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Chen Y, Zekelman LR, Zhang C, Xue T, Song Y, Makris N, Rathi Y, Golby AJ, Cai W, Zhang F, O'Donnell LJ. TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance. Med Image Anal 2024; 94:103120. [PMID: 38458095 PMCID: PMC11016451 DOI: 10.1016/j.media.2024.103120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 11/30/2023] [Accepted: 02/21/2024] [Indexed: 03/10/2024]
Abstract
We propose a geometric deep-learning-based framework, TractGeoNet, for performing regression using diffusion magnetic resonance imaging (dMRI) tractography and associated pointwise tissue microstructure measurements. By employing a point cloud representation, TractGeoNet can directly utilize tissue microstructure and positional information from all points within a fiber tract without the need to average or bin data along the streamline as traditionally required by dMRI tractometry methods. To improve regression performance, we propose a novel loss function, the Paired-Siamese Regression loss, which encourages the model to focus on accurately predicting the relative differences between regression label scores rather than just their absolute values. In addition, to gain insight into the brain regions that contribute most strongly to the prediction results, we propose a Critical Region Localization algorithm. This algorithm identifies highly predictive anatomical regions within the white matter fiber tracts for the regression task. We evaluate the effectiveness of the proposed method by predicting individual performance on two neuropsychological assessments of language using a dataset of 20 association white matter fiber tracts from 806 subjects from the Human Connectome Project Young Adult dataset. The results demonstrate superior prediction performance of TractGeoNet compared to several popular regression models that have been applied to predict individual cognitive performance based on neuroimaging features. Of the twenty tracts studied, we find that the left arcuate fasciculus tract is the most highly predictive of the two studied language performance assessments. Within each tract, we localize critical regions whose microstructure and point information are highly and consistently predictive of language performance across different subjects and across multiple independently trained models. These critical regions are widespread and distributed across both hemispheres and all cerebral lobes, including areas of the brain considered important for language function such as superior and anterior temporal regions, pars opercularis, and precentral gyrus. Overall, TractGeoNet demonstrates the potential of geometric deep learning to enhance the study of the brain's white matter fiber tracts and to relate their structure to human traits such as language performance.
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Affiliation(s)
- Yuqian Chen
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; School of Computer Science, The University of Sydney, Sydney, NSW, Australia
| | - Leo R Zekelman
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Speech and Hearing Bioscience and Technology, Harvard Medical School, Boston, MA, USA
| | - Chaoyi Zhang
- School of Computer Science, The University of Sydney, Sydney, NSW, Australia
| | - Tengfei Xue
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; School of Computer Science, The University of Sydney, Sydney, NSW, Australia
| | - Yang Song
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Nikos Makris
- Departments of Psychiatry and Neurology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yogesh Rathi
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alexandra J Golby
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Weidong Cai
- School of Computer Science, The University of Sydney, Sydney, NSW, Australia
| | - Fan Zhang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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5
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Fan XR, Wang YS, Chang D, Yang N, Rong MJ, Zhang Z, He Y, Hou X, Zhou Q, Gong ZQ, Cao LZ, Dong HM, Nie JJ, Chen LZ, Zhang Q, Zhang JX, Zhang L, Li HJ, Bao M, Chen A, Chen J, Chen X, Ding J, Dong X, Du Y, Feng C, Feng T, Fu X, Ge LK, Hong B, Hu X, Huang W, Jiang C, Li L, Li Q, Li S, Liu X, Mo F, Qiu J, Su XQ, Wei GX, Wu Y, Xia H, Yan CG, Yan ZX, Yang X, Zhang W, Zhao K, Zhu L, Zuo XN. A longitudinal resource for population neuroscience of school-age children and adolescents in China. Sci Data 2023; 10:545. [PMID: 37604823 PMCID: PMC10442366 DOI: 10.1038/s41597-023-02377-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 07/11/2023] [Indexed: 08/23/2023] Open
Abstract
During the past decade, cognitive neuroscience has been calling for population diversity to address the challenge of validity and generalizability, ushering in a new era of population neuroscience. The developing Chinese Color Nest Project (devCCNP, 2013-2022), the first ten-year stage of the lifespan CCNP (2013-2032), is a two-stages project focusing on brain-mind development. The project aims to create and share a large-scale, longitudinal and multimodal dataset of typically developing children and adolescents (ages 6.0-17.9 at enrolment) in the Chinese population. The devCCNP houses not only phenotypes measured by demographic, biophysical, psychological and behavioural, cognitive, affective, and ocular-tracking assessments but also neurotypes measured with magnetic resonance imaging (MRI) of brain morphometry, resting-state function, naturalistic viewing function and diffusion structure. This Data Descriptor introduces the first data release of devCCNP including a total of 864 visits from 479 participants. Herein, we provided details of the experimental design, sampling strategies, and technical validation of the devCCNP resource. We demonstrate and discuss the potential of a multicohort longitudinal design to depict normative brain growth curves from the perspective of developmental population neuroscience. The devCCNP resource is shared as part of the "Chinese Data-sharing Warehouse for In-vivo Imaging Brain" in the Chinese Color Nest Project (CCNP) - Lifespan Brain-Mind Development Data Community ( https://ccnp.scidb.cn ) at the Science Data Bank.
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Affiliation(s)
- Xue-Ru Fan
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Yin-Shan Wang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Da Chang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Ning Yang
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Meng-Jie Rong
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Zhe Zhang
- College of Education, Hebei Normal University, Shijiazhuang, 050024, China
| | - Ye He
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Xiaohui Hou
- Laboratory of Cognitive Neuroscience and Education, School of Education Science, Nanning Normal University, Nanning, 530299, China
| | - Quan Zhou
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Zhu-Qing Gong
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Li-Zhi Cao
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Hao-Ming Dong
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
- Changping Laboratory, Beijing, 102206, China
| | - Jing-Jing Nie
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Li-Zhen Chen
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China
| | - Qing Zhang
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Jia-Xin Zhang
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Lei Zhang
- School of Government, Shanghai University of Political Science and Law, Shanghai, 201701, China
| | - Hui-Jie Li
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Min Bao
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Antao Chen
- School of Psychology, Research Center for Exercise and Brain Science, Shanghai University of Sport, Shanghai, 200438, China
- Faculty of Psychology, Southwest University, Chongqing, 400715, China
| | - Jing Chen
- School of Psychology, Research Center for Exercise and Brain Science, Shanghai University of Sport, Shanghai, 200438, China
- Faculty of Psychology, Southwest University, Chongqing, 400715, China
| | - Xu Chen
- Faculty of Psychology, Southwest University, Chongqing, 400715, China
| | - Jinfeng Ding
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Xue Dong
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Yi Du
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Chen Feng
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Tingyong Feng
- Faculty of Psychology, Southwest University, Chongqing, 400715, China
| | - Xiaolan Fu
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li-Kun Ge
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Bao Hong
- NYU-ECNU Institute of Brain and Cognitive Science at New York University Shanghai, Shanghai, 200062, China
- School of Psychology and Cognitive Science, East China Normal University, Shanghai, 200062, China
| | - Xiaomeng Hu
- Department of Psychology, Renmin University of China, Beijing, 100872, China
| | - Wenjun Huang
- NYU-ECNU Institute of Brain and Cognitive Science at New York University Shanghai, Shanghai, 200062, China
- School of Psychology and Cognitive Science, East China Normal University, Shanghai, 200062, China
| | - Chao Jiang
- Beijing Key Laboratory of Learning and Cognition, School of Psychology, Capital Normal University, Beijing, 100048, China
| | - Li Li
- NYU-ECNU Institute of Brain and Cognitive Science at New York University Shanghai, Shanghai, 200062, China
- Faculty of Arts and Science, New York University Shanghai, Shanghai, 200122, China
| | - Qi Li
- Beijing Key Laboratory of Learning and Cognition, School of Psychology, Capital Normal University, Beijing, 100048, China
| | - Su Li
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Xun Liu
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Fan Mo
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Brain and Cognitive Science, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiang Qiu
- Faculty of Psychology, Southwest University, Chongqing, 400715, China
| | - Xue-Quan Su
- Laboratory of Cognitive Neuroscience and Education, School of Education Science, Nanning Normal University, Nanning, 530299, China
| | - Gao-Xia Wei
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Yiyang Wu
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Haishuo Xia
- Faculty of Psychology, Southwest University, Chongqing, 400715, China
| | - Chao-Gan Yan
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Zhi-Xiong Yan
- Laboratory of Cognitive Neuroscience and Education, School of Education Science, Nanning Normal University, Nanning, 530299, China
| | - Xiaohong Yang
- Department of Psychology, Renmin University of China, Beijing, 100872, China
| | - Wenfang Zhang
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Ke Zhao
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Psychology and Cognitive Science, East China Normal University, Shanghai, 200062, China
| | - Liqi Zhu
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China
| | - Xi-Nian Zuo
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, 100875, China.
- Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Developmental Population Neuroscience Research Center, International Data Group/McGovern Institute for Brain Research, Beijing Normal University, Beijing, 100875, China.
- CAS Key Laboratory of Behavioral Science, Institute of Psychology, Beijing, 100101, China.
- Laboratory of Cognitive Neuroscience and Education, School of Education Science, Nanning Normal University, Nanning, 530299, China.
- School of Education, Hunan University of Science and Technology, Hunan Xiangtan, 411201, China.
- National Basic Science Data Center, Beijing, 100190, China.
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