Towards Brain MRI Foundation Models for the Clinic: Findings from the FOMO25 Challenge
For the clinical brain MRI community, this work provides a benchmark and insights into the practical deployment of foundation models under realistic data heterogeneity and label scarcity.
The FOMO25 challenge evaluated 19 self-supervised foundation models for brain MRI on clinical data, finding that out-of-domain pretraining outperforms supervised in-domain baselines, but no single objective benefits all tasks and scaling model size does not reliably improve performance.
Clinical deployment of automated brain MRI analysis faces a fundamental challenge: clinical data is heterogeneous and noisy, and high-quality labels are prohibitively costly to obtain. Self-supervised learning (SSL) can address this by leveraging the vast amounts of unlabeled data produced in clinical workflows to train robust \textit{foundation models} that adapt out-of-domain with minimal supervision. However, the development of foundation models for brain MRI has been limited by small pretraining datasets and in-domain benchmarking focused on high-quality, research-grade data. To address this gap, we organized the FOMO25 challenge as a satellite event at MICCAI 2025. FOMO25 provided participants with a large pretraining dataset, FOMO60K, and evaluated models on data sourced directly from clinical workflows in few-shot and out-of-domain settings. Tasks covered infarct classification, meningioma segmentation, and brain age regression, and considered both models trained on FOMO60K (method track) and any data (open track). Nineteen foundation models from sixteen teams were evaluated using a standardized containerized pipeline. Results show that (a) self-supervised pretraining improves generalization on clinical data under domain shift, with the strongest models trained \textit{out-of-domain} surpassing supervised baselines trained \textit{in-domain}. (b) No single pretraining objective benefits all tasks: MAE favors segmentation, hybrid reconstruction-contrastive objectives favor classification, and (c) strong performance was achieved by small pretrained models, and improvements from scaling model size and training duration did not yield reliable benefits.