mkurman Overview
TotalSegmentator segments 104+ anatomical structures in CT images using nnUNet-based models. Run full-body, organ, or bone segmentation with a single CLI command.
Installation
uv pip install TotalSegmentator
CLI Usage
# Full body segmentation (all 104 structures)
TotalSegmentator -i input_ct.nii.gz -o output_seg.nii.gz
# Organ-only segmentation (liver, kidneys, spleen, etc.)
TotalSegmentator -i input_ct.nii.gz -o organ_seg.nii.gz -ta organ
# Appendicular bones
TotalSegmentator -i input_ct.nii.gz -o bone_seg.nii.gz -ta appendicular_bones
Python API
from totalsegmentator.python_api import totalsegmentator
segmentation = totalsegmentator("input_ct.nii.gz", "output_seg.nii.gz")
Workflow
- Obtain CT scan in NIfTI format
- Run
TotalSegmentator -i input.nii.gz -o output.nii.gz - Task types:
total(104 structures),organ,vertebra,ribs,appendicular_bones - Output is a multi-label segmentation mask
- Extract volumes per label for quantitative analysis