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Bug fixes to anatomical workflow #40

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Merged
kaitj merged 3 commits into from
Feb 6, 2026
Merged

Bug fixes to anatomical workflow #40

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f4406e0
Fix output path of composite warp
kaitj Feb 6, 2026
e197291
Fix fslmaths parameters since niwrap update"
kaitj Feb 6, 2026
a0435ba
Inline renaming of anatomical files
kaitj Feb 6, 2026
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4 changes: 3 additions & 1 deletion src/rbc/core/anatomical/registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -144,4 +144,6 @@ def ants_registration(
print_out_composite_warp_file=True,
),
)
return SimpleNamespace(forward=fwd.output, inverse=rev.output)
return SimpleNamespace(
forward=fwd.output.output_image_outfile, inverse=rev.output.output_image_outfile
)
4 changes: 2 additions & 2 deletions src/rbc/core/anatomical/segmentation.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,8 +53,8 @@ def fsl_tissue_segmentation(in_file: Path, output_prefix: str) -> SimpleNamespac
tissue_type: fsl.fslmaths(
input_files=[tissues.root / f"{output_prefix}_pve_{idx}.nii.gz"],
operations=[
fsl.fslmaths_operation(thr=0.95),
fsl.fslmaths_operation(bin_=True),
fsl.fslmaths_operation_thr(thr=0.95),
fsl.fslmaths_operation_bin(bin_=True),
],
output=f"{tissue_type}_mask.nii.gz",
).output_file
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15 changes: 7 additions & 8 deletions src/rbc/workflows/anatomical.py
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Expand Up @@ -42,16 +42,15 @@ def single_session(in_t1w: Path, output_dir: Path) -> None:
)

# Prep files to save
t1w_outputs = [
(extracted_t1w.brain_extracted_image, "brain", "T1w"),
(extracted_t1w.brain_mask, "T1w", "mask"),
(tissue_masks.csf, "csf", "mask"),
(tissue_masks.gm, "gm", "mask"),
(tissue_masks.wm, "wm", "mask"),
]
renamed_files = [
rename(out_file, bids(desc=desc, suffix=suffix, ext=".nii.gz"))
for out_file, desc, suffix in t1w_outputs
for out_file, desc, suffix in [
(extracted_t1w.brain_extracted_image, "brain", "T1w"),
(extracted_t1w.brain_mask, "T1w", "mask"),
(tissue_masks.csf, "csf", "mask"),
(tissue_masks.gm, "gm", "mask"),
(tissue_masks.wm, "wm", "mask"),
]
]
niwrap_helper.save(
[*renamed_files, transforms.forward, transforms.inverse],
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