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fixes bugs introduced in download-osf PR #280

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merged 2 commits into from
Feb 16, 2024
Merged

fixes bugs introduced in download-osf PR #280

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3ab2631
fixes bugs introduced in #277
akhanf Feb 16, 2024
7a6d33d
forgot conversion to str
akhanf Feb 16, 2024
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14 changes: 7 additions & 7 deletions hippunfold/workflow/rules/gifti.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -466,7 +466,7 @@ rule metric_to_nii:
params:
interp="-nearest-vertex 1",
refflatnii=lambda wildcards, input: Path(input.atlas_dir)
/ config["atlas_files"]["multihist7"]["label_nii"],
/ config["atlas_files"]["multihist7"]["label_nii"].format(**wildcards),
output:
metric_nii=bids(
root=work,
Expand Down Expand Up @@ -531,11 +531,11 @@ rule unfolded_registration:
warpfn="tmp1Warp.nii.gz",
invwarpfn="tmp1InverseWarp.nii.gz",
refthickness=lambda wildcards, input: Path(input.atlas_dir)
/ config["atlas_files"][wildcards.atlas]["thickness"],
/ config["atlas_files"][wildcards.atlas]["thickness"].format(**wildcards),
refcurvature=lambda wildcards, input: Path(input.atlas_dir)
/ config["atlas_files"][wildcards.atlas]["curvature"],
/ config["atlas_files"][wildcards.atlas]["curvature"].format(**wildcards),
refgyrification=lambda wildcards, input: Path(input.atlas_dir)
/ config["atlas_files"][wildcards.atlas]["gyrification"],
/ config["atlas_files"][wildcards.atlas]["gyrification"].format(**wildcards),
output:
warp=bids(
root=work,
Expand Down Expand Up @@ -1058,7 +1058,7 @@ rule resample_atlas_to_refvol:
atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas,
params:
atlas=lambda wildcards, input: Path(input.atlas_dir)
/ config["atlas_files"][wildcards.atlas]["label_nii"],
/ config["atlas_files"][wildcards.atlas]["label_nii"].format(**wildcards),
output:
label_nii=bids(
root=work,
Expand Down Expand Up @@ -1110,7 +1110,7 @@ rule nii_to_label_gii:
atlas_dir=lambda wildcards: Path(download_dir) / "atlas" / wildcards.atlas,
params:
label_list=lambda wildcards, input: Path(input.atlas_dir)
/ config["atlas_files"][wildcards.atlas]["label_list"],
/ config["atlas_files"][wildcards.atlas]["label_list"].format(**wildcards),
structure_type=lambda wildcards: hemi_to_structure[wildcards.hemi],
output:
label_gii=bids(
Expand All @@ -1131,7 +1131,7 @@ rule nii_to_label_gii:
shadow:
"minimal"
shell:
"wb_command -volume-to-surface-mapping {params.label_list} {input.surf} temp.shape.gii -enclosing && "
"wb_command -volume-to-surface-mapping {input.label_nii} {input.surf} temp.shape.gii -enclosing && "
"wb_command -metric-label-import temp.shape.gii {params.label_list} {output.label_gii} && "
"wb_command -set-structure {output.label_gii} {params.structure_type}"

Expand Down
22 changes: 12 additions & 10 deletions hippunfold/workflow/rules/nnunet.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -203,15 +203,13 @@ rule unflip_nnunet_nii:
def get_f3d_ref(wildcards, input):

if config["modality"] == "T2w":
nii = (
Path(input.template_dir)
/ config["template_files"][config["template"]]["crop_ref"]
)
nii = Path(input.template_dir) / config["template_files"][config["template"]][
"crop_ref"
].format(**wildcards)
elif config["modality"] == "T1w":
nii = (
Path(input.template_dir)
/ config["template_files"][config["template"]]["crop_refT1w"]
)
nii = Path(input.template_dir) / config["template_files"][config["template"]][
"crop_refT1w"
].format(**wildcards)
else:
raise ValueError("modality not supported for nnunet!")
return nii
Expand Down Expand Up @@ -302,8 +300,12 @@ rule qc_nnunet_dice:
template_dir=Path(download_dir) / "template" / config["template"],
params:
hipp_lbls=[1, 2, 7, 8],
ref=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["template"]]["Mask_crop"],
ref=lambda wildcards, input: (
Path(input.template_dir)
/ config["template_files"][config["template"]]["Mask_crop"].format(
**wildcards
)
),
output:
dice=report(
bids(
Expand Down
2 changes: 1 addition & 1 deletion hippunfold/workflow/rules/preproc_seg.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ rule warp_seg_to_corobl_crop:
template_dir=Path(download_dir) / "template" / config["template"],
params:
ref=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["template"]]["crop_ref"],
/ config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
output:
nii=bids(
root=work,
Expand Down
12 changes: 8 additions & 4 deletions hippunfold/workflow/rules/preproc_t1.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -72,9 +72,11 @@ else:

def reg_to_template_cmd(wildcards, input, output):

ref = (
ref = str(
Path(input.template_dir)
/ config["template_files"][config["template"]][wildcards.modality],
/ config["template_files"][config["template"]][wildcards.modality].format(
**wildcards
),
)
if config["no_reg_template"]:
cmd = f"reg_resample -flo {input.flo} -ref {ref} -res {output.warped_subj} -aff {input.xfm_identity}; cp {input.xfm_identity} {output.xfm_ras}"
Expand Down Expand Up @@ -183,7 +185,9 @@ rule compose_template_xfm_corobl:
template_dir=Path(download_dir) / "template" / config["template"],
params:
std_to_cor=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["template"]]["xfm_corobl"],
/ config["template_files"][config["template"]]["xfm_corobl"].format(
**wildcards
),
output:
sub_to_cor=bids(
root=work,
Expand Down Expand Up @@ -288,7 +292,7 @@ rule warp_t1_to_corobl_crop:
template_dir=Path(download_dir) / "template" / config["template"],
params:
ref=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["template"]]["crop_ref"],
/ config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
output:
t1=bids(
root=work,
Expand Down
9 changes: 4 additions & 5 deletions hippunfold/workflow/rules/preproc_t2.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -308,10 +308,9 @@ def get_cmd_compose_t2_xfm_corobl(wildcards, input):
# xfm0: t2 to template
xfm0 = input.t2_to_std
# xfm1: template to corobl
xfm1 = (
Path(input.template_dir)
/ config["template_files"][config["template"]]["xfm_corobl"]
)
xfm1 = Path(input.template_dir) / config["template_files"][config["template"]][
"xfm_corobl"
].format(**wildcards)

return "c3d_affine_tool -itk {xfm0} -itk {xfm1} -mult -oitk {output}"

Expand Down Expand Up @@ -394,7 +393,7 @@ rule warp_t2_to_corobl_crop:
template_dir=Path(download_dir) / "template" / config["template"],
params:
ref=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["template"]]["crop_ref"],
/ config["template_files"][config["template"]]["crop_ref"].format(**wildcards),
output:
nii=bids(
root=work,
Expand Down
8 changes: 6 additions & 2 deletions hippunfold/workflow/rules/qc.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -10,8 +10,12 @@ rule qc_reg_to_template:
),
template_dir=Path(download_dir) / "template" / config["template"],
params:
ref=lambda wildcards, input: Path(input.template_dir)
/ config["template_files"][config["template"]][wildcards.native_modality],
ref=lambda wildcards, input: str(
Path(input.template_dir)
/ config["template_files"][config["template"]][
wildcards.native_modality
].format(**wildcards)
),
output:
png=report(
bids(
Expand Down
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