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CortexMAE (ViT-B MAE foundation model for fMRI) -- CortexMAE volume (MNI cortical-surface 2D strip)
Description
CortexMAE (MedARC-AI, arXiv 2510.13768) is a ViT-B masked autoencoder pretrained on 2.1K hours of HCP fMRI BOLD data. The architecture is the standard MAE (encoder + lighter decoder + MSE loss on reconstructed patches) with separate Q/K/V Linears (the original MAE convention) and separable spatial + temporal positional embeddings (mae-st style).
v0 ships the parcel variant only (cortex_mae_parcel --
Schaefer-400 1D parcellation input). The flat (2D brain map)
and volume (3D MNI cortex) variants are queued as follow-ups
(#157 + #158) on top of the same shared transformer body.
Intended use
MNI cortical-surface backbone. Despite the volume name, the input space is a (465, 512) 2D grid (cortical surface points × MNI flattened band), NOT a 3D MNI volume. Input (1, 16, 465, 512). Output: cls embedding (1, 768) + patch embeddings (1860, 768) over 4 temporal x 465 spatial patches (each spanning the full 512 strip width).
Usage
from ilex.models.cortex_mae import CortexMAE
model = CortexMAE.from_pretrained('ilex-hub/cortex_mae.volume.1')
Authors
MedARC-AI (research collective)
Citation
Adkinson R. et al. (2025). CortexMAE -- A masked autoencoder foundation model for fMRI. arXiv 2510.13768.
References
- Adkinson R. et al. (2025). CortexMAE -- A masked autoencoder foundation model for fMRI. arXiv 2510.13768.
- Feichtenhofer C. et al. (2022). Masked autoencoders as spatiotemporal learners (MAE-ST). NeurIPS.
- Upstream code -- github.com/MedARC-AI/CortexMAE (Apache-2.0); weights -- huggingface.co/medarc/CortexMAE (CC-BY-NC-4.0).
License
HF Hub license tag: cc-by-nc-4.0
Effective terms: CC-BY-NC-4.0 on the released checkpoint weights (huggingface.co/medarc/CortexMAE, LICENSE.models). The upstream code (github.com/MedARC-AI/CortexMAE) is separately Apache-2.0. Non-commercial restriction on the weights requires gated distribution with explicit acknowledgement. The ilex JAX / Equinox port code is separately Apache-2.0 / GPL-3.0; non-commercial use only continues to apply to the weights regardless of the port-code licence.
Upstream license reference: https://creativecommons.org/licenses/by-nc/4.0/
Copyright
CortexMAE upstream code is copyright (c) MedARC-AI, Apache-2.0 on the code (github.com/MedARC-AI/CortexMAE, LICENSE) and CC-BY-NC-4.0 on the released checkpoint weights (huggingface.co/medarc/CortexMAE, LICENSE.models). The non-commercial restriction on the weights is preserved through gated HuggingFace distribution; the ilex JAX / Equinox port code is separately Apache-2.0 / GPL-3.0.
Upstream source
Original weights / reference implementation: https://github.com/MedARC-AI/CortexMAE
Provenance
This artefact was produced by ilex's
save/load pipeline. The architecture is implemented in
ilex.models.cortex_mae.CortexMAE and the weights have been converted
from their upstream format. See the upstream source above
for the canonical reference.
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