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

ABSTRACT: Neuroimaging has entered the era of big data. However, the advancement of preprocessing pipelines falls behind the rapid expansion of data volume, causing substantial computational challenges. Here we present DeepPrep, a pipeline empowered by deep learning and a workflow manager. Evaluated on over 55,000 scans, DeepPrep demonstrates tenfold acceleration, scalability and robustness compared to the state-of-the-art pipeline, thereby meeting the scalability requirements of neuroimaging.

SUBMITTER: Ren J 

PROVIDER: S-EPMC11903312 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature

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

Ren Jianxun J   An Ning N   Lin Cong C   Zhang Youjia Y   Sun Zhenyu Z   Zhang Wei W   Li Shiyi S   Guo Ning N   Cui Weigang W   Hu Qingyu Q   Wang Weiwei W   Wu Xuehai X   Wang Yinyan Y   Jiang Tao T   Satterthwaite Theodore D TD   Wang Danhong D   Liu Hesheng H  

Nature methods 20250206 3

Neuroimaging has entered the era of big data. However, the advancement of preprocessing pipelines falls behind the rapid expansion of data volume, causing substantial computational challenges. Here we present DeepPrep, a pipeline empowered by deep learning and a workflow manager. Evaluated on over 55,000 scans, DeepPrep demonstrates tenfold acceleration, scalability and robustness compared to the state-of-the-art pipeline, thereby meeting the scalability requirements of neuroimaging. ...[more]

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