| --- |
| 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. |
| |
