autods_pet.roi.liver#

Liver reference ROI: mask refinement and PET statistics.

class autods_pet.roi.liver.LiverROI(liver_label=5, erosion_mm=10.0, max_hole_volume_mm3=None, stats=None)[source]#

Bases: object

Liver reference ROI extraction and refinement.

Parameters:

  • liver_label (int (default: 5)) – TotalSegmentator label for liver (default 5).

  • erosion_mm (float (default: 10.0)) – Erosion radius in mm.

  • max_hole_volume_mm3 (float | None (default: None)) – If set, only fill holes smaller than this volume (mm³). Large holes (e.g. portal vein) are preserved.

  • stats (list[str] | None (default: None)) – Statistics to compute (e.g. ["median"]). Defaults to ["median"].

refine(whole_seg)[source]#

Refine TotalSegmentator liver label into a core-parenchyma mask.

Pipeline: extract label -> keep largest component -> fill holes -> erode to avoid partial-volume at boundaries.

Parameters:

whole_seg (Image) – TotalSegmentator multilabel segmentation.

Returns:

Result with refined_mask and shrinkage populated.

Return type:

ROIResult

extract(whole_seg, pet)[source]#

Refine mask and compute PET statistics in one call.

Parameters:

  • whole_seg (Image) – TotalSegmentator multilabel segmentation.

  • pet (Image) – PET SUV image (must share geometry with whole_seg).

Returns:

Result with refined_mask, shrinkage, and stats populated.

Return type:

ROIResult

Raises:

ValueError – If whole_seg and pet have mismatched geometry.