Links: [Paper] | [Pretraining Code] | [FOMO300K] | [FOMO260K] | [FOMO50K] | [FOMO45K]
This repository contains the preprocessing scripts to reproduce the FOMO-MRI datasets described in the paper:
A large-scale heterogeneous 3D magnetic resonance brain imaging dataset for self-supervised learning
The repository for pretraining and finetuning models as described in the paper is available here: https://github.com/Sllambias/asparagus
The FOMO-MRI collection contains brain MRI scans from 900+ diverse sources, designed for self-supervised learning research. The collection is organized around two supersets — FOMO300K (raw) and FOMO50K (a co-registered, skull-stripped subset) — each with an openly licensed counterpart (FOMO260K and FOMO45K respectively) that excludes constituent datasets requiring Data Use Agreements. All datasets include varied acquisition protocols, scanner types, and patient populations.
The preprocessed datasets are available on HuggingFace:
| Dataset | Scans | Access | Description |
|---|---|---|---|
| FOMO300K | 306,207 | Gated (auto-approved) | The full superset across the collection. Gated because some constituent datasets require Data Use Agreements. |
| FOMO260K | 260,927 | Open (CC-BY-NC-SA) | The freely accessible subset of FOMO300K. No login or access request required. |
| FOMO50K | 49,193 | Gated (auto-approved) | A co-registered, skull-stripped, and/or defaced subset of FOMO300K. |
| FOMO45K | 46,149 | Open (CC-BY-NC-SA) | The freely accessible subset of FOMO50K. No login or access request required. |
⚠️ Do not combine datasets from this collection. Because each dataset is a subset of FOMO300K, combining them will result in duplicated scans.
FOMO300K_preprocessing/- Preprocessing scripts and dataset generation for FOMO300K (and its open subset FOMO260K)FOMO50K_preprocessing/- FOMO50K subset preprocessing with coregistration and skull-stripping (and its open subset FOMO45K)scripts/- Analysis and visualization scripts
If you use any of the FOMO-MRI datasets, please cite:
@article{Cerri2026large,
title={A large-scale heterogeneous 3D magnetic resonance brain imaging dataset for self-supervised learning},
author={Cerri, Stefano and Munk, Asbj{\o}rn and Llambias, Sebastian N{\o}rgaard and Ambsdorf, Jakob and Machnio, Julia and Nersesjan, Vardan and Hedeager Krag, Christian and Liu, Peirong and Rocamora Garc{\'\i}a, Pablo and Mehdipour Ghazi, Mostafa and Boesen, Mikael and Benros, Michael Eriksen and Iglesias, Juan Eugenio and Nielsen, Mads},
journal={arXiv preprint arXiv:2506.14432},
year={2026},
url={https://arxiv.org/abs/2506.14432}
}