README.md

---
library_name: ilex
tags:
- jax
- equinox
- ilex
- neuroimaging
- skull
license: mit
license_link: https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/
---

# SynthStrip -- Main model

## Description

SynthStrip skull-stripping network ported to JAX / Equinox from the FreeSurfer mri_synthstrip reference implementation. The network is trained with synthesis-based domain randomisation and is contrast-agnostic across modalities (T1w, T2w, FLAIR, DWI, etc.). It outputs a signed distance transform (SDT) of the brain surface; downstream tooling thresholds the SDT to obtain a binary brain mask.

## Intended use

General-purpose adult skull stripping. The 90% case.

## Usage

```python
from ilex.models.synthstrip import SynthStrip
model = SynthStrip.from_pretrained('ilex-hub/synthstrip.1')
```

## Authors

Hoopes A., Mora J. S., Dalca A. V., Fischl B., Hoffmann M.

## Citation

Hoopes A., Mora J. S., Dalca A. V., Fischl B., Hoffmann M. (2022). SynthStrip: Skull-Stripping for Any Brain Image. NeuroImage, 260:119474. doi:10.1016/j.neuroimage.2022.119474

### References

- Hoopes A., Mora J. S., Dalca A. V., Fischl B., Hoffmann M. (2022). SynthStrip: Skull-Stripping for Any Brain Image. NeuroImage, 260:119474. doi:10.1016/j.neuroimage.2022.119474
- Kelley W. et al. (2024). Boosting Skull-Stripping Performance for Pediatric Brain Images. IEEE International Symposium on Biomedical Imaging (ISBI).
- Hoffmann M. (2025). Domain-Randomized Deep Learning for Neuroimage Analysis. IEEE Signal Processing Magazine.

## License

HF Hub license tag: `mit`

**Effective terms:** MIT or CC-BY-4.0, at the licensee's option, per the upstream FreeSurfer offer at the license_url. The HF Hub tag is `mit` for searchability; the dual nature of the offer survives in this field and in the README License section.

Upstream license reference: https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/

### Copyright

Network architecture and training code: copyright (c) 2022 The General Hospital Corporation, distributed as part of FreeSurfer (GPL-2.0). Pretrained weights: dual-licensed by upstream as MIT or CC-BY-4.0 (see https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/). JAX / Equinox port: copyright (c) the ilex authors, released under the Apache-2.0 / GPL-3.0 dual license used by ilex itself.

## Upstream source

Original weights / reference implementation: https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/

## Provenance

This artefact was produced by [ilex](https://github.com/hypercoil/ilex)'s
save/load pipeline. The architecture is implemented in
`ilex.models.synthstrip.SynthStrip` and the weights have been converted
from their upstream format. See the upstream source above
for the canonical reference.