A Universal Atlas-Free fMRI Foundation Model
Summary of the linked study; findings refer to that study’s own comparisons.
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Evidence boundary: Reported improvements refer to the benchmark tasks and foundation-model baselines evaluated in the paper, not every possible fMRI application.
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Self-supervised fMRI foundation models have shown promising transfer performance, yet most rely on predefined region-level parcellations that discard fine-grained voxel information and introduce atlas-dependent biases. We propose Omni-fMRI, an atlas-free foundation model that operates directly on voxel-level signals. To enable scalable pretraining on 49,497 fMRI sessions across nine datasets, Omni-fMRI introduces a dynamic patching mechanism that substantially reduces computational cost while preserving informative spatial structure. To support reproducibility and fair comparison, we establish a comprehensive benchmark suite spanning 11 datasets and a diverse set of resting-state and task-based fMRI tasks. Experimental results demonstrate that Omni-fMRI consistently outperforms existing foundation models, providing a scalable and reproducible framework for atlas-free brain representation learning.
Omni-fMRI adaptively allocates coarse and fine voxel patches, aligns them through a dual-path embedding, then reconstructs each scale with dedicated prediction heads.
@article{wang2026omnifmri,
title={Omni-fMRI: A Universal Atlas-Free fMRI Foundation Model},
author={Wang, Mo and Ye, Wenhao and Xia, Junfeng and Zhang, Junxiang and Pan, Xuanye and Xu, Minghao and Deng, Haotian and Wen, Hongkai and Liu, Quanying},
journal={arXiv preprint arXiv:2601.23090},
year={2026},
url={https://arxiv.org/abs/2601.23090},
doi={10.48550/arXiv.2601.23090}
}