Towards Generalisable Foundation Models for 3D Brain MRI

Abstract: Foundation models in AI are transforming medical imaging by enabling general-purpose feature learning from large-scale, unlabeled datasets. In this work, we introduce BrainFound, a self-supervised foundation model for brain MRI, built by extending DINO-v2, a vision transformer originally designed for 2D natural images. BrainFound adapts DINO-v2 to model full 3D brain anatomy by incorporating volumetric information from sequential MRI slices, moving beyond conventional single-slice paradigms. It supports both single- and multimodal inputs, enabling a broad range of downstream tasks, including disease detection and image segmentation, while generalising across varied imaging protocols and clinical scenarios. We show that BrainFound consistently outperforms existing self-supervised pretraining strategies and supervised baselines, particularly in label-scarce and multi-contrast settings. By integrating information from diverse 3D MRI modalities (e.g., T1, T2, FLAIR), it enhances diagnostic accuracy and reduces dependency on extensive expert annotations. This flexibility makes BrainFound a scalable and practical solution for 3D neuroimaging pipelines, with significant potential for clinical deployment and research innovation.