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Zhao K, Wang D, Wang D, Chen P, Wei Y, Tu L, Chen Y, Tang Y, Yao H, Zhou B, Lu J, Wang P, Liao Z, Chen Y, Han Y, Zhang X, Liu Y. Macroscale connectome topographical structure reveals the biomechanisms of brain dysfunction in Alzheimer's disease. SCIENCE ADVANCES 2024; 10:eado8837. [PMID: 39392880 DOI: 10.1126/sciadv.ado8837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 09/11/2024] [Indexed: 10/13/2024]
Abstract
The intricate spatial configurations of brain networks offer essential insights into understanding the specific patterns of brain abnormalities and the underlying biological mechanisms associated with Alzheimer's disease (AD), normal aging, and other neurodegenerative disorders. This study investigated alterations in the topographical structure of the brain related to aging and neurodegenerative diseases by analyzing brain gradients derived from structural MRI data across multiple cohorts (n = 7323). The analysis identified distinct gradient patterns in AD, aging, and other neurodegenerative conditions. Gene enrichment analysis indicated that inorganic ion transmembrane transport was the most significant term in normal aging, while chemical synaptic transmission is a common enrichment term across various neurodegenerative diseases. Moreover, the findings show that each disorder exhibits unique dysfunctional neurophysiological characteristics. These insights are pivotal for elucidating the distinct biological mechanisms underlying AD, thereby enhancing our understanding of its unique clinical phenotypes in contrast to normal aging and other neurodegenerative disorders.
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Affiliation(s)
- Kun Zhao
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Dawei Wang
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, China
- Research Institute of Shandong University: Magnetic Field-free Medicine & Functional Imaging, Jinan, China
- Shandong Key Laboratory: Magnetic Field-free Medicine & Functional Imaging (MF), Jinan, China
| | - Dong Wang
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Pindong Chen
- School of Artificial Intelligence, University of Chinese Academy of Sciences & Brainnetome Center, Chinese Academy of Sciences, Beijing, China
| | - Yongbin Wei
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Liyun Tu
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Yuqi Chen
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Yi Tang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Hongxiang Yao
- Department of Radiology, the Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Bo Zhou
- Department of Neurology, the Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Jie Lu
- Department of Radiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Pan Wang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Zhengluan Liao
- Department of Psychiatry, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Yan Chen
- Department of Psychiatry, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Ying Han
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Beijing, China
- Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Xi Zhang
- Department of Neurology, the Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Yong Liu
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences & Brainnetome Center, Chinese Academy of Sciences, Beijing, China
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Li C, Zhang G, Zhao B, Xie D, Du H, Duan X, Hu Y, Zhang L. Advances of surgical robotics: image-guided classification and application. Natl Sci Rev 2024; 11:nwae186. [PMID: 39144738 PMCID: PMC11321255 DOI: 10.1093/nsr/nwae186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 08/16/2024] Open
Abstract
Surgical robotics application in the field of minimally invasive surgery has developed rapidly and has been attracting increasingly more research attention in recent years. A common consensus has been reached that surgical procedures are to become less traumatic and with the implementation of more intelligence and higher autonomy, which is a serious challenge faced by the environmental sensing capabilities of robotic systems. One of the main sources of environmental information for robots are images, which are the basis of robot vision. In this review article, we divide clinical image into direct and indirect based on the object of information acquisition, and into continuous, intermittent continuous, and discontinuous according to the target-tracking frequency. The characteristics and applications of the existing surgical robots in each category are introduced based on these two dimensions. Our purpose in conducting this review was to analyze, summarize, and discuss the current evidence on the general rules on the application of image technologies for medical purposes. Our analysis gives insight and provides guidance conducive to the development of more advanced surgical robotics systems in the future.
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Affiliation(s)
- Changsheng Li
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Gongzi Zhang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100141, China
| | - Baoliang Zhao
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongsheng Xie
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Hailong Du
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100141, China
| | - Xingguang Duan
- School of Mechatronical Engineering, Beijing Institute of Technology, Beijing 100081, China
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Ying Hu
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lihai Zhang
- Department of Orthopedics, Chinese PLA General Hospital, Beijing 100141, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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Kumar PR, Jha RK, Katti A. Brain tissue segmentation in neurosurgery: a systematic analysis for quantitative tractography approaches. Acta Neurol Belg 2024; 124:1-15. [PMID: 36609837 DOI: 10.1007/s13760-023-02170-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 12/31/2022] [Indexed: 01/09/2023]
Abstract
Diffusion magnetic resonance imaging (dMRI) is a cutting-edge imaging method that provides a macro-scale in vivo map of the white matter pathways in the brain. The measurement of brain microstructure and the enhancement of tractography rely heavily on dMRI tissue segmentation. Anatomical MRI technique (e.g., T1- and T2-weighted imaging) is the most widely used method for segmentation in dMRI. In comparison to anatomical MRI, dMRI suffers from higher image distortions, lower image quality, and making inter-modality registration more difficult. The dMRI tractography study of brain connectivity has become a major part of the neuroimaging landscape in recent years. In this research, we provide a high-level overview of the methods used to segment several brain tissues types, including grey and white matter and cerebrospinal fluid, to enable quantitative studies of structural connectivity in the brain in health and illness. In the first part of our review, we discuss the three main phases in the quantitative analysis of tractography, which are correction, segmentation, and quantification. Methodological possibilities are described for each phase, along with their popularity and potential benefits and drawbacks. After that, we will look at research that used quantitative tractography approaches to examine the white and grey matter of the brain, with an emphasis on neurodevelopment, ageing, neurological illnesses, mental disorders, and neurosurgery as possible applications. Even though there have been substantial advancements in methodological technology and the spectrum of applications, there is still no consensus regarding the "optimal" approach in the quantitative analysis of tractography. As a result, researchers should tread carefully when interpreting the findings of quantitative analysis of tractography.
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Affiliation(s)
- Puranam Revanth Kumar
- Department of Electronics and Communication Engineering, IcfaiTech (Faculty of Science and Technology), IFHE University, Hyderabad, 501203, India.
| | - Rajesh Kumar Jha
- Department of Electronics and Communication Engineering, IcfaiTech (Faculty of Science and Technology), IFHE University, Hyderabad, 501203, India
| | - Amogh Katti
- Department of Computer Science and Engineering, Gitam School of Technology, GITAM University, Hyderabad, 502329, India
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Liu H, Ma Z, Wei L, Chen Z, Peng Y, Jiao Z, Bai H, Jing B. A radiomics-based brain network in T1 images: construction, attributes, and applications. Cereb Cortex 2024; 34:bhae016. [PMID: 38300184 PMCID: PMC10839838 DOI: 10.1093/cercor/bhae016] [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: 11/28/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
T1 image is a widely collected imaging sequence in various neuroimaging datasets, but it is rarely used to construct an individual-level brain network. In this study, a novel individualized radiomics-based structural similarity network was proposed from T1 images. In detail, it used voxel-based morphometry to obtain the preprocessed gray matter images, and radiomic features were then extracted on each region of interest in Brainnetome atlas, and an individualized radiomics-based structural similarity network was finally built using the correlational values of radiomic features between any pair of regions of interest. After that, the network characteristics of individualized radiomics-based structural similarity network were assessed, including graph theory attributes, test-retest reliability, and individual identification ability (fingerprinting). At last, two representative applications for individualized radiomics-based structural similarity network, namely mild cognitive impairment subtype discrimination and fluid intelligence prediction, were exemplified and compared with some other networks on large open-source datasets. The results revealed that the individualized radiomics-based structural similarity network displays remarkable network characteristics and exhibits advantageous performances in mild cognitive impairment subtype discrimination and fluid intelligence prediction. In summary, the individualized radiomics-based structural similarity network provides a distinctive, reliable, and informative individualized structural brain network, which can be combined with other networks such as resting-state functional connectivity for various phenotypic and clinical applications.
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Affiliation(s)
- Han Liu
- Department of Radiology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56, Nanlishilu Road, Xicheng District, Beijing 100045, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, School of Biomedical Engineering, Capital Medical University, No. 10, Xitoutiao Youanmenwai, Fengtai District, Beijing 100069, China
| | - Zhe Ma
- Department of Radiology, Henan Cancer Hospital, The Affiliated Cancer Hospital of Zhengzhou University, 127 Dongming Road, Jinshui District, Zhengzhou, Henan 450008, China
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, School of Biomedical Engineering, Capital Medical University, No. 10, Xitoutiao Youanmenwai, Fengtai District, Beijing 100069, China
| | - Lijiang Wei
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, School of Biomedical Engineering, Capital Medical University, No. 10, Xitoutiao Youanmenwai, Fengtai District, Beijing 100069, China
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, No. 19, Xinjiekouwai Street, Haidian District, Beijing 100875, China
| | - Zhenpeng Chen
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, School of Biomedical Engineering, Capital Medical University, No. 10, Xitoutiao Youanmenwai, Fengtai District, Beijing 100069, China
| | - Yun Peng
- Department of Radiology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, No. 56, Nanlishilu Road, Xicheng District, Beijing 100045, China
| | - Zhicheng Jiao
- Department of Diagnostic Imaging, Brown University, 593 Eddy Street, Providence, Rhode Island 02903, United States
| | - Harrison Bai
- Department of Radiology and Radiological Sciences, Johns Hopkins University, 1800 Orleans Street, Baltimore, Maryland 21205, United States
| | - Bin Jing
- Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, School of Biomedical Engineering, Capital Medical University, No. 10, Xitoutiao Youanmenwai, Fengtai District, Beijing 100069, China
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Zhao K, Chen P, Alexander-Bloch A, Wei Y, Dyrba M, Yang F, Kang X, Wang D, Fan D, Ye S, Tang Y, Yao H, Zhou B, Lu J, Yu C, Wang P, Liao Z, Chen Y, Huang L, Zhang X, Han Y, Li S, Liu Y. A neuroimaging biomarker for Individual Brain-Related Abnormalities In Neurodegeneration (IBRAIN): a cross-sectional study. EClinicalMedicine 2023; 65:102276. [PMID: 37954904 PMCID: PMC10632687 DOI: 10.1016/j.eclinm.2023.102276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 11/14/2023] Open
Abstract
Background Alzheimer's disease (AD) is a prevalent neurodegenerative disorder that poses a worldwide public health challenge. A neuroimaging biomarker would significantly improve early diagnosis and intervention, ultimately enhancing the quality of life for affected individuals and reducing the burden on healthcare systems. Methods Cross-sectional and longitudinal data (10,099 participants with 13,380 scans) from 12 independent datasets were used in the present study (this study was performed between September 1, 2021 and February 15, 2023). The Individual Brain-Related Abnormalities In Neurodegeneration (IBRAIN) score was developed via integrated regional- and network-based measures under an ensemble machine learning model based on structural MRI data. We systematically assessed whether IBRAIN could be a neuroimaging biomarker for AD. Findings IBRAIN accurately differentiated individuals with AD from NCs (AUC = 0.92) and other neurodegenerative diseases, including Frontotemporal dementia (FTD), Parkinson's disease (PD), Vascular dementia (VaD) and Amyotrophic Lateral Sclerosis (ALS) (AUC = 0.92). IBRAIN was significantly correlated to clinical measures and gene expression, enriched in immune process and protein metabolism. The IBRAIN score exhibited a significant ability to reveal the distinct progression of prodromal AD (i.e., Mild cognitive impairment, MCI) (Hazard Ratio (HR) = 6.52 [95% CI: 4.42∼9.62], p < 1 × 10-16), which offers similar powerful performance with Cerebrospinal Fluid (CSF) Aβ (HR = 3.78 [95% CI: 2.63∼5.43], p = 2.13 × 10-14) and CSF Tau (HR = 3.77 [95% CI: 2.64∼5.39], p = 9.53 × 10-15) based on the COX and Log-rank test. Notably, the IBRAIN shows comparable sensitivity (beta = -0.70, p < 1 × 10-16) in capturing longitudinal changes in individuals with conversion to AD than CSF Aβ (beta = -0.26, p = 4.40 × 10-9) and CSF Tau (beta = 0.12, p = 1.02 × 10-5). Interpretation Our findings suggested that IBRAIN is a biologically relevant, specific, and sensitive neuroimaging biomarker that can serve as a clinical measure to uncover prodromal AD progression. It has strong potential for application in future clinical practice and treatment trials. Funding Science and Technology Innovation 2030 Major Projects, the National Natural Science Foundation of China, Beijing Natural Science Funds, the Fundamental Research Funds for the CentralUniversity, and the Startup Funds for Talents at Beijing Normal University.
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Affiliation(s)
- Kun Zhao
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Pindong Chen
- School of Artificial Intelligence, University of Chinese Academy of Sciences & Brainnetome Centre, Chinese Academy of Sciences, Beijing, China
| | - Aaron Alexander-Bloch
- Department of Psychiatry, University of Pennsylvania, Philadelphia, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, USA
| | - Yongbin Wei
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
| | - Martin Dyrba
- German Centre for Neurodegenerative Diseases (DZNE), Rostock, Germany
| | - Fan Yang
- CAS Key Laboratory of Molecular Imaging, Institute of Automation, Beijing, China
| | - Xiaopeng Kang
- School of Artificial Intelligence, University of Chinese Academy of Sciences & Brainnetome Centre, Chinese Academy of Sciences, Beijing, China
| | - Dawei Wang
- Department of Radiology, Qilu Hospital of Shandong University, Ji'nan, China
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Shan Ye
- Department of Neurology, Peking University Third Hospital, Beijing, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing, China
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing, China
| | - Yi Tang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Hongxiang Yao
- Department of Radiology, The Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Bo Zhou
- Department of Neurology, The Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Jie Lu
- Department of Radiology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Chunshui Yu
- Department of Radiology, Tianjin Medical University General Hospital, Tianjin, China
| | - Pan Wang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Zhengluan Liao
- Department of Psychiatry, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Yan Chen
- Department of Psychiatry, People's Hospital of Hangzhou Medical College, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Longjian Huang
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xi Zhang
- Department of Neurology, The Second Medical Centre, National Clinical Research Centre for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
| | - Ying Han
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
- National Clinical Research Centre for Geriatric Disorders, Beijing, China
- Centre of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Shuyu Li
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Yong Liu
- School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China
- School of Artificial Intelligence, University of Chinese Academy of Sciences & Brainnetome Centre, Chinese Academy of Sciences, Beijing, China
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Wang D, Fan Q, Xiao X, He H, Yang Y, Li Y. Structural Fingerprinting of the Frontal Aslant Tract: Predicting Cognitive Control Capacity and Obsessive-Compulsive Symptoms. J Neurosci 2023; 43:7016-7027. [PMID: 37696666 PMCID: PMC10586535 DOI: 10.1523/jneurosci.0628-23.2023] [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: 04/04/2023] [Revised: 06/29/2023] [Accepted: 08/18/2023] [Indexed: 09/13/2023] Open
Abstract
White matter of the human brain is influenced by common genetic variations and shaped by neural activity-dependent experiences. Variations in microstructure of cerebral white matter across individuals and even across fiber tracts might underlie differences in cognitive capacity and vulnerabilities to mental disorders. The frontoparietal and cingulo-opercular networks of the brain constitute the central system supporting cognitive functions, and functional connectivity of these networks has been used to distinguish individuals known as "functional fingerprinting." The frontal aslant tract (FAT) that passes through the two networks has been implicated in executive functions. However, whether FAT can be used as a "structural fingerprint" to distinguish individuals and predict an individual's cognitive function and dysfunction is unknown. Here we investigated the fingerprinting property of FAT microstructural profiles using three independent diffusion MRI datasets with repeated scans on human participants including both females and males. We found that diffusion and geometric profiles of FAT can be used to distinguish individuals with a high accuracy. Next, we demonstrated that fractional anisotropy in different FAT segments predicted distinct cognitive functions, including working memory, inhibitory control, and relational reasoning. Finally, we assessed the contribution of altered FAT microstructural profiles to cognitive dysfunction in unmedicated patients with obsessive-compulsive disorders. We found that the altered microstructure in FAT was associated with the severity of obsessive-compulsive symptoms. Collectively, our findings suggest that the microstructural profiles of FAT can identify individuals with a high accuracy and may serve as an imaging marker for predicting an individual's cognitive capacity and disease severity.SIGNIFICANCE STATEMENT The frontoparietal network and cingulo-opercular network of the brain constitute a dual-network architecture for human cognitive functions, and functional connectivity of these two networks can be used as a "functional fingerprint" to distinguish individuals. However, the structural underpinnings of these networks subserving individual heterogeneities in their functional connectivity and cognitive ability remain unknown. We show here that the frontal aslant tract (FAT) that passes through the two networks distinguishes individuals with a high accuracy. Further, we demonstrate that the diffusion profiles of FAT predict distinct cognitive functions in healthy subjects and are associated with the clinical symptoms in patients with obsessive-compulsive disorders. Our findings suggest that the FAT may serve as a unique structural fingerprint underlying individual cognitive capability.
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Affiliation(s)
- Danni Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
| | - Qing Fan
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, People's Republic of China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, People's Republic of China
| | - Xiang Xiao
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
| | - Hongjian He
- Center for Brain Imaging Science and Technology, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Hangzhou 310027, People's Republic of China
- School of Physics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Yihong Yang
- Neuroimaging Research Branch, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
| | - Yao Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
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Liu M, Zhu AH, Maiti P, Thomopoulos SI, Gadewar S, Chai Y, Kim H, Jahanshad N. Style transfer generative adversarial networks to harmonize multisite MRI to a single reference image to avoid overcorrection. Hum Brain Mapp 2023; 44:4875-4892. [PMID: 37471702 PMCID: PMC10472922 DOI: 10.1002/hbm.26422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/30/2023] [Accepted: 06/25/2023] [Indexed: 07/22/2023] Open
Abstract
Recent work within neuroimaging consortia have aimed to identify reproducible, and often subtle, brain signatures of psychiatric or neurological conditions. To allow for high-powered brain imaging analyses, it is often necessary to pool MR images that were acquired with different protocols across multiple scanners. Current retrospective harmonization techniques have shown promise in removing site-related image variation. However, most statistical approaches may over-correct for technical, scanning-related, variation as they cannot distinguish between confounded image-acquisition based variability and site-related population variability. Such statistical methods often require that datasets contain subjects or patient groups with similar clinical or demographic information to isolate the acquisition-based variability. To overcome this limitation, we consider site-related magnetic resonance (MR) imaging harmonization as a style transfer problem rather than a domain transfer problem. Using a fully unsupervised deep-learning framework based on a generative adversarial network (GAN), we show that MR images can be harmonized by inserting the style information encoded from a single reference image, without knowing their site/scanner labels a priori. We trained our model using data from five large-scale multisite datasets with varied demographics. Results demonstrated that our style-encoding model can harmonize MR images, and match intensity profiles, without relying on traveling subjects. This model also avoids the need to control for clinical, diagnostic, or demographic information. We highlight the effectiveness of our method for clinical research by comparing extracted cortical and subcortical features, brain-age estimates, and case-control effect sizes before and after the harmonization. We showed that our harmonization removed the site-related variances, while preserving the anatomical information and clinical meaningful patterns. We further demonstrated that with a diverse training set, our method successfully harmonized MR images collected from unseen scanners and protocols, suggesting a promising tool for ongoing collaborative studies. Source code is released in USC-IGC/style_transfer_harmonization (github.com).
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Affiliation(s)
- Mengting Liu
- School of Biomedical EngineeringSun Yat‐sen UniversityShenzhenChina
- USC Mark and Mary Stevens Neuroimaging and Informatics InstituteKeck School of Medicine of USC, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Alyssa H. Zhu
- USC Mark and Mary Stevens Neuroimaging and Informatics InstituteKeck School of Medicine of USC, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Piyush Maiti
- USC Mark and Mary Stevens Neuroimaging and Informatics InstituteKeck School of Medicine of USC, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Sophia I. Thomopoulos
- USC Mark and Mary Stevens Neuroimaging and Informatics InstituteKeck School of Medicine of USC, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Shruti Gadewar
- USC Mark and Mary Stevens Neuroimaging and Informatics InstituteKeck School of Medicine of USC, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Yaqiong Chai
- USC Mark and Mary Stevens Neuroimaging and Informatics InstituteKeck School of Medicine of USC, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Hosung Kim
- USC Mark and Mary Stevens Neuroimaging and Informatics InstituteKeck School of Medicine of USC, University of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Neda Jahanshad
- USC Mark and Mary Stevens Neuroimaging and Informatics InstituteKeck School of Medicine of USC, University of Southern CaliforniaLos AngelesCaliforniaUSA
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Yamashita M, Kagitani-Shimono K, Hirano Y, Hamatani S, Nishitani S, Yao A, Kurata S, Kosaka H, Jung M, Yoshida T, Sasaki T, Matsumoto K, Kato Y, Nakanishi M, Tachibana M, Mohri I, Tsuchiya KJ, Tsujikawa T, Okazawa H, Shimizu E, Taniike M, Tomoda A, Mizuno Y. Child Developmental MRI (CDM) project: protocol for a multi-centre, cross-sectional study on elucidating the pathophysiology of attention-deficit/hyperactivity disorder and autism spectrum disorder through a multi-dimensional approach. BMJ Open 2023; 13:e070157. [PMID: 37355265 PMCID: PMC10314540 DOI: 10.1136/bmjopen-2022-070157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 06/07/2023] [Indexed: 06/26/2023] Open
Abstract
INTRODUCTION Neuroimaging studies on attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) have demonstrated differences in extensive brain structure, activity and network. However, there remains heterogeneity and inconsistency across these findings, presumably because of the diversity of the disorders themselves, small sample sizes, and site and parameter differences in MRI scanners, and their overall pathogenesis remains unclear. To address these gaps in the literature, we will apply the travelling-subject approach to correct site differences in MRI scanners and clarify brain structure and network characteristics of children with ADHD and ASD using large samples collected in a multi-centre collaboration. In addition, we will investigate the relationship between these characteristics and genetic, epigenetic, biochemical markers, and behavioural and psychological measures. METHODS AND ANALYSIS We will collect resting-state functional MRI (fMRI) and T1-weighted and diffusion-weighted MRI data from 15 healthy adults as travelling subjects and 300 children (ADHD, n=100; ASD, n=100; and typical development, n=100) with multi-dimensional assessments. We will also apply data from more than 1000 samples acquired in our previous neuroimaging studies on ADHD and ASD. ETHICS AND DISSEMINATION The study protocol has been approved by the Research Ethics Committee of the University of Fukui Hospital (approval no: 20220601). Our study findings will be submitted to scientific peer-reviewed journals and conferences.
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Affiliation(s)
- Masatoshi Yamashita
- Research Centre for Child Mental Development, University of Fukui, Fukui, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
| | - Kuriko Kagitani-Shimono
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Molecular Research Centre for Children's Mental Development, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Paediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshiyuki Hirano
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Research Centre for Child Mental Development, Chiba University, Chiba, Japan
| | - Sayo Hamatani
- Research Centre for Child Mental Development, University of Fukui, Fukui, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Research Centre for Child Mental Development, Chiba University, Chiba, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Shota Nishitani
- Research Centre for Child Mental Development, University of Fukui, Fukui, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
| | - Akiko Yao
- Research Centre for Child Mental Development, University of Fukui, Fukui, Japan
| | - Sawa Kurata
- Research Centre for Child Mental Development, University of Fukui, Fukui, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Hirotaka Kosaka
- Research Centre for Child Mental Development, University of Fukui, Fukui, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Minyoung Jung
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Department of Neuropsychiatry, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
- Cognitive Science Research Group, Korea Brain Research Institute, Daegu, Korea (the Republic of)
| | - Tokiko Yoshida
- Research Centre for Child Mental Development, Chiba University, Chiba, Japan
| | - Tsuyoshi Sasaki
- Department of Child Psychiatry and Psychiatry, Chiba University Hospital, Chiba, Japan
| | - Koji Matsumoto
- Department of Radiology, Chiba University Hospital, Chiba, Japan
| | - Yoko Kato
- Department of Paediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Mariko Nakanishi
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Molecular Research Centre for Children's Mental Development, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Paediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masaya Tachibana
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Molecular Research Centre for Children's Mental Development, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Paediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ikuko Mohri
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Molecular Research Centre for Children's Mental Development, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Paediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Kenji J Tsuchiya
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Research Centre for Child Mental Development, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tetsuya Tsujikawa
- Department of Radiology, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Hidehiko Okazawa
- Biomedical Imaging Research Centre, University of Fukui, Fukui, Japan
| | - Eiji Shimizu
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Research Centre for Child Mental Development, Chiba University, Chiba, Japan
| | - Masako Taniike
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Molecular Research Centre for Children's Mental Development, Osaka University Graduate School of Medicine, Osaka, Japan
- Department of Paediatrics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Akemi Tomoda
- Research Centre for Child Mental Development, University of Fukui, Fukui, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
| | - Yoshifumi Mizuno
- Research Centre for Child Mental Development, University of Fukui, Fukui, Japan
- United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University and University of Fukui, Osaka, Japan
- Department of Child and Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, Japan
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9
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Solanes A, Gosling CJ, Fortea L, Ortuño M, Lopez-Soley E, Llufriu S, Madero S, Martinez-Heras E, Pomarol-Clotet E, Solana E, Vieta E, Radua J, Radua J. Removing the effects of the site in brain imaging machine-learning - Measurement and extendable benchmark. Neuroimage 2023; 265:119800. [PMID: 36481413 DOI: 10.1016/j.neuroimage.2022.119800] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 11/17/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Multisite machine-learning neuroimaging studies, such as those conducted by the ENIGMA Consortium, need to remove the differences between sites to avoid effects of the site (EoS) that may prevent or fraudulently help the creation of prediction models, leading to impoverished or inflated prediction accuracy. Unfortunately, we have shown earlier that current Methods Aiming to Remove the EoS (MAREoS, e.g., ComBat) cannot remove complex EoS (e.g., including interactions between regions). And complex EoS may bias the accuracy. To overcome this hurdle, groups worldwide are developing novel MAREoS. However, we cannot assess their effectiveness because EoS may either inflate or shrink the accuracy, and MAREoS may both remove the EoS and degrade the data. In this work, we propose a strategy to measure the effectiveness of a MAREoS in removing different types of EoS. FOR MAREOS DEVELOPERS, we provide two multisite MRI datasets with only simple true effects (i.e., detectable by most machine-learning algorithms) and two with only simple EoS (i.e., removable by most MAREoS). First, they should use these datasets to fit machine-learning algorithms after applying the MAREoS. Second, they should use the formulas we provide to calculate the relative accuracy change associated with the MAREoS in each dataset and derive an EoS-removal effectiveness statistic. We also offer similar datasets and formulas for complex true effects and EoS that include first-order interactions. FOR MACHINE-LEARNING RESEARCHERS, we provide an extendable benchmark website to show: a) the types of EoS they should remove for each given machine-learning algorithm and b) the effectiveness of each MAREoS for removing each type of EoS. Relevantly, a MAREoS only able to remove the simple EoS may suffice for simple machine-learning algorithms, whereas more complex algorithms need a MAREoS that can remove more complex EoS. For instance, ComBat removes all simple EoS as needed for predictions based on simple lasso algorithms, but it leaves residual complex EoS that may bias the predictions based on standard support vector machine algorithms.
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Affiliation(s)
- Aleix Solanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Department of Psychiatry and Forensic Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Corentin J Gosling
- DysCo Lab, Paris Nanterre University, Nanterre, France; Laboratoire de Psychopathologie et Processus de Santé, Université de Paris, Paris, France; Centre for Innovation in Mental Health (CIMH), School of Psychology, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
| | - Lydia Fortea
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; University of Barcelona, Barcelona, Spain
| | - María Ortuño
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Elisabet Lopez-Soley
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; University of Barcelona, Barcelona, Spain; Center of Neuroimmunology, Laboratory of Advanced Imaging in Neuroimmunological Diseases, Hospital Clinic Barcelona
| | - Sara Llufriu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; University of Barcelona, Barcelona, Spain; Center of Neuroimmunology, Laboratory of Advanced Imaging in Neuroimmunological Diseases, Hospital Clinic Barcelona
| | - Santiago Madero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; University of Barcelona, Barcelona, Spain; Barcelona Bipolar Disorders and Depressive Unit, Institute of Neurosciences, Hospital Clinic, Barcelona, Spain
| | - Eloy Martinez-Heras
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; University of Barcelona, Barcelona, Spain; Center of Neuroimmunology, Laboratory of Advanced Imaging in Neuroimmunological Diseases, Hospital Clinic Barcelona
| | - Edith Pomarol-Clotet
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; FIDMAG Germanes Hospitalàries Research Foundation, Barcelona, Spain; Benito Menni CASM, Sant Boi de Llobregat, Barcelona, Spain
| | - Elisabeth Solana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; University of Barcelona, Barcelona, Spain; Center of Neuroimmunology, Laboratory of Advanced Imaging in Neuroimmunological Diseases, Hospital Clinic Barcelona
| | - Eduard Vieta
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; University of Barcelona, Barcelona, Spain; Barcelona Bipolar Disorders and Depressive Unit, Institute of Neurosciences, Hospital Clinic, Barcelona, Spain
| | - Joaquim Radua
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Madrid, Spain; University of Barcelona, Barcelona, Spain; Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, United Kingdom; Centre for Psychiatric Research and Education, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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10
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Theaud G, Edde M, Dumont M, Zotti C, Zucchelli M, Deslauriers-Gauthier S, Deriche R, Jodoin PM, Descoteaux M. DORIS: A diffusion MRI-based 10 tissue class deep learning segmentation algorithm tailored to improve anatomically-constrained tractography. FRONTIERS IN NEUROIMAGING 2022; 1:917806. [PMID: 37555143 PMCID: PMC10406193 DOI: 10.3389/fnimg.2022.917806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/09/2022] [Indexed: 08/10/2023]
Abstract
Modern tractography algorithms such as anatomically-constrained tractography (ACT) are based on segmentation maps of white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF). These maps are generally estimated from a T1-weighted (T1w) image and then registered in diffusion weighted images (DWI) space. Registration of T1w to diffusion space and partial volume estimation are challenging and rarely voxel-perfect. Diffusion-based segmentation would, thus, potentially allow not to have higher quality anatomical priors injected in the tractography process. On the other hand, even if FA-based tractography is possible without T1 registration, the literature shows that this technique suffers from multiple issues such as holes in the tracking mask and a high proportion of generated broken and anatomically implausible streamlines. Therefore, there is an important need for a tissue segmentation algorithm that works directly in the native diffusion space. We propose DORIS, a DWI-based deep learning segmentation algorithm. DORIS outputs 10 different tissue classes including WM, GM, CSF, ventricles, and 6 other subcortical structures (putamen, pallidum, hippocampus, caudate, amygdala, and thalamus). DORIS was trained and validated on a wide range of subjects, including 1,000 individuals from 22 to 90 years old from clinical and research DWI acquisitions, from 5 public databases. In the absence of a "true" ground truth in diffusion space, DORIS used a silver standard strategy from Freesurfer output registered onto the DWI. This strategy is extensively evaluated and discussed in the current study. Segmentation maps provided by DORIS are quantitatively compared to Freesurfer and FSL-fast and the impacts on tractography are evaluated. Overall, we show that DORIS is fast, accurate, and reproducible and that DORIS-based tractograms produce bundles with a longer mean length and fewer anatomically implausible streamlines.
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Affiliation(s)
- Guillaume Theaud
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, QC, Canada
- Imeka Solutions Inc., Sherbrooke, QC, Canada
| | - Manon Edde
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, QC, Canada
| | | | | | - Mauro Zucchelli
- Athena Project-Team, Inria Sophia Antipolis-Méditerranée, Université Côte D'Azur, Nice, France
| | | | - Rachid Deriche
- Athena Project-Team, Inria Sophia Antipolis-Méditerranée, Université Côte D'Azur, Nice, France
| | - Pierre-Marc Jodoin
- Imeka Solutions Inc., Sherbrooke, QC, Canada
- Videos & Images Theory and Analytics Laboratory (VITAL), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, QC, Canada
- Imeka Solutions Inc., Sherbrooke, QC, Canada
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11
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Zeng R, Lv J, Wang H, Zhou L, Barnett M, Calamante F, Wang C. FOD-Net: A deep learning method for fiber orientation distribution angular super resolution. Med Image Anal 2022; 79:102431. [PMID: 35397471 DOI: 10.1016/j.media.2022.102431] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
Mapping the human connectome using fiber-tracking permits the study of brain connectivity and yields new insights into neuroscience. However, reliable connectome reconstruction using diffusion magnetic resonance imaging (dMRI) data acquired by widely available clinical protocols remains challenging, thus limiting the connectome/tractography clinical applications. Here we develop fiber orientation distribution (FOD) network (FOD-Net), a deep-learning-based framework for FOD angular super-resolution. Our method enhances the angular resolution of FOD images computed from common clinical-quality dMRI data, to obtain FODs with quality comparable to those produced from advanced research scanners. Super-resolved FOD images enable superior tractography and structural connectome reconstruction from clinical protocols. The method was trained and tested with high-quality data from the Human Connectome Project (HCP) and further validated with a local clinical 3.0T scanner as well as with another public available multicenter-multiscanner dataset. Using this method, we improve the angular resolution of FOD images acquired with typical single-shell low-angular-resolution dMRI data (e.g., 32 directions, b=1000s/mm2) to approximate the quality of FODs derived from time-consuming, multi-shell high-angular-resolution dMRI research protocols. We also demonstrate tractography improvement, removing spurious connections and bridging missing connections. We further demonstrate that connectomes reconstructed by super-resolved FODs achieve comparable results to those obtained with more advanced dMRI acquisition protocols, on both HCP and clinical 3.0T data. Advances in deep-learning approaches used in FOD-Net facilitate the generation of high quality tractography/connectome analysis from existing clinical MRI environments. Our code is freely available at https://github.com/ruizengalways/FOD-Net.
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Affiliation(s)
- Rui Zeng
- School of Biomedical Engineering, The University of Sydney, Sydney 2050, Australia; Brain and Mind Centre, The University of Sydney, Sydney 2050, Australia
| | - Jinglei Lv
- School of Biomedical Engineering, The University of Sydney, Sydney 2050, Australia; Brain and Mind Centre, The University of Sydney, Sydney 2050, Australia
| | - He Wang
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China; Human Phenome Institute, Fudan University, Shanghai, China
| | - Luping Zhou
- School of Computer Science, The University of Sydney, Sydney 2050, Australia
| | - Michael Barnett
- Brain and Mind Centre, The University of Sydney, Sydney 2050, Australia; Sydney Neuroimaging Analysis Centre, Sydney 2050, Australia
| | - Fernando Calamante
- School of Biomedical Engineering, The University of Sydney, Sydney 2050, Australia; Brain and Mind Centre, The University of Sydney, Sydney 2050, Australia; Sydney Imaging, The University of Sydney, Sydney 2050, Australia
| | - Chenyu Wang
- Brain and Mind Centre, The University of Sydney, Sydney 2050, Australia; Sydney Neuroimaging Analysis Centre, Sydney 2050, Australia.
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12
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Yeh FC, Irimia A, Bastos DCDA, Golby AJ. Tractography methods and findings in brain tumors and traumatic brain injury. Neuroimage 2021; 245:118651. [PMID: 34673247 PMCID: PMC8859988 DOI: 10.1016/j.neuroimage.2021.118651] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/05/2021] [Accepted: 10/11/2021] [Indexed: 12/31/2022] Open
Abstract
White matter fiber tracking using diffusion magnetic resonance imaging (dMRI) provides a noninvasive approach to map brain connections, but improving anatomical accuracy has been a significant challenge since the birth of tractography methods. Utilizing tractography in brain studies therefore requires understanding of its technical limitations to avoid shortcomings and pitfalls. This review explores tractography limitations and how different white matter pathways pose different challenges to fiber tracking methodologies. We summarize the pros and cons of commonly-used methods, aiming to inform how tractography and its related analysis may lead to questionable results. Extending these experiences, we review the clinical utilization of tractography in patients with brain tumors and traumatic brain injury, starting from tensor-based tractography to more advanced methods. We discuss current limitations and highlight novel approaches in the context of these two conditions to inform future tractography developments.
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Affiliation(s)
- Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| | - Andrei Irimia
- Ethel Percy Andrus Gerontology Center, Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA; Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, California, USA
| | | | - Alexandra J Golby
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA; Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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13
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Cai LY, Yang Q, Kanakaraj P, Nath V, Newton AT, Edmonson HA, Luci J, Conrad BN, Price GR, Hansen CB, Kerley CI, Ramadass K, Yeh FC, Kang H, Garyfallidis E, Descoteaux M, Rheault F, Schilling KG, Landman BA. MASiVar: Multisite, multiscanner, and multisubject acquisitions for studying variability in diffusion weighted MRI. Magn Reson Med 2021; 86:3304-3320. [PMID: 34270123 PMCID: PMC9087815 DOI: 10.1002/mrm.28926] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/18/2022]
Abstract
PURPOSE Diffusion-weighted imaging allows investigators to identify structural, microstructural, and connectivity-based differences between subjects, but variability due to session and scanner biases is a challenge. METHODS To investigate DWI variability, we present MASiVar, a multisite data set consisting of 319 diffusion scans acquired at 3 T from b = 1000 to 3000 s/mm2 across 14 healthy adults, 83 healthy children (5 to 8 years), three sites, and four scanners as a publicly available, preprocessed, and de-identified data set. With the adult data, we demonstrate the capacity of MASiVar to simultaneously quantify the intrasession, intersession, interscanner, and intersubject variability of four common DWI processing approaches: (1) a tensor signal representation, (2) a multi-compartment neurite orientation dispersion and density model, (3) white-matter bundle segmentation, and (4) structural connectomics. Respectively, we evaluate region-wise fractional anisotropy, mean diffusivity, and principal eigenvector; region-wise CSF volume fraction, intracellular volume fraction, and orientation dispersion index; bundle-wise shape, volume, fractional anisotropy, and length; and whole connectome correlation and maximized modularity, global efficiency, and characteristic path length. RESULTS We plot the variability in these measures at each level and find that it consistently increases with intrasession to intersession to interscanner to intersubject effects across all processing approaches and that sometimes interscanner variability can approach intersubject variability. CONCLUSIONS This study demonstrates the potential of MASiVar to more globally investigate DWI variability across multiple levels and processing approaches simultaneously and suggests harmonization between scanners for multisite analyses should be considered before inference of group differences on subjects.
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Affiliation(s)
- Leon Y. Cai
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Qi Yang
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Praitayini Kanakaraj
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Vishwesh Nath
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Allen T. Newton
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, USA
| | | | - Jeffrey Luci
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, USA
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Benjamin N. Conrad
- Neuroscience Graduate Program, Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Psychology and Human Development, Peabody College, Vanderbilt University, Nashville, Tennessee, USA
| | - Gavin R. Price
- Department of Psychology and Human Development, Peabody College, Vanderbilt University, Nashville, Tennessee, USA
| | - Colin B. Hansen
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Cailey I. Kerley
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Karthik Ramadass
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Hakmook Kang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Maxime Descoteaux
- Department of Computer Science, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Francois Rheault
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
- Department of Computer Science, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Kurt G. Schilling
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Bennett A. Landman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, Tennessee, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, Tennessee, USA
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14
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Schilling KG, Tax CM, Rheault F, Hansen C, Yang Q, Yeh FC, Cai L, Anderson AW, Landman BA. Fiber tractography bundle segmentation depends on scanner effects, vendor effects, acquisition resolution, diffusion sampling scheme, diffusion sensitization, and bundle segmentation workflow. Neuroimage 2021; 242:118451. [PMID: 34358660 PMCID: PMC9933001 DOI: 10.1016/j.neuroimage.2021.118451] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/08/2021] [Accepted: 08/03/2021] [Indexed: 01/08/2023] Open
Abstract
When investigating connectivity and microstructure of white matter pathways of the brain using diffusion tractography bundle segmentation, it is important to understand potential confounds and sources of variation in the process. While cross-scanner and cross-protocol effects on diffusion microstructure measures are well described (in particular fractional anisotropy and mean diffusivity), it is unknown how potential sources of variation effect bundle segmentation results, which features of the bundle are most affected, where variability occurs, nor how these sources of variation depend upon the method used to reconstruct and segment bundles. In this study, we investigate six potential sources of variation, or confounds, for bundle segmentation: variation (1) across scan repeats, (2) across scanners, (3) across vendors (4) across acquisition resolution, (5) across diffusion schemes, and (6) across diffusion sensitization. We employ four different bundle segmentation workflows on two benchmark multi-subject cross-scanner and cross-protocol databases, and investigate reproducibility and biases in volume overlap, shape geometry features of fiber pathways, and microstructure features within the pathways. We find that the effects of acquisition protocol, in particular acquisition resolution, result in the lowest reproducibility of tractography and largest variation of features, followed by vendor-effects, scanner-effects, and finally diffusion scheme and b-value effects which had similar reproducibility as scan-rescan variation. However, confounds varied both across pathways and across segmentation workflows, with some bundle segmentation workflows more (or less) robust to sources of variation. Despite variability, bundle dissection is consistently able to recover the same location of pathways in the deep white matter, with variation at the gray matter/ white matter interface. Next, we show that differences due to the choice of bundle segmentation workflows are larger than any other studied confound, with low-to-moderate overlap of the same intended pathway when segmented using different methods. Finally, quantifying microstructure features within a pathway, we show that tractography adds variability over-and-above that which exists due to noise, scanner effects, and acquisition effects. Overall, these confounds need to be considered when harmonizing diffusion datasets, interpreting or combining data across sites, and when attempting to understand the successes and limitations of different methodologies in the design and development of new tractography or bundle segmentation methods.
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Affiliation(s)
- Kurt G. Schilling
- Department of Radiology & Radiological Science, Vanderbilt University Medical Center, Nashville, TN, United States,Vanderbilt Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Chantal M.W. Tax
- Cardiff University Brain Research Imaging Centre (CUBRIC), Cardiff University, Cardiff, United Kingdom
| | - Francois Rheault
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States
| | - Colin Hansen
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States
| | - Qi Yang
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States
| | - Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh, United States
| | - Leon Cai
- Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States
| | - Adam W. Anderson
- Department of Radiology & Radiological Science, Vanderbilt University Medical Center, Nashville, TN, United States,Vanderbilt Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, United States,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
| | - Bennett A. Landman
- Department of Radiology & Radiological Science, Vanderbilt University Medical Center, Nashville, TN, United States,Vanderbilt Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, United States,Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, United States,Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States
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15
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Liu M, Maiti P, Thomopoulos S, Zhu A, Chai Y, Kim H, Jahanshad N. Style Transfer Using Generative Adversarial Networks for Multi-Site MRI Harmonization. MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION : MICCAI ... INTERNATIONAL CONFERENCE ON MEDICAL IMAGE COMPUTING AND COMPUTER-ASSISTED INTERVENTION 2021; 12903:313-322. [PMID: 35647615 PMCID: PMC9137427 DOI: 10.1007/978-3-030-87199-4_30] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Large data initiatives and high-powered brain imaging analyses require the pooling of MR images acquired across multiple scanners, often using different protocols. Prospective cross-site harmonization often involves the use of a phantom or traveling subjects. However, as more datasets are becoming publicly available, there is a growing need for retrospective harmonization, pooling data from sites not originally coordinated together. Several retrospective harmonization techniques have shown promise in removing cross-site image variation. However, most unsupervised methods cannot distinguish between image-acquisition based variability and cross-site population variability, so they require that datasets contain subjects or patient groups with similar clinical or demographic information. To overcome this limitation, we consider cross-site MRI image harmonization as a style transfer problem rather than a domain transfer problem. Using a fully unsupervised deep-learning framework based on a generative adversarial network (GAN), we show that MR images can be harmonized by inserting the style information encoded from a reference image directly, without knowing their site/scanner labels a priori. We trained our model using data from five large-scale multi-site datasets with varied demographics. Results demonstrated that our style-encoding model can harmonize MR images, and match intensity profiles, successfully, without relying on traveling subjects. This model also avoids the need to control for clinical, diagnostic, or demographic information. Moreover, we further demonstrated that if we included diverse enough images into the training set, our method successfully harmonized MR images collected from unseen scanners and protocols, suggesting a promising novel tool for ongoing collaborative studies.
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Affiliation(s)
- Mengting Liu
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Piyush Maiti
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Sophia Thomopoulos
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Alyssa Zhu
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Yaqiong Chai
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Hosung Kim
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Neda Jahanshad
- USC Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
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16
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Wu Z, Gao Y, Potter T, Benoit J, Shen J, Schulz PE, Zhang Y. Interactions Between Aging and Alzheimer's Disease on Structural Brain Networks. Front Aging Neurosci 2021; 13:639795. [PMID: 34177548 PMCID: PMC8222527 DOI: 10.3389/fnagi.2021.639795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Normative aging and Alzheimer's disease (AD) propagation alter anatomical connections among brain parcels. However, the interaction between the trajectories of age- and AD-linked alterations in the topology of the structural brain network is not well understood. In this study, diffusion-weighted magnetic resonance imaging (MRI) datasets of 139 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database were used to document their structural brain networks. The 139 participants consist of 45 normal controls (NCs), 37 with early mild cognitive impairment (EMCI), 27 with late mild cognitive impairment (LMCI), and 30 AD patients. All subjects were further divided into three subgroups based on their age (56-65, 66-75, and 71-85 years). After the structural connectivity networks were built using anatomically-constrained deterministic tractography, their global and nodal topological properties were estimated, including network efficiency, characteristic path length, transitivity, modularity coefficient, clustering coefficient, and betweenness. Statistical analyses were then performed on these metrics using linear regression, and one- and two-way ANOVA testing to examine group differences and interactions between aging and AD propagation. No significant interactions were found between aging and AD propagation in the global topological metrics (network efficiency, characteristic path length, transitivity, and modularity coefficient). However, nodal metrics (clustering coefficient and betweenness centrality) of some cortical parcels exhibited significant interactions between aging and AD propagation, with affected parcels including left superior temporal, right pars triangularis, and right precentral. The results collectively confirm the age-related deterioration of structural networks in MCI and AD patients, providing novel insight into the cross effects of aging and AD disorder on brain structural networks. Some early symptoms of AD may also be due to age-associated anatomic vulnerability interacting with early anatomic changes associated with AD.
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Affiliation(s)
- Zhanxiong Wu
- School of Electronic Information, Hangzhou Dianzi University, Hangzhou, China
| | - Yunyuan Gao
- Department of Intelligent Control and Robotics Institute, College of Automation, Hangzhou Dianzi University, Hangzhou, China
| | - Thomas Potter
- Department of Biomedical Engineering, University of Houston, Houston, TX, United States
| | - Julia Benoit
- Texas Institute for Measurement Evaluation and Statistics, Department of Basic Vision Sciences, University of Houston, Houston, TX, United States
| | - Jian Shen
- Neurosurgery Department, The First Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Paul E. Schulz
- Department of Neurology, The McGovern Medical School of UTHealth-Houston, Houston, TX, United States
| | - Yingchun Zhang
- Department of Biomedical Engineering, University of Houston, Houston, TX, United States
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17
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Elaldi A, Dey N, Kim H, Gerig G. Equivariant Spherical Deconvolution: Learning Sparse Orientation Distribution Functions from Spherical Data. INFORMATION PROCESSING IN MEDICAL IMAGING : PROCEEDINGS OF THE ... CONFERENCE 2021; 12729:267-278. [PMID: 37576905 PMCID: PMC10422024 DOI: 10.1007/978-3-030-78191-0_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
We present a rotation-equivariant self-supervised learning framework for the sparse deconvolution of non-negative scalar fields on the unit sphere. Spherical signals with multiple peaks naturally arise in Diffusion MRI (dMRI), where each voxel consists of one or more signal sources corresponding to anisotropic tissue structure such as white matter. Due to spatial and spectral partial voluming, clinically-feasible dMRI struggles to resolve crossing-fiber white matter configurations, leading to extensive development in spherical deconvolution methodology to recover underlying fiber directions. However, these methods are typically linear and struggle with small crossing-angles and partial volume fraction estimation. In this work, we improve on current methodologies by nonlinearly estimating fiber structures via self-supervised spherical convolutional networks with guaranteed equivariance to spherical rotation. We perform validation via extensive single and multi-shell synthetic benchmarks demonstrating competitive performance against common base-lines. We further show improved downstream performance on fiber tractography measures on the Tractometer benchmark dataset. Finally, we show downstream improvements in terms of tractography and partial volume estimation on a multi-shell dataset of human subjects.
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Affiliation(s)
- Axel Elaldi
- Department of Computer Science and Engineering, New York University, New York, USA
| | - Neel Dey
- Department of Computer Science and Engineering, New York University, New York, USA
| | - Heejong Kim
- Department of Computer Science and Engineering, New York University, New York, USA
| | - Guido Gerig
- Department of Computer Science and Engineering, New York University, New York, USA
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18
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Zhang F, Breger A, Cho KIK, Ning L, Westin CF, O'Donnell LJ, Pasternak O. Deep learning based segmentation of brain tissue from diffusion MRI. Neuroimage 2021; 233:117934. [PMID: 33737246 PMCID: PMC8139182 DOI: 10.1016/j.neuroimage.2021.117934] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/12/2020] [Accepted: 03/01/2021] [Indexed: 02/06/2023] Open
Abstract
Segmentation of brain tissue types from diffusion MRI (dMRI) is an important task, required for quantification of brain microstructure and for improving tractography. Current dMRI segmentation is mostly based on anatomical MRI (e.g., T1- and T2-weighted) segmentation that is registered to the dMRI space. However, such inter-modality registration is challenging due to more image distortions and lower image resolution in dMRI as compared with anatomical MRI. In this study, we present a deep learning method for diffusion MRI segmentation, which we refer to as DDSeg. Our proposed method learns tissue segmentation from high-quality imaging data from the Human Connectome Project (HCP), where registration of anatomical MRI to dMRI is more precise. The method is then able to predict a tissue segmentation directly from new dMRI data, including data collected with different acquisition protocols, without requiring anatomical data and inter-modality registration. We train a convolutional neural network (CNN) to learn a tissue segmentation model using a novel augmented target loss function designed to improve accuracy in regions of tissue boundary. To further improve accuracy, our method adds diffusion kurtosis imaging (DKI) parameters that characterize non-Gaussian water molecule diffusion to the conventional diffusion tensor imaging parameters. The DKI parameters are calculated from the recently proposed mean-kurtosis-curve method that corrects implausible DKI parameter values and provides additional features that discriminate between tissue types. We demonstrate high tissue segmentation accuracy on HCP data, and also when applying the HCP-trained model on dMRI data from other acquisitions with lower resolution and fewer gradient directions.
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Affiliation(s)
- Fan Zhang
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anna Breger
- Faculty of Mathematics, University of Vienna, Wien, Austria
| | - Kang Ik Kevin Cho
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lipeng Ning
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carl-Fredrik Westin
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren J O'Donnell
- Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ofer Pasternak
- 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
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19
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Koike S, Tanaka SC, Okada T, Aso T, Yamashita A, Yamashita O, Asano M, Maikusa N, Morita K, Okada N, Fukunaga M, Uematsu A, Togo H, Miyazaki A, Murata K, Urushibata Y, Autio J, Ose T, Yoshimoto J, Araki T, Glasser MF, Van Essen DC, Maruyama M, Sadato N, Kawato M, Kasai K, Okamoto Y, Hanakawa T, Hayashi T. Brain/MINDS beyond human brain MRI project: A protocol for multi-level harmonization across brain disorders throughout the lifespan. Neuroimage Clin 2021; 30:102600. [PMID: 33741307 PMCID: PMC8209465 DOI: 10.1016/j.nicl.2021.102600] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 01/31/2021] [Accepted: 02/12/2021] [Indexed: 01/03/2023]
Abstract
Psychiatric and neurological disorders are afflictions of the brain that can affect individuals throughout their lifespan. Many brain magnetic resonance imaging (MRI) studies have been conducted; however, imaging-based biomarkers are not yet well established for diagnostic and therapeutic use. This article describes an outline of the planned study, the Brain/MINDS Beyond human brain MRI project (BMB-HBM, FY2018 ~ FY2023), which aims to establish clinically-relevant imaging biomarkers with multi-site harmonization by collecting data from healthy traveling subjects (TS) at 13 research sites. Collection of data in psychiatric and neurological disorders across the lifespan is also scheduled at 13 sites, whereas designing measurement procedures, developing and analyzing neuroimaging protocols, and databasing are done at three research sites. A high-quality scanning protocol, Harmonization Protocol (HARP), was established for five high-quality 3 T scanners to obtain multimodal brain images including T1 and T2-weighted, resting-state and task functional and diffusion-weighted MRI. Data are preprocessed and analyzed using approaches developed by the Human Connectome Project. Preliminary results in 30 TS demonstrated cortical thickness, myelin, functional connectivity measures are comparable across 5 scanners, suggesting sensitivity to subject-specific connectome. A total of 75 TS and more than two thousand patients with various psychiatric and neurological disorders are scheduled to participate in the project, allowing a mixed model statistical harmonization. The HARP protocols are publicly available online, and all the imaging, demographic and clinical information, harmonizing database will also be made available by 2024. To the best of our knowledge, this is the first project to implement a prospective, multi-level harmonization protocol with multi-site TS data. It explores intractable brain disorders across the lifespan and may help to identify the disease-specific pathophysiology and imaging biomarkers for clinical practice.
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Affiliation(s)
- Shinsuke Koike
- Center for Evolutionary Cognitive Sciences (ECS), Graduate School of Art and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan; University of Tokyo Institute for Diversity & Adaptation of Human Mind (UTIDAHM), Meguro-ku, Tokyo 153-8902, Japan; University of Tokyo Center for Integrative Science of Human Behavior (CiSHuB), 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan; The International Research Center for Neurointelligence (WPI-IRCN), Institutes for Advanced Study (UTIAS), University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Saori C Tanaka
- Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institutes International (ATR), Kyoto 619-0288, Japan
| | - Tomohisa Okada
- Human Brain Research Center, Kyoto University, Kyoto 606-8507, Japan
| | - Toshihiko Aso
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan
| | - Ayumu Yamashita
- Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institutes International (ATR), Kyoto 619-0288, Japan
| | - Okito Yamashita
- Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institutes International (ATR), Kyoto 619-0288, Japan
| | - Michiko Asano
- Center for Evolutionary Cognitive Sciences (ECS), Graduate School of Art and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Norihide Maikusa
- Center for Evolutionary Cognitive Sciences (ECS), Graduate School of Art and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan; Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Kodaira-shi, Tokyo 187-8551, Japan
| | - Kentaro Morita
- Department of Rehabilitation, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Naohiro Okada
- University of Tokyo Institute for Diversity & Adaptation of Human Mind (UTIDAHM), Meguro-ku, Tokyo 153-8902, Japan; The International Research Center for Neurointelligence (WPI-IRCN), Institutes for Advanced Study (UTIAS), University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan; Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Masaki Fukunaga
- Division of Cerebral Integration, Department of System Neuroscience, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
| | - Akiko Uematsu
- Center for Evolutionary Cognitive Sciences (ECS), Graduate School of Art and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
| | - Hiroki Togo
- Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Kodaira-shi, Tokyo 187-8551, Japan
| | - Atsushi Miyazaki
- Tamagawa University Brain Science Institute, 6-1-1 Tamagawagakuen, Machida, Tokyo 194-8610, Japan
| | | | | | - Joonas Autio
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan
| | - Takayuki Ose
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan
| | - Junichiro Yoshimoto
- Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institutes International (ATR), Kyoto 619-0288, Japan
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Matthew F Glasser
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO USA; Department of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - David C Van Essen
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO USA
| | - Megumi Maruyama
- Research Enhancement Strategy Office, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
| | - Norihiro Sadato
- Division of Cerebral Integration, Department of System Neuroscience, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
| | - Mitsuo Kawato
- Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institutes International (ATR), Kyoto 619-0288, Japan; Center for Advanced Intelligence Project, RIKEN, Tokyo 103-0027, Japan
| | - Kiyoto Kasai
- University of Tokyo Institute for Diversity & Adaptation of Human Mind (UTIDAHM), Meguro-ku, Tokyo 153-8902, Japan; University of Tokyo Center for Integrative Science of Human Behavior (CiSHuB), 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan; The International Research Center for Neurointelligence (WPI-IRCN), Institutes for Advanced Study (UTIAS), University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan; Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yasumasa Okamoto
- Department of Psychiatry and Neurosciences, Hiroshima University, Hiroshima 734-8551, Japan
| | - Takashi Hanakawa
- Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Kodaira-shi, Tokyo 187-8551, Japan; Department of Integrated Neuroanatomy and Neuroimaging, Kyoto University Graduate School of Medicine, Kyoto 606-8303, Japan
| | - Takuya Hayashi
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan.
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20
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Kim REY, Lee M, Kang DW, Wang SM, Kim NY, Lee MK, Lim HK, Kim D. Deep Learning-Based Segmentation to Establish East Asian Normative Volumes Using Multisite Structural MRI. Diagnostics (Basel) 2020; 11:diagnostics11010013. [PMID: 33374745 PMCID: PMC7824436 DOI: 10.3390/diagnostics11010013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 11/16/2022] Open
Abstract
Normative brain magnetic resonance imaging (MRI) is essential to interpret the state of an individual's brain health. However, a normative study is often expensive for small research groups. Although several attempts have been made to establish brain MRI norms, the focus has been limited to certain age ranges. This study aimed to establish East Asian normative brain data using multi-site MRI and determine the robustness of these data for clinical research. Normative MRI was gathered covering a wide range of cognitively normal East Asian populations (age: 18-96 years) from two open sources and three research sites. Eight sub-regional volumes were extracted in the left and right hemispheres using an in-house deep learning-based tool. Repeated measure consistency and multicenter reliability were determined using intraclass correlation coefficients and compared to a widely used tool, FreeSurfer. Our results showed highly consistent outcomes with high reliability across sites. Our method outperformed FreeSurfer in repeated measure consistency for most structures and multicenter reliability for all structures. The normative MRI we constructed was able to identify sub-regional differences in mild cognitive impairments and dementia after covariate adjustments. Our investigation suggests it is possible to provide a sound normative reference for neurodegenerative or aging research.
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Affiliation(s)
- Regina E. Y. Kim
- Research Institute, NEUROPHET Inc., Seoul 06247, Korea; (R.E.Y.K.); (M.L.)
- Institute of Human Genomic Study, College of Medicine, Korea University, Seoul 15355, Korea
- Department of Psychiatry, University of Iowa, Iowa City, IA 52240, USA
| | - Minho Lee
- Research Institute, NEUROPHET Inc., Seoul 06247, Korea; (R.E.Y.K.); (M.L.)
| | - Dong Woo Kang
- Department of Psychiatry, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Sheng-Min Wang
- Department of Psychiatry, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Korea; (S.-M.W.); (N.-Y.K.)
| | - Nak-Young Kim
- Department of Psychiatry, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Korea; (S.-M.W.); (N.-Y.K.)
| | - Min Kyoung Lee
- Department of Radiology, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Hyun Kook Lim
- Department of Psychiatry, Yeouido St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 07345, Korea; (S.-M.W.); (N.-Y.K.)
- Correspondence: (H.K.L.); (D.K.); Tel.: +82-70-5223-4414 (D.K.)
| | - Donghyeon Kim
- Research Institute, NEUROPHET Inc., Seoul 06247, Korea; (R.E.Y.K.); (M.L.)
- Correspondence: (H.K.L.); (D.K.); Tel.: +82-70-5223-4414 (D.K.)
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