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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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Luppi AI, Gellersen HM, Liu ZQ, Peattie ARD, Manktelow AE, Adapa R, Owen AM, Naci L, Menon DK, Dimitriadis SI, Stamatakis EA. Systematic evaluation of fMRI data-processing pipelines for consistent functional connectomics. Nat Commun 2024; 15:4745. [PMID: 38834553 PMCID: PMC11150439 DOI: 10.1038/s41467-024-48781-5] [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: 10/04/2022] [Accepted: 05/10/2024] [Indexed: 06/06/2024] Open
Abstract
Functional interactions between brain regions can be viewed as a network, enabling neuroscientists to investigate brain function through network science. Here, we systematically evaluate 768 data-processing pipelines for network reconstruction from resting-state functional MRI, evaluating the effect of brain parcellation, connectivity definition, and global signal regression. Our criteria seek pipelines that minimise motion confounds and spurious test-retest discrepancies of network topology, while being sensitive to both inter-subject differences and experimental effects of interest. We reveal vast and systematic variability across pipelines' suitability for functional connectomics. Inappropriate choice of data-processing pipeline can produce results that are not only misleading, but systematically so, with the majority of pipelines failing at least one criterion. However, a set of optimal pipelines consistently satisfy all criteria across different datasets, spanning minutes, weeks, and months. We provide a full breakdown of each pipeline's performance across criteria and datasets, to inform future best practices in functional connectomics.
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Affiliation(s)
- Andrea I Luppi
- Division of Anaesthesia, University of Cambridge, Cambridge, UK.
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- St John's College, University of Cambridge, Cambridge, UK.
- Montreal Neurological Institute, McGill University, Montreal, Canada.
| | - Helena M Gellersen
- German Center for Neurodegenerative Diseases, Magdeburg, Germany
- Department of Psychology, University of Cambridge, Cambridge, UK
| | - Zhen-Qi Liu
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Alexander R D Peattie
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anne E Manktelow
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Ram Adapa
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Adrian M Owen
- Department of Psychology, Western Institute for Neuroscience (WIN), Western University, London, ON, Canada
- Department of Physiology and Pharmacology, Western Institute for Neuroscience (WIN), Western University, London, ON, Canada
| | - Lorina Naci
- Trinity College Institute of Neuroscience, School of Psychology, Trinity College Dublin, Dublin, Ireland
| | - David K Menon
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
| | - Stavros I Dimitriadis
- Department of Clinical Psychology and Psychobiology, University of Barcelona, Barcelona, Spain
- Institut de Neurociències, University of Barcelona, Barcelona, Spain
- Neuroinformatics Group, Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, Wales, UK
- Neuroscience and Mental Health Research Institute, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, Wales, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, Wales, UK
- Integrative Neuroimaging Lab, Thessaloniki, Greece
| | - Emmanuel A Stamatakis
- Division of Anaesthesia, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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3
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Lizarraga A, Ripp I, Sala A, Shi K, Düring M, Koch K, Yakushev I. Similarity between structural and proxy estimates of brain connectivity. J Cereb Blood Flow Metab 2024; 44:284-295. [PMID: 37773727 PMCID: PMC10993877 DOI: 10.1177/0271678x231204769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/01/2023] [Accepted: 08/18/2023] [Indexed: 10/01/2023]
Abstract
Functional magnetic resonance and diffusion weighted imaging have so far made a major contribution to delineation of the brain connectome at the macroscale. While functional connectivity (FC) was shown to be related to structural connectivity (SC) to a certain degree, their spatial overlap is unknown. Even less clear are relations of SC with estimates of connectivity from inter-subject covariance of regional F18-fluorodeoxyglucose uptake (FDGcov) and grey matter volume (GMVcov). Here, we asked to what extent SC underlies three proxy estimates of brain connectivity: FC, FDGcov and GMVcov. Simultaneous PET/MR acquisitions were performed in 56 healthy middle-aged individuals. Similarity between four networks was assessed using Spearman correlation and convergence ratio (CR), a measure of spatial overlap. Spearman correlation coefficient was 0.27 for SC-FC, 0.40 for SC-FDGcov, and 0.15 for SC-GMVcov. Mean CRs were 51% for SC-FC, 48% for SC-FDGcov, and 37% for SC-GMVcov. These results proved to be reproducible and robust against image processing steps. In sum, we found a relevant similarity of SC with FC and FDGcov, while GMVcov consistently showed the weakest similarity. These findings indicate that white matter tracts underlie FDGcov to a similar degree as FC, supporting FDGcov as estimate of functional brain connectivity.
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Affiliation(s)
- Aldana Lizarraga
- Department of Nuclear Medicine, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Isabelle Ripp
- Department of Nuclear Medicine, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Arianna Sala
- Department of Nuclear Medicine, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
- Coma Science Group, GIGA Consciousness, University of Liege; Centre du Cerveau2, University Hospital of Liege, Avenue de L'Hôpital 1, Liege, Belgium
| | - Kuangyu Shi
- Department of Nuclear Medicine, University Hospital Bern, Bern, Switzerland
| | - Marco Düring
- Medical Image Analysis Center (MIAC AG) and Qbig, Department of Biomedical Engineering, University of Basel, Basel, Switzerland
| | - Kathrin Koch
- Department of Neuroradiology, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Igor Yakushev
- Department of Nuclear Medicine, School of Medicine, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
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4
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Girard G, Rafael-Patiño J, Truffet R, Aydogan DB, Adluru N, Nair VA, Prabhakaran V, Bendlin BB, Alexander AL, Bosticardo S, Gabusi I, Ocampo-Pineda M, Battocchio M, Piskorova Z, Bontempi P, Schiavi S, Daducci A, Stafiej A, Ciupek D, Bogusz F, Pieciak T, Frigo M, Sedlar S, Deslauriers-Gauthier S, Kojčić I, Zucchelli M, Laghrissi H, Ji Y, Deriche R, Schilling KG, Landman BA, Cacciola A, Basile GA, Bertino S, Newlin N, Kanakaraj P, Rheault F, Filipiak P, Shepherd TM, Lin YC, Placantonakis DG, Boada FE, Baete SH, Hernández-Gutiérrez E, Ramírez-Manzanares A, Coronado-Leija R, Stack-Sánchez P, Concha L, Descoteaux M, Mansour L S, Seguin C, Zalesky A, Marshall K, Canales-Rodríguez EJ, Wu Y, Ahmad S, Yap PT, Théberge A, Gagnon F, Massi F, Fischi-Gomez E, Gardier R, Haro JLV, Pizzolato M, Caruyer E, Thiran JP. Tractography passes the test: Results from the diffusion-simulated connectivity (disco) challenge. Neuroimage 2023; 277:120231. [PMID: 37330025 PMCID: PMC10771037 DOI: 10.1016/j.neuroimage.2023.120231] [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: 03/02/2023] [Revised: 05/12/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023] Open
Abstract
Estimating structural connectivity from diffusion-weighted magnetic resonance imaging is a challenging task, partly due to the presence of false-positive connections and the misestimation of connection weights. Building on previous efforts, the MICCAI-CDMRI Diffusion-Simulated Connectivity (DiSCo) challenge was carried out to evaluate state-of-the-art connectivity methods using novel large-scale numerical phantoms. The diffusion signal for the phantoms was obtained from Monte Carlo simulations. The results of the challenge suggest that methods selected by the 14 teams participating in the challenge can provide high correlations between estimated and ground-truth connectivity weights, in complex numerical environments. Additionally, the methods used by the participating teams were able to accurately identify the binary connectivity of the numerical dataset. However, specific false positive and false negative connections were consistently estimated across all methods. Although the challenge dataset doesn't capture the complexity of a real brain, it provided unique data with known macrostructure and microstructure ground-truth properties to facilitate the development of connectivity estimation methods.
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Affiliation(s)
- 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), Lausanne, Switzerland.
| | - Jonathan Rafael-Patiño
- Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland; Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Raphaël Truffet
- Univ Rennes, Inria, CNRS, Inserm, IRISA UMR 6074, Empenn ERL U-1228, Rennes, France
| | - Dogu Baran Aydogan
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland; Department of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland; Department of Psychiatry, Helsinki University Hospital, Helsinki, Finland
| | - Nagesh Adluru
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Radiology, University of Wisconsin-Madison, Madison, WI, United States
| | - Veena A Nair
- Department of Radiology, University of Wisconsin-Madison, Madison, WI, United States
| | - Vivek Prabhakaran
- Department of Radiology, University of Wisconsin-Madison, Madison, WI, United States
| | - Barbara B Bendlin
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Andrew L Alexander
- Waisman Center, University of Wisconsin-Madison, Madison, WI, United States; Department of Medical Physics, University of Wisconsin-Madison, Madison, WI, United States; Department of Psychiatry, University of Wisconsin-Madison, Madison, WI, United States
| | - Sara Bosticardo
- Diffusion Imaging and Connectivity Estimation (DICE) Lab, Department of Computer Science, University of Verona, Verona, Italy; Translational Imaging in Neurology (ThINk), Department of Biomedical Engineering, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Ilaria Gabusi
- Diffusion Imaging and Connectivity Estimation (DICE) Lab, Department of Computer Science, University of Verona, Verona, Italy; Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy
| | - Mario Ocampo-Pineda
- Diffusion Imaging and Connectivity Estimation (DICE) Lab, Department of Computer Science, University of Verona, Verona, Italy
| | - Matteo Battocchio
- Diffusion Imaging and Connectivity Estimation (DICE) Lab, Department of Computer Science, University of Verona, Verona, Italy; Sherbrooke Connectivity Imaging Laboratory (SCIL), Department of Computer Science, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Zuzana Piskorova
- Diffusion Imaging and Connectivity Estimation (DICE) Lab, Department of Computer Science, University of Verona, Verona, Italy; Brno Faculty of Electrical Engineering and Communication, Department of mathematics, University of Technology, Brno, Czech Republic
| | - Pietro Bontempi
- Diffusion Imaging and Connectivity Estimation (DICE) Lab, Department of Computer Science, University of Verona, Verona, Italy
| | - Simona Schiavi
- 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
| | | | - Dominika Ciupek
- Sano Centre for Computational Personalised Medicine, Kraków, Poland
| | - Fabian Bogusz
- AGH University of Science and Technology, Kraków, Poland
| | - Tomasz Pieciak
- AGH University of Science and Technology, Kraków, Poland; Laboratorio de Procesado de Imagen (LPI), ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Matteo Frigo
- Athena Project Team, Centre Inria d'Université Côte d'Azur, France
| | - Sara Sedlar
- Athena Project Team, Centre Inria d'Université Côte d'Azur, France
| | | | - Ivana Kojčić
- Athena Project Team, Centre Inria d'Université Côte d'Azur, France
| | - Mauro Zucchelli
- Athena Project Team, Centre Inria d'Université Côte d'Azur, France
| | - Hiba Laghrissi
- Athena Project Team, Centre Inria d'Université Côte d'Azur, France; Institut de Biologie de Valrose, Université Côte d'Azur, Nice, France
| | - Yang Ji
- Athena Project Team, Centre Inria d'Université Côte d'Azur, France
| | - Rachid Deriche
- Athena Project Team, Centre Inria d'Université Côte d'Azur, France
| | - Kurt G Schilling
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bennett A Landman
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, United States; Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, United States
| | - Alberto Cacciola
- Brain Mapping Lab, Department of Biomedical, Dental Sciences and Morphological and Functional Images, University of Messina, Messina, Italy; Center for Complex Network Intelligence (CCNI), Tsinghua Laboratory of Brain and Intelligence (THBI), Tsinghua University, Beijing, China; Department of Biomedical Engineering, Tsinghua University, Beijing, China
| | - Gianpaolo Antonio Basile
- Brain Mapping Lab, Department of Biomedical, Dental Sciences and Morphological and Functional Images, University of Messina, Messina, Italy
| | - Salvatore Bertino
- Brain Mapping Lab, Department of Biomedical, Dental Sciences and Morphological and Functional Images, University of Messina, Messina, Italy
| | - Nancy Newlin
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, United States
| | - Praitayini Kanakaraj
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, United States
| | - Francois Rheault
- Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN, United States
| | - Patryk Filipiak
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, NYU Langone Health, New York, NY, United States
| | - Timothy M Shepherd
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, NYU Langone Health, New York, NY, United States
| | - Ying-Chia Lin
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, NYU Langone Health, New York, NY, United States
| | - Dimitris G Placantonakis
- Department of Neurosurgery, Perlmutter Cancer Center, Neuroscience Institute, Kimmel Center for Stem Cell Biology, NYU Langone Health, New York, NY, United States
| | - Fernando E Boada
- Department of Radiology, Stanford University, Stanford, CA, United States
| | - Steven H Baete
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, NYU Langone Health, New York, NY, United States
| | - Erick Hernández-Gutiérrez
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Department of Computer Science, University of Sherbrooke, Sherbrooke, QC, Canada
| | | | - Ricardo Coronado-Leija
- Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, NYU Langone Health, New York, NY, United States
| | - Pablo Stack-Sánchez
- Computer Science Department, Centro de Investigación en Matemáticas A.C, Guanajuato, México
| | - Luis Concha
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Department of Computer Science, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Sina Mansour L
- Department of Biomedical Engineering, The University of Melbourne, Parkville, Victoria, Australia; Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Parkville, Victoria, Australia
| | - Caio Seguin
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Parkville, Victoria, Australia; School of Biomedical Engineering, The University of Sydney, Sydney, Australia; Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, United States
| | - Andrew Zalesky
- Department of Biomedical Engineering, The University of Melbourne, Parkville, Victoria, Australia; Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne and Melbourne Health, Parkville, Victoria, Australia
| | - Kenji Marshall
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; McGill University, Montréal, QC, Canada
| | - Erick J Canales-Rodríguez
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ye Wu
- Department of Radiology and Biomedical Research Imaging Center (BRIC), The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States; School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Sahar Ahmad
- Department of Radiology and Biomedical Research Imaging Center (BRIC), The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Pew-Thian Yap
- Department of Radiology and Biomedical Research Imaging Center (BRIC), The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Antoine Théberge
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Department of Computer Science, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Florence Gagnon
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Department of Computer Science, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Frédéric Massi
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Department of Computer Science, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Elda Fischi-Gomez
- 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), Lausanne, Switzerland
| | - Rémy Gardier
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Juan Luis Villarreal Haro
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marco Pizzolato
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Emmanuel Caruyer
- Univ Rennes, Inria, CNRS, Inserm, IRISA UMR 6074, Empenn ERL U-1228, Rennes, France
| | - 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), Lausanne, Switzerland
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5
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Borrelli P, Savini G, Cavaliere C, Palesi F, Grazia Bruzzone M, Aquino D, Biagi L, Bosco P, Carne I, Ferraro S, Giulietti G, Napolitano A, Nigri A, Pavone L, Pirastru A, Redolfi A, Tagliavini F, Tosetti M, Salvatore M, Gandini Wheeler-Kingshott CAM, Aiello M. Normative values of the topological metrics of the structural connectome: A multi-site reproducibility study across the Italian Neuroscience network. Phys Med 2023; 112:102610. [PMID: 37331082 DOI: 10.1016/j.ejmp.2023.102610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 03/20/2023] [Accepted: 05/30/2023] [Indexed: 06/20/2023] Open
Abstract
PURPOSE The use of topological metrics to derive quantitative descriptors from structural connectomes is receiving increasing attention but deserves specific studies to investigate their reproducibility and variability in the clinical context. This work exploits the harmonization of diffusion-weighted acquisition for neuroimaging data performed by the Italian Neuroscience and Neurorehabilitation Network initiative to obtain normative values of topological metrics and to investigate their reproducibility and variability across centers. METHODS Different topological metrics, at global and local level, were calculated on multishell diffusion-weighted data acquired at high-field (e.g. 3 T) Magnetic Resonance Imaging scanners in 13 different centers, following the harmonization of the acquisition protocol, on young and healthy adults. A "traveling brains" dataset acquired on a subgroup of subjects at 3 different centers was also analyzed as reference data. All data were processed following a common processing pipeline that includes data pre-processing, tractography, generation of structural connectomes and calculation of graph-based metrics. The results were evaluated both with statistical analysis of variability and consistency among sites with the traveling brains range. In addition, inter-site reproducibility was assessed in terms of intra-class correlation variability. RESULTS The results show an inter-center and inter-subject variability of <10%, except for "clustering coefficient" (variability of 30%). Statistical analysis identifies significant differences among sites, as expected given the wide range of scanners' hardware. CONCLUSIONS The results show low variability of connectivity topological metrics across sites running a harmonised protocol.
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Affiliation(s)
| | | | | | - Fulvia Palesi
- Department of Brain and Behavioral Sciences, Università degli Studi di Pavia, Pavia, Italy
| | - Maria Grazia Bruzzone
- Neuroradiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Domenico Aquino
- Neuroradiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Laura Biagi
- Laboratory of Medical Physics and Magnetic Resonance, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Paolo Bosco
- Laboratory of Medical Physics and Magnetic Resonance, IRCCS Stella Maris Foundation, Pisa, Italy
| | - Irene Carne
- Neuroradiology Unit, IRCCS Istituti Clinici Scientifici Maugeri, Pavia, Italy
| | - Stefania Ferraro
- Neuroradiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giovanni Giulietti
- Neuroimaging Laboratory, IRCCS Santa Lucia Foundation, Rome, Italy; SAIMLAL Department, Sapienza University of Rome, Rome, Italy
| | - Antonio Napolitano
- Medical Physics, IRCCS Istituto Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Anna Nigri
- Neuroradiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | | | | | - Alberto Redolfi
- Laboratory of Neuroinformatics, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Fabrizio Tagliavini
- Scientific Direction, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Michela Tosetti
- Laboratory of Medical Physics and Magnetic Resonance, IRCCS Stella Maris Foundation, Pisa, Italy
| | | | - Claudia A M Gandini Wheeler-Kingshott
- Department of Brain and Behavioral Sciences, Università degli Studi di Pavia, Pavia, Italy; NMR Research Unit, Department of Neuroinflammation, Queen Square MS Centre, UCL Queen Square Institute of Neurology, Faculty of Brain Sciences, University College London, London, United Kingdom
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6
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Madole JW, Buchanan CR, Rhemtulla M, Ritchie SJ, Bastin ME, Deary IJ, Cox SR, Tucker-Drob EM. Strong intercorrelations among global graph-theoretic indices of structural connectivity in the human brain. Neuroimage 2023; 275:120160. [PMID: 37169117 DOI: 10.1016/j.neuroimage.2023.120160] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/06/2023] [Accepted: 05/08/2023] [Indexed: 05/13/2023] Open
Abstract
Graph-theoretic metrics derived from neuroimaging data have been heralded as powerful tools for uncovering neural mechanisms of psychological traits, psychiatric disorders, and neurodegenerative diseases. In N = 8,185 human structural connectomes from UK Biobank, we examined the extent to which 11 commonly-used global graph-theoretic metrics index distinct versus overlapping information with respect to interindividual differences in brain organization. Using unthresholded, FA-weighted networks we found that all metrics other than Participation Coefficient were highly intercorrelated, both with each other (mean |r| = 0.788) and with a topologically-naïve summary index of brain structure (mean edge weight; mean |r| = 0.873). In a series of sensitivity analyses, we found that overlap between metrics is influenced by the sparseness of the network and the magnitude of variation in edge weights. Simulation analyses representing a range of population network structures indicated that individual differences in global graph metrics may be intrinsically difficult to separate from mean edge weight. In particular, Closeness, Characteristic Path Length, Global Efficiency, Clustering Coefficient, and Small Worldness were nearly perfectly collinear with one another (mean |r| = 0.939) and with mean edge weight (mean |r| = 0.952) across all observed and simulated conditions. Global graph-theoretic measures are valuable for their ability to distill a high-dimensional system of neural connections into summary indices of brain organization, but they may be of more limited utility when the goal is to index separable components of interindividual variation in specific properties of the human structural connectome.
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Affiliation(s)
- James W Madole
- Department of Psychology, University of Texas at Austin, Austin, TX, USA; VA Puget Sound Health Care System, Seattle Division, Seattle, WA, USA.
| | - Colin R Buchanan
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK; Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, Edinburgh, UK
| | - Mijke Rhemtulla
- Department of Psychology, University of California, Davis, CA, USA
| | - Stuart J Ritchie
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Mark E Bastin
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK; Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK; Scottish Imaging Network, A Platform for Scientific Excellence (SINAPSE) Collaboration, Edinburgh, UK
| | - Elliot M Tucker-Drob
- Department of Psychology, University of Texas at Austin, Austin, TX, USA; Population Research Center and Center on Aging and Population Sciences, University of Texas at Austin, Austin, TX, USA
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7
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Dimitriadis SI, Perry G, Lancaster TM, Tansey KE, Singh KD, Holmans P, Pocklington A, Davey Smith G, Zammit S, Hall J, O’Donovan MC, Owen MJ, Jones DK, Linden DE. Genetic risk for schizophrenia is associated with increased proportion of indirect connections in brain networks revealed by a semi-metric analysis: evidence from population sample stratified for polygenic risk. Cereb Cortex 2023; 33:2997-3011. [PMID: 35830871 PMCID: PMC10016061 DOI: 10.1093/cercor/bhac256] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 02/02/2023] Open
Abstract
Research studies based on tractography have revealed a prominent reduction of asymmetry in some key white-matter tracts in schizophrenia (SCZ). However, we know little about the influence of common genetic risk factors for SCZ on the efficiency of routing on structural brain networks (SBNs). Here, we use a novel recall-by-genotype approach, where we sample young adults from a population-based cohort (ALSPAC:N genotyped = 8,365) based on their burden of common SCZ risk alleles as defined by polygenic risk score (PRS). We compared 181 individuals at extremes of low (N = 91) or high (N = 90) SCZ-PRS under a robust diffusion MRI-based graph theoretical SBN framework. We applied a semi-metric analysis revealing higher SMR values for the high SCZ-PRS group compared with the low SCZ-PRS group in the left hemisphere. Furthermore, a hemispheric asymmetry index showed a higher leftward preponderance of indirect connections for the high SCZ-PRS group compared with the low SCZ-PRS group (PFDR < 0.05). These findings might indicate less efficient structural connectivity in the higher genetic risk group. This is the first study in a population-based sample that reveals differences in the efficiency of SBNs associated with common genetic risk variants for SCZ.
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Affiliation(s)
- S I Dimitriadis
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Neuroinformatics Group, School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - G Perry
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - T M Lancaster
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Department of Psychology, Bath University, Claverton Down BA2 7AY, Bath, Wales, UK
| | - K E Tansey
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Queens Road BS8 1QU, Bristol, Wales, UK
| | - K D Singh
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - P Holmans
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - A Pocklington
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - G Davey Smith
- MRC Integrative Epidemiology Unit (IEU), University of Bristol, Queens Road BS8 1QU, Bristol, Wales, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road BS8 1NU, Bristol, Wales, UK
| | - S Zammit
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road BS8 1NU, Bristol, Wales, UK
| | - J Hall
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - M C O’Donovan
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - M J Owen
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - D K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
| | - D E Linden
- Neuroscience and Mental Health Research Institute (NMHI), College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff School of Medicine, Cardiff University, Maindy Road CF24 4HQ, Cardiff, Wales, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, 1-5 Whiteladies Road BS8 1NU, Bristol, Wales, UK
- School for Mental Health and Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 40 UNS40 6229 ER, Maastricht, The Netherlands
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Messaritaki E, Foley S, Barawi K, Ettinger U, Jones DK. Increased structural connectivity in high schizotypy. Netw Neurosci 2023; 7:213-233. [PMID: 37334008 PMCID: PMC10270715 DOI: 10.1162/netn_a_00279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/14/2022] [Indexed: 09/23/2023] Open
Abstract
The link between brain structural connectivity and schizotypy was explored in two healthy participant cohorts, collected at two different neuroimaging centres, comprising 140 and 115 participants, respectively. The participants completed the Schizotypal Personality Questionnaire (SPQ), through which their schizotypy scores were calculated. Diffusion-MRI data were used to perform tractography and to generate the structural brain networks of the participants. The edges of the networks were weighted with the inverse radial diffusivity. Graph theoretical metrics of the default mode, sensorimotor, visual, and auditory subnetworks were derived and their correlation coefficients with the schizotypy scores were calculated. To the best of our knowledge, this is the first time that graph theoretical measures of structural brain networks are investigated in relation to schizotypy. A positive correlation was found between the schizotypy score and the mean node degree and mean clustering coefficient of the sensorimotor and the default mode subnetworks. The nodes driving these correlations were the right postcentral gyrus, the left paracentral lobule, the right superior frontal gyrus, the left parahippocampal gyrus, and the bilateral precuneus, that is, nodes that exhibit compromised functional connectivity in schizophrenia. Implications for schizophrenia and schizotypy are discussed.
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Affiliation(s)
- Eirini Messaritaki
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
| | - Sonya Foley
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
| | - Kali Barawi
- School of Medicine, Cardiff University, Cardiff, UK
| | | | - Derek K. Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
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9
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Jiang L, He J, Pan H, Wu D, Jiang T, Liu J. Seizure detection algorithm based on improved functional brain network structure feature extraction. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2022.104053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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10
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Dimitriadis SI. Assessing the Repeatability of Multi-Frequency Multi-Layer Brain Network Topologies Across Alternative Researcher's Choice Paths. Neuroinformatics 2023; 21:71-88. [PMID: 36372844 DOI: 10.1007/s12021-022-09610-6] [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] [Accepted: 10/05/2022] [Indexed: 11/15/2022]
Abstract
There is a growing interest in the neuroscience community on the advantages of multilayer functional brain networks. Researchers usually treated different frequencies separately at distinct functional brain networks. However, there is strong evidence that these networks share complementary information while their interdependencies could reveal novel findings. For this purpose, neuroscientists adopt multilayer networks, which can be described mathematically as an extension of trivial single-layer networks. Multilayer networks have become popular in neuroscience due to their advantage to integrate different sources of information. Here, Ι will focus on the multi-frequency multilayer functional connectivity analysis on resting-state fMRI (rs-fMRI) recordings. However, constructing a multilayer network depends on selecting multiple pre-processing steps that can affect the final network topology. Here, I analyzed the rs-fMRI dataset from a single human performing scanning over a period of 18 months (84 scans in total), and the rs-fMRI dataset containing 25 subjects with 3 repeat scans. I focused on assessing the reproducibility of multi-frequency multilayer topologies exploring the effect of two filtering methods for extracting frequencies from BOLD activity, three connectivity estimators, with or without a topological filtering scheme, and two spatial scales. Finally, I untangled specific combinations of researchers' choices that yield consistently brain networks with repeatable topologies, giving me the chance to recommend best practices over consistent topologies.
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Affiliation(s)
- Stavros I Dimitriadis
- Department of Clinical Psychology and Psychobiology, Faculty of Psychology, University of Barcelona, Passeig de la Vall d'Hebron, 171, 08035, Barcelona, Spain.
- Institut de Neurociències, University of Barcelona, Campus Mundet, Edifici de PonentPasseig de la Vall d'Hebron, 171, 08035, Barcelona, Spain.
- Integrative Neuroimaging Lab, 55133, Thessaloniki, Greece.
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Wales, CF24 4HQ, Cardiff, UK.
- Neuroinformatics Group, School of Psychology, College of Biomedical and Life Sciences, Cardiff University Brain Research Imaging Centre (CUBRIC), CF24 4HQ, Cardiff, Wales, UK.
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK.
- Neuroscience and Mental Health Research Institute, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, CF24 4HQ, Cardiff, Wales, UK.
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, College of Biomedical and Life Sciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK.
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11
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Mirza-Davies A, Foley S, Caseras X, Baker E, Holmans P, Escott-Price V, Jones DK, Harrison JR, Messaritaki E. The impact of genetic risk for Alzheimer's disease on the structural brain networks of young adults. Front Neurosci 2022; 16:987677. [PMID: 36532292 PMCID: PMC9748570 DOI: 10.3389/fnins.2022.987677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction We investigated the structural brain networks of 562 young adults in relation to polygenic risk for Alzheimer's disease, using magnetic resonance imaging (MRI) and genotype data from the Avon Longitudinal Study of Parents and Children. Methods Diffusion MRI data were used to perform whole-brain tractography and generate structural brain networks for the whole-brain connectome, and for the default mode, limbic and visual subnetworks. The mean clustering coefficient, mean betweenness centrality, characteristic path length, global efficiency and mean nodal strength were calculated for these networks, for each participant. The connectivity of the rich-club, feeder and local connections was also calculated. Polygenic risk scores (PRS), estimating each participant's genetic risk, were calculated at genome-wide level and for nine specific disease pathways. Correlations were calculated between the PRS and (a) the graph theoretical metrics of the structural networks and (b) the rich-club, feeder and local connectivity of the whole-brain networks. Results In the visual subnetwork, the mean nodal strength was negatively correlated with the genome-wide PRS (r = -0.19, p = 1.4 × 10-3), the mean betweenness centrality was positively correlated with the plasma lipoprotein particle assembly PRS (r = 0.16, p = 5.5 × 10-3), and the mean clustering coefficient was negatively correlated with the tau-protein binding PRS (r = -0.16, p = 0.016). In the default mode network, the mean nodal strength was negatively correlated with the genome-wide PRS (r = -0.14, p = 0.044). The rich-club and feeder connectivities were negatively correlated with the genome-wide PRS (r = -0.16, p = 0.035; r = -0.15, p = 0.036). Discussion We identified small reductions in brain connectivity in young adults at risk of developing Alzheimer's disease in later life.
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Affiliation(s)
- Anastasia Mirza-Davies
- School of Medicine, University Hospital Wales, Cardiff University, Cardiff, United Kingdom
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Sonya Foley
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Xavier Caseras
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Emily Baker
- UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Peter Holmans
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Valentina Escott-Price
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
- UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Derek K. Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Judith R. Harrison
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
- Institute for Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Eirini Messaritaki
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
- BRAIN Biomedical Research Unit, School of Medicine, Cardiff University, Cardiff, United Kingdom
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12
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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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13
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Seider NA, Adeyemo B, Miller R, Newbold DJ, Hampton JM, Scheidter KM, Rutlin J, Laumann TO, Roland JL, Montez DF, Van AN, Zheng A, Marek S, Kay BP, Bretthorst GL, Schlaggar BL, Greene DJ, Wang Y, Petersen SE, Barch DM, Gordon EM, Snyder AZ, Shimony JS, Dosenbach NUF. Accuracy and reliability of diffusion imaging models. Neuroimage 2022; 254:119138. [PMID: 35339687 PMCID: PMC9841915 DOI: 10.1016/j.neuroimage.2022.119138] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/01/2022] [Accepted: 03/22/2022] [Indexed: 01/19/2023] Open
Abstract
Diffusion imaging aims to non-invasively characterize the anatomy and integrity of the brain's white matter fibers. We evaluated the accuracy and reliability of commonly used diffusion imaging methods as a function of data quantity and analysis method, using both simulations and highly sampled individual-specific data (927-1442 diffusion weighted images [DWIs] per individual). Diffusion imaging methods that allow for crossing fibers (FSL's BedpostX [BPX], DSI Studio's Constant Solid Angle Q-Ball Imaging [CSA-QBI], MRtrix3's Constrained Spherical Deconvolution [CSD]) estimated excess fibers when insufficient data were present and/or when the data did not match the model priors. To reduce such overfitting, we developed a novel Bayesian Multi-tensor Model-selection (BaMM) method and applied it to the popular ball-and-stick model used in BedpostX within the FSL software package. BaMM was robust to overfitting and showed high reliability and the relatively best crossing-fiber accuracy with increasing amounts of diffusion data. Thus, sufficient data and an overfitting resistant analysis method enhance precision diffusion imaging. For potential clinical applications of diffusion imaging, such as neurosurgical planning and deep brain stimulation (DBS), the quantities of data required to achieve diffusion imaging reliability are lower than those needed for functional MRI.
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Affiliation(s)
- Nicole A Seider
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Babatunde Adeyemo
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Ryland Miller
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Dillan J Newbold
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Neurology, New York University Langone Medical Center, New York, NY 10016, United States of America
| | - Jacqueline M Hampton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Kristen M Scheidter
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Jerrel Rutlin
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Timothy O Laumann
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Jarod L Roland
- Department of Neurological Surgery, Washington University School of Medicine, St Louis, MO 63110 United States of America
| | - David F Montez
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Andrew N Van
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO 63110, United States of America
| | - Annie Zheng
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Scott Marek
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Benjamin P Kay
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - G Larry Bretthorst
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Chemistry, Washington University in St Louis, St. Louis, MO 63110, United States of America
| | - Bradley L Schlaggar
- Kennedy Krieger Institute, Baltimore, MD 21205, United States of America; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States of America; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States of America
| | - Deanna J Greene
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, United States of America
| | - Yong Wang
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Obstetrics and Gynecology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO 63110, United States of America
| | - Steven E Petersen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO 63110, United States of America; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Psychological and Brain Sciences, Washington University in St. Louis, MO 63110, United States of America
| | - Deanna M Barch
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Psychological and Brain Sciences, Washington University in St. Louis, MO 63110, United States of America
| | - Evan M Gordon
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Abraham Z Snyder
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Joshua S Shimony
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Nico U F Dosenbach
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Biomedical Engineering, Washington University in St Louis, St. Louis, MO 63110, United States of America; Program in Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, United States of America
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14
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De Brito Robalo BM, Vlegels N, Leemans A, Reijmer YD, Biessels GJ. Impact of thresholding on the consistency and sensitivity of diffusion MRI-based brain networks in patients with cerebral small vessel disease. Brain Behav 2022; 12:e2523. [PMID: 35413156 PMCID: PMC9120729 DOI: 10.1002/brb3.2523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Thresholding of low-weight connections of diffusion MRI-based brain networks has been proposed to remove false-positive connections. It has been previously established that this yields more reproducible scan-rescan network architecture in healthy subjects. In patients with brain disease, network measures are applied to assess inter-individual variation and changes over time. Our aim was to investigate whether thresholding also achieves improved consistency in network architecture in patients, while maintaining sensitivity to disease effects for these applications. METHODS We applied fixed-density and absolute thresholding on brain networks in patients with cerebral small vessel disease (SVD, n = 86; ≈24 months follow-up), as a clinically relevant exemplar condition. In parallel, we applied the same methods in healthy young subjects (n = 44; scan-rescan interval ≈4 months) as a frame of reference. Consistency of network architecture was assessed with dice similarity of edges and intraclass correlation coefficient (ICC) of edge-weights and hub-scores. Sensitivity to disease effects in patients was assessed by evaluating interindividual variation, changes over time, and differences between those with high and low white matter hyperintensity burden, using correlation analyses and mixed ANOVA. RESULTS Compared to unthresholded networks, both thresholding methods generated more consistent architecture over time in patients (unthresholded: dice = .70; ICC: .70-.78; thresholded: dice = .77; ICC: .73-.83). However, absolute thresholding created fragmented nodes. Similar observations were made in the reference group. Regarding sensitivity to disease effects in patients, fixed-density thresholds that were optimal in terms of consistency (densities: .10-.30) preserved interindividual variation in global efficiency and node strength as well as the sensitivity to detect effects of time and group. Absolute thresholding produced larger fluctuations of interindividual variation. CONCLUSIONS Our results indicate that thresholding of low-weight connections, particularly when using fixed-density thresholding, results in more consistent network architecture in patients with longer rescan intervals, while preserving sensitivity to disease effects.
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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
| | - Naomi Vlegels
- Department of Neurology and Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Alexander Leemans
- PROVIDI Lab, Image Sciences Institute, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Yael D Reijmer
- 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
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15
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Li W, Zhao J, Shen C, Zhang J, Hu J, Xiao M, Zhang J, Chen M. Regional Brain Fusion: Graph Convolutional Network for Alzheimer's Disease Prediction and Analysis. Front Neuroinform 2022; 16:886365. [PMID: 35571869 PMCID: PMC9100702 DOI: 10.3389/fninf.2022.886365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/30/2022] [Indexed: 11/24/2022] Open
Abstract
Alzheimer's disease (AD) has raised extensive concern in healthcare and academia as one of the most prevalent health threats to the elderly. Due to the irreversible nature of AD, early and accurate diagnoses are significant for effective prevention and treatment. However, diverse clinical symptoms and limited neuroimaging accuracy make diagnoses challenging. In this article, we built a brain network for each subject, which assembles several commonly used neuroimaging data simply and reasonably, including structural magnetic resonance imaging (MRI), diffusion-weighted imaging (DWI), and amyloid positron emission tomography (PET). Based on some existing research results, we applied statistical methods to analyze (i) the distinct affinity of AD burden on each brain region, (ii) the topological lateralization between left and right hemispheric sub-networks, and (iii) the asymmetry of the AD attacks on the left and right hemispheres. In the light of advances in graph convolutional networks for graph classifications and summarized characteristics of brain networks and AD pathologies, we proposed a regional brain fusion-graph convolutional network (RBF-GCN), which is constructed with an RBF framework mainly, including three sub-modules, namely, hemispheric network generation module, multichannel GCN module, and feature fusion module. In the multichannel GCN module, the improved GCN by our proposed adaptive native node attribute (ANNA) unit embeds within each channel independently. We not only fully verified the effectiveness of the RBF framework and ANNA unit but also achieved competitive results in multiple sets of AD stages' classification tasks using hundreds of experiments over the ADNI clinical dataset.
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Affiliation(s)
- Wenchao Li
- Intelligent Information Processing Laboratory, Hangzhou Dianzi University, Hangzhou, China
| | - Jiaqi Zhao
- Research Center for Healthcare Data Science, Zhejiang Lab, Hangzhou, China
| | - Chenyu Shen
- Intelligent Information Processing Laboratory, Hangzhou Dianzi University, Hangzhou, China
| | - Jingwen Zhang
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, United States
| | - Ji Hu
- Intelligent Information Processing Laboratory, Hangzhou Dianzi University, Hangzhou, China
| | - Mang Xiao
- Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiyong Zhang
- Intelligent Information Processing Laboratory, Hangzhou Dianzi University, Hangzhou, China
- *Correspondence: Jiyong Zhang
| | - Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, NC, United States
- Minghan Chen
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16
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Clarke H, Messaritaki E, Dimitriadis SI, Metzler-Baddeley C. Dementia Risk Factors Modify Hubs but Leave Other Connectivity Measures Unchanged in Asymptomatic Individuals: A Graph Theoretical Analysis. Brain Connect 2022; 12:26-40. [PMID: 34030485 PMCID: PMC8867081 DOI: 10.1089/brain.2020.0935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background: Alzheimer's disease (AD) is the most common form of dementia with genetic and environmental risk contributing to its development. Graph theoretical analyses of brain networks constructed from structural and functional magnetic resonance imaging (MRI) measurements have identified connectivity changes in AD and individuals with mild cognitive impairment. However, brain connectivity in asymptomatic individuals at risk of AD remains poorly understood. Methods: We analyzed diffusion-weighted MRI data from 161 asymptomatic individuals (38-71 years) from the Cardiff Ageing and Risk of Dementia Study (CARDS). We calculated white matter tracts and constructed whole-brain, default mode network (DMN) and visual structural brain networks that incorporate multiple structural metrics as edge weights. We then calculated the relationship of three AD risk factors, namely Apolipoprotein-E ɛ4 (APOE4) genotype, family history of dementia (FH), and central obesity (Waist-Hip-Ratio [WHR]), on graph theoretical measures and hubs. Results: We observed no risk-related differences in clustering coefficients, characteristic path lengths, eccentricity, diameter, and radius across the whole-brain, DMN or visual system. However, a hub in the right paracentral lobule was present in all the high-risk groups (FH, APOE4, obese), but absent in low-risk groups (no FH, APOE4-ve, healthy WHR). Discussion: We identified no risk-related effects on graph theoretical metrics in the structural brain networks of cognitively healthy individuals. However, high risk was associated with a hub in the right paracentral lobule, a medial fronto-parietal cortical area with motor and sensory functions. This finding is consistent with accumulating evidence for right parietal cortex contributions in AD. If this phenotype is shown to predict symptom development in longitudinal studies, it could be used as an early biomarker of AD. Impact statement Alzheimer's disease (AD) is a common form of dementia that to date has no cure. Identifying early biomarkers will aid the discovery and development of treatments that may slow AD progression in the future. In this article, we report that asymptomatic individuals at heightened risk of dementia due to their family history, Apolipoprotein-E ɛ4 genotype, and central adiposity have a hub in the right paracentral lobule, which is absent in low-risk groups. If this phenotype were to predict the development of symptoms in a longitudinal study of the same cohort, it could provide an early biomarker of disease progression.
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Affiliation(s)
- Hannah Clarke
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
- School of Medicine, UK Dementia Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Eirini Messaritaki
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
- BRAIN Biomedical Research Unit, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Stavros I. Dimitriadis
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
- Neuroinformatics Group, Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff University, Cardiff, United Kingdom
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
- School of Psychology, Cardiff University, Cardiff, United Kingdom
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Claudia Metzler-Baddeley
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom
- Neuroscience and Mental Health Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
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17
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Borrelli P, Cavaliere C, Salvatore M, Jovicich J, Aiello M. Structural Brain Network Reproducibility: Influence of Different Diffusion Acquisition and Tractography Reconstruction Schemes on Graph Metrics. Brain Connect 2021; 12:754-767. [PMID: 34605673 DOI: 10.1089/brain.2021.0123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Graph metrics of structural brain networks demonstrate to be a powerful tool for investigating brain topology at a large scale. However, the variability of the results related to applying different magnetic resonance acquisition schemes and tractography reconstruction techniques is not fully characterized. Materials and Methods: The present work aims to evaluate the influence of different combinations of diffusion acquisition schemes (single and multishell), diffusion models (tensor and spherical deconvolution), and tractography reconstruction approaches (deterministic and probabilistic) on the reproducibility of graph metrics derived from structural connectome on test/retest (TRT) data released by the Human Connectome Project. From each implemented experimental setup, both global and local graph metrics were evaluated and their reproducibility was estimated by the intraclass correlation coefficient (ICC). Moreover, the percentage relative standard deviation (pRSD) from the ICC values of local graph metrics was calculated to quantify how much the reproducibility varied across nodes within each experimental setup. Results: The presented results show that different combinations of diffusion acquisition schemes, diffusion models, and tractography algorithms can strongly affect the reproducibility of global and local graph metrics. The combination of constrained spherical deconvolution (CSD) and deterministic tractography gave generally high reproducibility (ICCs >0.75) and lowest pRSD for the considered graph metrics, meanwhile probabilistic CSD with a high b-value returned the highest reproducibility. Notably, the introduction of streamline selection filters on CSD can substantially affect the reproducibility. Discussion: This work demonstrates that the TRT reproducibility of graph metrics is generally high but can vary substantially with different combinations of acquisition and reconstruction schemes. Impact statement This work demonstrates the influence of different diffusion acquisition schemes, diffusion models, and tractography reconstruction approaches on the reproducibility of graph metrics derived from structural connectome. The presented findings impact on the choice of both acquisition protocol and processing pipeline for topological analyses to produce reproducible measurements for brain network studies.
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Affiliation(s)
| | | | | | - Jorge Jovicich
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
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18
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Kurokawa R, Kamiya K, Koike S, Nakaya M, Uematsu A, Tanaka SC, Kamagata K, Okada N, Morita K, Kasai K, Abe O. Cross-scanner reproducibility and harmonization of a diffusion MRI structural brain network: A traveling subject study of multi-b acquisition. Neuroimage 2021; 245:118675. [PMID: 34710585 DOI: 10.1016/j.neuroimage.2021.118675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/26/2021] [Accepted: 10/21/2021] [Indexed: 01/18/2023] Open
Abstract
Characterization of brain networks by diffusion MRI (dMRI) has rapidly evolved, and there are ongoing movements toward data sharing and multi-center studies. To extract meaningful information from multi-center data, methods to correct for the bias caused by scanner differences, that is, harmonization, are urgently needed. In this work, we report the cross-scanner differences in structural network analyses using data from nine traveling subjects (four males and five females, 21-49 years-old) who underwent scanning using four 3T scanners (public database available from the Brain/MINDS Beyond Human Brain MRI project (http://mriportal.umin.jp/)). The reliability and reproducibility were compared to those of data from another set of four subjects (all males, 29-42 years-old) who underwent scan-rescan (interval, 105-147 days) with the same scanner as well as scan-rescan data from the Human Connectome Project database. The results demonstrated that the reliability of the edge weights and graph theory metrics was lower for data including different scanners, compared to the scan-rescan with the same scanner. Besides, systematic differences between scanners were observed, indicating the risk of bias in comparing networks obtained from different scanners directly. We further demonstrate that it is feasible to reduce inter-scanner variabilities while preserving the inter-subject differences among healthy individuals by modeling the scanner effects at the level of network matrices, when traveling-subject data are available for calibration between scanners. The present data and results are expected to serve as a basis for developing and evaluating novel harmonization methods.
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Affiliation(s)
- Ryo Kurokawa
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Kouhei Kamiya
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Radiology, Toho University, Tokyo, Japan; Department of Radiology, Juntendo University, Tokyo, Japan.
| | - Shinsuke Koike
- Center for Evolutionary Cognitive Sciences (ECS), Graduate School of Art and Sciences, The University of Tokyo, Tokyo, Japan; University of Tokyo Institute for Diversity & Adaptation of Human Mind (UTIDAHM), Tokyo, Japan; University of Tokyo Center for Integrative Science of Human Behavior (CiSHuB), Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan.
| | - Moto Nakaya
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Akiko Uematsu
- Center for Evolutionary Cognitive Sciences (ECS), Graduate School of Art and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Saori C Tanaka
- Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institutes International (ATR), Kyoto, Japan.
| | - Koji Kamagata
- Department of Radiology, Juntendo University, Tokyo, Japan.
| | - Naohiro Okada
- University of Tokyo Institute for Diversity & Adaptation of Human Mind (UTIDAHM), Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan; Department of Neuropsychiatry, The University of Tokyo, Tokyo, Japan.
| | - Kentaro Morita
- Department of Neuropsychiatry, The University of Tokyo, Tokyo, Japan.
| | - Kiyoto Kasai
- University of Tokyo Institute for Diversity & Adaptation of Human Mind (UTIDAHM), Tokyo, Japan; University of Tokyo Center for Integrative Science of Human Behavior (CiSHuB), Tokyo, Japan; The International Research Center for Neurointelligence (WPI-IRCN), Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan; Department of Neuropsychiatry, The University of Tokyo, Tokyo, Japan.
| | - Osamu Abe
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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19
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Marimpis AD, Dimitriadis SI, Goebel R. Dyconnmap: Dynamic connectome mapping-A neuroimaging python module. Hum Brain Mapp 2021; 42:4909-4939. [PMID: 34250674 PMCID: PMC8449119 DOI: 10.1002/hbm.25589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/10/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022] Open
Abstract
Despite recent progress in the analysis of neuroimaging data sets, our comprehension of the main mechanisms and principles which govern human brain cognition and function remains incomplete. Network neuroscience makes substantial efforts to manipulate these challenges and provide real answers. For the last decade, researchers have been modelling brain structure and function via a graph or network that comprises brain regions that are either anatomically connected via tracts or functionally via a more extensive repertoire of functional associations. Network neuroscience is a relatively new multidisciplinary scientific avenue of the study of complex systems by pursuing novel ways to analyze, map, store and model the essential elements and their interactions in complex neurobiological systems, particularly the human brain, the most complex system in nature. Due to a rapid expansion of neuroimaging data sets' size and complexity, it is essential to propose and adopt new empirical tools to track dynamic patterns between neurons and brain areas and create comprehensive maps. In recent years, there is a rapid growth of scientific interest in moving functional neuroimaging analysis beyond simplified group or time‐averaged approaches and sophisticated algorithms that can capture the time‐varying properties of functional connectivity. We describe algorithms and network metrics that can capture the dynamic evolution of functional connectivity under this perspective. We adopt the word ‘chronnectome’ (integration of the Greek word ‘Chronos’, which means time, and connectome) to describe this specific branch of network neuroscience that explores how mutually informed brain activity correlates across time and brain space in a functional way. We also describe how good temporal mining of temporally evolved dynamic functional networks could give rise to the detection of specific brain states over which our brain evolved. This characteristic supports our complex human mind. The temporal evolution of these brain states and well‐known network metrics could give rise to new analytic trends. Functional brain networks could also increase the multi‐faced nature of the dynamic networks revealing complementary information. Finally, we describe a python module (https://github.com/makism/dyconnmap) which accompanies this article and contains a collection of dynamic complex network analytics and measures and demonstrates its great promise for the study of a healthy subject's repeated fMRI scans.
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Affiliation(s)
- Avraam D Marimpis
- Cognitive Neuroscience Department, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands.,Neuroinformatics Group, Cardiff University Brain Research Imaging Center (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.,Brain Innovation B.V, Maastricht, The Netherlands
| | - Stavros I Dimitriadis
- Neuroinformatics Group, Cardiff University Brain Research Imaging Center (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.,Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, United Kingdom.,Cardiff University Brain Research Imaging Center (CUBRIC), School of Psychology, Cardiff University, Cardiff, United Kingdom.,School of Psychology, Cardiff University, Cardiff, United Kingdom.,Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom.,MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Rainer Goebel
- Cognitive Neuroscience Department, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, The Netherlands.,Brain Innovation B.V, Maastricht, The Netherlands
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20
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Dimitriadis SI, Messaritaki E, K Jones D. The impact of graph construction scheme and community detection algorithm on the repeatability of community and hub identification in structural brain networks. Hum Brain Mapp 2021; 42:4261-4280. [PMID: 34170066 PMCID: PMC8356981 DOI: 10.1002/hbm.25545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/14/2021] [Indexed: 12/20/2022] Open
Abstract
A critical question in network neuroscience is how nodes cluster together to form communities, to form the mesoscale organisation of the brain. Various algorithms have been proposed for identifying such communities, each identifying different communities within the same network. Here, (using test–retest data from the Human Connectome Project), the repeatability of thirty‐three community detection algorithms, each paired with seven different graph construction schemes were assessed. Repeatability of community partition depended heavily on both the community detection algorithm and graph construction scheme. Hard community detection algorithms (in which each node is assigned to only one community) outperformed soft ones (in which each node can belong to more than one community). The highest repeatability was observed for the fast multi‐scale community detection algorithm paired with a graph construction scheme that combines nine white matter metrics. This pair also gave the highest similarity between representative group community affiliation and individual community affiliation. Connector hubs had higher repeatability than provincial hubs. Our results provide a workflow for repeatable identification of structural brain networks communities, based on the optimal pairing of community detection algorithm and graph construction scheme.
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Affiliation(s)
- Stavros I Dimitriadis
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK.,Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.,School of Psychology, Cardiff University, Cardiff, UK.,Neuroinformatics Group, Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff University, Cardiff, UK.,Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK.,MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Eirini Messaritaki
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK.,Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.,School of Psychology, Cardiff University, Cardiff, UK.,BRAIN Biomedical Research Unit, Cardiff University, Cardiff, UK
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK.,School of Psychology, Cardiff University, Cardiff, UK
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21
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Messaritaki E, Foley S, Schiavi S, Magazzini L, Routley B, Jones DK, Singh KD. Predicting MEG resting-state functional connectivity from microstructural information. Netw Neurosci 2021; 5:477-504. [PMID: 34189374 PMCID: PMC8233113 DOI: 10.1162/netn_a_00187] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/01/2021] [Indexed: 12/18/2022] Open
Abstract
Understanding how human brain microstructure influences functional connectivity is an important endeavor. In this work, magnetic resonance imaging data from 90 healthy participants were used to calculate structural connectivity matrices using the streamline count, fractional anisotropy, radial diffusivity, and a myelin measure (derived from multicomponent relaxometry) to assign connection strength. Unweighted binarized structural connectivity matrices were also constructed. Magnetoencephalography resting-state data from those participants were used to calculate functional connectivity matrices, via correlations of the Hilbert envelopes of beamformer time series in the delta, theta, alpha, and beta frequency bands. Nonnegative matrix factorization was performed to identify the components of the functional connectivity. Shortest path length and search-information analyses of the structural connectomes were used to predict functional connectivity patterns for each participant. The microstructure-informed algorithms predicted the components of the functional connectivity more accurately than they predicted the total functional connectivity. This provides a methodology to understand functional mechanisms better. The shortest path length algorithm exhibited the highest prediction accuracy. Of the weights of the structural connectivity matrices, the streamline count and the myelin measure gave the most accurate predictions, while the fractional anisotropy performed poorly. Overall, different structural metrics paint very different pictures of the structural connectome and its relationship to functional connectivity.
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Affiliation(s)
- Eirini Messaritaki
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Maindy Road, Cardiff, UK
| | - Sonya Foley
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Maindy Road, Cardiff, UK
| | - Simona Schiavi
- Department of Computer Science, University of Verona, Verona, Italy
| | - Lorenzo Magazzini
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Maindy Road, Cardiff, UK
| | - Bethany Routley
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Maindy Road, Cardiff, UK
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Maindy Road, Cardiff, UK
| | - Krish D Singh
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Maindy Road, Cardiff, UK
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22
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Yeh CH, Jones DK, Liang X, Descoteaux M, Connelly A. Mapping Structural Connectivity Using Diffusion MRI: Challenges and Opportunities. J Magn Reson Imaging 2021; 53:1666-1682. [PMID: 32557893 PMCID: PMC7615246 DOI: 10.1002/jmri.27188] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022] Open
Abstract
Diffusion MRI-based tractography is the most commonly-used technique when inferring the structural brain connectome, i.e., the comprehensive map of the connections in the brain. The utility of graph theory-a powerful mathematical approach for modeling complex network systems-for analyzing tractography-based connectomes brings important opportunities to interrogate connectome data, providing novel insights into the connectivity patterns and topological characteristics of brain structural networks. When applying this framework, however, there are challenges, particularly regarding methodological and biological plausibility. This article describes the challenges surrounding quantitative tractography and potential solutions. In addition, challenges related to the calculation of global network metrics based on graph theory are discussed.Evidence Level: 5Technical Efficacy: Stage 1.
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Affiliation(s)
- Chun-Hung Yeh
- Institute for Radiological Research, Chang Gung University and Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Child and Adolescent Psychiatry, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Derek K. Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK
- Mary Mackillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| | - Xiaoyun Liang
- Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
- Mary Mackillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| | - Maxime Descoteaux
- Sherbrooke Connectivity Imaging Laboratory (SCIL), Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Alan Connelly
- Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia
- Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia
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23
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Jung K, Eickhoff SB, Popovych OV. Tractography density affects whole-brain structural architecture and resting-state dynamical modeling. Neuroimage 2021; 237:118176. [PMID: 34000399 DOI: 10.1016/j.neuroimage.2021.118176] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 11/24/2022] Open
Abstract
Dynamical modeling of the resting-state brain dynamics essentially relies on the empirical neuroimaging data utilized for the model derivation and validation. There is however still no standardized data processing for magnetic resonance imaging pipelines and the structural and functional connectomes involved in the models. In this study, we thus address how the parameters of diffusion-weighted data processing for structural connectivity (SC) can influence the validation results of the whole-brain mathematical models informed by SC. For this, we introduce a set of simulation conditions including the varying number of total streamlines of the whole-brain tractography (WBT) used for extraction of SC, cortical parcellations based on functional and anatomical brain properties and distinct model fitting modalities. The main objective of this study is to explore how the quality of the model validation can vary across the considered simulation conditions. We observed that the graph-theoretical network properties of structural connectome can be affected by varying tractography density and strongly relate to the model performance. We also found that the optimal number of the total streamlines of WBT can vary for different brain atlases. Consequently, we suggest a way how to improve the model performance based on the network properties and the optimal parameter configurations from multiple WBT conditions. Furthermore, the population of subjects can be stratified into subgroups with divergent behaviors induced by the varying WBT density such that different recommendations can be made with respect to the data processing for individual subjects and brain parcellations.
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Affiliation(s)
- Kyesam Jung
- Institute of Neuroscience and Medicine, Brain and Behavior (INM-7), Research Center Jülich, Germany; Institute for Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Germany.
| | - Simon B Eickhoff
- Institute of Neuroscience and Medicine, Brain and Behavior (INM-7), Research Center Jülich, Germany; Institute for Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Germany.
| | - Oleksandr V Popovych
- Institute of Neuroscience and Medicine, Brain and Behavior (INM-7), Research Center Jülich, Germany; Institute for Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Germany.
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24
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Boshkovski T, Kocarev L, Cohen-Adad J, Mišić B, Lehéricy S, Stikov N, Mancini M. The R1-weighted connectome: complementing brain networks with a myelin-sensitive measure. Netw Neurosci 2021; 5:358-372. [PMID: 34189369 PMCID: PMC8233108 DOI: 10.1162/netn_a_00179] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/11/2020] [Indexed: 11/05/2022] Open
Abstract
Myelin plays a crucial role in how well information travels between brain regions. Complementing the structural connectome, obtained with diffusion MRI tractography, with a myelin-sensitive measure could result in a more complete model of structural brain connectivity and give better insight into white-matter myeloarchitecture. In this work we weight the connectome by the longitudinal relaxation rate (R1), a measure sensitive to myelin, and then we assess its added value by comparing it with connectomes weighted by the number of streamlines (NOS). Our analysis reveals differences between the two connectomes both in the distribution of their weights and the modular organization. Additionally, the rank-based analysis shows that R1 can be used to separate transmodal regions (responsible for higher-order functions) from unimodal regions (responsible for low-order functions). Overall, the R1-weighted connectome provides a different perspective on structural connectivity taking into account white matter myeloarchitecture. In the present work, we show that by using a myelin-sensitive measure we can complement the diffusion MRI-based connectivity and provide a different picture of the brain organization. We show that the R1-weighted average distribution does not follow the same trend as the number of streamlines strength distribution, and the two connectomes exhibit different modular organization. We also show that unimodal cortical regions tend to be connected by more streamlines, but the connections exhibit a lower R1-weighted average, while the transmodal regions have higher R1-weighted average but fewer streamlines. This could imply that the unimodal regions require more connections with lower myelination, whereas the transmodal regions rely on connections with higher myelination.
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Affiliation(s)
| | - Ljupco Kocarev
- Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | | | | | - Stéphane Lehéricy
- Paris Brain Institute (ICM), Centre for NeuroImaging Research (CENIR), Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013, Paris, France
| | - Nikola Stikov
- NeuroPoly Lab, Polytechnique Montreal, Montreal, QC, Canada
| | - Matteo Mancini
- NeuroPoly Lab, Polytechnique Montreal, Montreal, QC, Canada
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25
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Luppi AI, Stamatakis EA. Combining network topology and information theory to construct representative brain networks. Netw Neurosci 2021; 5:96-124. [PMID: 33688608 PMCID: PMC7935031 DOI: 10.1162/netn_a_00170] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/23/2020] [Indexed: 01/21/2023] Open
Abstract
Network neuroscience employs graph theory to investigate the human brain as a complex network, and derive generalizable insights about the brain's network properties. However, graph-theoretical results obtained from network construction pipelines that produce idiosyncratic networks may not generalize when alternative pipelines are employed. This issue is especially pressing because a wide variety of network construction pipelines have been employed in the human network neuroscience literature, making comparisons between studies problematic. Here, we investigate how to produce networks that are maximally representative of the broader set of brain networks obtained from the same neuroimaging data. We do so by minimizing an information-theoretic measure of divergence between network topologies, known as the portrait divergence. Based on functional and diffusion MRI data from the Human Connectome Project, we consider anatomical, functional, and multimodal parcellations at three different scales, and 48 distinct ways of defining network edges. We show that the highest representativeness can be obtained by using parcellations in the order of 200 regions and filtering functional networks based on efficiency-cost optimization-though suitable alternatives are also highlighted. Overall, we identify specific node definition and thresholding procedures that neuroscientists can follow in order to derive representative networks from their human neuroimaging data.
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Affiliation(s)
- Andrea I Luppi
- Division of Anesthesia, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Emmanuel A Stamatakis
- Division of Anesthesia, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
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26
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Poudel GR, Dominguez D JF, Verhelst H, Vander Linden C, Deblaere K, Jones DK, Cerin E, Vingerhoets G, Caeyenberghs K. Network diffusion modeling predicts neurodegeneration in traumatic brain injury. Ann Clin Transl Neurol 2020; 7:270-279. [PMID: 32105414 PMCID: PMC7086000 DOI: 10.1002/acn3.50984] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/10/2019] [Indexed: 02/03/2023] Open
Abstract
Objective Traumatic brain injury (TBI) is a heterogeneous disease with multiple neurological deficits that evolve over time. It is also associated with an increased incidence of neurodegenerative diseases. Accordingly, clinicians need better tools to predict a patient’s long‐term prognosis. Methods Diffusion‐weighted and anatomical MRI data were collected from 17 adolescents (mean age = 15y8mo) with moderate‐to‐severe TBI and 19 healthy controls. Using a network diffusion model (NDM), we examined the effect of progressive deafferentation and gray matter thinning in young TBI patients. Moreover, using a novel automated inference method, we identified several injury epicenters in order to determine the neural degenerative patterns in each TBI patient. Results We were able to identify the subject‐specific patterns of degeneration in each patient. In particular, the hippocampus, temporal cortices, and striatum were frequently found to be the epicenters of degeneration across the TBI patients. Orthogonal transformation of the predicted degeneration, using principal component analysis, identified distinct spatial components in the temporal–hippocampal network and the cortico‐striatal network, confirming the vulnerability of these networks to injury. The NDM model, best predictive of the degeneration, was significantly correlated with time since injury, indicating that NDM can potentially capture the pathological progression in the chronic phase of TBI. Interpretation These findings suggest that network spread may help explain patterns of distant gray matter thinning, which would be consistent with Wallerian degeneration of the white matter connections (i.e., “diaschisis”) from diffuse axonal injuries and multifocal contusive injuries, and the neurodegenerative patterns of abnormal protein aggregation and transmission, which are hallmarks of brain changes in TBI. NDM approaches could provide highly subject‐specific biomarkers relevant for disease monitoring and personalized therapies in TBI.
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Affiliation(s)
- Govinda R Poudel
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Juan F Dominguez D
- Cognitive Neuroscience Unit, School of Psychology, Deakin University, Burwood, VIC, Australia
| | - Helena Verhelst
- Department of Experimental Psychology, Faculty of Psychology and Educational Sciences, Ghent University, Ghent, Oost-Vlaanderen, Belgium
| | | | - Karel Deblaere
- Department of Neuroradiology, Ghent University Hospital, Ghent, Oost-Vlaanderen, Belgium
| | - Derek K Jones
- Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, Wales, United Kingdom
| | - Ester Cerin
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, Australia
| | - Guy Vingerhoets
- Department of Experimental Psychology, Faculty of Psychology and Educational Sciences, Ghent University, Ghent, Oost-Vlaanderen, Belgium
| | - Karen Caeyenberghs
- Cognitive Neuroscience Unit, School of Psychology, Deakin University, Burwood, VIC, Australia
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