DeepPrep: An accelerated, scalable, and robust pipeline for neuroimaging preprocessing empowered by deep learning

Jianxun Ren; Ning An; Lin Cong; Youjia Zhang; Zhenyu Sun; Wei Zhang; Shiyi Li; Ning Guo; Weigang Cui; Qingyu Hu; Weiwei Wang; Xuehai Wu; Yinyan Wang; Tao Jiang; Theodore Daniel Satterthwaite; Danhong Wang; Hesheng Liu

doi:10.1038/s41592-025-02599-1

NeuroscienceNature MethodsFeb 6, 2025

Peer-reviewed journal article

DeepPrep: An accelerated, scalable, and robust pipeline for neuroimaging preprocessing empowered by deep learning

Jianxun Ren iD, Ning An iD, Lin Cong iD, Youjia Zhang iD, Zhenyu Sun iD, Wei Zhang iD, Shiyi Li iD, Ning Guo iD, Weigang Cui iD, Qingyu Hu iD, Weiwei Wang iD, Xuehai Wu iD, Yinyan Wang iD, Tao Jiang iD, Theodore Daniel Satterthwaite iD, Danhong Wang iD, Hesheng Liu iD

Abstract

Neuroimaging has entered the era of big data. However, the advancement of preprocessing pipelines falls behind the rapid expansion of data volume, causing significant computational challenges. Here, we present DeepPrep, a pipeline empowered by deep learning and workflow manager. Evaluated on over 55,000 scans, DeepPrep demonstrates a 11-fold acceleration, exceptional scalability, and robustness compared to the current state-of-the-art pipeline, providing a promising solution to meet the scalability requirements of neuroimaging.

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