A Foundation Model for Brain MRI with Dynamic Modality Integration (Student Abstract)

Abstract We introduce a single–backbone foundation model for brain MRI that supports dynamic modality integration: it operates with arbitrary, possibly unseen, combinations of MRI sequences at pretrain and transfer. The encoder is conditioned by text-derived modality embeddings via conditional layer normalization, while a variance–covariance penalty discourages feature collapse. Unlike expert-based designs that grow with each new sequence, our approach scales without adding modality-specific branches. Pretrained self-supervised on ∼60,000 heterogeneous MRIs, the model learns modality-aware yet modality-agnostic features. We outline evaluation on segmentation and classification under missing/unseen modalities and cross-center shifts, and present early feasibility on multiple sclerosis lesion segmentation under limited data. This work moves toward robust, protocol-agnostic MRI foundation models suited to real clinical variability.