fsm_seg.hypothalamic_subunits.1

FSM-family small-FOV segmentation -- Hypothalamic subunits (11 labels)

Description

A small 3-level neurite UNet shared by five FreeSurfer segmentation tools, ported to JAX / Equinox from the FreeSurfer bundled reference implementations. The architecture is a compact variant of the SynthSeg / SynthSR UNet body (nb_features=24, nb_levels=3, conv_size=3, feat_mult=2, nb_conv_per_level=2, per-level BatchNorm, ELU activation, 1-channel T1 input, softmax head). Five published variants share this architecture exactly; they differ only in the number of output labels and in the recommended inference field of view. The variant id is recorded in the bundle's card, so loading by repo id selects the appropriate weights without changing the JAX class.

Intended use

Segmentation of the hypothalamus and its anterior, tuberal, and posterior subunits from a single T1w volume conformed to a 160 mm cube FoV.

Usage

from ilex.models.fsm_seg import FSMSeg
model = FSMSeg.from_pretrained('ilex-hub/fsm_seg.hypothalamic_subunits.1')

Authors

Greve D. N., Billot B., Cordero-Grande L., Van Leemput K., Fischl B., Iglesias J. E.; with substantial overlap across variants -- per-variant first authors are listed under references.

Citation

Per variant. sclimbic: Greve D. N., Billot B., Cordero-Grande L., et al. (2021). NeuroImage 244:118610. doi:10.1016/j.neuroimage.2021.118610. hypothalamic_subunits: Billot B., Bocchetta M., Todd E., Dalca A. V., Rohrer J. D., Iglesias J. E. (2020). NeuroImage 223:117287. doi:10.1016/j.neuroimage.2020.117287. entowm, mca-dura, vsinus: FreeSurfer 8.x release notes (no separate primary publications).

References

• Greve D. N., Billot B., Cordero-Grande L., et al. (2021). A deep learning toolbox for automatic segmentation of subcortical limbic structures from MRI images. NeuroImage, 244:118610. doi:10.1016/j.neuroimage.2021.118610. (sclimbic variant.)
• Billot B., Bocchetta M., Todd E., Dalca A. V., Rohrer J. D., Iglesias J. E. (2020). Automated segmentation of the hypothalamus and associated subunits in brain MRI. NeuroImage, 223:117287. doi:10.1016/j.neuroimage.2020.117287. (hypothalamic_subunits variant.)
• mri_entowm_seg, mri_mcadura_seg, mri_vsinus_seg are FreeSurfer utility variants of the sclimbic architecture; the underlying network is the same and the FreeSurfer release notes document their introduction without separate primary publications.

License

HF Hub license tag: other HF Hub license slug: freesurfer-software-license

Effective terms: FreeSurfer Software License: academic / non-commercial use only. Pending explicit upstream confirmation that re-hosting on HF Hub is acceptable. Resolve before flipping published: true.

Upstream license reference: https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense

Copyright

Network architectures, training code, and pretrained weights: copyright (c) the respective upstream authors, distributed as part of the FreeSurfer software bundle under the FreeSurfer Software License (FSLA; permissive academic / non-commercial research offering). See https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense for the binding terms. JAX / Equinox port code: 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/

Provenance

This artefact was produced by ilex's save/load pipeline. The architecture is implemented in ilex.models.fsm_seg.FSMSeg and the weights have been converted from their upstream format. See the upstream source above for the canonical reference.