DeepPrep: an accelerated, scalable and robust pipeline for neuroimaging preprocessing empowered by deep learning
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.
Authors
- Youjia Zhang (ORCID: https://orcid.org/0000-0002-5671-3232)
- Ning An (ORCID: https://orcid.org/0009-0003-4255-7675)
- Xuehai Wu
- Qingyu Hu (ORCID: https://orcid.org/0009-0007-5968-7854)
- Ning Guo (ORCID: https://orcid.org/0000-0002-0829-7262)
- Theodore Daniel Satterthwaite (ORCID: https://orcid.org/0000-0001-7072-9399)
- Hesheng Liu (ORCID: https://orcid.org/0000-0002-7233-1509)
- Weigang Cui (ORCID: https://orcid.org/0000-0002-7983-9161)
- Tao Jiang (ORCID: https://orcid.org/0000-0002-7008-6351)
- Zhenyu Sun (ORCID: https://orcid.org/0000-0001-5788-9339)
- Danhong Wang (ORCID: https://orcid.org/0000-0001-6780-3033)
- Lin Cong (ORCID: https://orcid.org/0009-0000-1693-608X)
- Wei Zhang (ORCID: https://orcid.org/0000-0002-4960-3190)
- Jianxun Ren (ORCID: https://orcid.org/0000-0002-7885-4546)
- Yinyan Wang (ORCID: https://orcid.org/0000-0003-1606-2284)
- Weiwei Wang (ORCID: https://orcid.org/0000-0002-1613-4009)
- Shiyi Li
Institutions
- Children's Hospital of Philadelphia (US)
- Harvard University (US)
- Capital Medical University (CN)
- Peking University (CN)
- Suzhou University of Technology (CN)
- Fudan University (CN)
- Beijing Tian Tan Hospital (CN)
- Massachusetts General Hospital (US)
- Beijing Institute of Neurosurgery (CN)
- Athinoula A. Martinos Center for Biomedical Imaging (US)
- Lifespan (US)
- Huashan Hospital (CN)
- Risun (China) (CN)
- University of Pennsylvania (US)
Publication Details
- Journal
- Nature Methods
- Published
- 2025-02-06
- DOI
- https://doi.org/10.1038/s41592-025-02599-1
- Citations
- 11
- Primary Topic
- Functional Brain Connectivity Studies
- Type
- article
- Field-Weighted Citation Impact
- 14.31
Funders
- National Natural Science Foundation of China
- China Postdoctoral Science Foundation