total-segmentator

name	total-segmentator
description	Tool for robust segmentation of 104+ anatomical structures in CT images. Uses nnUNet-based models for whole-body, organ, and bone segmentation. One-line CLI for comprehensive body-part segmentation.
tags	["medical-image-segmentation","ct-anatomy-segmentation","whole-body-ct","nnunet-inference","total-segmentator"]

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

1. Obtain CT scan in NIfTI format
2. Run TotalSegmentator -i input.nii.gz -o output.nii.gz
3. Task types: total (104 structures), organ, vertebra, ribs, appendicular_bones
4. Output is a multi-label segmentation mask
5. Extract volumes per label for quantitative analysis