totalsegmentator-konfai 1.4.5

Fast and lightweight TotalSegmentator CLI powered by the KonfAI framework.

TotalSegmentator-KonfAI

Fast and lightweight TotalSegmentator inference using the KonfAI framework

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🧩 Overview

TotalSegmentator-KonfAI is a lightweight command-line interface (CLI) for running TotalSegmentator models a multi-organ medical image segmentation, through the KonfAI deep learning framework.

It provides fast inference for segmentation tasks, even on low-resource hardware.
Models are automatically downloaded from Hugging Face Hub.

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🚀 Installation

From PyPI:

pip install totalsegmentator-konfai

From source:

git clone https://github.com/vboussot/TotalSegmentator-KonfAI.git
cd TotalSegmentator-KonfAI
pip install .

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⚙️ Usage

Perform segmentation on an input volume:

totalsegmentator-konfai -i path/to/image.nii.gz -o path/to/seg.nii.gz

Optional arguments

Flag	Description	Default
-i, --input	Path to the input medical image	required
-o, --output	Path to save the segmentation	Seg.nii.gz
-ta, --task	Choose model type: total or total_mr	total
-f, --fast	Use faster low-resolution model (≈3 mm)	False
-g, --gpu	GPU list (e.g. 0 or 0,1)	CPU if unset
--cpu	Number of CPU cores (used if no GPU)	1
-q, --quiet	Suppress console output	False

Example

totalsegmentator-konfai -i patient01.nii.gz -o seg_patient01.nii.gz --gpu 0 --task total --fast

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🧠 Features

• ⚡ Fast inference using KonfAI
• 🤗 Automatic model download from Hugging Face
• 🧩 Multi-model support
• 🧾 Multi-format compatibility: supports all major medical image formats handled by ITK

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📖 Reference

This package is based on the original TotalSegmentator by
Wasserthal et al., a deep learning framework for whole-body CT and MR segmentation.

For scientific use, please cite the original TotalSegmentator work in addition to this CLI tool.

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🧾 License

Released under the Apache 2.0 License.
The original TotalSegmentator and KonfAI licenses remain with their respective authors.

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🔗 Links

• 🧠 Original TotalSegmentator: github.com/wasserth/TotalSegmentator
• ⚙️ KonfAI Framework: github.com/vboussot/KonfAI
• 🤗 Model Hub: huggingface.co/VBoussot/TotalSegmentator-KonfAI
• 📦 PyPI Package: pypi.org/project/totalsegmentator-konfai

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