# Scaling Vision Transformers for Functional MRI with Flat Maps

arXiv: https://arxiv.org/abs/2510.13768 · HTML: https://mlsanity.com/paper/2510.13768/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 63 of its 152 references that are in the map.
- First posted on arXiv 15 Oct 2025.

## Builds on (most cited first, 30 of 63)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Microsoft COCO: Common Objects in Context](https://mlsanity.com/paper/1405.0312/) (2014)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [wav2vec 2.0: A Framework for Self-Supervised Learning of Speech Representations](https://mlsanity.com/paper/2006.11477/) (2020)
- [Training Compute-Optimal Large Language Models](https://mlsanity.com/paper/2203.15556/) (2022)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [The Kinetics Human Action Video Dataset](https://mlsanity.com/paper/1705.06950/) (2017)
- [ViViT: A Video Vision Transformer](https://mlsanity.com/paper/2103.15691/) (2021)
- [Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour](https://mlsanity.com/paper/1706.02677/) (2017)
- [VideoMAE: Masked Autoencoders are Data-Efficient Learners for Self-Supervised Video Pre-Training](https://mlsanity.com/paper/2203.12602/) (2022)
- [Self-Supervised Learning from Images with a Joint-Embedding Predictive Architecture](https://mlsanity.com/paper/2301.08243/) (2023)
- [Vision Transformers Need Registers](https://mlsanity.com/paper/2309.16588/) (2023)
- [VideoMAE V2: Scaling Video Masked Autoencoders with Dual Masking](https://mlsanity.com/paper/2303.16727/) (2023)
- [Masked Autoencoders As Spatiotemporal Learners](https://mlsanity.com/paper/2205.09113/) (2022)
- [Large Brain Model for Learning Generic Representations with Tremendous EEG Data in BCI](https://mlsanity.com/paper/2405.18765/) (2024)
- [Perception Encoder: The best visual embeddings are not at the output of the network](https://mlsanity.com/paper/2504.13181/) (2025)
- [Improving Reproducibility in Machine Learning Research (A Report from the NeurIPS 2019 Reproducibility Program)](https://mlsanity.com/paper/2003.12206/) (2020)
- [Hiera: A Hierarchical Vision Transformer without the Bells-and-Whistles](https://mlsanity.com/paper/2306.00989/) (2023)
- [A Cookbook of Self-Supervised Learning](https://mlsanity.com/paper/2304.12210/) (2023)
- [BENDR: using transformers and a contrastive self-supervised learning task to learn from massive amounts of EEG data](https://mlsanity.com/paper/2101.12037/) (2021)

## Built on by (most cited first, 5 of 5)

- [Meta-learning In-Context Enables Training-Free Cross Subject Brain Decoding](https://mlsanity.com/paper/2604.08537/) (2026)
- [Flow Matching with In-Context Priors for Out-of-Distribution Brain Dynamics](https://mlsanity.com/paper/2606.11833/) (2026)
- [Real-time Reconstruction of Human Visual Perception from fMRI](https://mlsanity.com/paper/2607.22753/) (2026)
- [FlatClip: Reusing Image Foundation Models for fMRI Representation Learning via Cortical Flatmaps](https://mlsanity.com/paper/2609.31204/) (2026)
- [Natural Image Autoencoder-Based fMRI Representations for Trait and State Prediction](https://mlsanity.com/paper/2609.34167/) (2026)

## Abstract (arXiv)

We study the problem of training self-supervised foundation models for functional MRI. Our main contributions are: (1) we introduce a new model family (CortexMAE) trained using the masked autoencoder framework on 2.1K hours of open fMRI data, and (2) we release the first open evaluation suite (Brainmarks) for fMRI foundation models. Our core innovation is simple: we adapt the Vision Transformer to fMRI by first converting each 3D fMRI volume to a 2D map using a cortical flat map projection. We directly compare flat maps to both parcellation and volume-based representations. While each has its advantages, flat maps generally perform best. We perform the first systematic scaling analysis for fMRI and observe strict power law scaling, albeit with limits. Finally, we use Brainmarks to do controlled benchmark comparisons. On subject-level trait prediction, we report a challenging null result: no single model achieves clear state-of-the-art performance. Moreover, all models struggle to outperform a simple functional connectivity baseline. On cognitive state decoding, we observe more robust performance, and in this setting our CortexMAE family outperforms prior models by a large margin. Code, models, and datasets are available at https://github.com/MedARC-AI/CortexMAE and https://github.com/MedARC-AI/Brainmarks.