https://github.com/mu40/babyseg
Brain segmentation across the first years of life
https://github.com/mu40/babyseg
brain-segmentation deep-learning domain-randomization mri neuroimaging nifti
Last synced: 23 days ago
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Brain segmentation across the first years of life
- Host: GitHub
- URL: https://github.com/mu40/babyseg
- Owner: mu40
- License: mit
- Created: 2025-10-19T11:46:47.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2026-02-18T13:04:14.000Z (4 months ago)
- Last Synced: 2026-02-18T17:36:48.406Z (4 months ago)
- Topics: brain-segmentation, deep-learning, domain-randomization, mri, neuroimaging, nifti
- Language: Python
- Homepage: https://babyseg.io
- Size: 195 KB
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# BabySeg
BabySeg is a brain segmentation tool for infants and young children, designed to delineate anatomical structures in MRI without preprocessing.
The tool can integrate information from multiple NIfTI image volumes of variable contrast, shape, and resolution in any order, provided that (1) their header geometries are correct, and (2) they are properly aligned in world space.
## Running BabySeg
The recommended way to run BabySeg is in a [container](docker/README.md).
## Video
Watch a 30-minute [video](https://www.youtube.com/watch?v=UZwUZQXhnBo) recording of a talk introducing the motivation and methodology behind BabySeg.
## Attribution
If you find this work useful, please cite the relevant papers below.
BabySeg [method](https://arxiv.org/abs/2512.05114):
```bibtex
@inproceedings{hoffmann2025deep,
title={{Deep infant brain segmentation from multi-contrast MRI}},
author={Hoffmann, Malte and Z{\"o}llei, Lilla and Dalca, Adrian V},
booktitle={{Asilomar Conference on Signals, Systems, and Computers}},
pages={974--981},
year={2025},
publisher={IEEE}
}
```
Data [engine](https://arxiv.org/abs/2507.13458):
```bibtex
@article{hoffmann2025domain,
title={Domain-randomized deep learning for neuroimage analysis},
author={Hoffmann, Malte},
journal={IEEE Signal Processing Magazine},
volume={42},
number={4},
pages={78--90},
year={2025},
publisher={IEEE}
}
```
## Support
Read the [FAQ](doc/faq.md), post questions to the FreeSurfer [mailing list](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport), or file bugs on GitHub.