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Meier TB, Savitz J, España LY, Goeckner BD, Kent Teague T, van der Horn HJ, Tugan Muftuler L, Mayer AR, Brett BL. Association of concussion history with psychiatric symptoms, limbic system structure, and kynurenine pathway metabolites in healthy, collegiate-aged athletes. Brain Behav Immun 2025; 123:619-630. [PMID: 39414174 PMCID: PMC11624060 DOI: 10.1016/j.bbi.2024.10.015] [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: 04/24/2024] [Revised: 09/30/2024] [Accepted: 10/11/2024] [Indexed: 10/18/2024] Open
Abstract
Psychiatric outcomes are commonly observed in individuals with repeated concussions, though their underlying mechanism is unknown. One potential mechanism linking concussion with psychiatric symptoms is inflammation-induced activation of the kynurenine pathway, which is thought to play a role in the pathogenesis of mood disorders. Here, we investigated the association of prior concussion with multiple psychiatric-related outcomes in otherwise healthy male and female collegiate-aged athletes (N = 212) with varying histories of concussion recruited from the community. Specially, we tested the hypotheses that concussion history is associated with worse psychiatric symptoms, limbic system structural abnormalities (hippocampal volume, white matter microstructure assessed using neurite orientation dispersion and density imaging; NODDI), and elevations in kynurenine pathway (KP) metabolites (e.g., Quinolinic acid; QuinA). Given known sex-effects on concussion risk and recovery, psychiatric outcomes, and the kynurenine pathway, the moderating effect of sex was considered for all analyses. More concussions were associated with greater depression, anxiety, and anhedonia symptoms in female athletes (ps ≤ 0.005) and greater depression symptoms in male athletes (p = 0.011). More concussions were associated with smaller bilateral hippocampal tail (ps < 0.010) and left hippocampal body (p < 0.001) volumes across male and female athletes. Prior concussion was also associated with elevations in the orientation dispersion index (ODI) and lower intracellular volume fraction in several white matter tracts including the in uncinate fasciculus, cingulum-gyrus, and forceps major and minor, with evidence of female-specific associations in select regions. Regarding serum KP metabolites, more concussions were associated with elevated QuinA in females and lower tryptophan in males (ps ≤ 0.010). Finally, serum levels of QuinA were associated with elevated ODI (male and female athletes) and worse anxiety symptoms (females only), while higher ODI in female athletes and smaller hippocampal volumes in male athletes were associated with more severe anxiety and depression symptoms (ps ≤ 0.05). These data suggest that cumulative concussion is associated with psychiatric symptoms and limbic system structure in healthy athletes, with increased susceptibility to these effects in female athletes. Moreover, the associations of outcomes with serum KP metabolites highlight the KP as one potential molecular pathway underlying these observations.
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Affiliation(s)
- Timothy B Meier
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, the United States of America; Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, the United States of America; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, the United States of America.
| | - Jonathan Savitz
- Laureate Institute for Brain Research, Tulsa, OK 74136, the United States of America; Oxley College of Health Sciences, The University of Tulsa, Tulsa, OK 74119, the United States of America
| | - Lezlie Y España
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, the United States of America
| | - Bryna D Goeckner
- Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, the United States of America
| | - T Kent Teague
- Department of Psychiatry, The University of Oklahoma School of Community Medicine, Tulsa, OK 74135, the United States of America; Department of Surgery, The University of Oklahoma School of Community Medicine, Tulsa, OK 74135, the United States of America; Department of Pharmaceutical Sciences, University of Oklahoma College of Pharmacy, Tulsa, OK 74135, the United States of America
| | - Harm Jan van der Horn
- The Mind Research Network/Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, the United States of America; University of Groningen, University Medical Center Groningen, the Netherlands
| | - L Tugan Muftuler
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, the United States of America
| | - Andrew R Mayer
- The Mind Research Network/Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, the United States of America; Departments of Neurology and Psychiatry, University of New Mexico School of Medicine, Albuquerque, NM, the United States of America; Department of Psychology, University of New Mexico, Albuquerque, NM, the United States of America
| | - Benjamin L Brett
- Department of Neurosurgery, Medical College of Wisconsin, Milwaukee, WI, the United States of America; Department of Neurology, Medical College of Wisconsin, Milwaukee, WI, the United States of America
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Al-Sharif NB, Zavaliangos-Petropulu A, Narr KL. A review of diffusion MRI in mood disorders: mechanisms and predictors of treatment response. Neuropsychopharmacology 2024; 50:211-229. [PMID: 38902355 PMCID: PMC11525636 DOI: 10.1038/s41386-024-01894-3] [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: 04/08/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024]
Abstract
By measuring the molecular diffusion of water molecules in brain tissue, diffusion MRI (dMRI) provides unique insight into the microstructure and structural connections of the brain in living subjects. Since its inception, the application of dMRI in clinical research has expanded our understanding of the possible biological bases of psychiatric disorders and successful responses to different therapeutic interventions. Here, we review the past decade of diffusion imaging-based investigations with a specific focus on studies examining the mechanisms and predictors of therapeutic response in people with mood disorders. We present a brief overview of the general application of dMRI and key methodological developments in the field that afford increasingly detailed information concerning the macro- and micro-structural properties and connectivity patterns of white matter (WM) pathways and their perturbation over time in patients followed prospectively while undergoing treatment. This is followed by a more in-depth summary of particular studies using dMRI approaches to examine mechanisms and predictors of clinical outcomes in patients with unipolar or bipolar depression receiving pharmacological, neurostimulation, or behavioral treatments. Limitations associated with dMRI research in general and with treatment studies in mood disorders specifically are discussed, as are directions for future research. Despite limitations and the associated discrepancies in findings across individual studies, evolving research strongly indicates that the field is on the precipice of identifying and validating dMRI biomarkers that could lead to more successful personalized treatment approaches and could serve as targets for evaluating the neural effects of novel treatments.
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Affiliation(s)
- Noor B Al-Sharif
- Departments of Neurology and Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
| | - Artemis Zavaliangos-Petropulu
- Departments of Neurology and Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Katherine L Narr
- Departments of Neurology and Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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Gao C, Yang Q, Kim ME, Khairi NM, Cai LY, Newlin NR, Kanakaraj P, Remedios LW, Krishnan AR, Yu X, Yao T, Zhang P, Schilling KG, Moyer D, Archer DB, Resnick SM, Landman BA. Characterizing patterns of diffusion tensor imaging variance in aging brains. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.08.22.23294381. [PMID: 37662348 PMCID: PMC10473788 DOI: 10.1101/2023.08.22.23294381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Purpose As large analyses merge data across sites, a deeper understanding of variance in statistical assessment across the sources of data becomes critical for valid analyses. Diffusion tensor imaging (DTI) exhibits spatially varying and correlated noise, so care must be taken with distributional assumptions. Here we characterize the role of physiology, subject compliance, and the interaction of subject with the scanner in the understanding of DTI variability, as modeled in spatial variance of derived metrics in homogeneous regions. Approach We analyze DTI data from 1035 subjects in the Baltimore Longitudinal Study of Aging (BLSA), with ages ranging from 22.4 to 103 years old. For each subject, up to 12 longitudinal sessions were conducted. We assess variance of DTI scalars within regions of interest (ROIs) defined by four segmentation methods and investigate the relationships between the variance and covariates, including baseline age, time from the baseline (referred to as "interval"), motion, sex, and whether it is the first scan or the second scan in the session. Results Covariate effects are heterogeneous and bilaterally symmetric across ROIs. Inter-session interval is positively related ( p ≪ 0.001 ) to FA variance in the cuneus and occipital gyrus, but negatively ( p ≪ 0.001 ) in the caudate nucleus. Males show significantly ( p ≪ 0.001 ) higher FA variance in the right putamen, thalamus, body of the corpus callosum, and cingulate gyrus. In 62 out of 176 ROIs defined by the Eve type-1 atlas, an increase in motion is associated ( p < 0.05 ) with a decrease in FA variance. Head motion increases during the rescan of DTI ( Δ μ = 0.045 millimeters per volume). Conclusions The effects of each covariate on DTI variance, and their relationships across ROIs are complex. Ultimately, we encourage researchers to include estimates of variance when sharing data and consider models of heteroscedasticity in analysis. This work provides a foundation for study planning to account for regional variations in metric variance.
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Affiliation(s)
- Chenyu Gao
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, United States
| | - Qi Yang
- Vanderbilt University, Department of Computer Science, Nashville, United States
| | - Michael E. Kim
- Vanderbilt University, Department of Computer Science, Nashville, United States
| | - Nazirah Mohd Khairi
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, United States
| | - Leon Y. Cai
- Vanderbilt University, Department of Biomedical Engineering, Nashville, United States
| | - Nancy R. Newlin
- Vanderbilt University, Department of Computer Science, Nashville, United States
| | | | - Lucas W. Remedios
- Vanderbilt University, Department of Computer Science, Nashville, United States
| | - Aravind R. Krishnan
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, United States
| | - Xin Yu
- Vanderbilt University, Department of Computer Science, Nashville, United States
| | - Tianyuan Yao
- Vanderbilt University, Department of Computer Science, Nashville, United States
| | - Panpan Zhang
- Vanderbilt University Medical Center, Department of Biostatistics, Nashville, United States
| | - Kurt G. Schilling
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, USA
- Vanderbilt University, Vanderbilt University Institute of Imaging Science, Nashville, USA
| | - Daniel Moyer
- Vanderbilt University, Department of Computer Science, Nashville, United States
| | - Derek B. Archer
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University School of Medicine, Nashville, USA
- Vanderbilt University Medical Center, Vanderbilt Genetics Institute, Nashville, USA
| | - Susan M. Resnick
- National Institute on Aging, Laboratory of Behavioral Neuroscience, Baltimore, United States
| | - Bennett A. Landman
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, United States
- Vanderbilt University, Department of Computer Science, Nashville, United States
- Vanderbilt University, Department of Biomedical Engineering, Nashville, United States
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, USA
- Vanderbilt University, Vanderbilt University Institute of Imaging Science, Nashville, USA
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Gao C, Yang Q, Kim ME, Khairi NM, Cai LY, Newlin NR, Kanakaraj P, Remedios LW, Krishnan AR, Yu X, Yao T, Zhang P, Schilling KG, Moyer D, Archer DB, Resnick SM, Landman BA. Characterizing patterns of diffusion tensor imaging variance in aging brains. J Med Imaging (Bellingham) 2024; 11:044007. [PMID: 39185477 PMCID: PMC11344569 DOI: 10.1117/1.jmi.11.4.044007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/27/2024] Open
Abstract
Purpose As large analyses merge data across sites, a deeper understanding of variance in statistical assessment across the sources of data becomes critical for valid analyses. Diffusion tensor imaging (DTI) exhibits spatially varying and correlated noise, so care must be taken with distributional assumptions. Here, we characterize the role of physiology, subject compliance, and the interaction of the subject with the scanner in the understanding of DTI variability, as modeled in the spatial variance of derived metrics in homogeneous regions. Approach We analyze DTI data from 1035 subjects in the Baltimore Longitudinal Study of Aging, with ages ranging from 22.4 to 103 years old. For each subject, up to 12 longitudinal sessions were conducted. We assess the variance of DTI scalars within regions of interest (ROIs) defined by four segmentation methods and investigate the relationships between the variance and covariates, including baseline age, time from the baseline (referred to as "interval"), motion, sex, and whether it is the first scan or the second scan in the session. Results Covariate effects are heterogeneous and bilaterally symmetric across ROIs. Inter-session interval is positively related ( p ≪ 0.001 ) to FA variance in the cuneus and occipital gyrus, but negatively ( p ≪ 0.001 ) in the caudate nucleus. Males show significantly ( p ≪ 0.001 ) higher FA variance in the right putamen, thalamus, body of the corpus callosum, and cingulate gyrus. In 62 out of 176 ROIs defined by the Eve type-1 atlas, an increase in motion is associated ( p < 0.05 ) with a decrease in FA variance. Head motion increases during the rescan of DTI ( Δ μ = 0.045 mm per volume). Conclusions The effects of each covariate on DTI variance and their relationships across ROIs are complex. Ultimately, we encourage researchers to include estimates of variance when sharing data and consider models of heteroscedasticity in analysis. This work provides a foundation for study planning to account for regional variations in metric variance.
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Affiliation(s)
- Chenyu Gao
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, Tennessee, United States
| | - Qi Yang
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Michael E. Kim
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Nazirah Mohd Khairi
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, Tennessee, United States
| | - Leon Y. Cai
- Vanderbilt University, Department of Biomedical Engineering, Nashville, Tennessee, United States
| | - Nancy R. Newlin
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Praitayini Kanakaraj
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Lucas W. Remedios
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Aravind R. Krishnan
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, Tennessee, United States
| | - Xin Yu
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Tianyuan Yao
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Panpan Zhang
- Vanderbilt University Medical Center, Department of Biostatistics, Nashville, Tennessee, United States
| | - Kurt G. Schilling
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, Tennessee, United States
- Vanderbilt University, Vanderbilt University Institute of Imaging Science, Nashville, Tennessee, United States
| | - Daniel Moyer
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
| | - Derek B. Archer
- Vanderbilt Memory and Alzheimer’s Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States
- Vanderbilt University Medical Center, Vanderbilt Genetics Institute, Nashville, Tennessee, United States
| | - Susan M. Resnick
- National Institute on Aging, Laboratory of Behavioral Neuroscience, Baltimore, Maryland, United States
| | - Bennett A. Landman
- Vanderbilt University, Department of Electrical and Computer Engineering, Nashville, Tennessee, United States
- Vanderbilt University, Department of Computer Science, Nashville, Tennessee, United States
- Vanderbilt University, Department of Biomedical Engineering, Nashville, Tennessee, United States
- Vanderbilt University Medical Center, Department of Radiology and Radiological Sciences, Nashville, Tennessee, United States
- Vanderbilt University, Vanderbilt University Institute of Imaging Science, Nashville, Tennessee, United States
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Wei YC, Kung YC, Lin CP, Chen CK, Lin C, Tseng RY, Chen YL, Huang WY, Chen PY, Chong ST, Shyu YC, Chang WC, Yeh CH. White matter alterations and their associations with biomarkers and behavior in subjective cognitive decline individuals: a fixel-based analysis. BEHAVIORAL AND BRAIN FUNCTIONS : BBF 2024; 20:12. [PMID: 38778325 PMCID: PMC11110460 DOI: 10.1186/s12993-024-00238-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Subjective cognitive decline (SCD) is an early stage of dementia linked to Alzheimer's disease pathology. White matter changes were found in SCD using diffusion tensor imaging, but there are known limitations in voxel-wise tensor-based methods. Fixel-based analysis (FBA) can help understand changes in white matter fibers and how they relate to neurodegenerative proteins and multidomain behavior data in individuals with SCD. METHODS Healthy adults with normal cognition were recruited in the Northeastern Taiwan Community Medicine Research Cohort in 2018-2022 and divided into SCD and normal control (NC). Participants underwent evaluations to assess cognitive abilities, mental states, physical activity levels, and susceptibility to fatigue. Neurodegenerative proteins were measured using an immunomagnetic reduction technique. Multi-shell diffusion MRI data were collected and analyzed using whole-brain FBA, comparing results between groups and correlating them with multidomain assessments. RESULTS The final enrollment included 33 SCD and 46 NC participants, with no significant differences in age, sex, or education between the groups. SCD had a greater fiber-bundle cross-section than NC (pFWE < 0.05) at bilateral frontal superior longitudinal fasciculus II (SLFII). These white matter changes correlate negatively with plasma Aβ42 level (r = -0.38, p = 0.01) and positively with the AD8 score for subjective cognitive complaints (r = 0.42, p = 0.004) and the Hamilton Anxiety Rating Scale score for the degree of anxiety (Ham-A, r = 0.35, p = 0.019). The dimensional analysis of FBA metrics and blood biomarkers found positive correlations of plasma neurofilament light chain with fiber density at the splenium of corpus callosum (pFWE < 0.05) and with fiber-bundle cross-section at the right thalamus (pFWE < 0.05). Further examination of how SCD grouping interacts between the correlations of FBA metrics and multidomain assessments showed interactions between the fiber density at the corpus callosum with letter-number sequencing cognitive score (pFWE < 0.01) and with fatigue to leisure activities (pFWE < 0.05). CONCLUSION Based on FBA, our investigation suggests white matter structural alterations in SCD. The enlargement of SLFII's fiber cross-section is linked to plasma Aβ42 and neuropsychiatric symptoms, which suggests potential early axonal dystrophy associated with Alzheimer's pathology in SCD. The splenium of the corpus callosum is also a critical region of axonal degeneration and cognitive alteration for SCD.
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Affiliation(s)
- Yi-Chia Wei
- Department of Neurology, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Yi-Chia Kung
- Department of Radiology, Tri-Service General Hospital, National Defense Medical Center, Taipei, 114, Taiwan
| | - Ching-Po Lin
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan
| | - Chih-Ken Chen
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
- Department of Psychiatry, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
| | - Chemin Lin
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
- Department of Psychiatry, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
| | - Rung-Yu Tseng
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan, 333, Taiwan
| | - Yao-Liang Chen
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan, 333, Taiwan
- Department of Radiology, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
| | - Wen-Yi Huang
- Department of Neurology, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
| | - Pin-Yuan Chen
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, 333, Taiwan
- Department of Neurosurgery, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
| | - Shin-Tai Chong
- Institute of Neuroscience, National Yang Ming Chiao Tung University, Taipei, 112, Taiwan
| | - Yu-Chiau Shyu
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung, 204, Taiwan
- Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, 333, Taiwan
| | - Wei-Chou Chang
- Department of Radiology, Tri-Service General Hospital, National Defense Medical Center, Taipei, 114, Taiwan
| | - Chun-Hung Yeh
- Department of Medical Imaging and Radiological Sciences, Chang Gung University, Taoyuan, 333, Taiwan.
- Department of Psychiatry, Chang Gung Memorial Hospital at Linkou, Taoyuan, 333, Taiwan.
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Yu X, Tang Y, Yang Q, Lee HH, Bao S, Huo Y, Landman BA. Enhancing Hierarchical Transformers for Whole Brain Segmentation with Intracranial Measurements Integration. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2024; 12930:129300K. [PMID: 39220623 PMCID: PMC11364374 DOI: 10.1117/12.3009084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Whole brain segmentation with magnetic resonance imaging (MRI) enables the non-invasive measurement of brain regions, including total intracranial volume (TICV) and posterior fossa volume (PFV). Enhancing the existing whole brain segmentation methodology to incorporate intracranial measurements offers a heightened level of comprehensiveness in the analysis of brain structures. Despite its potential, the task of generalizing deep learning techniques for intracranial measurements faces data availability constraints due to limited manually annotated atlases encompassing whole brain and TICV/PFV labels. In this paper, we enhancing the hierarchical transformer UNesT for whole brain segmentation to achieve segmenting whole brain with 133 classes and TICV/PFV simultaneously. To address the problem of data scarcity, the model is first pretrained on 4859 T1-weighted (T1w) 3D volumes sourced from 8 different sites. These volumes are processed through a multi-atlas segmentation pipeline for label generation, while TICV/PFV labels are unavailable. Subsequently, the model is finetuned with 45 T1w 3D volumes from Open Access Series Imaging Studies (OASIS) where both 133 whole brain classes and TICV/PFV labels are available. We evaluate our method with Dice similarity coefficients(DSC). We show that our model is able to conduct precise TICV/PFV estimation while maintaining the 132 brain regions performance at a comparable level. Code and trained model are available at: https://github.com/MASILab/UNesT/wholebrainSeg.
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Affiliation(s)
- Xin Yu
- Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Yucheng Tang
- Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
- Nvidia Corporation
| | - Qi Yang
- Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Ho Hin Lee
- Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Shunxing Bao
- Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yuankai Huo
- Computer Science, Vanderbilt University, Nashville, TN, USA
- Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Computer Science, Vanderbilt University, Nashville, TN, USA
- Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, USA
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Zu Z, Choi S, Zhao Y, Gao Y, Li M, Schilling KG, Ding Z, Gore JC. The missing third dimension-Functional correlations of BOLD signals incorporating white matter. SCIENCE ADVANCES 2024; 10:eadi0616. [PMID: 38277462 PMCID: PMC10816695 DOI: 10.1126/sciadv.adi0616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024]
Abstract
Correlations between magnetic resonance imaging (MRI) blood oxygenation level-dependent (BOLD) signals from pairs of gray matter areas are used to infer their functional connectivity, but they are unable to describe how white matter is engaged in brain networks. Recently, evidence that BOLD signals in white matter are robustly detectable and are modulated by neural activities has accumulated. We introduce a three-way correlation between BOLD signals from pairs of gray matter volumes (nodes) and white matter bundles (edges) to define the communication connectivity through each white matter bundle. Using MRI images from publicly available databases, we show, for example, that the three-way connectivity is influenced by age. By integrating functional MRI signals from white matter as a third component in network analyses, more comprehensive descriptions of brain function may be obtained.
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Affiliation(s)
- Zhongliang Zu
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Soyoung Choi
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yu Zhao
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yurui Gao
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Muwei Li
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kurt G. Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Zhaohua Ding
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37232, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN 37232, USA
| | - John C. Gore
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37232, USA
- Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37232, USA
- Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
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8
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Goeckner BD, Brett BL, Mayer AR, España LY, Banerjee A, Muftuler LT, Meier TB. Associations of prior concussion severity with brain microstructure using mean apparent propagator magnetic resonance imaging. Hum Brain Mapp 2024; 45:e26556. [PMID: 38158641 PMCID: PMC10789198 DOI: 10.1002/hbm.26556] [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: 03/16/2023] [Revised: 10/16/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024] Open
Abstract
Magnetic resonance imaging (MRI) diffusion studies have shown chronic microstructural tissue abnormalities in athletes with history of concussion, but with inconsistent findings. Concussions with post-traumatic amnesia (PTA) and/or loss of consciousness (LOC) have been connected to greater physiological injury. The novel mean apparent propagator (MAP) MRI is expected to be more sensitive to such tissue injury than the conventional diffusion tensor imaging. This study examined effects of prior concussion severity on microstructure with MAP-MRI. Collegiate-aged athletes (N = 111, 38 females; ≥6 months since most recent concussion, if present) completed semistructured interviews to determine the presence of prior concussion and associated injury characteristics, including PTA and LOC. MAP-MRI metrics (mean non-Gaussian diffusion [NG Mean], return-to-origin probability [RTOP], and mean square displacement [MSD]) were calculated from multi-shell diffusion data, then evaluated for associations with concussion severity through group comparisons in a primary model (athletes with/without prior concussion) and two secondary models (athletes with/without prior concussion with PTA and/or LOC, and athletes with/without prior concussion with LOC only). Bayesian multilevel modeling estimated models in regions of interest (ROI) in white matter and subcortical gray matter, separately. In gray matter, the primary model showed decreased NG Mean and RTOP in the bilateral pallidum and decreased NG Mean in the left putamen with prior concussion. In white matter, lower NG Mean with prior concussion was present in all ROI across all models and was further decreased with LOC. However, only prior concussion with LOC was associated with decreased RTOP and increased MSD across ROI. Exploratory analyses conducted separately in male and female athletes indicate associations in the primary model may differ by sex. Results suggest microstructural measures in gray matter are associated with a general history of concussion, while a severity-dependent association of prior concussion may exist in white matter.
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Affiliation(s)
- Bryna D. Goeckner
- Department of BiophysicsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Benjamin L. Brett
- Department of NeurosurgeryMedical College of WisconsinMilwaukeeWisconsinUSA
- Department of NeurologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Andrew R. Mayer
- The Mind Research Network/Lovelace Biomedical and Environmental Research InstituteAlbuquerqueNew MexicoUSA
- Departments of Neurology and PsychiatryUniversity of New Mexico School of MedicineAlbuquerqueNew MexicoUSA
- Department of PsychologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Lezlie Y. España
- Department of NeurosurgeryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Anjishnu Banerjee
- Department of BiostatisticsMedical College of WisconsinMilwaukeeWisconsinUSA
| | - L. Tugan Muftuler
- Department of NeurosurgeryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Timothy B. Meier
- Department of NeurosurgeryMedical College of WisconsinMilwaukeeWisconsinUSA
- Department of Biomedical EngineeringMedical College of WisconsinMilwaukeeWisconsinUSA
- Department of Cell Biology, Neurobiology and AnatomyMedical College of WisconsinMilwaukeeWisconsinUSA
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9
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Liu W, Zhuo Z, Liu Y, Ye C. One-shot segmentation of novel white matter tracts via extensive data augmentation and adaptive knowledge transfer. Med Image Anal 2023; 90:102968. [PMID: 37729793 DOI: 10.1016/j.media.2023.102968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/24/2023] [Accepted: 09/11/2023] [Indexed: 09/22/2023]
Abstract
The use of convolutional neural networks (CNNs) has allowed accurate white matter (WM) tract segmentation on diffusion magnetic resonance imaging (dMRI). To train the CNN-based segmentation models, a large number of scans on which WM tracts are annotated need to be collected, and these annotated scans can be accumulated over a long period of time. However, when novel WM tracts that are different from existing annotated WM tracts are of interest, additional annotations are required for their segmentation. Due to the cost of manual annotations, methods have been developed for few-shot segmentation of novel WM tracts, where the segmentation knowledge is transferred from existing WM tracts to novel WM tracts and the amount of annotated data for novel WM tracts is reduced. Despite these developments, it is desirable to further reduce the amount of annotated data to the one-shot setting with a single annotated image. To address this problem, we develop an approach to one-shot segmentation of novel WM tracts. Our method follows the existing pretraining/fine-tuning framework that transfers segmentation knowledge from existing to novel WM tracts. First, as there is extremely scarce annotated data in the one-shot setting, we design several different data augmentation strategies so that extensive data augmentation can be performed to obtain extra synthetic training data. The data augmentation strategies are based on image masking and thus applicable to the one-shot setting. Second, to address overfitting and knowledge forgetting in the fine-tuning stage that can be more severe given limited training data, we propose an adaptive knowledge transfer strategy that selects the network weights to be updated. The data augmentation and adaptive knowledge transfer strategies are combined to train the segmentation model. Considering that the different data augmentation strategies can generate synthetic data that contain potentially conflicting information, we apply the data augmentation strategies separately, each leading to a different segmentation model. The results predicted by the different models are fused to produce the final segmentation. We validated our method on two brain dMRI datasets, including a public dataset and an in-house dataset. Different settings were considered for the validation, and the results show that the proposed method improves the one-shot segmentation of novel WM tracts.
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Affiliation(s)
- Wan Liu
- School of Integrated Circuits and Electronics, Beijing Institute of Technology, Beijing, China
| | - Zhizheng Zhuo
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yaou Liu
- Department of Radiology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Chuyang Ye
- School of Integrated Circuits and Electronics, Beijing Institute of Technology, Beijing, China.
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10
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Petersen MV, McIntyre CC. Comparison of Anatomical Pathway Models with Tractography Estimates of the Pallidothalamic, Cerebellothalamic, and Corticospinal Tracts. Brain Connect 2023; 13:237-246. [PMID: 36772800 PMCID: PMC10178936 DOI: 10.1089/brain.2022.0068] [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] [Indexed: 02/12/2023] Open
Abstract
Introduction: Models of structural connectivity in the human brain are typically simulated using tractographic approaches. However, the nonlinear fitting of anatomical pathway atlases to de novo subject brains represents a simpler alternative that is hypothesized to provide more anatomically realistic results. Therefore, the goal of this study was to perform a side-by-side comparison of the streamline estimates generated by either pathway atlas fits or tractographic reconstructions in the same subjects. Methods: Our analyses focused on reconstruction of the corticospinal tract (CST), cerebellothalamic (CBT), and pallidothalamic (PT) pathways using example datasets from the Human Connectome Project (HCP). We used MRtrix3 to explore whole brain, as well as manual seed-to-target, tractography approaches. In parallel, we performed nonlinear fits of an axonal pathway atlas to each HCP dataset using Advanced Normalization Tools (ANTs). Results: The different methods produced notably different estimates for each pathway in each subject. The fitted atlas pathways were highly stereotyped and exhibited low variability in their streamline trajectories. Manual tractography resulted in pathway estimates that generally corresponded with the fitted atlas pathways, but with a higher degree of variability in the individual streamlines. Pathway reconstructions derived from whole-brain tractography exhibited the highest degree of variability and struggled to create anatomically realistic representations for either the CBT or PT pathways. Conclusion: The speed, simplicity, reproducibility, and realism of anatomical pathway model fits makes them an appealing option for some forms of structural connectivity modeling in the human brain. Impact statement Axonal pathway modeling is an important component of deep brain stimulation (DBS) research studies that seek to identify the brain connections that are directly activated by stimulation. The corticospinal tract, cerebellothalamic (CBT), and pallidothalamic (PT) pathways are specifically relevant to the study of subthalamic DBS for the treatment of Parkinson's disease. Our results suggest that anatomical pathway model fits of the CBT and PT pathways to de novo subject brains represent a more anatomically realistic option than tractographic approaches when studying subthalamic DBS.
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Affiliation(s)
- Mikkel V. Petersen
- Center of Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Cameron C. McIntyre
- Department of Biomedical Engineering and Duke University, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University, Durham, North Carolina, USA
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11
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Chandio BQ, Olivetti E, Romero-Bascones D, Harezlak J, Garyfallidis E. BundleWarp, streamline-based nonlinear registration of white matter tracts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522802. [PMID: 36711974 PMCID: PMC9881938 DOI: 10.1101/2023.01.04.522802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Nonlinear registration plays a central role in most neuroimage analysis methods and pipelines, such as in tractography-based individual and group-level analysis methods. However, nonlinear registration is a non-trivial task, especially when dealing with tractography data that digitally represent the underlying anatomy of the brain's white matter. Furthermore, such process often changes the structure of the data, causing artifacts that can suppress the underlying anatomical and structural details. In this paper, we introduce BundleWarp, a novel and robust streamline-based nonlinear registration method for the registration of white matter tracts. BundleWarp intelligently warps two bundles while preserving the bundles' crucial topological features. BundleWarp has two main steps. The first step involves the solution of an assignment problem that matches corresponding streamlines from the two bundles (iterLAP step). The second step introduces streamline-specific point-based deformations while keeping the topology of the bundle intact (mlCPD step). We provide comparisons against streamline-based linear registration and image-based nonlinear registration methods. BundleWarp quantitatively and qualitatively outperforms both, and we show that BundleWarp can deform and, at the same time, preserve important characteristics of the original anatomical shape of the bundles. Results are shown on 1,728 pairs of bundle registrations across 27 different bundle types. In addition, we present an application of BundleWarp for quantifying bundle shape differences using the generated deformation fields.
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Affiliation(s)
- Bramsh Qamar Chandio
- Department of Intelligent Systems Engineering, Indiana University Bloomington, USA
| | | | - David Romero-Bascones
- Biomedical Engineering Department, Faculty of Engineering (MU-ENG), Mondragon Unibertsitatea, Spain
- Moorfields Eye Hospital NHS Foundation Trust, UK
| | - Jaroslaw Harezlak
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, USA
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12
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Conrad BN, Pollack C, Yeo DJ, Price GR. Structural and functional connectivity of the inferior temporal numeral area. Cereb Cortex 2022; 33:6152-6170. [PMID: 36587366 PMCID: PMC10183753 DOI: 10.1093/cercor/bhac492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 01/02/2023] Open
Abstract
A growing body of evidence suggests that in adults, there is a spatially consistent "inferior temporal numeral area" (ITNA) in the occipitotemporal cortex that appears to preferentially process Arabic digits relative to non-numerical symbols and objects. However, very little is known about why the ITNA is spatially segregated from regions that process other orthographic stimuli such as letters, and why it is spatially consistent across individuals. In the present study, we used diffusion-weighted imaging and functional magnetic resonance imaging to contrast structural and functional connectivity between left and right hemisphere ITNAs and a left hemisphere letter-preferring region. We found that the left ITNA had stronger structural and functional connectivity than the letter region to inferior parietal regions involved in numerical magnitude representation and arithmetic. Between hemispheres, the left ITNA showed stronger structural connectivity with the left inferior frontal gyrus (Broca's area), while the right ITNA showed stronger structural connectivity to the ipsilateral inferior parietal cortex and stronger functional coupling with the bilateral IPS. Based on their relative connectivity, our results suggest that the left ITNA may be more readily involved in mapping digits to verbal number representations, while the right ITNA may support the mapping of digits to quantity representations.
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Affiliation(s)
- Benjamin N Conrad
- Department of Psychology & Human Development, Peabody College, Vanderbilt University, 230 Appleton Place, Nashville, TN, 37203, USA
| | - Courtney Pollack
- Department of Psychology & Human Development, Peabody College, Vanderbilt University, 230 Appleton Place, Nashville, TN, 37203, USA
| | - Darren J Yeo
- Department of Psychology & Human Development, Peabody College, Vanderbilt University, 230 Appleton Place, Nashville, TN, 37203, USA.,Division of Psychology, School of Social Sciences, Nanyang Technological University, 48 Nanyang Avenue, Singapore, 639818
| | - Gavin R Price
- Department of Psychology & Human Development, Peabody College, Vanderbilt University, 230 Appleton Place, Nashville, TN, 37203, USA.,Department of Psychology, University of Exeter, Washington Singer Building Perry Road, Exeter, EX4 4QG, United Kingdom
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13
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Billot A, Thiebaut de Schotten M, Parrish TB, Thompson CK, Rapp B, Caplan D, Kiran S. Structural disconnections associated with language impairments in chronic post-stroke aphasia using disconnectome maps. Cortex 2022; 155:90-106. [PMID: 35985126 PMCID: PMC9623824 DOI: 10.1016/j.cortex.2022.06.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 09/14/2021] [Accepted: 06/10/2022] [Indexed: 11/16/2022]
Abstract
Inconsistent findings have been reported about the impact of structural disconnections on language function in post-stroke aphasia. This study investigated patterns of structural disconnections associated with chronic language impairments using disconnectome maps. Seventy-six individuals with post-stroke aphasia underwent a battery of language assessments and a structural MRI scan. Support-vector regression disconnectome-symptom mapping analyses were performed to examine the correlations between disconnectome maps, representing the probability of disconnection at each white matter voxel and different language scores. To further understand whether significant disconnections were primarily representing focal damage or a more extended network of seemingly preserved but disconnected areas beyond the lesion site, results were qualitatively compared to support-vector regression lesion-symptom mapping analyses. Part of the left white matter perisylvian network was similarly disconnected in 90% of the individuals with aphasia. Surrounding this common left perisylvian disconnectome, specific structural disconnections in the left fronto-temporo-parietal network were significantly associated with aphasia severity and with lower performance in auditory comprehension, syntactic comprehension, syntactic production, repetition and naming tasks. Auditory comprehension, repetition and syntactic processing deficits were related to disconnections in areas that overlapped with and extended beyond lesion sites significant in SVR-LSM analyses. In contrast, overall language abilities as measured by aphasia severity and naming seemed to be mostly explained by focal damage at the level of the insular and central opercular cortices, given the high overlap between SVR-DSM and SVR-LSM results for these scores. While focal damage seems to be sufficient to explain broad measures of language performance, the structural disconnections between language areas provide additional information on the neural basis of specific and persistent language impairments at the chronic stage beyond lesion volume. Leveraging routinely available clinical data, disconnectome mapping furthers our understanding of anatomical connectivity constraints that may limit the recovery of some language abilities in chronic post-stroke aphasia.
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Affiliation(s)
- Anne Billot
- Sargent College of Health & Rehabilitation Sciences, Boston University, Boston, MA, USA; School of Medicine, Boston University, Boston, MA, USA.
| | - Michel Thiebaut de Schotten
- Brain Connectivity and Behaviour Laboratory, Sorbonne Universities, Paris, France; Groupe d'Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives-UMR 5293, CNRS, CEA University of Bordeaux, Bordeaux, France
| | - Todd B Parrish
- Department of Radiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cynthia K Thompson
- Department of Communication Sciences and Disorders, Northwestern University, Evanston, IL, USA
| | - Brenda Rapp
- Department of Cognitive Science, Johns Hopkins University, Baltimore, MD, USA
| | - David Caplan
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Swathi Kiran
- Sargent College of Health & Rehabilitation Sciences, Boston University, Boston, MA, USA
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14
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Yeh FC. Population-based tract-to-region connectome of the human brain and its hierarchical topology. Nat Commun 2022; 13:4933. [PMID: 35995773 PMCID: PMC9395399 DOI: 10.1038/s41467-022-32595-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 08/05/2022] [Indexed: 12/25/2022] Open
Abstract
Connectome maps region-to-region connectivities but does not inform which white matter pathways form the connections. Here we constructed a population-based tract-to-region connectome to fill this information gap. The constructed connectome quantifies the population probability of a white matter tract innervating a cortical region. The results show that ~85% of the tract-to-region connectome entries are consistent across individuals, whereas the remaining (~15%) have substantial individual differences requiring individualized mapping. Further hierarchical clustering on cortical regions revealed dorsal, ventral, and limbic networks based on the tract-to-region connective patterns. The clustering results on white matter bundles revealed the categorization of fiber bundle systems in the association pathways. This tract-to-region connectome provides insights into the connective topology between cortical regions and white matter bundles. The derived hierarchical relation further offers a categorization of gray and white matter structures. The brain connectome maps region-to-region connections but often ignores the role of the connecting pathways. Here, the authors mapped the tract-to-region relations to reveal the hierarchical relation of fiber bundles and dorsal, ventral, and limbic networks.
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Affiliation(s)
- Fang-Cheng Yeh
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA. .,Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
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15
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Yang Q, Hansen CB, Cai LY, Rheault F, Lee HH, Bao S, Chandio BQ, Williams O, Resnick SM, Garyfallidis E, Anderson AW, Descoteaux M, Schilling KG, Landman BA. Learning white matter subject-specific segmentation from structural MRI. Med Phys 2022; 49:2502-2513. [PMID: 35090192 PMCID: PMC9053869 DOI: 10.1002/mp.15495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 12/20/2021] [Accepted: 01/10/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Mapping brain white matter (WM) is essential for building an understanding of brain anatomy and function. Tractography-based methods derived from diffusion-weighted MRI (dMRI) are the principal tools for investigating WM. These procedures rely on time-consuming dMRI acquisitions that may not always be available, especially for legacy or time-constrained studies. To address this problem, we aim to generate WM tracts from structural magnetic resonance imaging (MRI) image by deep learning. METHODS Following recently proposed innovations in structural anatomical segmentation, we evaluate the feasibility of training multiply spatial localized convolution neural networks to learn context from fixed spatial patches from structural MRI on standard template. We focus on six widely used dMRI tractography algorithms (TractSeg, RecoBundles, XTRACT, Tracula, automated fiber quantification (AFQ), and AFQclipped) and train 125 U-Net models to learn these techniques from 3870 T1-weighted images from the Baltimore Longitudinal Study of Aging, the Human Connectome Project S1200 release, and scans acquired at Vanderbilt University. RESULTS The proposed framework identifies fiber bundles with high agreement against tractography-based pathways with a median Dice coefficient from 0.62 to 0.87 on a test cohort, achieving improved subject-specific accuracy when compared to population atlas-based methods. We demonstrate the generalizability of the proposed framework on three externally available datasets. CONCLUSIONS We show that patch-wise convolutional neural network can achieve robust bundle segmentation from T1w. We envision the use of this framework for visualizing the expected course of WM pathways when dMRI is not available.
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Affiliation(s)
- Qi Yang
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Colin B. Hansen
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Leon Y. Cai
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Francois Rheault
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Ho Hin Lee
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Shunxing Bao
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Bramsh Qamar Chandio
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, USA
| | - Owen Williams
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, Maryland, USA
| | - Susan M. Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Baltimore, Maryland, USA
| | - Eleftherios Garyfallidis
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, Indiana, USA,Program of Neuroscience, Indiana University, Bloomington, Indiana, USA
| | - Adam W. Anderson
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA,Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, Canada
| | - Kurt G. Schilling
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Centre, Nashville, Tennessee, USA,Department of Radiology and Radiological Sciences, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
| | - Bennett A. Landman
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA,Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA,Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, Tennessee, USA,Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Centre, Nashville, Tennessee, USA,Department of Radiology and Radiological Sciences, Vanderbilt University Medical Centre, Nashville, Tennessee, USA
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16
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Rheault F, Bayrak RG, Wang X, Schilling KG, Greer JM, Hansen CB, Kerley C, Ramadass K, Remedios LW, Blaber JA, Williams O, Beason-Held LL, Resnick SM, Rogers BP, Landman BA. TractEM: Evaluation of protocols for deterministic tractography white matter atlas. Magn Reson Imaging 2022; 85:44-56. [PMID: 34666161 PMCID: PMC8629950 DOI: 10.1016/j.mri.2021.10.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/25/2021] [Accepted: 10/12/2021] [Indexed: 01/03/2023]
Abstract
Reproducible identification of white matter pathways across subjects is essential for the study of structural connectivity of the human brain. One of the key challenges is anatomical differences between subjects and human rater subjectivity in labeling. Labeling white matter regions of interest presents many challenges due to the need to integrate both local and global information. Clearly communicating the manual processes to capture this information is cumbersome, yet essential to lay a solid foundation for comprehensive atlases. Segmentation protocols must be designed so the interpretation of the requested tasks as well as locating structural landmarks is anatomically accurate, intuitive and reproducible. In this work, we quantified the reproducibility of a first iteration of an open/public multi-bundle segmentation protocol. This allowed us to establish a baseline for its reproducibility as well as to identify the limitations for future iterations. The protocol was tested/evaluated on both typical 3 T research acquisition Baltimore Longitudinal Study of Aging (BLSA) and high-acquisition quality Human Connectome Project (HCP) datasets. The results show that a rudimentary protocol can produce acceptable intra-rater and inter-rater reproducibility. However, this work highlights the difficulty in generalizing reproducible results and the importance of reaching consensus on anatomical description of white matter pathways. The protocol has been made available in open source to improve generalizability and reliability in collaboration. The goal is to improve upon the first iteration and initiate a discussion on the anatomical validity (or lack thereof) of some bundle definitions and the importance of reproducibility of tractography segmentation.
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Affiliation(s)
- Francois Rheault
- Electrical Engineering, Vanderbilt University, Nashville, TN, USA.
| | - Roza G Bayrak
- Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Xuan Wang
- Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Kurt G Schilling
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA
| | - Jasmine M Greer
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA
| | - Colin B Hansen
- Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Cailey Kerley
- Electrical Engineering, Vanderbilt University, Nashville, TN, USA
| | | | | | | | - Owen Williams
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Lori L Beason-Held
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Baxter P Rogers
- Vanderbilt University Institute of Imaging Science, Nashville, TN, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Electrical Engineering, Vanderbilt University, Nashville, TN, USA; Vanderbilt University Institute of Imaging Science, Nashville, TN, USA; Computer Science, Vanderbilt University, Nashville, TN, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA
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