into from
Jul 22, 2024
Merged

Template inject Lflip vs R #310

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e6967c8
bigbrain template laplace coords added
Jul 8, 2024
98ea109
bugfix for using L or R template injection
Jul 10, 2024
c8fe2b8
lint
Jul 10, 2024
4962b48
Merge branch 'master' into templateLflipvsR
jordandekraker Jul 16, 2024
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10 changes: 7 additions & 3 deletions hippunfold/config/snakebids.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -384,21 +384,25 @@ template_based_segmentation:
hemi:
- R
- L
CIVM:
dHCP:
hemi:
- R
- L

MBMv2:
hemi:
- R
MBMv3:
hemi:
- R
ABAv3:
CIVM:
hemi:
- R
- L
dHCP:
upenn:
hemi:
- R
ABAv3:
hemi:
- R
- L
Expand Down
80 changes: 58 additions & 22 deletions hippunfold/workflow/rules/shape_inject.smk
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Original file line number Diff line number Diff line change
@@ -1,3 +1,36 @@
# Template-based segmentation supports templates that have only a single hemisphere
# by mapping it to the flipped version of the other hemisphere.
# If a template has both L and R files, then we set hemi_constrained_wildcard to L|R.
# If a hemisphere is missing data, then we set it to flip that, e.g. if L missing, then use Lflip|R

hemi_constraints = []
if config["template"] in config["template_based_segmentation"]:
for hemi in config["hemi"]:
if hemi in config["template_based_segmentation"][config["template"]]["hemi"]:
hemi_constraints.append(hemi)
else:
hemi_constraints.append(f"{hemi}flip")

hemi_constrained_wildcard = "{{hemi,{constraints}}}".format(
constraints="|".join(hemi_constraints)
)


def flipped(wildcards):
"""function to map hemi in wildcards from Lflip to R, or Rflip to L,
for use in rules where e.g. the output wildcard is Lflip, but for the input, R is desired, such as
when mapping a R hemi dseg to the Lflip hemisphere of a subject."""

if wildcards.hemi == "L" or wildcards.hemi == "R":
return wildcards
elif wildcards.hemi == "Lflip":
wildcards.hemi = "R"
return wildcards
elif wildcards.hemi == "Rflip":
wildcards.hemi = "L"
return wildcard


def get_input_for_shape_inject(wildcards):
if config["modality"] == "cropseg":
seg = bids(
Expand All @@ -6,7 +39,7 @@ def get_input_for_shape_inject(wildcards):
**config["subj_wildcards"],
suffix="dseg.nii.gz",
space="corobl",
hemi="{hemi}"
hemi="{hemi}",
).format(**wildcards)
elif get_modality_key(config["modality"]) == "seg":
modality_suffix = get_modality_suffix(config["modality"])
Expand All @@ -18,7 +51,7 @@ def get_input_for_shape_inject(wildcards):
suffix="dseg.nii.gz",
space="corobl",
hemi="{hemi}",
from_="{modality_suffix}"
from_="{modality_suffix}",
).format(**wildcards, modality_suffix=modality_suffix),
)
else:
Expand All @@ -29,7 +62,7 @@ def get_input_for_shape_inject(wildcards):
suffix="dseg.nii.gz",
desc="nnunet",
space="corobl",
hemi="{hemi}"
hemi="{hemi}",
).format(**wildcards)
return seg

Expand All @@ -42,7 +75,7 @@ def get_input_splitseg_for_shape_inject(wildcards):
**config["subj_wildcards"],
suffix="dsegsplit",
space="corobl",
hemi="{hemi}"
hemi="{hemi}",
).format(**wildcards)

elif get_modality_key(config["modality"]) == "seg":
Expand All @@ -54,7 +87,7 @@ def get_input_splitseg_for_shape_inject(wildcards):
suffix="dsegsplit",
space="corobl",
hemi="{hemi}",
from_="{modality_suffix}"
from_="{modality_suffix}",
).format(**wildcards, modality_suffix=modality_suffix)
else:
seg = bids(
Expand All @@ -64,7 +97,7 @@ def get_input_splitseg_for_shape_inject(wildcards):
suffix="dsegsplit",
desc="nnunet",
space="corobl",
hemi="{hemi}"
hemi="{hemi}",
).format(**wildcards)
return seg

Expand Down Expand Up @@ -92,7 +125,7 @@ rule import_template_shape:
params:
template_seg=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["inject_template"]]["dseg"].format(
**wildcards
**flipped(wildcards)
),
output:
template_seg=bids(
Expand All @@ -101,6 +134,7 @@ rule import_template_shape:
space="template",
**config["subj_wildcards"],
desc="hipptissue",
hemi=hemi_constrained_wildcard,
suffix="dseg.nii.gz"
),
group:
Expand Down Expand Up @@ -164,6 +198,7 @@ rule template_shape_reg:
space="template",
**config["subj_wildcards"],
desc="hipptissue",
hemi="{hemi}",
suffix="dsegsplit"
),
subject_seg=get_input_splitseg_for_shape_inject,
Expand All @@ -183,7 +218,7 @@ rule template_shape_reg:
to="subject",
space="corobl",
type_="ras",
hemi="{hemi,Lflip|R}"
hemi=hemi_constrained_wildcard,
),
warp=bids(
root=work,
Expand All @@ -194,7 +229,7 @@ rule template_shape_reg:
from_="template",
to="subject",
space="corobl",
hemi="{hemi,Lflip|R}"
hemi=hemi_constrained_wildcard,
),
group:
"subj"
Expand All @@ -205,7 +240,7 @@ rule template_shape_reg:
bids(
root="logs",
**config["subj_wildcards"],
hemi="{hemi,Lflip|R}",
hemi=hemi_constrained_wildcard,
suffix="templateshapereg.txt"
),
shell:
Expand All @@ -222,6 +257,7 @@ rule template_shape_inject:
space="template",
**config["subj_wildcards"],
desc="hipptissue",
hemi="{hemi}",
suffix="dseg.nii.gz"
),
subject_seg=get_input_for_shape_inject,
Expand All @@ -235,7 +271,7 @@ rule template_shape_inject:
to="subject",
space="corobl",
type_="ras",
hemi="{hemi}"
hemi="{hemi}",
),
warp=bids(
root=work,
Expand All @@ -246,7 +282,7 @@ rule template_shape_inject:
from_="template",
to="subject",
space="corobl",
hemi="{hemi}"
hemi="{hemi}",
),
params:
interp_opt="-ri LABEL 0.2vox",
Expand All @@ -258,14 +294,14 @@ rule template_shape_inject:
suffix="dseg.nii.gz",
desc="inject",
space="corobl",
hemi="{hemi,Lflip|R}"
hemi=hemi_constrained_wildcard,
),
log:
bids(
root="logs",
**config["subj_wildcards"],
suffix="templateshapeinject.txt",
hemi="{hemi,Lflip|R}"
hemi=hemi_constrained_wildcard,
),
group:
"subj"
Expand All @@ -289,7 +325,7 @@ rule inject_init_laplace_coords:
to="subject",
space="corobl",
type_="ras",
hemi="{hemi}"
hemi="{hemi}",
),
warp=bids(
root=work,
Expand All @@ -300,7 +336,7 @@ rule inject_init_laplace_coords:
from_="template",
to="subject",
space="corobl",
hemi="{hemi}"
hemi="{hemi}",
),
template_dir=Path(download_dir) / "template" / config["inject_template"],
params:
Expand All @@ -319,7 +355,7 @@ rule inject_init_laplace_coords:
suffix="coords.nii.gz",
desc="init",
space="corobl",
hemi="{hemi,R|Lflip}"
hemi=hemi_constrained_wildcard,
),
log:
bids(
Expand All @@ -329,7 +365,7 @@ rule inject_init_laplace_coords:
label="{autotop}",
suffix="injectcoords.txt",
desc="init",
hemi="{hemi,R|Lflip}"
hemi=hemi_constrained_wildcard,
),
group:
"subj"
Expand Down Expand Up @@ -365,7 +401,7 @@ rule unflip_init_coords:
suffix="coords.nii.gz",
desc="init",
space="corobl",
hemi="{hemi,L}"
hemi="{hemi,L|R}"
),
container:
config["singularity"]["autotop"]
Expand All @@ -385,7 +421,7 @@ rule reinsert_subject_labels:
suffix="dseg.nii.gz",
desc="inject",
space="corobl",
hemi="{hemi}"
hemi="{hemi}",
),
subject_seg=get_input_for_shape_inject,
params:
Expand All @@ -400,7 +436,7 @@ rule reinsert_subject_labels:
suffix="dseg.nii.gz",
desc="postproc",
space="corobl",
hemi="{hemi,Lflip|R}"
hemi=hemi_constrained_wildcard,
),
group:
"subj"
Expand Down Expand Up @@ -429,7 +465,7 @@ rule unflip_postproc:
suffix="dseg.nii.gz",
desc="postproc",
space="corobl",
hemi="{hemi,L}",
hemi="{hemi,L|R}",
**config["subj_wildcards"]
),
container:
Expand Down
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