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
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'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.