mrsegmentator-konfai 1.4.5

Fast and lightweight MRSegmentator CLI powered by the KonfAI framework.

MRSegmentator-KonfAI

Fast and lightweight MRI segmentation built on the MRSegmentator model using the KonfAI framework

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🧩 Overview

MRSegmentator-KonfAI is a lightweight command-line interface (CLI) for running MRSegmentator
models through the KonfAI deep learning framework.

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

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🚀 Installation

From PyPI:

pip install mrsegmentator-konfai

From source:

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

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⚙️ Usage

Run inference on an MRI scan:

mrsegmentator-konfai -i path/to/input.nii.gz -o path/to/output_seg.nii.gz

Optional arguments

Flag	Description	Default
-i, --input	Path to the input MRI volume	required
-o, --output	Path to save the segmentation	Seg.nii.gz
-f, --folds	Number of model folds to ensemble (1–5)	2
-g, --gpu	List of GPUs to use (e.g. 0, 0,1)	CPU if unset
--cpu	Number of CPU cores to use (if no GPU)	1
-quiet	Suppress console output	off

Example:

mrsegmentator-konfai -i subject01.nii.gz -o seg_subject01.nii.gz --gpu 0 -f 3

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🧠 Features

• ⚡ Fast inference using KonfAI
• 🤗 Automatic model download from Hugging Face
• 🧩 Support for ensemble models (multi-fold prediction)
• 🧾 Multi-format compatibility: supports all major medical image formats handled by ITK

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📖 Reference

This package is based on the original MRSegmentator by
Henrik Haentze et al., a deep-learning-based method for full body MRI segmentation.

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

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🧾 License

This repository is released under the Apache 2.0 License.
Original MRSegmentator license and copyright remain with their respective authors.

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🔗 Links

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