# From 100,000+ images to winning the first brain MRI foundation model challenges: Sharing lessons and models

arXiv: https://arxiv.org/abs/2601.13166 · HTML: https://mlsanity.com/paper/2601.13166/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 10 references that are in the map.
- First posted on arXiv 19 Jan 2026.

## Builds on (most cited first, 7 of 7)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Revisiting MAE pre-training for 3D medical image segmentation](https://mlsanity.com/paper/2410.23132/) (2024)
- [An OpenMind for 3D medical vision self-supervised learning](https://mlsanity.com/paper/2412.17041/) (2024)
- [AMAES: Augmented Masked Autoencoder Pretraining on Public Brain MRI Data for 3D-Native Segmentation](https://mlsanity.com/paper/2408.00640/) (2024)
- [A large-scale heterogeneous 3D magnetic resonance brain imaging dataset for self-supervised learning](https://mlsanity.com/paper/2506.14432/) (2025)

## Built on by (most cited first, 1 of 1)

- [Towards Brain MRI Foundation Models for the Clinic: Findings from the FOMO25 Challenge](https://mlsanity.com/paper/2604.11679/) (2026)

## Abstract (arXiv)

Developing Foundation Models for medical image analysis is essential to overcome the unique challenges of radiological tasks. The first challenges of this kind for 3D brain MRI, SSL3D and FOMO25, were held at MICCAI 2025. Our solution ranked first in tracks of both contests. It relies on a U-Net CNN architecture combined with strategies leveraging anatomical priors and neuroimaging domain knowledge. Notably, our models trained 1-2 orders of magnitude faster and were 10 times smaller than competing transformer-based approaches. Models are available here: https://github.com/jbanusco/BrainFM4Challenges.