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Patel J, Schöttner M, Tarun A, Tourbier S, Alemán-Gómez Y, Hagmann P, Bolton TAW. Modeling the impact of MRI acquisition bias on structural connectomes: Harmonizing structural connectomes. Netw Neurosci 2024; 8:623-652. [PMID: 39355442 PMCID: PMC11340995 DOI: 10.1162/netn_a_00368] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/26/2024] [Indexed: 10/03/2024] Open
Abstract
One way to increase the statistical power and generalizability of neuroimaging studies is to collect data at multiple sites or merge multiple cohorts. However, this usually comes with site-related biases due to the heterogeneity of scanners and acquisition parameters, negatively impacting sensitivity. Brain structural connectomes are not an exception: Being derived from T1-weighted and diffusion-weighted magnetic resonance images, structural connectivity is impacted by differences in imaging protocol. Beyond minimizing acquisition parameter differences, removing bias with postprocessing is essential. In this work we create, from the exhaustive Human Connectome Project Young Adult dataset, a resampled dataset of different b-values and spatial resolutions, modeling a cohort scanned across multiple sites. After demonstrating the statistical impact of acquisition parameters on connectivity, we propose a linear regression with explicit modeling of b-value and spatial resolution, and validate its performance on separate datasets. We show that b-value and spatial resolution affect connectivity in different ways and that acquisition bias can be reduced using a linear regression informed by the acquisition parameters while retaining interindividual differences and hence boosting fingerprinting performance. We also demonstrate the generative potential of our model, and its generalization capability in an independent dataset reflective of typical acquisition practices in clinical settings.
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Affiliation(s)
- Jagruti Patel
- Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
| | - Mikkel Schöttner
- Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
| | - Anjali Tarun
- Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
| | - Sebastien Tourbier
- Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
| | - Yasser Alemán-Gómez
- Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
| | - Patric Hagmann
- Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
| | - Thomas A W Bolton
- Department of Radiology, Lausanne University Hospital and University of Lausanne (CHUV-UNIL), Lausanne, Switzerland
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2
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Xu X, Sun C, Yu H, Yan G, Zhu Q, Kong X, Pan Y, Xu H, Zheng T, Zhou C, Wang Y, Xiao J, Chen R, Li M, Zhang S, Hu H, Zou Y, Wang J, Wang G, Wu D. Site effects in multisite fetal brain MRI: morphological insights into early brain development. Eur Radiol 2024:10.1007/s00330-024-11084-w. [PMID: 39299951 DOI: 10.1007/s00330-024-11084-w] [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: 03/21/2024] [Revised: 06/06/2024] [Accepted: 08/26/2024] [Indexed: 09/22/2024]
Abstract
OBJECTIVE To evaluate multisite effects on fetal brain MRI. Specifically, to identify crucial acquisition factors affecting fetal brain structural measurements and developmental patterns, while assessing the effectiveness of existing harmonization methods in mitigating site effects. MATERIALS AND METHODS Between May 2017 and March 2022, T2-weighted fast spin-echo sequences in-utero MRI were performed on healthy fetuses from retrospectively recruited pregnant volunteers on four different scanners at four sites. A generalized additive model (GAM) was used to quantitatively assess site effects, including field strength (FS), manufacturer (M), in-plane resolution (R), and slice thickness (ST), on subcortical volume and cortical morphological measurements, including cortical thickness, curvature, and sulcal depth. Growth models were selected to elucidate the developmental trajectories of these morphological measurements. Welch's test was performed to evaluate the influence of site effects on developmental trajectories. The comBat-GAM harmonization method was applied to mitigate site-related biases. RESULTS The final analytic sample consisted of 340 MRI scans from 218 fetuses (mean GA, 30.1 weeks ± 4.4 [range, 21.7-40 weeks]). GAM results showed that lower FS and lower spatial resolution led to overestimations in selected brain regions of subcortical volumes and cortical morphological measurements. Only the peak cortical thickness in developmental trajectories was significantly influenced by the effects of FS and R. Notably, ComBat-GAM harmonization effectively removed site effects while preserving developmental patterns. CONCLUSION Our findings pinpointed the key acquisition factors in in-utero fetal brain MRI and underscored the necessity of data harmonization when pooling multisite data for fetal brain morphology investigations. KEY POINTS Question How do specific site MRI acquisition factors affect fetal brain imaging? Finding Lower FS and spatial resolution overestimated subcortical volumes and cortical measurements. Cortical thickness in developmental trajectories was influenced by FS and in-plane resolution. Clinical relevance This study provides important guidelines for the fetal MRI community when scanning fetal brains and underscores the necessity of data harmonization of cross-center fetal studies.
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Affiliation(s)
- Xinyi Xu
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Cong Sun
- Department of Radiology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hong Yu
- Dalian Municipal Women and Children's Medical Center (Group), Dalian, China
| | - Guohui Yan
- Department of Radiology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qingqing Zhu
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xianglei Kong
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yibin Pan
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Haoan Xu
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Tianshu Zheng
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Chi Zhou
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Yutian Wang
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Jiaxin Xiao
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
- School of Biomedical Engineering & Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Ruike Chen
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Mingyang Li
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China
| | - Songying Zhang
- Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province, Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Hongjie Hu
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Yu Zou
- Department of Radiology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jingshi Wang
- Dalian Municipal Women and Children's Medical Center (Group), Dalian, China.
| | - Guangbin Wang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Dan Wu
- Department of Biomedical Engineering, College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, China.
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3
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Zhou Z, Fischl B, Aganj I. Harmonization of Structural Brain Connectivity through Distribution Matching. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.05.611489. [PMID: 39314357 PMCID: PMC11418962 DOI: 10.1101/2024.09.05.611489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
The increasing prevalence of multi-site diffusion-weighted magnetic resonance imaging (dMRI) studies potentially offers enhanced statistical power for investigating brain structure. However, these studies face challenges due to variations in scanner hardware and acquisition protocols. While several methods exist for dMRI data harmonization, few specifically address structural brain connectivity. We introduce a new distribution-matching approach to harmonizing structural brain connectivity across different sites and scanners. We evaluate our method using structural brain connectivity data from two distinct datasets of OASIS-3 and ADNI-2, comparing its performance to the widely used ComBat method. Our approach is meant to align the statistical properties of connectivity data from these two datasets. We examine the impact of harmonization on the correlation of brain connectivity with the Mini-Mental State Examination score and age. Our results demonstrate that our distribution-matching technique more effectively harmonizes structural brain connectivity, often producing stronger and more significant correlations compared to ComBat. Qualitative assessments illustrate the desired distributional alignment of ADNI-2 with OASIS-3, while quantitative evaluations confirm robust performance. This work contributes to the growing field of dMRI harmonization, potentially improving the reliability and comparability of structural connectivity studies that combine data from different sources in neuroscientific and clinical research.
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Affiliation(s)
- Zhen Zhou
- Athinoula A. Martinos Center for Biomedical Imaging, Radiology Department, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bruce Fischl
- Athinoula A. Martinos Center for Biomedical Imaging, Radiology Department, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Iman Aganj
- Athinoula A. Martinos Center for Biomedical Imaging, Radiology Department, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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4
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Poortman SR, Barendse ME, Setiaman N, van den Heuvel MP, de Lange SC, Hillegers MH, van Haren NE. Age Trajectories of the Structural Connectome in Child and Adolescent Offspring of Individuals With Bipolar Disorder or Schizophrenia. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100336. [PMID: 39040431 PMCID: PMC11260845 DOI: 10.1016/j.bpsgos.2024.100336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/08/2024] [Accepted: 05/09/2024] [Indexed: 07/24/2024] Open
Abstract
Background Offspring of parents with severe mental illness (e.g., bipolar disorder or schizophrenia) are at elevated risk of developing psychiatric illness owing to both genetic predisposition and increased burden of environmental stress. Emerging evidence indicates a disruption of brain network connectivity in young offspring of patients with bipolar disorder and schizophrenia, but the age trajectories of these brain networks in this high-familial-risk population remain to be elucidated. Methods A total of 271 T1-weighted and diffusion-weighted scans were obtained from 174 offspring of at least 1 parent diagnosed with bipolar disorder (n = 74) or schizophrenia (n = 51) and offspring of parents without severe mental illness (n = 49). The age range was 8 to 23 years; 97 offspring underwent 2 scans. Anatomical brain networks were reconstructed into structural connectivity matrices. Network analysis was performed to investigate anatomical brain connectivity. Results Offspring of parents with schizophrenia had differential trajectories of connectivity strength and clustering compared with offspring of parents with bipolar disorder and parents without severe mental illness, of global efficiency compared with offspring of parents without severe mental illness, and of local connectivity compared with offspring of parents with bipolar disorder. Conclusions The findings of this study suggest that familial high risk of schizophrenia is related to deviations in age trajectories of global structural connectome properties and local connectivity strength.
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Affiliation(s)
- Simon R. Poortman
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Marjolein E.A. Barendse
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Sophia Children’s Hospital, Rotterdam, the Netherlands
| | - Nikita Setiaman
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Sophia Children’s Hospital, Rotterdam, the Netherlands
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, the Netherlands
| | - Martijn P. van den Heuvel
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Child Psychiatry, Amsterdam University Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Siemon C. de Lange
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Sleep and Cognition, Netherlands Institute for Neuroscience, an institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, the Netherlands
| | - Manon H.J. Hillegers
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Sophia Children’s Hospital, Rotterdam, the Netherlands
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, the Netherlands
| | - Neeltje E.M. van Haren
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Center, Sophia Children’s Hospital, Rotterdam, the Netherlands
- Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, the Netherlands
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5
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Newlin NR, Kim ME, Kanakaraj P, Yao T, Hohman T, Pechman KR, Beason-Held LL, Resnick SM, Archer D, Jefferson A, Landman BA, Moyer D. MidRISH: Unbiased harmonization of rotationally invariant harmonics of the diffusion signal. Magn Reson Imaging 2024; 111:113-119. [PMID: 38537892 PMCID: PMC11283839 DOI: 10.1016/j.mri.2024.03.033] [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: 08/09/2023] [Revised: 03/09/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
Data harmonization is necessary for removing confounding effects in multi-site diffusion image analysis. One such harmonization method, LinearRISH, scales rotationally invariant spherical harmonic (RISH) features from one site ("target") to the second ("reference") to reduce confounding scanner effects. However, reference and target site designations are not arbitrary and resultant diffusion metrics (fractional anisotropy, mean diffusivity) are biased by this choice. In this work we propose MidRISH: rather than scaling reference RISH features to target RISH features, we project both sites to a mid-space. We validate MidRISH with the following experiments: harmonizing scanner differences from 37 matched patients free of cognitive impairment, and harmonizing acquisition and study differences on 117 matched patients free of cognitive impairment. We find that MidRISH reduces bias of reference selection while preserving harmonization efficacy of LinearRISH. Users should be cautious when performing LinearRISH harmonization. To select a reference site is to choose diffusion metric effect-size. Our proposed method eliminates the bias-inducing site selection step.
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Affiliation(s)
- Nancy R Newlin
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA.
| | - Michael E Kim
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | | | - Tianyuan Yao
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Timothy Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kimberly R Pechman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, 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
| | - Derek Archer
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Angela Jefferson
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA; Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
| | - Daniel Moyer
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
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6
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Takemura H, Kruper JA, Miyata T, Rokem A. Tractometry of Human Visual White Matter Pathways in Health and Disease. Magn Reson Med Sci 2024; 23:316-340. [PMID: 38866532 PMCID: PMC11234945 DOI: 10.2463/mrms.rev.2024-0007] [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: 06/14/2024] Open
Abstract
Diffusion-weighted MRI (dMRI) provides a unique non-invasive view of human brain tissue properties. The present review article focuses on tractometry analysis methods that use dMRI to assess the properties of brain tissue within the long-range connections comprising brain networks. We focus specifically on the major white matter tracts that convey visual information. These connections are particularly important because vision provides rich information from the environment that supports a large range of daily life activities. Many of the diseases of the visual system are associated with advanced aging, and tractometry of the visual system is particularly important in the modern aging society. We provide an overview of the tractometry analysis pipeline, which includes a primer on dMRI data acquisition, voxelwise model fitting, tractography, recognition of white matter tracts, and calculation of tract tissue property profiles. We then review dMRI-based methods for analyzing visual white matter tracts: the optic nerve, optic tract, optic radiation, forceps major, and vertical occipital fasciculus. For each tract, we review background anatomical knowledge together with recent findings in tractometry studies on these tracts and their properties in relation to visual function and disease. Overall, we find that measurements of the brain's visual white matter are sensitive to a range of disorders and correlate with perceptual abilities. We highlight new and promising analysis methods, as well as some of the current barriers to progress toward integration of these methods into clinical practice. These barriers, such as variability in measurements between protocols and instruments, are targets for future development.
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Affiliation(s)
- Hiromasa Takemura
- Division of Sensory and Cognitive Brain Mapping, Department of System Neuroscience, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Hayama, Kanagawa, Japan
- Center for Information and Neural Networks (CiNet), Advanced ICT Research Institute, National Institute of Information and Communications Technology, Suita, Osaka, Japan
| | - John A Kruper
- Department of Psychology and eScience Institute, University of Washington, Seattle, WA, USA
| | - Toshikazu Miyata
- Division of Sensory and Cognitive Brain Mapping, Department of System Neuroscience, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
- Center for Information and Neural Networks (CiNet), Advanced ICT Research Institute, National Institute of Information and Communications Technology, Suita, Osaka, Japan
| | - Ariel Rokem
- Department of Psychology and eScience Institute, University of Washington, Seattle, WA, USA
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7
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Bano W, Pulli E, Cantonas L, Sorsa A, Hämäläinen J, Karlsson H, Karlsson L, Saukko E, Sainio T, Peuna A, Korja R, Aro M, Leppänen PH, Tuulari JJ, Merisaari H. Implementing ABCD study Ⓡ MRI sequences for multi-site cohort studies: Practical guide to necessary steps, preprocessing methods, and challenges. MethodsX 2024; 12:102789. [PMID: 38966716 PMCID: PMC11223117 DOI: 10.1016/j.mex.2024.102789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/31/2024] [Indexed: 07/06/2024] Open
Abstract
Large multi-site studies that combine magnetic resonance imaging (MRI) data across research sites present exceptional opportunities to advance neuroscience research. However, scanner or site variability and non-standardised image acquisition protocols, data processing and analysis pipelines can adversely affect the reliability and repeatability of MRI derived brain measures. We implemented a standardised MRI protocol based on that used in the Adolescent Brain Cognition Development (ABCD)Ⓡ study in two sites, and across four MRI scanners. Twice repeated measurements of a single healthy volunteer were obtained in two sites and in four 3T MRI scanners (vendors: Siemens, Philips, and GE). Imaging data included anatomical scans (T1 weighted, T2 weighted), diffusion weighted imaging (DWI) and resting state functional MRI (rs-fMRI). Standardised containerized pipelines were utilised to pre-process the data and different image quality metrics and test-retest variability of different brain metrics were evaluated. The implementation of the MRI protocols was possible with minor adjustments in acquisition (e.g. repetition time (TR), higher b-values) and exporting (DICOM formats) of images due to different technical performance of the scanners. This study provides practical insights into the implementation of standardised sequences and data processing for multisite studies, showcase the benefits of containerised preprocessing tools, and highlights the need for careful optimisation of multisite image acquisition.
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Affiliation(s)
- Wajiha Bano
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
| | - Elmo Pulli
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
| | - Lucia Cantonas
- Department of Psychology and Education, University of Jyväskylä, Finland
| | - Aino Sorsa
- Department of Psychology and Education, University of Jyväskylä, Finland
| | - Jarmo Hämäläinen
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
- Department of Psychology and Education, University of Jyväskylä, Finland
| | - Hasse Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
- Department of Clinical Medicine, Unit of Public Health, University of Turku, Finland
- Department of Child Psychiatry, Turku University Hospital, Turku, Finland
| | - Linnea Karlsson
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
- Department of Clinical Medicine, Unit of Public Health, University of Turku, Finland
- Department of Child Psychiatry, Turku University Hospital, Turku, Finland
| | - Ekaterina Saukko
- Department of Radiology, Turku University Hospital and University of Turku, Turku, Finland
| | - Teija Sainio
- Department of Medical Physics, Turku University Hospital and University of Turku, Turku, Finland
| | - Arttu Peuna
- Department of Diagnostic Services, Hospital Nova of Central Finland, Wellbeing Services County of Central Finland, Finland
| | - Riikka Korja
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
- Department of Psychology and Speech-Pathology, University of Turku, Finland
| | - Mikko Aro
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
- Department of Education, University of Jyväskylä, Finland
| | - Paavo H.T. Leppänen
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
- Department of Psychology and Education, University of Jyväskylä, Finland
| | - Jetro J. Tuulari
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
- Turku Collegium for Science and Medicine, University of Turku, Turku, Finland
- Department of Psychiatry, Turku University Hospital and University of Turku, Turku, Finland
| | - Harri Merisaari
- FinnBrain Birth Cohort Study, Turku Brain and Mind Center, Department of Clinical Medicine, University of Turku, Turku, Finland
- Centre for Population Health Research, Turku University Hospital and University of Turku, Turku, Finland
- Centre of Excellence in Learning Dynamics and Intervention Research (InterLearn), University of Jyväskylä and University of Turku, Finland
- Department of Radiology, Turku University Hospital and University of Turku, Turku, Finland
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8
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Saito Y, Kamagata K, Andica C, Maikusa N, Uchida W, Takabayashi K, Yoshida S, Hagiwara A, Fujita S, Akashi T, Wada A, Irie R, Shimoji K, Hori M, Kamiya K, Koike S, Hayashi T, Aoki S. Traveling Subject-Informed Harmonization Increases Reliability of Brain Diffusion Tensor and Neurite Mapping. Aging Dis 2023:AD.2023.1020. [PMID: 38029401 DOI: 10.14336/ad.2023.1020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Diffusion-weighted magnetic resonance imaging (dMRI) of brain has helped elucidate the microstructural changes of psychiatric and neurodegenerative disorders. Inconsistency between MRI models has hampered clinical application of dMRI-based metrics. Using harmonized dMRI data of 300 scans from 69 traveling subjects (TS) scanning the same individuals at multiple conditions with 13 MRI models and 2 protocols, the widely-used metrics such as diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) were evaluated before and after harmonization with a combined association test (ComBat) or TS-based general linear model (TS-GLM). Results showed that both ComBat and TS-GLM significantly reduced the effects of the MRI site, model, and protocol for diffusion metrics while maintaining the intersubject biological effects. The harmonization power of TS-GLM based on TS data model is more powerful than that of ComBat. In conclusion, our research demonstrated that although ComBat and TS-GLM harmonization approaches were effective at reducing the scanner effects of the site, model, and protocol for DTI and NODDI metrics in WM, they exhibited high retainability of biological effects. Therefore, we suggest that, after harmonizing DTI and NODDI metrics, a multisite study with large cohorts can accurately detect small pathological changes by retaining pathological effects.
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Affiliation(s)
- Yuya Saito
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
| | - Koji Kamagata
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
| | - Christina Andica
- Faculty of Health Data Science, Juntendo University, Chiba, Japan
| | - Norihide Maikusa
- Center for Evolutionary Cognitive Sciences, Graduate School of Art and Sciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Uchida
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
| | - Kaito Takabayashi
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
| | - Seina Yoshida
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
- Department of Radiological Sciences, Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, Japan
| | - Akifumi Hagiwara
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
| | - Shohei Fujita
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
- Department of Radiology, The University of Tokyo, Tokyo, Japan
| | - Toshiaki Akashi
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
| | - Akihiko Wada
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
| | - Ryusuke Irie
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
| | - Keigo Shimoji
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
- Faculty of Health Data Science, Juntendo University, Chiba, Japan
| | - Masaaki Hori
- Department of Radiology, Toho University Omori Medical Center, Tokyo Japan
| | - Kouhei Kamiya
- Department of Radiology, Toho University Omori Medical Center, Tokyo Japan
| | - Shinsuke Koike
- Center for Evolutionary Cognitive Sciences, Graduate School of Art and Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Hayashi
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Japan
- Department of Brain Connectomics, Kyoto University Graduate School of Medicine
| | - Shigeki Aoki
- Department of Radiology, Juntendo University Graduate School of Medicine, Tokyo Japan
- Faculty of Health Data Science, Juntendo University, Chiba, Japan
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9
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Chen Q, Abrigo J, Deng M, Shi L, Wang YX, Chu WC. Structural Network Topology Reveals Higher Brain Resilience in Individuals with Preclinical Alzheimer's Disease. Brain Connect 2023; 13:553-562. [PMID: 37551987 PMCID: PMC10771874 DOI: 10.1089/brain.2023.0013] [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: 08/09/2023] Open
Abstract
Introduction: The diagnosis of Alzheimer's disease (AD) requires the presence of amyloid and tau pathology, but it remains unclear how they affect the structural network in the pre-clinical stage. We aimed to assess differences in topological properties in cognitively normal (CN) individuals with varying levels of amyloid and tau pathology, as well as their association with AD pathology burden. Methods: A total of 68 CN individuals were included and stratified by normal/abnormal (-/+) amyloid (A) and tau (T) status based on positron emission tomography results, yielding three groups: A-T- (n = 19), A+T- (n = 28), and A+T+ (n = 21). Topological properties were measured from structural connectivity. Group differences and correlations with A and T were evaluated. Results: Compared with the A-T- group, the A+T+ group exhibited changes in the structural network topology. At the global level, higher assortativity was shown in the A+T+ group and was correlated with greater tau burden (r = 0.29, p = 0.02), while no difference in global efficiency was found across the three groups. At the local level, the A+T+ group showed disrupted topological properties in the left hippocampus compared with the A-T- group, characterized by lower local efficiency (p < 0.01) and a lower clustering coefficient (p = 0.014). Conclusions: The increased linkage in the higher level architecture of the white matter network reflected by assortativity may indicate increased brain resilience in the early pathological state. Our results encourage further investigation of the topological properties of the structural network in pre-clinical AD.
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Affiliation(s)
- Qianyun Chen
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jill Abrigo
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Min Deng
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lin Shi
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yi-Xiang Wang
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Winnie C.W. Chu
- Department of Imaging and Interventional Radiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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10
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Newlin NR, Kim ME, Kanakaraj P, Yao T, Hohman T, Pechman KR, Beason-Held LL, Resnick SM, Archer D, Jefferson A, Landman BA, Moyer D. MidRISH: Unbiased harmonization of rotationally invariant harmonics of the diffusion signal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.12.553099. [PMID: 37645973 PMCID: PMC10462069 DOI: 10.1101/2023.08.12.553099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Objective Data harmonization is necessary for removing confounding effects in multi-site diffusion image analysis. One such harmonization method, LinearRISH, scales rotationally invariant spherical harmonic (RISH) features from one site ("target") to the second ("reference") to reduce confounding scanner effects. However, reference and target site designations are not arbitrary and resultant diffusion metrics (fractional anisotropy, mean diffusivity) are biased by this choice. In this work we propose MidRISH: rather than scaling reference RISH features to target RISH features, we project both sites to a mid-space. Methods We validate MidRISH with the following experiments: harmonizing scanner differences from 37 matched patients free of cognitive impairment, and harmonizing acquisition and study differences on 117 matched patients free of cognitive impairment. Conclusion MidRISH reduces bias of reference selection while preserving harmonization efficacy of LinearRISH. Significance Users should be cautious when performing LinearRISH harmonization. To select a reference site is to choose diffusion metric effect-size. Our proposed method eliminates the bias-inducing site selection step.
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Affiliation(s)
- Nancy R Newlin
- Department of Computer Science at Vanderbilt University, Nashville, TN, USA
| | - Michael E Kim
- Department of Computer Science at Vanderbilt University, Nashville, TN, USA
| | | | - Tianyuan Yao
- Department of Computer Science at Vanderbilt University, Nashville, TN, USA
| | - Timothy Hohman
- VMAC, VUMC, Nashville, TN, USA and Vanderbilt University, Nashville, TN, 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
| | - Derek Archer
- VMAC, VUMC, Nashville, TN, USA and Vanderbilt University, Nashville, TN, USA
| | - Angela Jefferson
- VMAC, VUMC, Nashville, TN, USA and Vanderbilt University, Nashville, TN, USA
| | - Bennett A Landman
- Department of Computer Science at Vanderbilt University, Nashville, TN, USA
| | - Daniel Moyer
- Department of Computer Science at Vanderbilt University, Nashville, TN, USA
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11
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Hu F, Chen AA, Horng H, Bashyam V, Davatzikos C, Alexander-Bloch A, Li M, Shou H, Satterthwaite TD, Yu M, Shinohara RT. Image harmonization: A review of statistical and deep learning methods for removing batch effects and evaluation metrics for effective harmonization. Neuroimage 2023; 274:120125. [PMID: 37084926 PMCID: PMC10257347 DOI: 10.1016/j.neuroimage.2023.120125] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 04/23/2023] Open
Abstract
Magnetic resonance imaging and computed tomography from multiple batches (e.g. sites, scanners, datasets, etc.) are increasingly used alongside complex downstream analyses to obtain new insights into the human brain. However, significant confounding due to batch-related technical variation, called batch effects, is present in this data; direct application of downstream analyses to the data may lead to biased results. Image harmonization methods seek to remove these batch effects and enable increased generalizability and reproducibility of downstream results. In this review, we describe and categorize current approaches in statistical and deep learning harmonization methods. We also describe current evaluation metrics used to assess harmonization methods and provide a standardized framework to evaluate newly-proposed methods for effective harmonization and preservation of biological information. Finally, we provide recommendations to end-users to advocate for more effective use of current methods and to methodologists to direct future efforts and accelerate development of the field.
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Affiliation(s)
- Fengling Hu
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States.
| | - Andrew A Chen
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States
| | - Hannah Horng
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States
| | - Vishnu Bashyam
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Christos Davatzikos
- Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States; Penn-CHOP Lifespan Brain Institute, United States; Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, United States
| | - Mingyao Li
- Statistical Center for Single-Cell and Spatial Genomics, Perelman School of Medicine, University of Pennsylvania, United States
| | - Haochang Shou
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States; Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
| | - Theodore D Satterthwaite
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States; Penn-CHOP Lifespan Brain Institute, United States; The Penn Lifespan Informatics and Neuroimaging Center, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, United States
| | - Meichen Yu
- Indiana Alzheimer's Disease Research Center, Indiana University School of Medicine, United States
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Endeavor (PennSIVE), Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, 423 Guardian Dr, Philadelphia, PA 19104, United States; Center for Biomedical Image Computing and Analytics (CBICA), Perelman School of Medicine, United States
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12
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Zhang L, Pini L, Corbetta M. Different MRI structural processing methods do not impact functional connectivity computation. Sci Rep 2023; 13:8589. [PMID: 37237072 DOI: 10.1038/s41598-023-34645-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Resting-state functional magnetic resonance imaging (rs-fMRI) has become an increasingly popular technique. This technique can assess several features of brain connectivity, such as inter-regional temporal correlation (functional connectivity), from which graph measures of network organization can be derived. However, these measures are prone to a certain degree of variability depending on the analytical steps during preprocessing. Many studies have investigated the effect of different preprocessing steps on functional connectivity measures; however, no study investigated whether different structural reconstructions lead to different functional connectivity metrics. Here, we evaluated the impact of different structural segmentation strategies on functional connectivity outcomes. To this aim, we compared different metrics computed after two different registration strategies. The first strategy used structural information from the 3D T1-weighted image (unimodal), while the second strategy implemented a multimodal approach, where an additional registration step used the information from the T2-weighted image. The impact of these different approaches was evaluated on a sample of 58 healthy adults. As expected, different approaches led to significant differences in structural measures (i.e., cortical thickness, volume, and gyrification index), with the maximum impact on the insula cortex. However, these differences were only slightly translated to functional metrics. We reported no differences in graph measures and seed-based functional connectivity maps, but slight differences in the insula when we compared the mean functional strength for each parcel. Overall, these results suggested that functional metrics are only slightly different when using a unimodal compared to a multimodal approach, while the structural output can be significantly affected.
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Affiliation(s)
- Lu Zhang
- Padova Neuroscience Center, University of Padova, 35131, Padua, Italy
| | - Lorenzo Pini
- Padova Neuroscience Center, University of Padova, 35131, Padua, Italy
| | - Maurizio Corbetta
- Padova Neuroscience Center, University of Padova, 35131, Padua, Italy.
- Venetian Institute of Molecular Medicine (VIMM), 35129, Padua, Italy.
- Clinica Neurologica, Department of Neuroscience, University of Padova, 35131, Padua, Italy.
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13
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Yin G, Li T, Jin S, Wang N, Li J, Wu C, He H, Wang J. A comprehensive evaluation of multicentric reliability of single-subject cortical morphological networks on traveling subjects. Cereb Cortex 2023:7169131. [PMID: 37197789 DOI: 10.1093/cercor/bhad178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 04/29/2023] [Accepted: 04/30/2023] [Indexed: 05/19/2023] Open
Abstract
Despite the prevalence of research on single-subject cerebral morphological networks in recent years, whether they can offer a reliable way for multicentric studies remains largely unknown. Using two multicentric datasets of traveling subjects, this work systematically examined the inter-site test-retest (TRT) reliabilities of single-subject cerebral morphological networks, and further evaluated the effects of several key factors. We found that most graph-based network measures exhibited fair to excellent reliabilities regardless of different analytical pipelines. Nevertheless, the reliabilities were affected by choices of morphological index (fractal dimension > sulcal depth > gyrification index > cortical thickness), brain parcellation (high-resolution > low-resolution), thresholding method (proportional > absolute), and network type (binarized > weighted). For the factor of similarity measure, its effects depended on the thresholding method used (absolute: Kullback-Leibler divergence > Jensen-Shannon divergence; proportional: Jensen-Shannon divergence > Kullback-Leibler divergence). Furthermore, longer data acquisition intervals and different scanner software versions significantly reduced the reliabilities. Finally, we showed that inter-site reliabilities were significantly lower than intra-site reliabilities for single-subject cerebral morphological networks. Altogether, our findings propose single-subject cerebral morphological networks as a promising approach for multicentric human connectome studies, and offer recommendations on how to determine analytical pipelines and scanning protocols for obtaining reliable results.
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Affiliation(s)
- Guole Yin
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Ting Li
- Institute of Brain and Psychological Sciences, Sichuan Normal University, Chengdu 610066, China
| | - Suhui Jin
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Ningkai Wang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Junle Li
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Changwen Wu
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Hongjian He
- Center for Brain Imaging Science and Technology, College of Biomedical Engineering and Instrumental Science, Zhejiang University, Hangzhou 310058, China
| | - Jinhui Wang
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
- Key Laboratory of Cognition and Education Sciences, Ministry of Education, Beijing 100816, China
- Center for Studies of Psychological Application, South China Normal University, Guangzhou 510000, China
- Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou 510000, China
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14
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Newlin NR, Cai LY, Yao T, Archer D, Pechman KR, Schilling KG, Jefferson A, Resnick SM, Hohman TJ, Shafer AT, Landman BA. Comparing voxel- and feature-wise harmonization of complex graph measures from multiple sites for structural brain network investigation of aging. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2023; 12464:124642B. [PMID: 37123017 PMCID: PMC10139749 DOI: 10.1117/12.2653947] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Complex graph theory measures of brain structural connectomes derived from diffusion weighted images (DWI) provide insight into the network structure of the brain. Further, as the number of available DWI datasets grows, so does the ability to investigate associations in these measures with major biological factors, like age. However, one key hurdle that remains is the presence of scanner effects that can arise from different DWI datasets and confound multisite analyses. Two common approaches to correct these effects are voxel-wise and feature-wise harmonization. However, it is still unclear how to best leverage them for graph-theory analysis of an aging population. Thus, there is a need to better characterize the impact of each harmonization method and their ability to preserve age related features. We investigate this by characterizing four complex graph theory measures (modularity, characteristic path length, global efficiency, and betweenness centrality) in 48 participants aged 55 to 86 from Baltimore Longitudinal Study of Aging (BLSA) and Vanderbilt Memory and Aging Project (VMAP) before and after voxel- and feature-wise harmonization with the Null Space Deep Network (NSDN) and ComBat, respectively. First, we characterize across dataset coefficients of variation (CoV) and find the combination of NSDN and ComBat causes the greatest reduction in CoV followed by ComBat alone then NSDN alone. Second, we reproduce published associations of modularity with age after correcting for other covariates with linear models. We find that harmonization with ComBat or ComBat and NSDN together improves the significance of existing age effects, reduces model residuals, and qualitatively reduces separation between datasets. These results reinforce the efficiency of statistical harmonization on the feature-level with ComBat and suggest that harmonization on the voxel-level is synergistic but may have reduced effect after running through the multiple layers of the connectomics pipeline. Thus, we conclude that feature-wise harmonization improves statistical results, but the addition of biologically informed voxel-based harmonization offers further improvement.
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Affiliation(s)
- Nancy R Newlin
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Leon Y Cai
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Tianyuan Yao
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Derek Archer
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kimberly R Pechman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kurt G Schilling
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Angela Jefferson
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Susan M Resnick
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Timothy J Hohman
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Andrea T Shafer
- Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Bennett A Landman
- Department of Computer Science, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA
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15
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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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16
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Imms P, Clemente A, Deutscher E, Radwan AM, Akhlaghi H, Beech P, Wilson PH, Irimia A, Poudel G, Domínguez Duque JF, Caeyenberghs K. Exploring personalized structural connectomics for moderate to severe traumatic brain injury. Netw Neurosci 2023; 7:160-183. [PMID: 37334004 PMCID: PMC10270710 DOI: 10.1162/netn_a_00277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/06/2022] [Indexed: 10/03/2023] Open
Abstract
Graph theoretical analysis of the structural connectome has been employed successfully to characterize brain network alterations in patients with traumatic brain injury (TBI). However, heterogeneity in neuropathology is a well-known issue in the TBI population, such that group comparisons of patients against controls are confounded by within-group variability. Recently, novel single-subject profiling approaches have been developed to capture inter-patient heterogeneity. We present a personalized connectomics approach that examines structural brain alterations in five chronic patients with moderate to severe TBI who underwent anatomical and diffusion magnetic resonance imaging. We generated individualized profiles of lesion characteristics and network measures (including personalized graph metric GraphMe plots, and nodal and edge-based brain network alterations) and compared them against healthy reference cases (N = 12) to assess brain damage qualitatively and quantitatively at the individual level. Our findings revealed alterations of brain networks with high variability between patients. With validation and comparison to stratified, normative healthy control comparison cohorts, this approach could be used by clinicians to formulate a neuroscience-guided integrative rehabilitation program for TBI patients, and for designing personalized rehabilitation protocols based on their unique lesion load and connectome.
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Affiliation(s)
- Phoebe Imms
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Adam Clemente
- Healthy Brain and Mind Research Centre, School of Behavioural, Health, and Human Sciences, Faculty of Health Sciences, Australian Catholic University, Fitzroy, Victoria, Australia
| | - Evelyn Deutscher
- Cognitive Neuroscience Unit, School of Psychology, Faculty of Health, Deakin University, Burwood, Victoria, Australia
| | - Ahmed M. Radwan
- KU Leuven, Department of Imaging and Pathology, Translational MRI, Leuven, Belgium
| | - Hamed Akhlaghi
- Emergency Department, St. Vincent’s Hospital (Melbourne), Faculty of Health, Deakin University, Melbourne, Victoria, Australia
| | - Paul Beech
- Department of Radiology and Nuclear Medicine, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Peter H. Wilson
- Healthy Brain and Mind Research Centre, School of Behavioural, Health, and Human Sciences, Faculty of Health Sciences, Australian Catholic University, Fitzroy, Victoria, Australia
| | - Andrei Irimia
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Corwin D. Denney Research Center, Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, Dana and David Dornsife College of Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Govinda Poudel
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| | - Juan F. Domínguez Duque
- Cognitive Neuroscience Unit, School of Psychology, Faculty of Health, Deakin University, Burwood, Victoria, Australia
| | - Karen Caeyenberghs
- Cognitive Neuroscience Unit, School of Psychology, Faculty of Health, Deakin University, Burwood, Victoria, Australia
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17
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de Brito Robalo BM, de Luca A, Chen C, Dewenter A, Duering M, Hilal S, Koek HL, Kopczak A, Lam BYK, Leemans A, Mok V, Onkenhout LP, van den Brink H, Biessels GJ. Improved sensitivity and precision in multicentre diffusion MRI network analysis using thresholding and harmonization. Neuroimage Clin 2022; 36:103217. [PMID: 36240537 PMCID: PMC9668636 DOI: 10.1016/j.nicl.2022.103217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/22/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022]
Abstract
PURPOSE To investigate if network thresholding and raw data harmonization improve consistency of diffusion MRI (dMRI)-based brain networks while also increasing precision and sensitivity to detect disease effects in multicentre datasets. METHODS Brain networks were reconstructed from dMRI of five samples with cerebral small vessel disease (SVD; 629 patients, 166 controls), as a clinically relevant exemplar condition for studies on network integrity. We evaluated consistency of network architecture in age-matched controls, by calculating cross-site differences in connection probability and fractional anisotropy (FA). Subsequently we evaluated precision and sensitivity to disease effects by identifying connections with low FA in sporadic SVD patients relative to controls, using more severely affected patients with a pure form of genetically defined SVD as reference. RESULTS In controls, thresholding and harmonization improved consistency of network architecture, minimizing cross-site differences in connection probability and FA. In patients relative to controls, thresholding improved precision to detect disrupted connections by removing false positive connections (precision, before: 0.09-0.19; after: 0.38-0.70). Before harmonization, sensitivity was low within individual sites, with few connections surviving multiple testing correction (k = 0-25 connections). Harmonization and pooling improved sensitivity (k = 38), while also achieving higher precision when combined with thresholding (0.97). CONCLUSION We demonstrated that network consistency, precision and sensitivity to detect disease effects in SVD are improved by thresholding and harmonization. We recommend introducing these techniques to leverage large existing multicentre datasets to better understand the impact of disease on brain networks.
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Affiliation(s)
- Bruno M. de Brito Robalo
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands,Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Alberto de Luca
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands,Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Christopher Chen
- Memory, Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anna Dewenter
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | - Marco Duering
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany,Medical Image Analysis Center (MIAC AG) and Department of Biomedical Engineering, University of Basel, Basel, Switzerland
| | - Saima Hilal
- Memory, Aging and Cognition Center, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore
| | - Huiberdina L. Koek
- Department of Geriatric Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anna Kopczak
- Institute for Stroke and Dementia Research (ISD), University Hospital, LMU Munich, Germany
| | - Bonnie Yin Ka Lam
- Division of Neurology, Department of Medicine and Therapeutics, Gerald Choa Neuroscience Centre, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Alexander Leemans
- Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Vincent Mok
- Division of Neurology, Department of Medicine and Therapeutics, Gerald Choa Neuroscience Centre, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Laurien P. Onkenhout
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hilde van den Brink
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Geert Jan Biessels
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands,Corresponding author at: Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, P.O. Box 85500, 3508 GA Utrecht, the Netherlands.
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18
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Onicas AI, Ware AL, Harris AD, Beauchamp MH, Beaulieu C, Craig W, Doan Q, Freedman SB, Goodyear BG, Zemek R, Yeates KO, Lebel C. Multisite Harmonization of Structural DTI Networks in Children: An A-CAP Study. Front Neurol 2022; 13:850642. [PMID: 35785336 PMCID: PMC9247315 DOI: 10.3389/fneur.2022.850642] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
The analysis of large, multisite neuroimaging datasets provides a promising means for robust characterization of brain networks that can reduce false positives and improve reproducibility. However, the use of different MRI scanners introduces variability to the data. Managing those sources of variability is increasingly important for the generation of accurate group-level inferences. ComBat is one of the most promising tools for multisite (multiscanner) harmonization of structural neuroimaging data, but no study has examined its application to graph theory metrics derived from the structural brain connectome. The present work evaluates the use of ComBat for multisite harmonization in the context of structural network analysis of diffusion-weighted scans from the Advancing Concussion Assessment in Pediatrics (A-CAP) study. Scans were acquired on six different scanners from 484 children aged 8.00-16.99 years [Mean = 12.37 ± 2.34 years; 289 (59.7%) Male] ~10 days following mild traumatic brain injury (n = 313) or orthopedic injury (n = 171). Whole brain deterministic diffusion tensor tractography was conducted and used to construct a 90 x 90 weighted (average fractional anisotropy) adjacency matrix for each scan. ComBat harmonization was applied separately at one of two different stages during data processing, either on the (i) weighted adjacency matrices (matrix harmonization) or (ii) global network metrics derived using unharmonized weighted adjacency matrices (parameter harmonization). Global network metrics based on unharmonized adjacency matrices and each harmonization approach were derived. Robust scanner effects were found for unharmonized metrics. Some scanner effects remained significant for matrix harmonized metrics, but effect sizes were less robust. Parameter harmonized metrics did not differ by scanner. Intraclass correlations (ICC) indicated good to excellent within-scanner consistency between metrics calculated before and after both harmonization approaches. Age correlated with unharmonized network metrics, but was more strongly correlated with network metrics based on both harmonization approaches. Parameter harmonization successfully controlled for scanner variability while preserving network topology and connectivity weights, indicating that harmonization of global network parameters based on unharmonized adjacency matrices may provide optimal results. The current work supports the use of ComBat for removing multiscanner effects on global network topology.
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Affiliation(s)
- Adrian I. Onicas
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- MoMiLab Research Unit, IMT School for Advanced Studies Lucca, Lucca, Italy
| | - Ashley L. Ware
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Department of Neurology, University of Utah, Salt Lake City, UT, United States
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Ashley D. Harris
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- Department of Radiology, University of Calgary, Calgary, AB, Canada
| | - Miriam H. Beauchamp
- Department of Psychology, University of Montreal and CHU Sainte-Justine Hospital Research Center, Montreal, QC, Canada
| | - Christian Beaulieu
- Department of Biomedical Engineering, University of Alberta, Edmonton, AB, Canada
| | - William Craig
- University of Alberta and Stollery Children's Hospital, Edmonton, AB, Canada
| | - Quynh Doan
- Department of Pediatrics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Stephen B. Freedman
- Departments of Pediatrics and Emergency Medicine, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Bradley G. Goodyear
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
- Department of Radiology, University of Calgary, Calgary, AB, Canada
| | - Roger Zemek
- Department of Pediatrics and Emergency Medicine, Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Keith Owen Yeates
- Department of Psychology, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Catherine Lebel
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
- Department of Radiology, University of Calgary, Calgary, AB, Canada
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19
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Koch PJ, Girard G, Brügger J, Cadic-Melchior AG, Beanato E, Park CH, Morishita T, Wessel MJ, Pizzolato M, Canales-Rodríguez EJ, Fischi-Gomez E, Schiavi S, Daducci A, Piredda GF, Hilbert T, Kober T, Thiran JP, Hummel FC. Evaluating reproducibility and subject-specificity of microstructure-informed connectivity. Neuroimage 2022; 258:119356. [PMID: 35659995 DOI: 10.1016/j.neuroimage.2022.119356] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/01/2022] [Accepted: 06/01/2022] [Indexed: 11/30/2022] Open
Abstract
Tractography enables identifying and evaluating the healthy and diseased brain's white matter pathways from diffusion-weighted magnetic resonance imaging data. As previous evaluation studies have reported significant false-positive estimation biases, recent microstructure-informed tractography algorithms have been introduced to improve the trade-off between specificity and sensitivity. However, a major limitation for characterizing the performance of these techniques is the lack of ground truth brain data. In this study, we compared the performance of two relevant microstructure-informed tractography methods, SIFT2 and COMMIT, by assessing the subject specificity and reproducibility of their derived white matter pathways. Specifically, twenty healthy young subjects were scanned at eight different time points at two different sites. Subject specificity and reproducibility were evaluated using the whole-brain connectomes and a subset of 29 white matter bundles. Our results indicate that although the raw tractograms are more vulnerable to the presence of false-positive connections, they are highly reproducible, suggesting that the estimation bias is subject-specific. This high reproducibility was preserved when microstructure-informed tractography algorithms were used to filter the raw tractograms. Moreover, the resulting track-density images depicted a more uniform coverage of streamlines throughout the white matter, suggesting that these techniques could increase the biological meaning of the estimated fascicles. Notably, we observed an increased subject specificity by employing connectivity pre-processing techniques to reduce the underlaying noise and the data dimensionality (using principal component analysis), highlighting the importance of these tools for future studies. Finally, no strong bias from the scanner site or time between measurements was found. The largest intraindividual variance originated from the sole repetition of data measurements (inter-run).
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Affiliation(s)
- Philipp J Koch
- Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL), 1202 Geneva, Switzerland; Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL Valais), Clinique Romande de Réadaptation, 1951 Sion, Switzerland; Department of Neurology, University of Lübeck, 23562 Lübeck, Germany; Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, 23562 Lübeck, Germany
| | - Gabriel Girard
- CIBM Center for Biomedical Imaging, Switzerland; Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Switzerland.
| | - Julia Brügger
- Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL), 1202 Geneva, Switzerland; Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL Valais), Clinique Romande de Réadaptation, 1951 Sion, Switzerland
| | - Andéol G Cadic-Melchior
- Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL), 1202 Geneva, Switzerland; Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL Valais), Clinique Romande de Réadaptation, 1951 Sion, Switzerland
| | - Elena Beanato
- Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL), 1202 Geneva, Switzerland; Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL Valais), Clinique Romande de Réadaptation, 1951 Sion, Switzerland
| | - Chang-Hyun Park
- Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL), 1202 Geneva, Switzerland; Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL Valais), Clinique Romande de Réadaptation, 1951 Sion, Switzerland
| | - Takuya Morishita
- Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL), 1202 Geneva, Switzerland; Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL Valais), Clinique Romande de Réadaptation, 1951 Sion, Switzerland
| | - Maximilian J Wessel
- Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL), 1202 Geneva, Switzerland; Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL Valais), Clinique Romande de Réadaptation, 1951 Sion, Switzerland; Department of Neurology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Marco Pizzolato
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Switzerland; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Elda Fischi-Gomez
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Switzerland; Translational Machine Learning Lab, Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Simona Schiavi
- Diffusion Imaging and Connectivity Estimation (DICE) Lab, Department of Computer Science, University of Verona, Verona, Italy; Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DINOGMI), University of Genoa, Genoa, Italy
| | - Alessandro Daducci
- Diffusion Imaging and Connectivity Estimation (DICE) Lab, Department of Computer Science, University of Verona, Verona, Italy
| | - Gian Franco Piredda
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Switzerland; Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland
| | - Tom Hilbert
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Switzerland; Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland
| | - Tobias Kober
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Switzerland; Advanced Clinical Imaging Technology, Siemens Healthcare AG, Lausanne, Switzerland
| | - Jean-Philippe Thiran
- CIBM Center for Biomedical Imaging, Switzerland; Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Switzerland
| | - Friedhelm C Hummel
- Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL), 1202 Geneva, Switzerland; Defitech Chair of Clinical Neuroengineering, Center for Neuroprosthetics (CNP) and Brain Mind Institute (BMI), École Polytechnique Fédérale de Lausanne (EPFL Valais), Clinique Romande de Réadaptation, 1951 Sion, Switzerland; Clinical Neuroscience, University Hospital of Geneva (HUG), Geneva, Switzerland
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