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Park BY, Benkarim O, Weber CF, Kebets V, Fett S, Yoo S, Martino AD, Milham MP, Misic B, Valk SL, Hong SJ, Bernhardt BC. Connectome-wide structure-function coupling models implicate polysynaptic alterations in autism. Neuroimage 2024; 285:120481. [PMID: 38043839 DOI: 10.1016/j.neuroimage.2023.120481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 11/29/2023] [Accepted: 12/01/2023] [Indexed: 12/05/2023] Open
Abstract
Autism spectrum disorder (ASD) is one of the most common neurodevelopmental diagnoses. Although incompletely understood, structural and functional network alterations are increasingly recognized to be at the core of the condition. We utilized multimodal imaging and connectivity modeling to study structure-function coupling in ASD and probed mono- and polysynaptic mechanisms on structurally-governed network function. We examined multimodal magnetic resonance imaging data in 80 ASD and 61 neurotypical controls from the Autism Brain Imaging Data Exchange (ABIDE) II initiative. We predicted intrinsic functional connectivity from structural connectivity data in each participant using a Riemannian optimization procedure that varies the times that simulated signals can unfold along tractography-derived personalized connectomes. In both ASD and neurotypical controls, we observed improved structure-function prediction at longer diffusion time scales, indicating better modeling of brain function when polysynaptic mechanisms are accounted for. Prediction accuracy differences (∆prediction accuracy) were marked in transmodal association systems, such as the default mode network, in both neurotypical controls and ASD. Differences were, however, lower in ASD in a polysynaptic regime at higher simulated diffusion times. We compared regional differences in ∆prediction accuracy between both groups to assess the impact of polysynaptic communication on structure-function coupling. This analysis revealed that between-group differences in ∆prediction accuracy followed a sensory-to-transmodal cortical hierarchy, with an increased gap between controls and ASD in transmodal compared to sensory/motor systems. Multivariate associative techniques revealed that structure-function differences reflected inter-individual differences in autistic symptoms and verbal as well as non-verbal intelligence. Our network modeling approach sheds light on atypical structure-function coupling in autism, and suggests that polysynaptic network mechanisms are implicated in the condition and that these can help explain its wide range of associated symptoms.
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Affiliation(s)
- Bo-Yong Park
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada; Department of Data Science, Inha University, Incheon, South Korea; Department of Statistics and Data Science, Inha University, Incheon, South Korea; Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea.
| | - Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Clara F Weber
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Valeria Kebets
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Serena Fett
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Seulki Yoo
- Convergence Research Institute, Sungkyunkwan University, Suwon, South Korea
| | - Adriana Di Martino
- Center for the Developing Brain, Child Mind Institute, New York, United States
| | - Michael P Milham
- Center for the Developing Brain, Child Mind Institute, New York, United States
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Sofie L Valk
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Seok-Jun Hong
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada; Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea; Center for the Developing Brain, Child Mind Institute, New York, United States; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada.
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Urru A, Nakaki A, Benkarim O, Crovetto F, Segalés L, Comte V, Hahner N, Eixarch E, Gratacos E, Crispi F, Piella G, González Ballester MA. An automatic pipeline for atlas-based fetal and neonatal brain segmentation and analysis. Comput Methods Programs Biomed 2023; 230:107334. [PMID: 36682108 DOI: 10.1016/j.cmpb.2023.107334] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 11/29/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND OBJECTIVE The automatic segmentation of perinatal brain structures in magnetic resonance imaging (MRI) is of utmost importance for the study of brain growth and related complications. While different methods exist for adult and pediatric MRI data, there is a lack for automatic tools for the analysis of perinatal imaging. METHODS In this work, a new pipeline for fetal and neonatal segmentation has been developed. We also report the creation of two new fetal atlases, and their use within the pipeline for atlas-based segmentation, based on novel registration methods. The pipeline is also able to extract cortical and pial surfaces and compute features, such as curvature, local gyrification index, sulcal depth, and thickness. RESULTS Results show that the introduction of the new templates together with our segmentation strategy leads to accurate results when compared to expert annotations, as well as better performances when compared to a reference pipeline (developing Human Connectome Project (dHCP)), for both early and late-onset fetal brains. CONCLUSIONS These findings show the potential of the presented atlases and the whole pipeline for application in both fetal, neonatal, and longitudinal studies, which could lead to dramatic improvements in the understanding of perinatal brain development.
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Affiliation(s)
- Andrea Urru
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Ayako Nakaki
- BCNatal | Fetal Medicine Research Center (Hospital Clínic and Hospital Sant Joan de Déu), University of Barcelona, Barcelona, Spain; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Francesca Crovetto
- BCNatal | Fetal Medicine Research Center (Hospital Clínic and Hospital Sant Joan de Déu), University of Barcelona, Barcelona, Spain
| | - Laura Segalés
- BCNatal | Fetal Medicine Research Center (Hospital Clínic and Hospital Sant Joan de Déu), University of Barcelona, Barcelona, Spain
| | - Valentin Comte
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nadine Hahner
- BCNatal | Fetal Medicine Research Center (Hospital Clínic and Hospital Sant Joan de Déu), University of Barcelona, Barcelona, Spain; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Elisenda Eixarch
- BCNatal | Fetal Medicine Research Center (Hospital Clínic and Hospital Sant Joan de Déu), University of Barcelona, Barcelona, Spain; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centre for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Eduard Gratacos
- BCNatal | Fetal Medicine Research Center (Hospital Clínic and Hospital Sant Joan de Déu), University of Barcelona, Barcelona, Spain; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centre for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Fàtima Crispi
- BCNatal | Fetal Medicine Research Center (Hospital Clínic and Hospital Sant Joan de Déu), University of Barcelona, Barcelona, Spain; Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain; Centre for Biomedical Research on Rare Diseases (CIBERER), Barcelona, Spain
| | - Gemma Piella
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Miguel A González Ballester
- BCN MedTech, Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain; ICREA, Barcelona, Spain.
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3
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Hong SJ, Mottron L, Park BY, Benkarim O, Valk SL, Paquola C, Larivière S, Vos de Wael R, Degré-Pelletier J, Soulieres I, Ramphal B, Margolis A, Milham M, Di Martino A, Bernhardt BC. A convergent structure-function substrate of cognitive imbalances in autism. Cereb Cortex 2023; 33:1566-1580. [PMID: 35552620 PMCID: PMC9977381 DOI: 10.1093/cercor/bhac156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a common neurodevelopmental diagnosis showing substantial phenotypic heterogeneity. A leading example can be found in verbal and nonverbal cognitive skills, which vary from elevated to impaired compared with neurotypical individuals. Moreover, deficits in verbal profiles often coexist with normal or superior performance in the nonverbal domain. METHODS To study brain substrates underlying cognitive imbalance in ASD, we capitalized categorical and dimensional IQ profiling as well as multimodal neuroimaging. RESULTS IQ analyses revealed a marked verbal to nonverbal IQ imbalance in ASD across 2 datasets (Dataset-1: 155 ASD, 151 controls; Dataset-2: 270 ASD, 490 controls). Neuroimaging analysis in Dataset-1 revealed a structure-function substrate of cognitive imbalance, characterized by atypical cortical thickening and altered functional integration of language networks alongside sensory and higher cognitive areas. CONCLUSION Although verbal and nonverbal intelligence have been considered as specifiers unrelated to autism diagnosis, our results indicate that intelligence disparities are accentuated in ASD and reflected by a consistent structure-function substrate affecting multiple brain networks. Our findings motivate the incorporation of cognitive imbalances in future autism research, which may help to parse the phenotypic heterogeneity and inform intervention-oriented subtyping in ASD.
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Affiliation(s)
- Seok-Jun Hong
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada.,Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon 16419, South Korea.,Department of Biomedical Engineering, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon 16419, South Korea.,Center for the Developing Brain, Child Mind Institute, 101 East 56th Street, New York, NY 10022, United States
| | - Laurent Mottron
- Centre de Recherche du CIUSSSNIM and Department of Psychiatry and Addictology, Université de Montréal, 7070 boulevard Perras, Montréal, Quebec H1E 1A4, Canada
| | - Bo-Yong Park
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada.,Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Seobu-ro 2066, Jangan-gu, Suwon 16419, South Korea.,Department of Data Science, Inha Univerisity, Incheon 22212, South Korea
| | - Oualid Benkarim
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada
| | - Sofie L Valk
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada.,Otto Hahn group Cognitive neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraβe 1A. Leipzig D-04103, Germany.,Institute of Neuroscience and Medicine, Research Centre Wilhelm-Johnen-Strasse, Jülich 52425, Germany.,Institute of Systems Neuroscience, Heinrich Heine University, Moorenstr. 5, Düsseldorf 40225, Germany
| | - Casey Paquola
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada.,Institute of Neuroscience and Medicine, Research Centre Wilhelm-Johnen-Strasse, Jülich 52425, Germany
| | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada
| | - Reinder Vos de Wael
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada
| | - Janie Degré-Pelletier
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada.,Department of Psychology, Université du Québec à Montréal, 100 rue Sherbrooke Ouest, Montréal, Québec H2X 3P2, Canada
| | - Isabelle Soulieres
- Department of Psychology, Université du Québec à Montréal, 100 rue Sherbrooke Ouest, Montréal, Québec H2X 3P2, Canada
| | - Bruce Ramphal
- Department of Psychiatry, The New York State Psychiatric Institute and the College of Physicians Surgeons, Columbia University, 1051 Riverside Drive, New York, NY 10032, United States
| | - Amy Margolis
- Department of Psychiatry, The New York State Psychiatric Institute and the College of Physicians Surgeons, Columbia University, 1051 Riverside Drive, New York, NY 10032, United States
| | - Michael Milham
- Center for the Developing Brain, Child Mind Institute, 101 East 56th Street, New York, NY 10022, United States.,Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute, 140 Old Orangeburg Road, Orangeburg, NY 10962, United States
| | - Adriana Di Martino
- Autism Center, Child Mind Institute, 101 East 56th Street, New York, NY 10022, United States
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Department of Neurology and Neurosurgery and Montreal Neurological Institute and Hospital, McGill University, 3801 University Street, Montreal, Quebec H3A2B4, Canada
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Larivière S, Bayrak Ş, Vos de Wael R, Benkarim O, Herholz P, Rodriguez-Cruces R, Paquola C, Hong SJ, Misic B, Evans AC, Valk SL, Bernhardt BC. BrainStat: A toolbox for brain-wide statistics and multimodal feature associations. Neuroimage 2023; 266:119807. [PMID: 36513290 DOI: 10.1016/j.neuroimage.2022.119807] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/28/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Analysis and interpretation of neuroimaging datasets has become a multidisciplinary endeavor, relying not only on statistical methods, but increasingly on associations with respect to other brain-derived features such as gene expression, histological data, and functional as well as cognitive architectures. Here, we introduce BrainStat - a toolbox for (i) univariate and multivariate linear models in volumetric and surface-based brain imaging datasets, and (ii) multidomain feature association of results with respect to spatial maps of post-mortem gene expression and histology, task-based fMRI meta-analysis, as well as resting-state fMRI motifs across several common surface templates. The combination of statistics and feature associations into a turnkey toolbox streamlines analytical processes and accelerates cross-modal research. The toolbox is implemented in both Python and MATLAB, two widely used programming languages in the neuroimaging and neuroinformatics communities. BrainStat is openly available and complemented by an expandable documentation.
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Affiliation(s)
- Sara Larivière
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Şeyma Bayrak
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Reinder Vos de Wael
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Peer Herholz
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Raul Rodriguez-Cruces
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Casey Paquola
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Germany
| | - Seok-Jun Hong
- Child Mind Institute, New York, USA; Center for Neuroscience Imaging Research, Institute for Basic Science, and Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Alan C Evans
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Sofie L Valk
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Germany.
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada.
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5
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Cruces RR, Royer J, Herholz P, Larivière S, Vos de Wael R, Paquola C, Benkarim O, Park BY, Degré-Pelletier J, Nelson MC, DeKraker J, Leppert IR, Tardif C, Poline JB, Concha L, Bernhardt BC. Micapipe: A pipeline for multimodal neuroimaging and connectome analysis. Neuroimage 2022; 263:119612. [PMID: 36070839 PMCID: PMC10697132 DOI: 10.1016/j.neuroimage.2022.119612] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 08/20/2022] [Accepted: 09/03/2022] [Indexed: 11/25/2022] Open
Abstract
Multimodal magnetic resonance imaging (MRI) has accelerated human neuroscience by fostering the analysis of brain microstructure, geometry, function, and connectivity across multiple scales and in living brains. The richness and complexity of multimodal neuroimaging, however, demands processing methods to integrate information across modalities and to consolidate findings across different spatial scales. Here, we present micapipe, an open processing pipeline for multimodal MRI datasets. Based on BIDS-conform input data, micapipe can generate i) structural connectomes derived from diffusion tractography, ii) functional connectomes derived from resting-state signal correlations, iii) geodesic distance matrices that quantify cortico-cortical proximity, and iv) microstructural profile covariance matrices that assess inter-regional similarity in cortical myelin proxies. The above matrices can be automatically generated across established 18 cortical parcellations (100-1000 parcels), in addition to subcortical and cerebellar parcellations, allowing researchers to replicate findings easily across different spatial scales. Results are represented on three different surface spaces (native, conte69, fsaverage5), and outputs are BIDS-conform. Processed outputs can be quality controlled at the individual and group level. micapipe was tested on several datasets and is available at https://github.com/MICA-MNI/micapipe, documented at https://micapipe.readthedocs.io/, and containerized as a BIDS App http://bids-apps.neuroimaging.io/apps/. We hope that micapipe will foster robust and integrative studies of human brain microstructure, morphology, function, cand connectivity.
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Affiliation(s)
- Raúl R Cruces
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada.
| | - Jessica Royer
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada; Analytical Neurophysiology Laboratory, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada.
| | - Peer Herholz
- NeuroDataScience - ORIGAMI lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Reinder Vos de Wael
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Casey Paquola
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada; Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Jülich, Germany
| | - Oualid Benkarim
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Bo-Yong Park
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada; Department of Data Science, Inha University, Incheon, Republic of Korea; Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea
| | - Janie Degré-Pelletier
- Labo IDEA, Département de Psychologie, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Mark C Nelson
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Jordan DeKraker
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Ilana R Leppert
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Christine Tardif
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Jean-Baptiste Poline
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Luis Concha
- Instituto de Neurobiología, Universidad Nacional Autónoma de México, Campus Juriquilla, Mexico
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Québec, Canada.
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Royer J, Rodríguez-Cruces R, Tavakol S, Larivière S, Herholz P, Li Q, Vos de Wael R, Paquola C, Benkarim O, Park BY, Lowe AJ, Margulies D, Smallwood J, Bernasconi A, Bernasconi N, Frauscher B, Bernhardt BC. An Open MRI Dataset For Multiscale Neuroscience. Sci Data 2022; 9:569. [PMID: 36109562 PMCID: PMC9477866 DOI: 10.1038/s41597-022-01682-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/24/2022] [Indexed: 12/17/2022] Open
Abstract
AbstractMultimodal neuroimaging grants a powerful window into the structure and function of the human brain at multiple scales. Recent methodological and conceptual advances have enabled investigations of the interplay between large-scale spatial trends (also referred to as gradients) in brain microstructure and connectivity, offering an integrative framework to study multiscale brain organization. Here, we share a multimodal MRI dataset for Microstructure-Informed Connectomics (MICA-MICs) acquired in 50 healthy adults (23 women; 29.54 ± 5.62 years) who underwent high-resolution T1-weighted MRI, myelin-sensitive quantitative T1 relaxometry, diffusion-weighted MRI, and resting-state functional MRI at 3 Tesla. In addition to raw anonymized MRI data, this release includes brain-wide connectomes derived from (i) resting-state functional imaging, (ii) diffusion tractography, (iii) microstructure covariance analysis, and (iv) geodesic cortical distance, gathered across multiple parcellation scales. Alongside, we share large-scale gradients estimated from each modality and parcellation scale. Our dataset will facilitate future research examining the coupling between brain microstructure, connectivity, and function. MICA-MICs is available on the Canadian Open Neuroscience Platform data portal (https://portal.conp.ca) and the Open Science Framework (https://osf.io/j532r/).
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Park BY, Paquola C, Bethlehem RAI, Benkarim O, Mišić B, Smallwood J, Bullmore ET, Bernhardt BC. Adolescent development of multiscale structural wiring and functional interactions in the human connectome. Proc Natl Acad Sci U S A 2022; 119:e2116673119. [PMID: 35776541 PMCID: PMC9271154 DOI: 10.1073/pnas.2116673119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/30/2022] [Indexed: 01/03/2023] Open
Abstract
Adolescence is a time of profound changes in the physical wiring and function of the brain. Here, we analyzed structural and functional brain network development in an accelerated longitudinal cohort spanning 14 to 25 y (n = 199). Core to our work was an advanced in vivo model of cortical wiring incorporating MRI features of corticocortical proximity, microstructural similarity, and white matter tractography. Longitudinal analyses assessing age-related changes in cortical wiring identified a continued differentiation of multiple corticocortical structural networks in youth. We then assessed structure-function coupling using resting-state functional MRI measures in the same participants both via cross-sectional analysis at baseline and by studying longitudinal change between baseline and follow-up scans. At baseline, regions with more similar structural wiring were more likely to be functionally coupled. Moreover, correlating longitudinal structural wiring changes with longitudinal functional connectivity reconfigurations, we found that increased structural differentiation, particularly between sensory/unimodal and default mode networks, was reflected by reduced functional interactions. These findings provide insights into adolescent development of human brain structure and function, illustrating how structural wiring interacts with the maturation of macroscale functional hierarchies.
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Affiliation(s)
- Bo-yong Park
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
- Department of Data Science, Inha University, Incheon, 22212, Republic of Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, 16419, Republic of Korea
| | - Casey Paquola
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
- Institute of Neuroscience and Medicine, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Richard A. I. Bethlehem
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH, United Kingdom
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH, United Kingdom
| | - Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
| | | | - Bratislav Mišić
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
| | - Jonathan Smallwood
- Department of Psychology, Queen’s University, Kingston, ON, K7L 3N6, Canada
| | - Edward T. Bullmore
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, CB2 8AH, United Kingdom
| | - Boris C. Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, H3A 2B4, Canada
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Benkarim O, Paquola C, Park BY, Kebets V, Hong SJ, Vos de Wael R, Zhang S, Yeo BTT, Eickenberg M, Ge T, Poline JB, Bernhardt BC, Bzdok D. Population heterogeneity in clinical cohorts affects the predictive accuracy of brain imaging. PLoS Biol 2022; 20:e3001627. [PMID: 35486643 PMCID: PMC9094526 DOI: 10.1371/journal.pbio.3001627] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/11/2022] [Accepted: 04/11/2022] [Indexed: 12/18/2022] Open
Abstract
Brain imaging research enjoys increasing adoption of supervised machine learning for single-participant disease classification. Yet, the success of these algorithms likely depends on population diversity, including demographic differences and other factors that may be outside of primary scientific interest. Here, we capitalize on propensity scores as a composite confound index to quantify diversity due to major sources of population variation. We delineate the impact of population heterogeneity on the predictive accuracy and pattern stability in 2 separate clinical cohorts: the Autism Brain Imaging Data Exchange (ABIDE, n = 297) and the Healthy Brain Network (HBN, n = 551). Across various analysis scenarios, our results uncover the extent to which cross-validated prediction performances are interlocked with diversity. The instability of extracted brain patterns attributable to diversity is located preferentially in regions part of the default mode network. Collectively, our findings highlight the limitations of prevailing deconfounding practices in mitigating the full consequences of population diversity.
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Affiliation(s)
- Oualid Benkarim
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Casey Paquola
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Jülich, Germany
| | - Bo-yong Park
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
- Department of Data Science, Inha University, Incheon, South Korea
- Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon, South Korea
| | - Valeria Kebets
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Seok-Jun Hong
- Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon, South Korea
- Center for the Developing Brain, Child Mind Institute, New York, New York, United States of America
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Reinder Vos de Wael
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Shaoshi Zhang
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Centre for Sleep and Cognition (CSC) & Centre for Translational Magnetic Resonance Research (TMR), National University of Singapore, Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine (WisDM), National University of Singapore, Singapore, Singapore
| | - B. T. Thomas Yeo
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Centre for Sleep and Cognition (CSC) & Centre for Translational Magnetic Resonance Research (TMR), National University of Singapore, Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine (WisDM), National University of Singapore, Singapore, Singapore
| | | | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jean-Baptiste Poline
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Boris C. Bernhardt
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
| | - Danilo Bzdok
- McConnell Brain Imaging Centre (BIC), Montreal Neurological Institute (MNI), Faculty of Medicine, McGill University, Montreal, Canada
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, Canada
- School of Computer Science, McGill University, Montreal, Canada
- Mila—Quebec Artificial Intelligence Institute, Montreal, Canada
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9
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Yin S, Hong SJ, Di Martino A, Milham MP, Park BY, Benkarim O, Bethlehem RAI, Bernhardt BC, Paquola C. OUP accepted manuscript. Cereb Cortex 2022; 32:4565-4575. [PMID: 35059701 PMCID: PMC9574241 DOI: 10.1093/cercor/bhab502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/04/2022] Open
Abstract
Autism spectrum disorder (ASD) and anxiety disorders (ANX) are common neurodevelopmental conditions with several overlapping symptoms. Notably, many children and adolescents with ASD also have an ANX diagnosis, suggesting shared pathological mechanisms. Here, we leveraged structural imaging and phenotypic data from 112 youth (33 ASD, 37 ANX, 42 typically developing controls) to assess shared and distinct cortical thickness patterns of the disorders. ANX was associated with widespread increases in cortical thickness, while ASD related to a mixed pattern of subtle increases and decreases across the cortical mantle. Despite the qualitative difference in the case–control contrasts, the statistical maps from the ANX-vs-controls and ASD-vs-controls analyses were significantly correlated when correcting for spatial autocorrelation. Dimensional analysis, regressing trait anxiety and social responsiveness against cortical thickness measures, partially recapitulated diagnosis-based findings. Collectively, our findings provide evidence for a common axis of neurodevelopmental disturbances as well as distinct effects of ASD and ANX on cortical thickness.
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Affiliation(s)
- Shelly Yin
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Seok-Jun Hong
- Center for the Developing Brain and Autism Research Centre, Child Mind Institute, New York City, NY 10022, USA
| | - Adriana Di Martino
- Center for the Developing Brain and Autism Research Centre, Child Mind Institute, New York City, NY 10022, USA
| | - Michael P Milham
- Center for the Developing Brain and Autism Research Centre, Child Mind Institute, New York City, NY 10022, USA
| | - Bo-Yong Park
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal H3A 2B4, Canada
| | - Oualid Benkarim
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal H3A 2B4, Canada
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10
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Benkarim O, Paquola C, Park BY, Hong SJ, Royer J, Vos de Wael R, Lariviere S, Valk S, Bzdok D, Mottron L, C Bernhardt B. Connectivity alterations in autism reflect functional idiosyncrasy. Commun Biol 2021; 4:1078. [PMID: 34526654 PMCID: PMC8443598 DOI: 10.1038/s42003-021-02572-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/17/2021] [Indexed: 02/08/2023] Open
Abstract
Autism spectrum disorder (ASD) is commonly understood as an alteration of brain networks, yet case-control analyses against typically-developing controls (TD) have yielded inconsistent results. Here, we devised a novel approach to profile the inter-individual variability in functional network organization and tested whether such idiosyncrasy contributes to connectivity alterations in ASD. Studying a multi-centric dataset with 157 ASD and 172 TD, we obtained robust evidence for increased idiosyncrasy in ASD relative to TD in default mode, somatomotor and attention networks, but also reduced idiosyncrasy in lateral temporal cortices. Idiosyncrasy increased with age and significantly correlated with symptom severity in ASD. Furthermore, while patterns of functional idiosyncrasy were not correlated with ASD-related cortical thickness alterations, they co-localized with the expression patterns of ASD risk genes. Notably, we could demonstrate that patterns of atypical idiosyncrasy in ASD closely overlapped with connectivity alterations that are measurable with conventional case-control designs and may, thus, be a principal driver of inconsistency in the autism connectomics literature. These findings support important interactions between inter-individual heterogeneity in autism and functional signatures. Our findings provide novel biomarkers to study atypical brain development and may consolidate prior research findings on the variable nature of connectome level anomalies in autism.
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Affiliation(s)
- Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada.
| | - Casey Paquola
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Bo-Yong Park
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Seok-Jun Hong
- Center for the Developing Brain, Child Mind Institute, New York, NY, USA
- Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon, South Korea
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Jessica Royer
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Reinder Vos de Wael
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Sara Lariviere
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Sofie Valk
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- INM-7, FZ Jülich, Jülich, Germany
| | - Danilo Bzdok
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
- Department of Biomedical Engineering, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Mila - Quebec Artificial Intelligence Institute, Montreal, QC, Canada
| | - Laurent Mottron
- Centre de recherche du CIUSSSNIM et Département de Psychiatrie, Université de Montréal, Montreal, QC, Canada
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada.
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11
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Larivière S, Paquola C, Park BY, Royer J, Wang Y, Benkarim O, de Wael RV, Valk SL, Thomopoulos SI, Kirschner M, Lewis LB, Evans AC, Sisodiya SM, McDonald CR, Thompson PM, Bernhardt BC. The ENIGMA Toolbox: multiscale neural contextualization of multisite neuroimaging datasets. Nat Methods 2021; 18:698-700. [PMID: 34194050 PMCID: PMC8983056 DOI: 10.1038/s41592-021-01186-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sara Larivière
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Casey Paquola
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada,Institute of Neuroscience and Medicine (INM-1), Research Center, Jülich D-52425 Jülich, Germany
| | - Bo-yong Park
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada,Department of Data Science, Inha University, Incheon, South Korea
| | - Jessica Royer
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Yezhou Wang
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Oualid Benkarim
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Reinder Vos de Wael
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Sofie L. Valk
- Otto Hahn Research Group for Cognitive Neurogenetics, Max Planck Institute for Cognitive and Brain Sciences, Leipzig, Germany,INM-7, FZ Jülich, Jülich, Germany
| | - Sophia I. Thomopoulos
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, California, United States
| | - Matthias Kirschner
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric Hospital, University of Zurich, Switzerland
| | | | - Lindsay B. Lewis
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada,McGill Centre for Integrative Neuroscience, McGill University, Montreal, Quebec, Canada
| | - Alan C. Evans
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada,McGill Centre for Integrative Neuroscience, McGill University, Montreal, Quebec, Canada
| | - Sanjay M. Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom,Chalfont Centre for Epilepsy, Bucks, United Kingdom
| | - Carrie R. McDonald
- Department of Psychiatry, Center for Multimodal Imaging and Genetics, University of California San Diego, La Jolla, California, United States
| | - Paul M. Thompson
- Imaging Genetics Center, Mark & Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, California, United States
| | - Boris C. Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
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12
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Vos de Wael R, Royer J, Tavakol S, Wang Y, Paquola C, Benkarim O, Eichert N, Larivière S, Xu T, Misic B, Smallwood J, Valk SL, Bernhardt BC. Structural Connectivity Gradients of the Temporal Lobe Serve as Multiscale Axes of Brain Organization and Cortical Evolution. Cereb Cortex 2021; 31:5151-5164. [PMID: 34148082 PMCID: PMC8491677 DOI: 10.1093/cercor/bhab149] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The temporal lobe is implicated in higher cognitive processes and is one of the regions that underwent substantial reorganization during primate evolution. Its functions are instantiated, in part, by the complex layout of its structural connections. Here, we identified low-dimensional representations of structural connectivity variations in human temporal cortex and explored their microstructural underpinnings and associations to macroscale function. We identified three eigenmodes which described gradients in structural connectivity. These gradients reflected inter-regional variations in cortical microstructure derived from quantitative magnetic resonance imaging and postmortem histology. Gradient-informed models accurately predicted macroscale measures of temporal lobe function. Furthermore, the identified gradients aligned closely with established measures of functional reconfiguration and areal expansion between macaques and humans, highlighting their potential role in shaping temporal lobe function throughout primate evolution. Findings were replicated in several datasets. Our results provide robust evidence for three axes of structural connectivity in human temporal cortex with consistent microstructural underpinnings and contributions to large-scale brain network function.
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Affiliation(s)
- Reinder Vos de Wael
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Jessica Royer
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Shahin Tavakol
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Yezhou Wang
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Casey Paquola
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Nicole Eichert
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Sara Larivière
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | - Ting Xu
- Center for the Developing Brain, Child Mind Institute, New York, NY, NY 10022, USA
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, H3A 2B4, Canada
| | | | - Sofie L Valk
- Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, 04103, Germany
| | - Boris C Bernhardt
- Address correspondence to Boris C. Bernhardt, McConnell Brain Imaging Centre, Montreal Neurological Institute (NW-256), McGill University, 3801 Rue University, Montréal, QC H3A2B4, Canada.
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13
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Park BY, Hong SJ, Valk SL, Paquola C, Benkarim O, Bethlehem RAI, Di Martino A, Milham MP, Gozzi A, Yeo BTT, Smallwood J, Bernhardt BC. Differences in subcortico-cortical interactions identified from connectome and microcircuit models in autism. Nat Commun 2021; 12:2225. [PMID: 33850128 PMCID: PMC8044226 DOI: 10.1038/s41467-021-21732-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 02/05/2021] [Indexed: 01/14/2023] Open
Abstract
The pathophysiology of autism has been suggested to involve a combination of both macroscale connectome miswiring and microcircuit anomalies. Here, we combine connectome-wide manifold learning with biophysical simulation models to understand associations between global network perturbations and microcircuit dysfunctions in autism. We studied neuroimaging and phenotypic data in 47 individuals with autism and 37 typically developing controls obtained from the Autism Brain Imaging Data Exchange initiative. Our analysis establishes significant differences in structural connectome organization in individuals with autism relative to controls, with strong between-group effects in low-level somatosensory regions and moderate effects in high-level association cortices. Computational models reveal that the degree of macroscale anomalies is related to atypical increases of recurrent excitation/inhibition, as well as subcortical inputs into cortical microcircuits, especially in sensory and motor areas. Transcriptomic association analysis based on postmortem datasets identifies genes expressed in cortical and thalamic areas from childhood to young adulthood. Finally, supervised machine learning finds that the macroscale perturbations are associated with symptom severity scores on the Autism Diagnostic Observation Schedule. Together, our analyses suggest that atypical subcortico-cortical interactions are associated with both microcircuit and macroscale connectome differences in autism.
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Affiliation(s)
- Bo-Yong Park
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada.
- Department of Data Science, Inha University, Incheon, South Korea.
| | - Seok-Jun Hong
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
- Center for the Developing Brain, Child Mind Institute, New York City, NY, USA
- Center for Neuroscience Imaging Research, Institute for Basic Science, Sungkyunkwan University, Suwon, South Korea
- Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Sofie L Valk
- Forschungszentrum, Julich, Germany
- Max Planck Institute for Cognitive and Brain Sciences, Leipzig, Germany
| | - Casey Paquola
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Richard A I Bethlehem
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
- Brain Mapping Unit, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Adriana Di Martino
- Center for the Developing Brain, Child Mind Institute, New York City, NY, USA
| | - Michael P Milham
- Center for the Developing Brain, Child Mind Institute, New York City, NY, USA
| | - Alessandro Gozzi
- Istituto Italiano di Tecnologia, Centre for Neuroscience and Cognitive Systems @ UNITN, Rovereto, Italy
| | - B T Thomas Yeo
- Department of Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
- Centre for Sleep and Cognition (CSC) & Centre for Translational Magnetic Resonance Research (TMR), National University of Singapore, Singapore, Singapore
- N.1 Institute for Health & Institute for Digital Medicine (WisDM), National University of Singapore, Singapore, Singapore
- Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
- Integrative Sciences and Engineering Programme (ISEP), National University of Singapore, Singapore, Singapore
| | - Jonathan Smallwood
- Department of Psychology, York Neuroimaging Centre, University of York, York, UK
- Department of Psychology, Queen's University, Kingston, ON, Canada
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada.
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14
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Paquola C, Benkarim O, DeKraker J, Larivière S, Frässle S, Royer J, Tavakol S, Valk S, Bernasconi A, Bernasconi N, Khan A, Evans AC, Razi A, Smallwood J, Bernhardt BC. Convergence of cortical types and functional motifs in the human mesiotemporal lobe. eLife 2020; 9:e60673. [PMID: 33146610 PMCID: PMC7671688 DOI: 10.7554/elife.60673] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/03/2020] [Indexed: 01/24/2023] Open
Abstract
The mesiotemporal lobe (MTL) is implicated in many cognitive processes, is compromised in numerous brain disorders, and exhibits a gradual cytoarchitectural transition from six-layered parahippocampal isocortex to three-layered hippocampal allocortex. Leveraging an ultra-high-resolution histological reconstruction of a human brain, our study showed that the dominant axis of MTL cytoarchitectural differentiation follows the iso-to-allocortical transition and depth-specific variations in neuronal density. Projecting the histology-derived MTL model to in-vivo functional MRI, we furthermore determined how its cytoarchitecture underpins its intrinsic effective connectivity and association to large-scale networks. Here, the cytoarchitectural gradient was found to underpin intrinsic effective connectivity of the MTL, but patterns differed along the anterior-posterior axis. Moreover, while the iso-to-allocortical gradient parametrically represented the multiple-demand relative to task-negative networks, anterior-posterior gradients represented transmodal versus unimodal networks. Our findings establish that the combination of micro- and macrostructural features allow the MTL to represent dominant motifs of whole-brain functional organisation.
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Affiliation(s)
- Casey Paquola
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Oualid Benkarim
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Jordan DeKraker
- Brain and Mind Institute, University of Western OntarioLondonCanada
| | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Stefan Frässle
- Translational Neuromodeling Unit, Institute for Biomedical Engineering, University of Zurich & ETH ZurichZurichSwitzerland
| | - Jessica Royer
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Shahin Tavakol
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Sofie Valk
- Institute of Neuroscience and Medicine (INM-7: Brain and Behaviour), Research Centre JülichJülichGermany
- Institute of Systems Neuroscience, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Andrea Bernasconi
- Neuroimaging Of Epilepsy Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Neda Bernasconi
- Neuroimaging Of Epilepsy Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Ali Khan
- Brain and Mind Institute, University of Western OntarioLondonCanada
| | - Alan C Evans
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
- McGill Centre for Integrative Neuroscience, McGill UniversityMontrealCanada
| | | | | | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
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15
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Paquola C, Seidlitz J, Benkarim O, Royer J, Klimes P, Bethlehem RAI, Larivière S, Vos de Wael R, Rodríguez-Cruces R, Hall JA, Frauscher B, Smallwood J, Bernhardt BC. A multi-scale cortical wiring space links cellular architecture and functional dynamics in the human brain. PLoS Biol 2020; 18:e3000979. [PMID: 33253185 PMCID: PMC7728398 DOI: 10.1371/journal.pbio.3000979] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 12/10/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022] Open
Abstract
The vast net of fibres within and underneath the cortex is optimised to support the convergence of different levels of brain organisation. Here, we propose a novel coordinate system of the human cortex based on an advanced model of its connectivity. Our approach is inspired by seminal, but so far largely neglected models of cortico-cortical wiring established by postmortem anatomical studies and capitalises on cutting-edge in vivo neuroimaging and machine learning. The new model expands the currently prevailing diffusion magnetic resonance imaging (MRI) tractography approach by incorporation of additional features of cortical microstructure and cortico-cortical proximity. Studying several datasets and different parcellation schemes, we could show that our coordinate system robustly recapitulates established sensory-limbic and anterior-posterior dimensions of brain organisation. A series of validation experiments showed that the new wiring space reflects cortical microcircuit features (including pyramidal neuron depth and glial expression) and allowed for competitive simulations of functional connectivity and dynamics based on resting-state functional magnetic resonance imaging (rs-fMRI) and human intracranial electroencephalography (EEG) coherence. Our results advance our understanding of how cell-specific neurobiological gradients produce a hierarchical cortical wiring scheme that is concordant with increasing functional sophistication of human brain organisation. Our evaluations demonstrate the cortical wiring space bridges across scales of neural organisation and can be easily translated to single individuals.
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Affiliation(s)
- Casey Paquola
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Jakob Seidlitz
- Developmental Neurogenomics Unit, National Institute of Mental Health, Bethesda, Maryland, United States of America
| | - Oualid Benkarim
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Jessica Royer
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Petr Klimes
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | | | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Reinder Vos de Wael
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Raul Rodríguez-Cruces
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Jeffery A. Hall
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Birgit Frauscher
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | | | - Boris C. Bernhardt
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
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16
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Mckeown B, Strawson WH, Wang HT, Karapanagiotidis T, Vos de Wael R, Benkarim O, Turnbull A, Margulies D, Jefferies E, McCall C, Bernhardt B, Smallwood J. The relationship between individual variation in macroscale functional gradients and distinct aspects of ongoing thought. Neuroimage 2020; 220:117072. [PMID: 32585346 PMCID: PMC7573534 DOI: 10.1016/j.neuroimage.2020.117072] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/15/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022] Open
Abstract
Contemporary accounts of ongoing thought recognise it as a heterogeneous and multidimensional construct, varying in both form and content. An emerging body of evidence demonstrates that distinct types of experience are associated with unique neurocognitive profiles, that can be described at the whole-brain level as interactions between multiple large-scale networks. The current study sought to explore the possibility that whole-brain functional connectivity patterns at rest may be meaningfully related to patterns of ongoing thought that occurred over this period. Participants underwent resting-state functional magnetic resonance imaging (rs-fMRI) followed by a questionnaire retrospectively assessing the content and form of their ongoing thoughts during the scan. A non-linear dimension reduction algorithm was applied to the rs-fMRI data to identify components explaining the greatest variance in whole-brain connectivity patterns. Using these data, we examined whether specific types of thought measured at the end of the scan were predictive of individual variation along the first three low-dimensional components of functional connectivity at rest. Multivariate analyses revealed that individuals for whom the connectivity of the sensorimotor system was maximally distinct from the visual system were most likely to report thoughts related to finding solutions to problems or goals and least likely to report thoughts related to the past. These results add to an emerging literature that suggests that unique patterns of experience are associated with distinct distributed neurocognitive profiles and highlight that unimodal systems may play an important role in this process.
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Affiliation(s)
- Brontë Mckeown
- Department of Psychology, York Neuroimaging Centre, University of York, United Kingdom.
| | - Will H Strawson
- Neuroscience, Brighton and Sussex Medical School, University of Sussex, United Kingdom
| | - Hao-Ting Wang
- Sackler Centre for Consciousness Studies, University of Sussex, United Kingdom
| | | | - Reinder Vos de Wael
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Adam Turnbull
- Department of Psychology, York Neuroimaging Centre, University of York, United Kingdom
| | - Daniel Margulies
- Frontlab, Institut du Cerveau et de la Moelle épinière, UPMC UMRS 1127, Inserm U 1127, CNRS UMR, 7225, Paris, France
| | - Elizabeth Jefferies
- Department of Psychology, York Neuroimaging Centre, University of York, United Kingdom
| | - Cade McCall
- Department of Psychology, York Neuroimaging Centre, University of York, United Kingdom
| | - Boris Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Jonathan Smallwood
- Department of Psychology, York Neuroimaging Centre, University of York, United Kingdom
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17
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Park BY, Vos de Wael R, Paquola C, Larivière S, Benkarim O, Royer J, Tavakol S, Cruces RR, Li Q, Valk SL, Margulies DS, Mišić B, Bzdok D, Smallwood J, Bernhardt BC. Signal diffusion along connectome gradients and inter-hub routing differentially contribute to dynamic human brain function. Neuroimage 2020; 224:117429. [PMID: 33038538 DOI: 10.1016/j.neuroimage.2020.117429] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/13/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022] Open
Abstract
Human cognition is dynamic, alternating over time between externally-focused states and more abstract, often self-generated, patterns of thought. Although cognitive neuroscience has documented how networks anchor particular modes of brain function, mechanisms that describe transitions between distinct functional states remain poorly understood. Here, we examined how time-varying changes in brain function emerge within the constraints imposed by macroscale structural network organization. Studying a large cohort of healthy adults (n = 326), we capitalized on manifold learning techniques that identify low dimensional representations of structural connectome organization and we decomposed neurophysiological activity into distinct functional states and their transition patterns using Hidden Markov Models. Structural connectome organization predicted dynamic transitions anchored in sensorimotor systems and those between sensorimotor and transmodal states. Connectome topology analyses revealed that transitions involving sensorimotor states traversed short and intermediary distances and adhered strongly to communication mechanisms of network diffusion. Conversely, transitions between transmodal states involved spatially distributed hubs and increasingly engaged long-range routing. These findings establish that the structure of the cortex is optimized to allow neural states the freedom to vary between distinct modes of processing, and so provides a key insight into the neural mechanisms that give rise to the flexibility of human cognition.
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Affiliation(s)
- Bo-Yong Park
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada.
| | - Reinder Vos de Wael
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Casey Paquola
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Oualid Benkarim
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Jessica Royer
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Shahin Tavakol
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Raul R Cruces
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Qiongling Li
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Sofie L Valk
- Institute of Neuroscience and Medicine (INM-7: Brain & Behaviour), Research Centre Jülich, Jülich, Germany; Institute of Systems Neuroscience, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Daniel S Margulies
- Frontlab, Institut du Cerveau et de la Moelle épinière, UPMC UMRS 1127, Inserm U 1127, CNRS UMR 7225, Paris, France
| | - Bratislav Mišić
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Danilo Bzdok
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada; Mila - Quebec Artificial Intelligence Institute, Montreal, Quebec, Canada
| | - Jonathan Smallwood
- Department of Psychology, York Neuroimaging Centre, University of York, New York, United Kingdom
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Lab, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada.
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18
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Bernardino G, Benkarim O, Sanz-de la Garza M, Prat-Gonzàlez S, Sepulveda-Martinez A, Crispi F, Sitges M, Butakoff C, De Craene M, Bijnens B, González Ballester MA. Handling confounding variables in statistical shape analysis - application to cardiac remodelling. Med Image Anal 2020; 65:101792. [PMID: 32712526 DOI: 10.1016/j.media.2020.101792] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 04/01/2020] [Accepted: 07/17/2020] [Indexed: 11/15/2022]
Abstract
Statistical shape analysis is a powerful tool to assess organ morphologies and find shape changes associated to a particular disease. However, imbalance in confounding factors, such as demographics might invalidate the analysis if not taken into consideration. Despite the methodological advances in the field, providing new methods that are able to capture complex and regional shape differences, the relationship between non-imaging information and shape variability has been overlooked. We present a linear statistical shape analysis framework that finds shape differences unassociated to a controlled set of confounding variables. It includes two confounding correction methods: confounding deflation and adjustment. We applied our framework to a cardiac magnetic resonance imaging dataset, consisting of the cardiac ventricles of 89 triathletes and 77 controls, to identify cardiac remodelling due to the practice of endurance exercise. To test robustness to confounders, subsets of this dataset were generated by randomly removing controls with low body mass index, thus introducing imbalance. The analysis of the whole dataset indicates an increase of ventricular volumes and myocardial mass in athletes, which is consistent with the clinical literature. However, when confounders are not taken into consideration no increase of myocardial mass is found. Using the downsampled datasets, we find that confounder adjustment methods are needed to find the real remodelling patterns in imbalanced datasets.
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Affiliation(s)
- Gabriel Bernardino
- BCN Medtech, Dept. of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain.
| | | | | | - Susanna Prat-Gonzàlez
- Cardiovascular Institute, Hospital Clínic, Barcelona, Spain; IDIBAPS, Barcelona, Spain
| | - Alvaro Sepulveda-Martinez
- BCNatal, Hospital Clínic and Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; Fetal Medicine Unit, Department of Obstetrics and Gynecology, Hospital Clínico de la Universidad de Chile, Santiago de Chile, Chile
| | - Fátima Crispi
- IDIBAPS, Barcelona, Spain; BCNatal, Hospital Clínic and Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain; CIBER-ER, Barcelona, Spain
| | - Marta Sitges
- Cardiovascular Institute, Hospital Clínic, Barcelona, Spain; IDIBAPS, Barcelona, Spain; CIBER-CV, Barcelona, Spain
| | | | | | - Bart Bijnens
- BCN Medtech, Dept. of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain; IDIBAPS, Barcelona, Spain; ICREA, Barcelona, Spain
| | - Miguel A González Ballester
- BCN Medtech, Dept. of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain; ICREA, Barcelona, Spain
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19
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Vos de Wael R, Benkarim O, Paquola C, Lariviere S, Royer J, Tavakol S, Xu T, Hong SJ, Langs G, Valk S, Misic B, Milham M, Margulies D, Smallwood J, Bernhardt BC. BrainSpace: a toolbox for the analysis of macroscale gradients in neuroimaging and connectomics datasets. Commun Biol 2020; 3:103. [PMID: 32139786 PMCID: PMC7058611 DOI: 10.1038/s42003-020-0794-7] [Citation(s) in RCA: 192] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 01/24/2020] [Indexed: 11/21/2022] Open
Abstract
Understanding how cognitive functions emerge from brain structure depends on quantifying how discrete regions are integrated within the broader cortical landscape. Recent work established that macroscale brain organization and function can be described in a compact manner with multivariate machine learning approaches that identify manifolds often described as cortical gradients. By quantifying topographic principles of macroscale organization, cortical gradients lend an analytical framework to study structural and functional brain organization across species, throughout development and aging, and its perturbations in disease. Here, we present BrainSpace, a Python/Matlab toolbox for (i) the identification of gradients, (ii) their alignment, and (iii) their visualization. Our toolbox furthermore allows for controlled association studies between gradients with other brain-level features, adjusted with respect to null models that account for spatial autocorrelation. Validation experiments demonstrate the usage and consistency of our tools for the analysis of functional and microstructural gradients across different spatial scales.
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Affiliation(s)
- Reinder Vos de Wael
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Oualid Benkarim
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Casey Paquola
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Sara Lariviere
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Jessica Royer
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Shahin Tavakol
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Ting Xu
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
- Center for the Developing Brain, Child Mind Institute, New York, USA
| | - Seok-Jun Hong
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
- Center for the Developing Brain, Child Mind Institute, New York, USA
| | - Georg Langs
- Medical University of Vienna, Vienna, Austria
| | - Sofie Valk
- Institute for Neuroscience and Medicine; 7/Institute of Systems Neuroscience, Forschungszentrum Juelich - Heinrich Heine Universitaet Duesseldorf, Juelich, Germany
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Michael Milham
- Center for the Developing Brain, Child Mind Institute, New York, USA
| | - Daniel Margulies
- Frontlab, Institut du Cerveau et de la Moelle épinière, UPMC UMRS 1127, Inserm U 1127, CNRS UMR 7225, Paris, France
| | | | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.
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