Large-scale Multi-sequence Pretraining for Generalizable MRI Analysis in Versatile Clinical Applications

Zelin Qiu; Xi Wang; Zhuoyao Xie; Juan Zhou; Yu Wang; Lingjie Yang; Xinrui Jiang; Juyoung Bae; Moo Hyun Son; Qiang Ye; Dexuan Chen; Rui Zhang; Tao Li; Neeraj Ramesh Mahboobani; Varut Vardhanabhuti; Xiaohui Duan; Yinghua Zhao; Hao Chen

arXiv · 2508.07165

Large-scale Multi-sequence Pretraining for Generalizable MRI Analysis in Versatile Clinical Applications

Zelin Qiu·Xi Wang·Zhuoyao Xie·Juan Zhou·Yu Wang·Lingjie Yang·Xinrui Jiang·Juyoung Bae·Moo Hyun Son·Qiang Ye·Dexuan Chen·Rui Zhang·Tao Li·Neeraj Ramesh Mahboobani·Varut Vardhanabhuti·Xiaohui Duan·Yinghua Zhao·Hao Chen

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Abstract

Multi-sequence Magnetic Resonance Imaging (MRI) offers remarkable versatility, enabling the distinct visualization of different tissue types. Nevertheless, the inherent heterogeneity among MRI sequences poses significant challenges to the generalization capability of deep learning models. These challenges undermine model performance when faced with varying acquisition parameters, thereby severely restricting their clinical utility. In this study, we present PRISM, a foundation model PRe-trained with large-scale multI-Sequence MRI. We collected a total of 64 datasets from both public and private sources, encompassing a wide range of whole-body anatomical structures, with scans spanning diverse MRI sequences. Among them, 336,476 volumetric MRI scans from 34 datasets (8 public and 26 private) were curated to construct the largest multi-organ multi-sequence MRI pretraining corpus to date. We propose a novel pretraining paradigm that disentangles anatomically invariant features from sequence-specific variations in MRI, while preserving high-level semantic representations. We established a benchmark comprising 44 downstream tasks, including disease diagnosis, image segmentation, registration, progression prediction, and report generation. These tasks were evaluated on 32 public datasets and 5 private cohorts. PRISM consistently outperformed both non-pretrained models and existing foundation models, achieving first-rank results in 39 out of 44 downstream benchmarks with statistical significance improvements. These results underscore its ability to learn robust and generalizable representations across unseen data acquired under diverse MRI protocols. PRISM provides a scalable framework for multi-sequence MRI analysis, thereby enhancing the translational potential of AI in radiology. It delivers consistent performance across diverse imaging protocols, reinforcing its clinical applicability.

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Zelin Qiu, Xi Wang, Zhuoyao Xie, Juan Zhou, Yu Wang, Lingjie Yang, Xinrui Jiang, Juyoung Bae, Moo Hyun Son, Qiang Ye, Dexuan Chen, Rui Zhang, Tao Li, Neeraj Ramesh Mahboobani, Varut Vardhanabhuti, Xiaohui Duan, Yinghua Zhao, Hao Chen. 2025-08-25. Large-scale Multi-sequence Pretraining for Generalizable MRI Analysis in Versatile Clinical Applications. https://arxiv.org/abs/2508.07165

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