A generalizable brain extraction net (BEN) for multimodal MRI data from rodents, nonhuman primates, and humans
- Fudan University, China
- Helmholtz Zentrum München, Germany
- ShanghaiTech University, China
Abstract
Accurate brain tissue extraction on magnetic resonance imaging (MRI) data is crucial for analyzing brain structure and function. While several conventional tools have been optimized to handle human brain data, there have been no generalizable methods to extract brain tissues for multimodal MRI data from rodents, nonhuman primates, and humans. Therefore, developing a flexible and generalizable method for extracting whole brain tissue across species would allow researchers to analyze and compare experiment results more efficiently. Here, we propose a domain-adaptive and semi-supervised deep neural network, named the Brain Extraction Net (BEN), to extract brain tissues across species, MRI modalities, and MR scanners. We have evaluated BEN on 18 independent datasets, including 783 rodent MRI scans, 246 nonhuman primate MRI scans, and 4,601 human MRI scans, covering five species, four modalities, and six MR scanners with various magnetic field strengths. Compared to conventional toolboxes, the superiority of BEN is illustrated by its robustness, accuracy, and generalizability. Our proposed method not only provides a generalized solution for extracting brain tissue across species but also significantly improves the accuracy of atlas registration, thereby benefiting the downstream processing tasks. As a novel fully automated deep-learning method, BEN is designed as an open-source software to enable high-throughput processing of neuroimaging data across species in preclinical and clinical applications.
Data availability
All data (MRI data, source codes, pretrained weights and replicate demo notebooks for Figure 1-7) are included in the manuscript or available at https://github.com/yu02019/BEN.
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Article and author information
Author details
Funding
National Natural Science Foundation of China (81873893,82171903,92043301)
- Xiao-Yong Zhang
Fudan University (the Office of Global Partnerships (Key Projects Development Fund))
- Xiao-Yong Zhang
Shanghai Municipal Science and Technology Major Project (No.2018SHZDZX01)
- Xiao-Yong Zhang
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: Partial rodent MRI data collection were approved by the Animal Care and Use Committee of Fudan University, China. The rest rodent data (Rat-T2WI-9.4T and Rat-EPI-9.4T datasets) are publicly available (CARMI: https://openneuro.org/datasets/ds002870/versions/1.0.0). Marmoset MRI data collection were approved by the Animal Care and Use Committee of the Institute of Neuroscience, Chinese Academy of Sciences, China. Macaque MRI data are publicly available from the nonhuman PRIMatE Data Exchange (PRIME-DE) (https://fcon_1000.projects.nitrc.org/indi/indiPRIME.html).
Human subjects: The Zhangjiang International Brain Biobank (ZIB) protocols were approved by the Ethics Committee of Fudan University (AF/SC-03/20200722) and written informed consents were obtained from all volunteers. UK Biobank (UKB) and Adolescent Brain Cognitive Development (ABCD) are publicly available.
Reviewing Editor
- Saad Jbabdi, University of Oxford, United Kingdom
Publication history
- Received: June 20, 2022
- Accepted: December 21, 2022
- Accepted Manuscript published: December 22, 2022 (version 1)
Copyright
© 2022, Yu et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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A generalizable brain extraction net (BEN) for multimodal MRI data from rodents, nonhuman primates, and humans
eLife 11:e81217.
https://doi.org/10.7554/eLife.81217
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