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arXiv · 2508.05783

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

Mengyu Li·Guoyao Shen·Chad W. Farris·Xin Zhang
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Abstract

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.

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Mengyu Li, Guoyao Shen, Chad W. Farris, Xin Zhang. 2025-08-07. Few-Shot Deployment of Pretrained MRI Transformers in Brain Imaging Tasks. https://arxiv.org/abs/2508.05783

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