Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.
@article{arxiv.2509.00549,
title = {A Modality-agnostic Multi-task Foundation Model for Human Brain Imaging},
author = {Peirong Liu and Oula Puonti and Xiaoling Hu and Karthik Gopinath and Annabel Sorby-Adams and Daniel C. Alexander and W. Taylor Kimberly and Juan E. Iglesias},
journal= {arXiv preprint arXiv:2509.00549},
year = {2025}
}