# Few-Shot Deployment of Pretrained MRI Transformers in Brain Imaging Tasks

arXiv: https://arxiv.org/abs/2508.05783 · HTML: https://mlsanity.com/paper/2508.05783/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 48 references that are in the map.
- First posted on arXiv 7 Aug 2025.

## Builds on (most cited first, 19 of 19)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation](https://mlsanity.com/paper/2105.05537/) (2021)
- [A Survey on Deep Learning in Medical Image Analysis](https://mlsanity.com/paper/1702.05747/) (2017)
- [EfficientNetV2: Smaller Models and Faster Training](https://mlsanity.com/paper/2104.00298/) (2021)
- [UNETR: Transformers for 3D Medical Image Segmentation](https://mlsanity.com/paper/2103.10504/) (2021)
- [fastMRI: An Open Dataset and Benchmarks for Accelerated MRI](https://mlsanity.com/paper/1811.08839/) (2018)
- [Med3D: Transfer Learning for 3D Medical Image Analysis](https://mlsanity.com/paper/1904.00625/) (2019)
- [Deep Convolutional Neural Networks for Computer-Aided Detection: CNN Architectures, Dataset Characteristics and Transfer Learning](https://mlsanity.com/paper/1602.03409/) (2016)
- [Self-Supervision with Superpixels: Training Few-shot Medical Image Segmentation without Annotation](https://mlsanity.com/paper/2007.09886/) (2020)
- [SynthStrip: Skull-Stripping for Any Brain Image](https://mlsanity.com/paper/2203.09974/) (2022)
- [3D Deep Learning on Medical Images: A Review](https://mlsanity.com/paper/2004.00218/) (2020)
- [Few Shot Medical Image Segmentation with Cross Attention Transformer](https://mlsanity.com/paper/2303.13867/) (2023)
- [Weakly Supervised Few-Shot Segmentation Via Meta-Learning](https://mlsanity.com/paper/2109.01693/) (2021)
- [Learning to Reconstruct Accelerated MRI Through K-space Cold Diffusion without Noise](https://mlsanity.com/paper/2311.10162/) (2023)
- [Automated Classification of Body MRI Sequence Type Using Convolutional Neural Networks](https://mlsanity.com/paper/2402.08098/) (2024)

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

- [Vision Transformer-Conditioned UNet for Domain-Adaptive Semantic Segmentation](https://mlsanity.com/paper/2605.16393/) (2026)

## Abstract (arXiv)

Machine learning using transformers has shown great potential in medical imaging, but its real-world applicability remains limited due to the scarcity of annotated data. In this study, we propose a practical framework for the few-shot deployment of pretrained MRI transformers in diverse brain imaging tasks. By utilizing the Masked Autoencoder (MAE) pretraining strategy on a large-scale, multi-cohort brain MRI dataset comprising over 31 million slices, we obtain highly transferable latent representations that generalize well across tasks and datasets. For high-level tasks such as classification, a frozen MAE encoder combined with a lightweight linear head achieves state-of-the-art accuracy in MRI sequence identification with minimal supervision. For low-level tasks such as segmentation, we propose MAE-FUnet, a hybrid architecture that fuses multiscale CNN features with pretrained MAE embeddings. This model consistently outperforms other strong baselines in both skull stripping and multi-class anatomical segmentation under data-limited conditions. With extensive quantitative and qualitative evaluations, our framework demonstrates efficiency, stability, and scalability, suggesting its suitability for low-resource clinical environments and broader neuroimaging applications.