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

Journal: Nature methods
PMID: 39915693

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.

Authors

  • Jianxun Ren
    Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
  • Ning An
  • Cong Lin
    College of Electronics and Information Engineering, Guangdong Ocean University, Zhanjiang 524025, China.
  • Youjia Zhang
    Changping Laboratory, Beijing, China.
  • Zhenyu Sun
    Changping Laboratory, Beijing, China.
  • Wei Zhang
    The First Affiliated Hospital of Nanchang University, Nanchang, China.
  • Shiyi Li
    From the Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas.
  • Ning Guo
  • Weigang Cui
  • Qingyu Hu
    Changping Laboratory, Beijing, China.
  • Weiwei Wang
  • Xuehai Wu
    Mechanical and Aerospace Engineering Rutgers University-New Brunswick Piscataway NJ 08854 USA.
  • Yinyan Wang
    Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China. Electronic address: tiantanyinyan@126.com.
  • Tao Jiang
    Department of Respiratory and Critical Care Medicine, Center for Respiratory Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
  • Theodore D Satterthwaite
    Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA, USA.
  • Danhong Wang
    Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA.
  • Hesheng Liu
    Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA. hesheng.liu@mgh.harvard.edu.

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