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Protocol for Brain Magnetic Resonance Imaging and Extraction of Imaging-Derived Phenotypes from the China Phenobank Project

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Abstract

Imaging-derived phenotypes (IDPs) have been increasingly used in population-based cohort studies in recent years. As widely reported, magnetic resonance imaging (MRI) is an important imaging modality for assessing the anatomical structure and function of the brain with high resolution and excellent soft-tissue contrast. The purpose of this article was to describe the imaging protocol of the brain MRI in the China Phenobank Project (CHPP). Each participant underwent a 30-min brain MRI scan as part of a 2-h whole-body imaging protocol in CHPP. The brain imaging sequences included T1-magnetization that prepared rapid gradient echo, T2 fluid-attenuated inversion-recovery, magnetic resonance angiography, diffusion MRI, and resting-state functional MRI. The detailed descriptions of image acquisition, interpretation, and post-processing were provided in this article. The measured IDPs included volumes of brain subregions, cerebral vessel geometrical parameters, microstructural tracts, and function connectivity metrics.

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Data availability

The data supported the protocols of this study are available on request from the corresponding author.

Abbreviations

AAL:

Automated anatomical labeling

AD:

Axial diffusivity

ADC:

Apparent diffusion coefficient

ALFF:

Amplitude of low-frequency fluctuation

CAT:

Computational anatomy toolbox

CHPP:

China Phenobank Project

CSF:

Cerebrospinal fluid

DC:

Degree centrality

DWI:

Diffusion weighted imaging

DTI:

Diffusion tensor imaging

EPI:

Echo-echo planar imaging

FA:

Fractional anisotropy

FC:

Functional connectivity

FLAIR:

Fluid-attenuated inversion-recovery

GRE:

Gradient recalled echo

IDP:

Imaging-derived phenotype

MD:

Mean diffusivity

MPRAGE:

Magnetization prepared rapid gradient echo

MRI:

Magnetic resonance imaging

RD:

Radial diffusivity

ReHo:

Regional homogeneity

rfMRI:

Resting-state functional magnetic resonance imaging

ROI:

Region of interest

SAG:

Sagittal

SE-EPI:

Spin echo-echo planar imaging

T 1w:

T1-Weighted

T 2-FLAIR:

T2-Weighted fluid attenuated inversion recovery

TBSS:

Tract‑based spatial statistics

TOF-MRA:

Time of flight-magnetic resonance angiography

TRA:

Transverse

TSE:

Turbo spin echo

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Acknowledgements

The data and samples used for this protocol were obtained from CHPP. We would like to thank the CHPP participants and coordinators for their contribution to this dataset.

Funding

This study was funded by the Shanghai Municipal Science and Technology Major Project (No. 2017SHZDZX01).

Author information

Authors and Affiliations

  1. Human Phenome Institute, Fudan University, 825 Zhangheng Road, Pudong New District, Shanghai, 201203, China

    Chengyan Wang, Xueqin Xia, Xutong Kuang, Lizhen Lan, Yudan Wu, Na Zhang, Ji Tao, Xumei Hu, Wenzhao Cao, Jingchun Luo, He Wang & Mei Tian

  2. Department of Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China

    Zhang Shi

  3. Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China

    Yan Li & Naying He

  4. Department of Nuclear Medicine and Medical PET Center, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310003, China

    Shufang Qian & Le Xue

  5. Department of Computer Science, Hong Kong Baptist University, Hong Kong Special Administrative Region, 999077, China

    Yike Guo

  6. Data Science Institute, Imperial College London, London, SW72AZ, UK

    Yike Guo

  7. Philips Healthcare, Co., Shanghai, 200070, China

    Weibo Chen

  8. Department of Radiology, Huashan Hospital, National Center for Neurological Disorders, Fudan University, Shanghai, 200040, China

    Jun Zhang

  9. Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China

    He Wang

  10. Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, Fudan University, Shanghai, 200433, China

    He Wang

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  1. Chengyan Wang
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Contributions

CW, MT, HW: concept and design, data interpretation and analysis, supervision, drafting, revision and approval of final manuscript. ZS, YL, NH, YG, WC, JZ, JL: data interpretation and analysis, drafting, revision and approval of final manuscript. XX, XK, SQ, LX, LL, YW, NZ, JT, XH, WC: data collection, data analysis, drafting, revision and approval of final manuscript.

Corresponding author

Correspondence to Mei Tian.

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Ethics approval and consent to participate

The study was in agreement with the ethical guidelines of the 1975 Declaration of Helsinki and approved by the institutional review board of Fudan University. Informed consent was obtained from each subject.

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Not applicable.

Competing interests

MT is the Editorial Board Member of Phenomics, and she was not involved in reviewing this paper.

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Wang, C., Shi, Z., Li, Y. et al. Protocol for Brain Magnetic Resonance Imaging and Extraction of Imaging-Derived Phenotypes from the China Phenobank Project. Phenomics 3, 642–656 (2023). https://doi.org/10.1007/s43657-022-00083-w

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