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Ulusoy I, Geduk S. Improved brain effective connectivity modelling by dynamic Bayesian networks. J Neurosci Methods 2024; 409:110211. [PMID: 38968975 DOI: 10.1016/j.jneumeth.2024.110211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/10/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND If brain effective connectivity network modelling (ECN) could be accurately achieved, early diagnosis of neurodegenerative diseases would be possible. It has been observed in the literature that Dynamic Bayesian Network (DBN) based methods are more successful than others. However, DBNs have not been applied easily and tested much due to computational complexity problems in structure learning. NEW METHOD This study introduces an advanced method for modelling brain ECNs using improved discrete DBN (Improved- dDBN) which addresses the computational challenges previously limiting DBN application, offering solutions that enable accurate and fast structure modelling. RESULTS The practical data and prior sizes needed for the convergence to the globally correct network structure are proved to be much smaller than the theoretical ones using simulated dDBN data. Besides, Hill Climbing is shown to converge to the true structure at a reasonable iteration step size when the appropriate data and prior sizes are used. Finally, importance of data quantization methods are analysed. COMPARISON WITH EXISTING METHODS The Improved-dDBN method performs better and robust, when compared to the existing methods for realistic scenarios such as varying graph complexity, various input conditions, noise cases and non-stationary connections. The data used in these tests is the simulated fMRI BOLD time series proposed in the literature. CONCLUSIONS Improved-dDBN is a good candidate to be used on real datasets to accelerate developments in brain ECN modelling and neuroscience. Appropriate data and prior sizes can be identified based on the approach proposed in this study for global and fast convergence.
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Affiliation(s)
- Ilkay Ulusoy
- Department of Electrical and Electronics Engineering, Middle East Technical University, Ankara, Turkey.
| | - Salih Geduk
- Department of Electrical and Electronics Engineering, Middle East Technical University, Ankara, Turkey.
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2
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Tanner J, Faskowitz J, Teixeira AS, Seguin C, Coletta L, Gozzi A, Mišić B, Betzel RF. A multi-modal, asymmetric, weighted, and signed description of anatomical connectivity. Nat Commun 2024; 15:5865. [PMID: 38997282 PMCID: PMC11245624 DOI: 10.1038/s41467-024-50248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 07/01/2024] [Indexed: 07/14/2024] Open
Abstract
The macroscale connectome is the network of physical, white-matter tracts between brain areas. The connections are generally weighted and their values interpreted as measures of communication efficacy. In most applications, weights are either assigned based on imaging features-e.g. diffusion parameters-or inferred using statistical models. In reality, the ground-truth weights are unknown, motivating the exploration of alternative edge weighting schemes. Here, we explore a multi-modal, regression-based model that endows reconstructed fiber tracts with directed and signed weights. We find that the model fits observed data well, outperforming a suite of null models. The estimated weights are subject-specific and highly reliable, even when fit using relatively few training samples, and the networks maintain a number of desirable features. In summary, we offer a simple framework for weighting connectome data, demonstrating both its ease of implementation while benchmarking its utility for typical connectome analyses, including graph theoretic modeling and brain-behavior associations.
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Affiliation(s)
- Jacob Tanner
- Cognitive Science Program, Indiana University, Bloomington, IN, USA
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA
| | - Joshua Faskowitz
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | - Andreia Sofia Teixeira
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Caio Seguin
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA
| | | | - Alessandro Gozzi
- Functional Neuroimaging Lab, Istituto Italiano di Tecnologia, Center for Neuroscience and Cognitive Systems, Rovereto, Italy
| | - Bratislav Mišić
- McConnell Brain Imaging Centre, Montréal Neurological Institute, McGill University, Montréal, Canada
| | - Richard F Betzel
- Cognitive Science Program, Indiana University, Bloomington, IN, USA.
- School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, USA.
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA.
- Program in Neuroscience, Indiana University, Bloomington, IN, USA.
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3
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Zou A, Ji J, Lei M, Liu J, Song Y. Exploring Brain Effective Connectivity Networks Through Spatiotemporal Graph Convolutional Models. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2024; 35:7871-7883. [PMID: 36399590 DOI: 10.1109/tnnls.2022.3221617] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Learning brain effective connectivity networks (ECN) from functional magnetic resonance imaging (fMRI) data has gained much attention in recent years. With the successful applications of deep learning in numerous fields, several brain ECN learning methods based on deep learning have been reported in the literature. However, current methods ignore the deep temporal features of fMRI data and fail to fully employ the spatial topological relationship between brain regions. In this article, we propose a novel method for learning brain ECN based on spatiotemporal graph convolutional models (STGCM), named STGCMEC, in which we first adopt the temporal convolutional network to extract the deep temporal features of fMRI data and utilize the graph convolutional network to update the spatial features of each brain region by aggregating information from neighborhoods, which makes the features of brain regions more discriminative. Then, based on such features of brain regions, we design a joint loss function to guide STGCMEC to learn the brain ECN, which includes a task prediction loss and a graph regularization loss. The experimental results on a simulated dataset and a real Alzheimer's disease neuroimaging initiative (ADNI) dataset show that the proposed STGCMEC is able to better learn brain ECN compared with some state-of-the-art methods.
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4
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Zhang S, Jung K, Langner R, Florin E, Eickhoff SB, Popovych OV. Impact of data processing varieties on DCM estimates of effective connectivity from task-fMRI. Hum Brain Mapp 2024; 45:e26751. [PMID: 38864293 PMCID: PMC11167406 DOI: 10.1002/hbm.26751] [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: 06/20/2023] [Revised: 01/05/2024] [Accepted: 05/22/2024] [Indexed: 06/13/2024] Open
Abstract
Effective connectivity (EC) refers to directional or causal influences between interacting neuronal populations or brain regions and can be estimated from functional magnetic resonance imaging (fMRI) data via dynamic causal modeling (DCM). In contrast to functional connectivity, the impact of data processing varieties on DCM estimates of task-evoked EC has hardly ever been addressed. We therefore investigated how task-evoked EC is affected by choices made for data processing. In particular, we considered the impact of global signal regression (GSR), block/event-related design of the general linear model (GLM) used for the first-level task-evoked fMRI analysis, type of activation contrast, and significance thresholding approach. Using DCM, we estimated individual and group-averaged task-evoked EC within a brain network related to spatial conflict processing for all the parameters considered and compared the differences in task-evoked EC between any two data processing conditions via between-group parametric empirical Bayes (PEB) analysis and Bayesian data comparison (BDC). We observed strongly varying patterns of the group-averaged EC depending on the data processing choices. In particular, task-evoked EC and parameter certainty were strongly impacted by GLM design and type of activation contrast as revealed by PEB and BDC, respectively, whereas they were little affected by GSR and the type of significance thresholding. The event-related GLM design appears to be more sensitive to task-evoked modulations of EC, but provides model parameters with lower certainty than the block-based design, while the latter is more sensitive to the type of activation contrast than is the event-related design. Our results demonstrate that applying different reasonable data processing choices can substantially alter task-evoked EC as estimated by DCM. Such choices should be made with care and, whenever possible, varied across parallel analyses to evaluate their impact and identify potential convergence for robust outcomes.
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Affiliation(s)
- Shufei Zhang
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM‐7)Research Centre JülichJülichGermany
- Institute for Systems Neuroscience, Medical FacultyHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Kyesam Jung
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM‐7)Research Centre JülichJülichGermany
- Institute for Systems Neuroscience, Medical FacultyHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Robert Langner
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM‐7)Research Centre JülichJülichGermany
- Institute for Systems Neuroscience, Medical FacultyHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Esther Florin
- Institute of Clinical Neuroscience and Medical Psychology, Medical FacultyHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Simon B. Eickhoff
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM‐7)Research Centre JülichJülichGermany
- Institute for Systems Neuroscience, Medical FacultyHeinrich‐Heine University DüsseldorfDüsseldorfGermany
| | - Oleksandr V. Popovych
- Institute of Neuroscience and Medicine, Brain and Behaviour (INM‐7)Research Centre JülichJülichGermany
- Institute for Systems Neuroscience, Medical FacultyHeinrich‐Heine University DüsseldorfDüsseldorfGermany
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Xie K, Royer J, Larivière S, Rodriguez-Cruces R, Frässle S, Cabalo DG, Ngo A, DeKraker J, Auer H, Tavakol S, Weng Y, Abdallah C, Arafat T, Horwood L, Frauscher B, Caciagli L, Bernasconi A, Bernasconi N, Zhang Z, Concha L, Bernhardt BC. Atypical connectome topography and signal flow in temporal lobe epilepsy. Prog Neurobiol 2024; 236:102604. [PMID: 38604584 DOI: 10.1016/j.pneurobio.2024.102604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 12/18/2023] [Accepted: 04/07/2024] [Indexed: 04/13/2024]
Abstract
Temporal lobe epilepsy (TLE) is the most common pharmaco-resistant epilepsy in adults. While primarily associated with mesiotemporal pathology, recent evidence suggests that brain alterations in TLE extend beyond the paralimbic epicenter and impact macroscale function and cognitive functions, particularly memory. Using connectome-wide manifold learning and generative models of effective connectivity, we examined functional topography and directional signal flow patterns between large-scale neural circuits in TLE at rest. Studying a multisite cohort of 95 patients with TLE and 95 healthy controls, we observed atypical functional topographies in the former group, characterized by reduced differentiation between sensory and transmodal association cortices, with most marked effects in bilateral temporo-limbic and ventromedial prefrontal cortices. These findings were consistent across all study sites, present in left and right lateralized patients, and validated in a subgroup of patients with histopathological validation of mesiotemporal sclerosis and post-surgical seizure freedom. Moreover, they were replicated in an independent cohort of 30 TLE patients and 40 healthy controls. Further analyses demonstrated that reduced differentiation related to decreased functional signal flow into and out of temporolimbic cortical systems and other brain networks. Parallel analyses of structural and diffusion-weighted MRI data revealed that topographic alterations were independent of TLE-related cortical thinning but partially mediated by white matter microstructural changes that radiated away from paralimbic circuits. Finally, we found a strong association between the degree of functional alterations and behavioral markers of memory dysfunction. Our work illustrates the complex landscape of macroscale functional imbalances in TLE, which can serve as intermediate markers bridging microstructural changes and cognitive impairment.
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Affiliation(s)
- Ke Xie
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jessica Royer
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada; Analytical Neurophysiology Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Raul Rodriguez-Cruces
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Donna Gift Cabalo
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Alexander Ngo
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Jordan DeKraker
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Hans Auer
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Shahin Tavakol
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Yifei Weng
- Department of Medical Imaging, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chifaou Abdallah
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Thaera Arafat
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Linda Horwood
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada; Analytical Neurophysiology Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Birgit Frauscher
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada; Department of Neurology, Duke University School of Medicine and Department of Biomedical Engineering, Duke University Pratt School of Engineering, Durham, NC 27705, USA
| | - Lorenzo Caciagli
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Neurology, Inselspital, Sleep-Wake-Epilepsy-Center, Bern University Hospital, University of Bern, Bern, Switzerland; Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London WC1N 3 BG, United Kingdom
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Neda Bernasconi
- Neuroimaging of Epilepsy Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada
| | - Zhiqiang Zhang
- Department of Medical Imaging, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Luis Concha
- Institute of Neurobiology, Universidad Nacional Autónoma de Mexico (UNAM), Queretaro, Mexico
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC H3A 2B4, Canada.
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Avram M, Müller F, Preller KH, Razi A, Rogg H, Korda A, Holze F, Vizeli P, Ley L, Liechti ME, Borgwardt S. Effective Connectivity of Thalamocortical Interactions Following d-Amphetamine, LSD, and MDMA Administration. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2024; 9:522-532. [PMID: 37532129 DOI: 10.1016/j.bpsc.2023.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND While the exploration of serotonergic psychedelics as psychiatric medicines deepens, so does the pressure to better understand how these compounds act on the brain. METHODS We used a double-blind, placebo-controlled, crossover design and administered lysergic acid diethylamide (LSD), 3,4-methylenedioxymethamphetamine (MDMA), and d-amphetamine in 25 healthy participants. By using spectral dynamic causal modeling, we mapped substance-induced changes in effective connectivity between the thalamus and different cortex types (unimodal vs. transmodal) derived from a previous study with resting-state functional magnetic resonance imaging data. Due to the distinct pharmacological modes of action of the 3 substances, we were able to investigate specific effects mainly driven by different neurotransmitter systems on thalamocortical and corticothalamic interactions. RESULTS Compared with placebo, all 3 substances increased the effective connectivity from the thalamus to specific unimodal cortices, whereas the influence of these cortices on the thalamus was reduced. These results indicate increased bottom-up and decreased top-down information flow between the thalamus and some unimodal cortices. However, for the amphetamines, we found the opposite effects when examining the effective connectivity with transmodal cortices, including parts of the salience network. Intriguingly, LSD increased the effective connectivity from the thalamus to both unimodal and transmodal cortices, indicating a breach in the hierarchical organization of ongoing brain activity. CONCLUSIONS The results advance our knowledge about the action of psychedelics on the brain and refine current models aiming to explain the underlying neurobiological processes.
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Affiliation(s)
- Mihai Avram
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany; Center of Brain, Behavior, and Metabolism, University of Lübeck, Lübeck, Germany.
| | - Felix Müller
- Department of Psychiatry, University of Basel, Basel, Switzerland
| | - Katrin H Preller
- Pharmaco-Neuroimaging and Cognitive-Emotional Processing, Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric Hospital, University of Zürich, Zürich, Switzerland
| | - Adeel Razi
- Turner Institute for Brain and Mental Health, Monash University, Clayton, Victoria, Australia
| | - Helena Rogg
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Alexandra Korda
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany; Center of Brain, Behavior, and Metabolism, University of Lübeck, Lübeck, Germany
| | - Friederike Holze
- Division of Clinical Pharmacology and Toxicology, Department of Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Patrick Vizeli
- Division of Clinical Pharmacology and Toxicology, Department of Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Laura Ley
- Division of Clinical Pharmacology and Toxicology, Department of Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Matthias E Liechti
- Division of Clinical Pharmacology and Toxicology, Department of Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Stefan Borgwardt
- Translational Psychiatry, Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany; Center of Brain, Behavior, and Metabolism, University of Lübeck, Lübeck, Germany
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Medrano J, Friston K, Zeidman P. Linking fast and slow: The case for generative models. Netw Neurosci 2024; 8:24-43. [PMID: 38562283 PMCID: PMC10861163 DOI: 10.1162/netn_a_00343] [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: 08/08/2023] [Accepted: 10/11/2023] [Indexed: 04/04/2024] Open
Abstract
A pervasive challenge in neuroscience is testing whether neuronal connectivity changes over time due to specific causes, such as stimuli, events, or clinical interventions. Recent hardware innovations and falling data storage costs enable longer, more naturalistic neuronal recordings. The implicit opportunity for understanding the self-organised brain calls for new analysis methods that link temporal scales: from the order of milliseconds over which neuronal dynamics evolve, to the order of minutes, days, or even years over which experimental observations unfold. This review article demonstrates how hierarchical generative models and Bayesian inference help to characterise neuronal activity across different time scales. Crucially, these methods go beyond describing statistical associations among observations and enable inference about underlying mechanisms. We offer an overview of fundamental concepts in state-space modeling and suggest a taxonomy for these methods. Additionally, we introduce key mathematical principles that underscore a separation of temporal scales, such as the slaving principle, and review Bayesian methods that are being used to test hypotheses about the brain with multiscale data. We hope that this review will serve as a useful primer for experimental and computational neuroscientists on the state of the art and current directions of travel in the complex systems modelling literature.
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Affiliation(s)
- Johan Medrano
- The Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, UK
| | - Karl Friston
- The Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, UK
| | - Peter Zeidman
- The Wellcome Centre for Human Neuroimaging, UCL Queen Square Institute of Neurology, London, UK
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8
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Gosti G, Milanetti E, Folli V, de Pasquale F, Leonetti M, Corbetta M, Ruocco G, Della Penna S. A recurrent Hopfield network for estimating meso-scale effective connectivity in MEG. Neural Netw 2024; 170:72-93. [PMID: 37977091 DOI: 10.1016/j.neunet.2023.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
The architecture of communication within the brain, represented by the human connectome, has gained a paramount role in the neuroscience community. Several features of this communication, e.g., the frequency content, spatial topology, and temporal dynamics are currently well established. However, identifying generative models providing the underlying patterns of inhibition/excitation is very challenging. To address this issue, we present a novel generative model to estimate large-scale effective connectivity from MEG. The dynamic evolution of this model is determined by a recurrent Hopfield neural network with asymmetric connections, and thus denoted Recurrent Hopfield Mass Model (RHoMM). Since RHoMM must be applied to binary neurons, it is suitable for analyzing Band Limited Power (BLP) dynamics following a binarization process. We trained RHoMM to predict the MEG dynamics through a gradient descent minimization and we validated it in two steps. First, we showed a significant agreement between the similarity of the effective connectivity patterns and that of the interregional BLP correlation, demonstrating RHoMM's ability to capture individual variability of BLP dynamics. Second, we showed that the simulated BLP correlation connectomes, obtained from RHoMM evolutions of BLP, preserved some important topological features, e.g, the centrality of the real data, assuring the reliability of RHoMM. Compared to other biophysical models, RHoMM is based on recurrent Hopfield neural networks, thus, it has the advantage of being data-driven, less demanding in terms of hyperparameters and scalable to encompass large-scale system interactions. These features are promising for investigating the dynamics of inhibition/excitation at different spatial scales.
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Affiliation(s)
- Giorgio Gosti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro, 5, 00185, Rome, Italy; Istituto di Scienze del Patrimonio Culturale, Sede di Roma, Consiglio Nazionale delle Ricerche, CNR-ISPC, Via Salaria km, 34900 Rome, Italy.
| | - Edoardo Milanetti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185, Rome, Italy.
| | - Viola Folli
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; D-TAILS srl, Via di Torre Rossa, 66, 00165, Rome, Italy.
| | - Francesco de Pasquale
- Faculty of Veterinary Medicine, University of Teramo, 64100 Piano D'Accio, Teramo, Italy.
| | - Marco Leonetti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; Soft and Living Matter Laboratory, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche, Piazzale Aldo Moro, 5, 00185, Rome, Italy; D-TAILS srl, Via di Torre Rossa, 66, 00165, Rome, Italy.
| | - Maurizio Corbetta
- Department of Neuroscience, University of Padova, Via Belzoni, 160, 35121, Padova, Italy; Padova Neuroscience Center (PNC), University of Padova, Via Orus, 2/B, 35129, Padova, Italy; Veneto Institute of Molecular Medicine (VIMM), Via Orus, 2, 35129, Padova, Italy.
| | - Giancarlo Ruocco
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena, 291, 00161, Rome, Italy; Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185, Rome, Italy.
| | - Stefania Della Penna
- Department of Neuroscience, Imaging and Clinical Sciences, and Institute for Advanced Biomedical Technologies, "G. d'Annunzio" University of Chieti-Pescara, Via Luigi Polacchi, 11, 66100 Chieti, Italy.
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Manjunatha KKH, Baron G, Benozzo D, Silvestri E, Corbetta M, Chiuso A, Bertoldo A, Suweis S, Allegra M. Controlling target brain regions by optimal selection of input nodes. PLoS Comput Biol 2024; 20:e1011274. [PMID: 38215166 PMCID: PMC10810536 DOI: 10.1371/journal.pcbi.1011274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 01/25/2024] [Accepted: 12/04/2023] [Indexed: 01/14/2024] Open
Abstract
The network control theory framework holds great potential to inform neurostimulation experiments aimed at inducing desired activity states in the brain. However, the current applicability of the framework is limited by inappropriate modeling of brain dynamics, and an overly ambitious focus on whole-brain activity control. In this work, we leverage recent progress in linear modeling of brain dynamics (effective connectivity) and we exploit the concept of target controllability to focus on the control of a single region or a small subnetwork of nodes. We discuss when control may be possible with a reasonably low energy cost and few stimulation loci, and give general predictions on where to stimulate depending on the subset of regions one wishes to control. Importantly, using the robustly asymmetric effective connectome instead of the symmetric structural connectome (as in previous research), we highlight the fundamentally different roles in- and out-hubs have in the control problem, and the relevance of inhibitory connections. The large degree of inter-individual variation in the effective connectome implies that the control problem is best formulated at the individual level, but we discuss to what extent group results may still prove useful.
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Affiliation(s)
- Karan Kabbur Hanumanthappa Manjunatha
- Physics and Astronomy Department “Galileo Galilei”, University of Padova, Padova, Italy
- Modeling and Engineering Risk and Complexity, Scuola Superiore Meridionale, Napoli, Italy
| | - Giorgia Baron
- Information Engineering Department, University of Padova, Padova, Italy
| | - Danilo Benozzo
- Information Engineering Department, University of Padova, Padova, Italy
| | - Erica Silvestri
- Information Engineering Department, University of Padova, Padova, Italy
| | - Maurizio Corbetta
- Neuroscience Department, University of Padova, Padova, Italy
- Venetian Institute of Molecular Medicine (VIMM), Padova, Italy
- Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Alessandro Chiuso
- Information Engineering Department, University of Padova, Padova, Italy
| | - Alessandra Bertoldo
- Information Engineering Department, University of Padova, Padova, Italy
- Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Samir Suweis
- Physics and Astronomy Department “Galileo Galilei”, University of Padova, Padova, Italy
- Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Michele Allegra
- Physics and Astronomy Department “Galileo Galilei”, University of Padova, Padova, Italy
- Padova Neuroscience Center, University of Padova, Padova, Italy
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10
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Blain SD, Taylor SF, Lasagna CA, Angstadt M, Rutherford SE, Peltier S, Diwadkar VA, Tso IF. Aberrant Effective Connectivity During Eye Gaze Processing Is Linked to Social Functioning and Symptoms in Schizophrenia. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2023; 8:1228-1239. [PMID: 37648206 PMCID: PMC10840731 DOI: 10.1016/j.bpsc.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/02/2023] [Accepted: 08/19/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Patients with schizophrenia show abnormal gaze processing, which is associated with social dysfunction. These abnormalities are related to aberrant connectivity among brain regions that are associated with visual processing, social cognition, and cognitive control. In this study, we investigated 1) how effective connectivity during gaze processing is disrupted in schizophrenia and 2) how this may contribute to social dysfunction and clinical symptoms. METHODS Thirty-nine patients with schizophrenia/schizoaffective disorder (SZ) and 33 healthy control participants completed an eye gaze processing task during functional magnetic resonance imaging. Participants viewed faces with different gaze angles and performed explicit and implicit gaze processing. Four brain regions-the secondary visual cortex, posterior superior temporal sulcus, inferior parietal lobule, and posterior medial frontal cortex-were identified as nodes for dynamic causal modeling analysis. RESULTS Both the SZ and healthy control groups showed similar model structures for general gaze processing. Explicit gaze discrimination led to changes in effective connectivity, including stronger excitatory, bottom-up connections from the secondary visual cortex to the posterior superior temporal sulcus and inferior parietal lobule and inhibitory, top-down connections from the posterior medial frontal cortex to the secondary visual cortex. Group differences in top-down modulation from the posterior medial frontal cortex to the posterior superior temporal sulcus and inferior parietal lobule were noted, such that these inhibitory connections were attenuated in the healthy control group but further strengthened in the SZ group. Connectivity was associated with social dysfunction and symptom severity. CONCLUSIONS The SZ group showed notably stronger top-down inhibition during explicit gaze discrimination, which was associated with more social dysfunction but less severe symptoms among patients. These findings help pinpoint neural mechanisms of aberrant gaze processing and may serve as future targets for interventions that combine neuromodulation with social cognitive training.
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Affiliation(s)
- Scott D Blain
- Department of Psychiatry & Behavioral Health, The Ohio State University, Columbus, Ohio; Department of Psychiatry, University of Michigan, Ann Arbor, Michigan.
| | - Stephan F Taylor
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan; Department of Psychology, University of Michigan, Ann Arbor, Michigan
| | - Carly A Lasagna
- Department of Psychology, University of Michigan, Ann Arbor, Michigan
| | - Mike Angstadt
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan
| | - Saige E Rutherford
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan; Predictive Clinical Neuroscience Lab, Donders Center for Medical Neuroscience, Nijmegen, the Netherlands
| | - Scott Peltier
- Functional MRI Laboratory, University of Michigan, Ann Arbor, Michigan
| | - Vaibhav A Diwadkar
- Department of Psychiatry & Behavioral Neurosciences, Wayne State University, Detroit, Michigan
| | - Ivy F Tso
- Department of Psychiatry & Behavioral Health, The Ohio State University, Columbus, Ohio; Department of Psychiatry, University of Michigan, Ann Arbor, Michigan
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11
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Saberi A, Paquola C, Wagstyl K, Hettwer MD, Bernhardt BC, Eickhoff SB, Valk SL. The regional variation of laminar thickness in the human isocortex is related to cortical hierarchy and interregional connectivity. PLoS Biol 2023; 21:e3002365. [PMID: 37943873 PMCID: PMC10684102 DOI: 10.1371/journal.pbio.3002365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/28/2023] [Accepted: 10/06/2023] [Indexed: 11/12/2023] Open
Abstract
The human isocortex consists of tangentially organized layers with unique cytoarchitectural properties. These layers show spatial variations in thickness and cytoarchitecture across the neocortex, which is thought to support function through enabling targeted corticocortical connections. Here, leveraging maps of the 6 cortical layers based on 3D human brain histology, we aimed to quantitatively characterize the systematic covariation of laminar structure in the cortex and its functional consequences. After correcting for the effect of cortical curvature, we identified a spatial pattern of changes in laminar thickness covariance from lateral frontal to posterior occipital regions, which differentiated the dominance of infra- versus supragranular layer thickness. Corresponding to the laminar regularities of cortical connections along cortical hierarchy, the infragranular-dominant pattern of laminar thickness was associated with higher hierarchical positions of regions, mapped based on resting-state effective connectivity in humans and tract-tracing of structural connections in macaques. Moreover, we show that regions with similar laminar thickness patterns have a higher likelihood of structural connections and strength of functional connections. In sum, here we characterize the organization of laminar thickness in the human isocortex and its association with cortico-cortical connectivity, illustrating how laminar organization may provide a foundational principle of cortical function.
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Affiliation(s)
- Amin Saberi
- Otto Hahn Research Group for Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Institute of Neurosciences and Medicine (INM-7), Research Centre Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Casey Paquola
- Institute of Neurosciences and Medicine (INM-7), Research Centre Jülich, Jülich, Germany
| | - Konrad Wagstyl
- Wellcome Trust Centre for Neuroimaging, University College London, London, United Kingdom
| | - Meike D. Hettwer
- Otto Hahn Research Group for Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Institute of Neurosciences and Medicine (INM-7), Research Centre Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Max Planck School of Cognition, Leipzig, Germany
| | - Boris C. Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada
| | - Simon B. Eickhoff
- Institute of Neurosciences and Medicine (INM-7), Research Centre Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sofie L. Valk
- Otto Hahn Research Group for Cognitive Neurogenetics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
- Institute of Neurosciences and Medicine (INM-7), Research Centre Jülich, Jülich, Germany
- Institute of Systems Neuroscience, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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12
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Xie K, Royer J, Larivière S, Rodriguez-Cruces R, Frässle S, Cabalo DG, Ngo A, DeKraker J, Auer H, Tavakol S, Weng Y, Abdallah C, Horwood L, Frauscher B, Caciagli L, Bernasconi A, Bernasconi N, Zhang Z, Concha L, Bernhardt BC. Atypical connectome topography and signal flow in temporal lobe epilepsy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541934. [PMID: 37292996 PMCID: PMC10245853 DOI: 10.1101/2023.05.23.541934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Temporal lobe epilepsy (TLE) is one of the most common pharmaco-resistant epilepsies in adults. While hippocampal pathology is the hallmark of this condition, emerging evidence indicates that brain alterations extend beyond the mesiotemporal epicenter and affect macroscale brain function and cognition. We studied macroscale functional reorganization in TLE, explored structural substrates, and examined cognitive associations. We investigated a multisite cohort of 95 patients with pharmaco-resistant TLE and 95 healthy controls using state-of-the-art multimodal 3T magnetic resonance imaging (MRI). We quantified macroscale functional topographic organization using connectome dimensionality reduction techniques and estimated directional functional flow using generative models of effective connectivity. We observed atypical functional topographies in patients with TLE relative to controls, manifesting as reduced functional differentiation between sensory/motor networks and transmodal systems such as the default mode network, with peak alterations in bilateral temporal and ventromedial prefrontal cortices. TLE-related topographic changes were consistent in all three included sites and reflected reductions in hierarchical flow patterns between cortical systems. Integration of parallel multimodal MRI data indicated that these findings were independent of TLE-related cortical grey matter atrophy, but mediated by microstructural alterations in the superficial white matter immediately beneath the cortex. The magnitude of functional perturbations was robustly associated with behavioral markers of memory function. Overall, this work provides converging evidence for macroscale functional imbalances, contributing microstructural alterations, and their associations with cognitive dysfunction in TLE.
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Affiliation(s)
- Ke Xie
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Jessica Royer
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Sara Larivière
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Raul Rodriguez-Cruces
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Donna Gift Cabalo
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Alexander Ngo
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Jordan DeKraker
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Hans Auer
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Shahin Tavakol
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Yifei Weng
- Department of Medical Imaging, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chifaou Abdallah
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Linda Horwood
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Birgit Frauscher
- Analytical Neurophysiology Laboratory, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Lorenzo Caciagli
- Department of Biomedical Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Andrea Bernasconi
- Neuroimaging of Epilepsy Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Neda Bernasconi
- Neuroimaging of Epilepsy Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Zhiqiang Zhang
- Department of Medical Imaging, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Luis Concha
- Brain Connectivity Laboratory, Institute of Neurobiology, Universidad Nacional Autónoma de Mexico (UNAM), Mexico
| | - Boris C Bernhardt
- Multimodal Imaging and Connectome Analysis Laboratory, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
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13
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Bedford P, Hauke DJ, Wang Z, Roth V, Nagy-Huber M, Holze F, Ley L, Vizeli P, Liechti ME, Borgwardt S, Müller F, Diaconescu AO. The effect of lysergic acid diethylamide (LSD) on whole-brain functional and effective connectivity. Neuropsychopharmacology 2023:10.1038/s41386-023-01574-8. [PMID: 37185950 PMCID: PMC10267115 DOI: 10.1038/s41386-023-01574-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 05/17/2023]
Abstract
Psychedelics have emerged as promising candidate treatments for various psychiatric conditions, and given their clinical potential, there is a need to identify biomarkers that underlie their effects. Here, we investigate the neural mechanisms of lysergic acid diethylamide (LSD) using regression dynamic causal modelling (rDCM), a novel technique that assesses whole-brain effective connectivity (EC) during resting-state functional magnetic resonance imaging (fMRI). We modelled data from two randomised, placebo-controlled, double-blind, cross-over trials, in which 45 participants were administered 100 μg LSD and placebo in two resting-state fMRI sessions. We compared EC against whole-brain functional connectivity (FC) using classical statistics and machine learning methods. Multivariate analyses of EC parameters revealed predominantly stronger interregional connectivity and reduced self-inhibition under LSD compared to placebo, with the notable exception of weakened interregional connectivity and increased self-inhibition in occipital brain regions as well as subcortical regions. Together, these findings suggests that LSD perturbs the Excitation/Inhibition balance of the brain. Notably, whole-brain EC did not only provide additional mechanistic insight into the effects of LSD on the Excitation/Inhibition balance of the brain, but EC also correlated with global subjective effects of LSD and discriminated experimental conditions in a machine learning-based analysis with high accuracy (91.11%), highlighting the potential of using whole-brain EC to decode or predict subjective effects of LSD in the future.
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Affiliation(s)
- Peter Bedford
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Daniel J Hauke
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK.
| | - Zheng Wang
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
| | - Volker Roth
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Monika Nagy-Huber
- Department of Mathematics and Computer Science, University of Basel, Basel, Switzerland
| | - Friederike Holze
- Division of Clinical Pharmacology and Toxicology, Department of Biomedicine and Department of Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Laura Ley
- Division of Clinical Pharmacology and Toxicology, Department of Biomedicine and Department of Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Patrick Vizeli
- Division of Clinical Pharmacology and Toxicology, Department of Biomedicine and Department of Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Matthias E Liechti
- Division of Clinical Pharmacology and Toxicology, Department of Biomedicine and Department of Clinical Research, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Stefan Borgwardt
- Department of Psychiatry and Psychotherapy, Translational Psychiatry, Lübeck, Germany
| | - Felix Müller
- Department of Psychiatry (UPK), University of Basel, Basel, Switzerland
| | - Andreea O Diaconescu
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health (CAMH), Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Psychology, University of Toronto, Toronto, ON, Canada
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14
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Ji J, Zou A, Liu J, Yang C, Zhang X, Song Y. A Survey on Brain Effective Connectivity Network Learning. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2023; 34:1879-1899. [PMID: 34469315 DOI: 10.1109/tnnls.2021.3106299] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Human brain effective connectivity characterizes the causal effects of neural activities among different brain regions. Studies of brain effective connectivity networks (ECNs) for different populations contribute significantly to the understanding of the pathological mechanism associated with neuropsychiatric diseases and facilitate finding new brain network imaging markers for the early diagnosis and evaluation for the treatment of cerebral diseases. A deeper understanding of brain ECNs also greatly promotes brain-inspired artificial intelligence (AI) research in the context of brain-like neural networks and machine learning. Thus, how to picture and grasp deeper features of brain ECNs from functional magnetic resonance imaging (fMRI) data is currently an important and active research area of the human brain connectome. In this survey, we first show some typical applications and analyze existing challenging problems in learning brain ECNs from fMRI data. Second, we give a taxonomy of ECN learning methods from the perspective of computational science and describe some representative methods in each category. Third, we summarize commonly used evaluation metrics and conduct a performance comparison of several typical algorithms both on simulated and real datasets. Finally, we present the prospects and references for researchers engaged in learning ECNs.
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15
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Galioulline H, Frässle S, Harrison S, Pereira I, Heinzle J, Stephan KE. Predicting Future Depressive Episodes from Resting-State fMRI with Generative Embedding. Neuroimage 2023; 273:119986. [PMID: 36958617 DOI: 10.1016/j.neuroimage.2023.119986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 02/15/2023] [Accepted: 02/25/2023] [Indexed: 03/25/2023] Open
Abstract
After a first episode of major depressive disorder (MDD), there is substantial risk for a long-term remitting-relapsing course. Prevention and early interventions are thus critically important. Various studies have examined the feasibility of detecting at-risk individuals based on out-of-sample predictions about the future occurrence of depression. However, functional magnetic resonance imaging (MRI) has received very little attention for this purpose so far. Here, we explored the utility of generative models (i.e. different dynamic causal models, DCMs) as well as functional connectivity (FC) for predicting future episodes of depression in never-depressed adults, using a large dataset (N=906) of task-free ("resting state") fMRI data from the UK Biobank. Connectivity analyses were conducted using timeseries from pre-computed spatially independent components of different dimensionalities. Over a three year period, 50% of participants showed indications of at least one depressive episode, while the other 50% did not. Using nested cross-validation for training and a held-out test set (80/20 split), we systematically examined the combination of 8 connectivity feature sets and 17 classifiers. We found that a generative embedding procedure based on combining regression DCM (rDCM) with a support vector machine (SVM) enabled the best predictions, both on the training set (0.63 accuracy, 0.66 area under the curve, AUC) and the test set (0.62 accuracy, 0.64 AUC; p<0.001). However, on the test set, rDCM was only slightly superior to predictions based on FC (0.59 accuracy, 0.61 AUC). Interpreting model predictions based on SHAP (SHapley Additive exPlanations) values suggested that the most predictive connections were widely distributed and not confined to specific networks. Overall, our analyses suggest (i) ways of improving future fMRI-based generative embedding approaches for the early detection of individuals at-risk for depression and that (ii) achieving accuracies of clinical utility may require combination of fMRI with other data modalities.
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Affiliation(s)
- Herman Galioulline
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, 8032 Zurich, Switzerland.
| | - Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, 8032 Zurich, Switzerland
| | - Sam Harrison
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, 8032 Zurich, Switzerland
| | - Inês Pereira
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, 8032 Zurich, Switzerland
| | - Jakob Heinzle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, 8032 Zurich, Switzerland
| | - Klaas Enno Stephan
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, 8032 Zurich, Switzerland; Max Planck Institute for Metabolism Research, Cologne, Germany
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16
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Wang Y, Yan G, Wang X, Li S, Peng L, Tudorascu DL, Zhang T. A variational Bayesian approach to identifying whole-brain directed networks with fMRI data. Ann Appl Stat 2023. [DOI: 10.1214/22-aoas1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Yaotian Wang
- Department of Statistics, University of Pittsburgh
| | - Guofen Yan
- Department of Public Health Sciences, University of Virginia
| | - Xiaofeng Wang
- Department of Quantitative Health Sciences, Cleveland Clinic
| | - Shuoran Li
- Department of Statistics, University of Pittsburgh
| | - Lingyi Peng
- Department of Biostatistics, University of Pittsburgh
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17
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Hashemi M, Vattikonda AN, Jha J, Sip V, Woodman MM, Bartolomei F, Jirsa VK. Amortized Bayesian inference on generative dynamical network models of epilepsy using deep neural density estimators. Neural Netw 2023; 163:178-194. [PMID: 37060871 DOI: 10.1016/j.neunet.2023.03.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 03/24/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023]
Abstract
Whole-brain modeling of epilepsy combines personalized anatomical data with dynamical models of abnormal activities to generate spatio-temporal seizure patterns as observed in brain imaging data. Such a parametric simulator is equipped with a stochastic generative process, which itself provides the basis for inference and prediction of the local and global brain dynamics affected by disorders. However, the calculation of likelihood function at whole-brain scale is often intractable. Thus, likelihood-free algorithms are required to efficiently estimate the parameters pertaining to the hypothetical areas, ideally including the uncertainty. In this study, we introduce the simulation-based inference for the virtual epileptic patient model (SBI-VEP), enabling us to amortize the approximate posterior of the generative process from a low-dimensional representation of whole-brain epileptic patterns. The state-of-the-art deep learning algorithms for conditional density estimation are used to readily retrieve the statistical relationships between parameters and observations through a sequence of invertible transformations. We show that the SBI-VEP is able to efficiently estimate the posterior distribution of parameters linked to the extent of the epileptogenic and propagation zones from sparse intracranial electroencephalography recordings. The presented Bayesian methodology can deal with non-linear latent dynamics and parameter degeneracy, paving the way for fast and reliable inference on brain disorders from neuroimaging modalities.
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18
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Kobeleva X, Varoquaux G, Dagher A, Adhikari M, Grefkes C, Gilson M. Advancing brain network models to reconcile functional neuroimaging and clinical research. Neuroimage Clin 2022; 36:103262. [PMID: 36451365 PMCID: PMC9723311 DOI: 10.1016/j.nicl.2022.103262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/26/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022]
Abstract
Functional magnetic resonance imaging (fMRI) captures information on brain function beyond the anatomical alterations that are traditionally visually examined by neuroradiologists. However, the fMRI signals are complex in addition to being noisy, so fMRI still faces limitations for clinical applications. Here we review methods that have been proposed as potential solutions so far, namely statistical, biophysical and decoding models, with their strengths and weaknesses. We especially evaluate the ability of these models to directly predict clinical variables from their parameters (predictability) and to extract clinically relevant information regarding biological mechanisms and relevant features for classification and prediction (interpretability). We then provide guidelines for useful applications and pitfalls of such fMRI-based models in a clinical research context, looking beyond the current state of the art. In particular, we argue that the clinical relevance of fMRI calls for a new generation of models for fMRI data, which combine the strengths of both biophysical and decoding models. This leads to reliable and biologically meaningful model parameters, which thus fulfills the need for simultaneous interpretability and predictability. In our view, this synergy is fundamental for the discovery of new pharmacological and interventional targets, as well as the use of models as biomarkers in neurology and psychiatry.
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Affiliation(s)
- Xenia Kobeleva
- Department of Neurology, University of Bonn, Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE) Bonn, Bonn, Germany
| | | | - Alain Dagher
- Montreal Neurological Institute, McGill University, Montréal, Canada
| | - Mohit Adhikari
- Bio-imaging Lab, University of Antwerp, Antwerp, Belgium
| | - Christian Grefkes
- Department of Neurology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany; Institute of Neuroscience and Medicine (INM-1, INM-3), Research Centre Juelich, Juelich, Germany; Department of Neurology, Goethe University Frankfurt, Frankfurt, Germany
| | - Matthieu Gilson
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany; Center for Brain and Cognition, Department of Information and Telecommunication Technologies, Universitat Pompeu Fabra, Barcelona, Spain; Institut de Neurosciences des Systèmes, Aix-Marseille University, Marseille, France.
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19
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Jha J, Hashemi M, Vattikonda AN, Wang H, Jirsa V. Fully Bayesian estimation of virtual brain parameters with self-tuning Hamiltonian Monte Carlo. MACHINE LEARNING: SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1088/2632-2153/ac9037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract
Virtual brain models are data-driven patient-specific brain models integrating individual brain imaging data with neural mass modeling in a single computational framework, capable of autonomously generating brain activity and its associated brain imaging signals. Along the example of epilepsy, we develop an efficient and accurate Bayesian methodology estimating the parameters linked to the extent of the epileptogenic zone. State-of-the-art advances in Bayesian inference using Hamiltonian Monte Carlo (HMC) algorithms have remained elusive for large-scale differential-equations based models due to their slow convergence. We propose appropriate priors and a novel reparameterization to facilitate efficient exploration of the posterior distribution in terms of computational time and convergence diagnostics. The methodology is illustrated for in-silico dataset and then, applied to infer the personalized model parameters based on the empirical stereotactic electroencephalography (SEEG) recordings of retrospective patients. This improved methodology may pave the way to render HMC methods sufficiently easy and efficient to use, thus applicable in personalized medicine.
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20
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Li G, Yap PT. From descriptive connectome to mechanistic connectome: Generative modeling in functional magnetic resonance imaging analysis. Front Hum Neurosci 2022; 16:940842. [PMID: 36061504 PMCID: PMC9428697 DOI: 10.3389/fnhum.2022.940842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/28/2022] [Indexed: 01/28/2023] Open
Abstract
As a newly emerging field, connectomics has greatly advanced our understanding of the wiring diagram and organizational features of the human brain. Generative modeling-based connectome analysis, in particular, plays a vital role in deciphering the neural mechanisms of cognitive functions in health and dysfunction in diseases. Here we review the foundation and development of major generative modeling approaches for functional magnetic resonance imaging (fMRI) and survey their applications to cognitive or clinical neuroscience problems. We argue that conventional structural and functional connectivity (FC) analysis alone is not sufficient to reveal the complex circuit interactions underlying observed neuroimaging data and should be supplemented with generative modeling-based effective connectivity and simulation, a fruitful practice that we term "mechanistic connectome." The transformation from descriptive connectome to mechanistic connectome will open up promising avenues to gain mechanistic insights into the delicate operating principles of the human brain and their potential impairments in diseases, which facilitates the development of effective personalized treatments to curb neurological and psychiatric disorders.
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Affiliation(s)
- Guoshi Li
- Department of Radiology, University of North Carolina, Chapel Hill, NC, United States,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, United States,*Correspondence: Guoshi Li,
| | - Pew-Thian Yap
- Department of Radiology, University of North Carolina, Chapel Hill, NC, United States,Biomedical Research Imaging Center, University of North Carolina, Chapel Hill, NC, United States
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21
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Ou Y, Dai P, Zhou X, Xiong T, Li Y, Chen Z, Zou B. A strategy of model space search for dynamic causal modeling in task fMRI data exploratory analysis. Phys Eng Sci Med 2022; 45:867-882. [PMID: 35849323 DOI: 10.1007/s13246-022-01156-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/18/2022] [Indexed: 12/01/2022]
Abstract
Dynamic causal modeling (DCM) is a tool used for effective connectivity (EC) estimation in neuroimage analysis. But it is a model-driven analysis method, and the structure of the EC network needs to be determined in advance based on a large amount of prior knowledge. This characteristic makes it difficult to apply DCM to the exploratory brain network analysis. The exploratory analysis of DCM can be realized from two perspectives: one is to reduce the computational cost of the model; the other is to reduce the model space. From the perspective of model space reduction, a model space exploration strategy is proposed, including two algorithms. One algorithm, named GreedyEC, starts with reducing EC from full model, and the other, named GreedyROI, start with adding EC from one node model. Then the two algorithms were applied to the task state functional magnetic resonance imaging (fMRI) data of visual object recognition and selected the best DCM model from the perspective of model comparison based on Bayesian model compare method. Results show that combining the results of the two algorithms can further improve the effect of DCM exploratory analysis. For convenience in application, the algorithms were encapsulated into MATLAB function based on SPM to help neuroscience researchers to analyze the brain causal information flow network. The strategy provides a model space exploration tool that may obtain the best model from the perspective of model comparison and lower the threshold of DCM analysis.
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Affiliation(s)
- Yilin Ou
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Peishan Dai
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
- Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Central South University, Changsha, 410083, China.
| | - Xiaoyan Zhou
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Tong Xiong
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Yang Li
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Central South University, Changsha, 410083, China
| | - Zailiang Chen
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Central South University, Changsha, 410083, China
| | - Beiji Zou
- School of Computer Science and Engineering, Central South University, Changsha, 410083, China
- Hunan Engineering Research Center of Machine Vision and Intelligent Medicine, Central South University, Changsha, 410083, China
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22
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Wein S, Schüller A, Tomé AM, Malloni WM, Greenlee MW, Lang EW. Forecasting brain activity based on models of spatiotemporal brain dynamics: A comparison of graph neural network architectures. Netw Neurosci 2022; 6:665-701. [PMID: 36607180 PMCID: PMC9810370 DOI: 10.1162/netn_a_00252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/02/2022] [Indexed: 01/10/2023] Open
Abstract
Comprehending the interplay between spatial and temporal characteristics of neural dynamics can contribute to our understanding of information processing in the human brain. Graph neural networks (GNNs) provide a new possibility to interpret graph-structured signals like those observed in complex brain networks. In our study we compare different spatiotemporal GNN architectures and study their ability to model neural activity distributions obtained in functional MRI (fMRI) studies. We evaluate the performance of the GNN models on a variety of scenarios in MRI studies and also compare it to a VAR model, which is currently often used for directed functional connectivity analysis. We show that by learning localized functional interactions on the anatomical substrate, GNN-based approaches are able to robustly scale to large network studies, even when available data are scarce. By including anatomical connectivity as the physical substrate for information propagation, such GNNs also provide a multimodal perspective on directed connectivity analysis, offering a novel possibility to investigate the spatiotemporal dynamics in brain networks.
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Affiliation(s)
- S. Wein
- CIML, Biophysics, University of Regensburg, Regensburg, Germany,Experimental Psychology, University of Regensburg, Regensburg, Germany,* Corresponding Author:
| | - A. Schüller
- CIML, Biophysics, University of Regensburg, Regensburg, Germany
| | - A. M. Tomé
- IEETA, DETI, Universidade de Aveiro, Aveiro, Portugal
| | - W. M. Malloni
- Experimental Psychology, University of Regensburg, Regensburg, Germany
| | - M. W. Greenlee
- Experimental Psychology, University of Regensburg, Regensburg, Germany
| | - E. W. Lang
- CIML, Biophysics, University of Regensburg, Regensburg, Germany
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23
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Mijalkov M, Volpe G, Pereira JB. Directed Brain Connectivity Identifies Widespread Functional Network Abnormalities in Parkinson's Disease. Cereb Cortex 2022; 32:593-607. [PMID: 34331060 PMCID: PMC8805861 DOI: 10.1093/cercor/bhab237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/19/2021] [Accepted: 06/17/2021] [Indexed: 11/14/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by topological abnormalities in large-scale functional brain networks, which are commonly analyzed using undirected correlations in the activation signals between brain regions. This approach assumes simultaneous activation of brain regions, despite previous evidence showing that brain activation entails causality, with signals being typically generated in one region and then propagated to other ones. To address this limitation, here, we developed a new method to assess whole-brain directed functional connectivity in participants with PD and healthy controls using antisymmetric delayed correlations, which capture better this underlying causality. Our results show that whole-brain directed connectivity, computed on functional magnetic resonance imaging data, identifies widespread differences in the functional networks of PD participants compared with controls, in contrast to undirected methods. These differences are characterized by increased global efficiency, clustering, and transitivity combined with lower modularity. Moreover, directed connectivity patterns in the precuneus, thalamus, and cerebellum were associated with motor, executive, and memory deficits in PD participants. Altogether, these findings suggest that directional brain connectivity is more sensitive to functional network differences occurring in PD compared with standard methods, opening new opportunities for brain connectivity analysis and development of new markers to track PD progression.
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Affiliation(s)
- Mite Mijalkov
- Address correspondence to Mite Mijalkov and Joana B. Pereira, Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, Karolinska Institutet, Neo 7th floor, Blickagången 16, 141 83 Huddinge, Sweden. (M.M.); (J.B.P.)
| | | | - Joana B Pereira
- Address correspondence to Mite Mijalkov and Joana B. Pereira, Department of Neurobiology, Care Sciences and Society, Division of Clinical Geriatrics, Karolinska Institutet, Neo 7th floor, Blickagången 16, 141 83 Huddinge, Sweden. (M.M.); (J.B.P.)
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24
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Frässle S, Stephan KE. Test-retest reliability of regression dynamic causal modeling. Netw Neurosci 2022; 6:135-160. [PMID: 35356192 PMCID: PMC8959103 DOI: 10.1162/netn_a_00215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/08/2021] [Indexed: 11/04/2022] Open
Abstract
Abstract
Regression dynamic causal modeling (rDCM) is a novel and computationally highly efficient method for inferring effective connectivity at the whole-brain level. While face and construct validity of rDCM have already been demonstrated, here we assessed its test-retest reliability—a test-theoretical property of particular importance for clinical applications—together with group-level consistency of connection-specific estimates and consistency of whole-brain connectivity patterns over sessions. Using the Human Connectome Project dataset for eight different paradigms (tasks and rest) and two different parcellation schemes, we found that rDCM provided highly consistent connectivity estimates at the group level across sessions. Second, while test-retest reliability was limited when averaging over all connections (range of mean intraclass correlation coefficient 0.24–0.42 over tasks), reliability increased with connection strength, with stronger connections showing good to excellent test-retest reliability. Third, whole-brain connectivity patterns by rDCM allowed for identifying individual participants with high (and in some cases perfect) accuracy. Comparing the test-retest reliability of rDCM connectivity estimates with measures of functional connectivity, rDCM performed favorably—particularly when focusing on strong connections. Generally, for all methods and metrics, task-based connectivity estimates showed greater reliability than those from the resting state. Our results underscore the potential of rDCM for human connectomics and clinical applications.
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Affiliation(s)
- Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Klaas E. Stephan
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Max Planck Institute for Metabolism Research, Cologne, Germany
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25
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Grimm C, Frässle S, Steger C, von Ziegler L, Sturman O, Shemesh N, Peleg-Raibstein D, Burdakov D, Bohacek J, Stephan KE, Razansky D, Wenderoth N, Zerbi V. Optogenetic activation of striatal D1R and D2R cells differentially engages downstream connected areas beyond the basal ganglia. Cell Rep 2021; 37:110161. [PMID: 34965430 DOI: 10.1016/j.celrep.2021.110161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 10/20/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
The basal ganglia (BG) are a group of subcortical nuclei responsible for motor and executive function. Central to BG function are striatal cells expressing D1 (D1R) and D2 (D2R) dopamine receptors. D1R and D2R cells are considered functional antagonists that facilitate voluntary movements and inhibit competing motor patterns, respectively. However, whether they maintain a uniform function across the striatum and what influence they exert outside the BG is unclear. Here, we address these questions by combining optogenetic activation of D1R and D2R cells in the mouse ventrolateral caudoputamen with fMRI. Striatal D1R/D2R stimulation evokes distinct activity within the BG-thalamocortical network and differentially engages cerebellar and prefrontal regions. Computational modeling of effective connectivity confirms that changes in D1R/D2R output drive functional relationships between these regions. Our results suggest a complex functional organization of striatal D1R/D2R cells and hint toward an interconnected fronto-BG-cerebellar network modulated by striatal D1R and D2R cells.
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Affiliation(s)
- Christina Grimm
- Neural Control of Movement Lab, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland; Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland
| | - Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zürich and ETH Zürich, Zürich, Switzerland
| | - Céline Steger
- Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland; Center for MR Research, University Children's Hospital Zurich, Zürich, Switzerland
| | - Lukas von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland; Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland
| | - Oliver Sturman
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland; Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland
| | - Noam Shemesh
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Daria Peleg-Raibstein
- Laboratory of Neurobehavioral Dynamics, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, Zürich, Switzerland; Institute for Biomedical Engineering and Institute of Pharmacology and Toxicology, Faculty of Medicine, University of Zurich, Zürich, Switzerland
| | - Denis Burdakov
- Laboratory of Neurobehavioral Dynamics, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, Zürich, Switzerland; Institute for Biomedical Engineering and Institute of Pharmacology and Toxicology, Faculty of Medicine, University of Zurich, Zürich, Switzerland; Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland; Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland
| | - Klaas Enno Stephan
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zürich and ETH Zürich, Zürich, Switzerland
| | - Daniel Razansky
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zürich, Zürich, Switzerland; Institute of Biological and Medical Imaging (IBMI), Technical University of Munich and Helmholtz Center Munich, Munich, Germany; Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland
| | - Nicole Wenderoth
- Neural Control of Movement Lab, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland; Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland
| | - Valerio Zerbi
- Neural Control of Movement Lab, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland; Neuroscience Center Zurich, ETH Zürich and University of Zurich, Zürich, Switzerland.
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26
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Valeriani D, Simonyan K. The dynamic connectome of speech control. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200256. [PMID: 34482717 DOI: 10.1098/rstb.2020.0256] [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] [Indexed: 02/06/2023] Open
Abstract
Speech production relies on the orchestrated control of multiple brain regions. The specific, directional influences within these networks remain poorly understood. We used regression dynamic causal modelling to infer the whole-brain directed (effective) connectivity from functional magnetic resonance imaging data of 36 healthy individuals during the production of meaningful English sentences and meaningless syllables. We identified that the two dynamic connectomes have distinct architectures that are dependent on the complexity of task production. The speech was regulated by a dynamic neural network, the most influential nodes of which were centred around superior and inferior parietal areas and influenced the whole-brain network activity via long-ranging coupling with primary sensorimotor, prefrontal, temporal and insular regions. By contrast, syllable production was controlled by a more compressed, cost-efficient network structure, involving sensorimotor cortico-subcortical integration via superior parietal and cerebellar network hubs. These data demonstrate the mechanisms by which the neural network reorganizes the connectivity of its influential regions, from supporting the fundamental aspects of simple syllabic vocal motor output to multimodal information processing of speech motor output. This article is part of the theme issue 'Vocal learning in animals and humans'.
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Affiliation(s)
- Davide Valeriani
- Department of Otolaryngology - Head and Neck Surgery, Massachusetts Eye and Ear, 243 Charles Street, Boston, MA 02114, USA.,Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA
| | - Kristina Simonyan
- Department of Otolaryngology - Head and Neck Surgery, Massachusetts Eye and Ear, 243 Charles Street, Boston, MA 02114, USA.,Department of Otolaryngology-Head and Neck Surgery, Harvard Medical School, 243 Charles Street, Boston, MA 02114, USA.,Department of Neurology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
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27
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Li H, Wang Y, Yan G, Sun Y, Tanabe S, Liu CC, Quigg MS, Zhang T. A Bayesian State-Space Approach to Mapping Directional Brain Networks. J Am Stat Assoc 2021. [DOI: 10.1080/01621459.2020.1865985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Huazhang Li
- Department of Statistics, University of Virginia, Charlottesville, VA
| | - Yaotian Wang
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA
| | - Guofen Yan
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Yinge Sun
- Department of Statistics, University of Virginia, Charlottesville, VA
| | - Seiji Tanabe
- Department of Psychology, University of Virginia, Charlottesville, VA
| | - Chang-Chia Liu
- Department of Neurosurgery, University of Virginia, Charlottesville, VA
| | - Mark S. Quigg
- Department of Neurology, University of Virginia, Charlottesville, VA
| | - Tingting Zhang
- Department of Statistics, University of Pittsburgh, Pittsburgh, PA
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28
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Abrevaya G, Dumas G, Aravkin AY, Zheng P, Gagnon-Audet JC, Kozloski J, Polosecki P, Lajoie G, Cox D, Dawson SP, Cecchi G, Rish I. Learning Brain Dynamics With Coupled Low-Dimensional Nonlinear Oscillators and Deep Recurrent Networks. Neural Comput 2021; 33:2087-2127. [PMID: 34310676 DOI: 10.1162/neco_a_01401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 02/19/2021] [Indexed: 01/16/2023]
Abstract
Many natural systems, especially biological ones, exhibit complex multivariate nonlinear dynamical behaviors that can be hard to capture by linear autoregressive models. On the other hand, generic nonlinear models such as deep recurrent neural networks often require large amounts of training data, not always available in domains such as brain imaging; also, they often lack interpretability. Domain knowledge about the types of dynamics typically observed in such systems, such as a certain type of dynamical systems models, could complement purely data-driven techniques by providing a good prior. In this work, we consider a class of ordinary differential equation (ODE) models known as van der Pol (VDP) oscil lators and evaluate their ability to capture a low-dimensional representation of neural activity measured by different brain imaging modalities, such as calcium imaging (CaI) and fMRI, in different living organisms: larval zebrafish, rat, and human. We develop a novel and efficient approach to the nontrivial problem of parameters estimation for a network of coupled dynamical systems from multivariate data and demonstrate that the resulting VDP models are both accurate and interpretable, as VDP's coupling matrix reveals anatomically meaningful excitatory and inhibitory interactions across different brain subsystems. VDP outperforms linear autoregressive models (VAR) in terms of both the data fit accuracy and the quality of insight provided by the coupling matrices and often tends to generalize better to unseen data when predicting future brain activity, being comparable to and sometimes better than the recurrent neural networks (LSTMs). Finally, we demonstrate that our (generative) VDP model can also serve as a data-augmentation tool leading to marked improvements in predictive accuracy of recurrent neural networks. Thus, our work contributes to both basic and applied dimensions of neuroimaging: gaining scientific insights and improving brain-based predictive models, an area of potentially high practical importance in clinical diagnosis and neurotechnology.
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Affiliation(s)
- Germán Abrevaya
- Departamento de Física, FCEyN, UBA and IFIBA, CONICET, 1428 Buenos Aires, Argentina
| | - Guillaume Dumas
- Mila-Quebec Artificial Intelligence Institute, and CHU Sainte-Justine Research Center, Department of Psychiatry, Universitéde Montréal, Montreal H3A OE8, Canada
| | | | - Peng Zheng
- University of Washington, Seattle, WA 98195, U.S.A.
| | | | - James Kozloski
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598, U.S.A.
| | - Pablo Polosecki
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598, U.S.A.
| | - Guillaume Lajoie
- Mila-Quebec Artificial Intelligence Institute, Universitéde Montréal, Montreal H3A OE8, Canada
| | - David Cox
- MIT-IBM Watson AI Lab, Cambridge, MA 02139, U.S.A.
| | - Silvina Ponce Dawson
- Departamento de Física, FCEyN, UBA and IFIBA, CONICET, 1428 Buenos Aires, Argentina
| | - Guillermo Cecchi
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598, U.S.A.
| | - Irina Rish
- Mila-Quebec Artificial Intelligence Institute, Université de Montréal, Montreal H3A OE8, Canada
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29
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Ji S, Ma H, Yao M, Guo M, Li S, Chen N, Liu X, Shao X, Yao Z, Hu B. Aberrant Temporal Variability in Brain Regions during Risk Decision Making in Patients with Bipolar I Disorder: A Dynamic Effective Connectivity Study. Neuroscience 2021; 469:68-78. [PMID: 34153355 DOI: 10.1016/j.neuroscience.2021.06.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022]
Abstract
Bipolar I disorder (BD-I) is associated with high-risk behaviors, such as suicide attempts and addictive substance abuse. Understanding brain activity exposure to risk decision making provides evidence for the treatment of BD-I patients. This study aimed to investigate the temporal dynamics of brain connectivity underlying risk decision making in patients with BD-I. A total of 101 subjects (48 BD-I patients and 53 age- and gender-matched healthy controls (HCs)) were included in this research. We analyzed the fMRI data acquired during Balloon Analog Risk Task (BART) performance. Voxel-wise dynamic effective connectivity (dEC) was employed to measure the activities in 264 brain regions. The coefficient of variation (CV) was calculated as temporal dynamics of brain connectivity. Finally, we used structural equation modeling (SEM) to determine the relationships of dEC in brain regions with clinical symptoms, behavior performances in patients. Results showed that BD-I patients exhibited increased dynamics in four lobes and exhibited decreased in three frontal regions. Besides, SEM results showed that the impulsive symptoms of patients were affected by the dEC during both resting and task states. Moreover, the dEC of left supramarginal gyrus (SMG) influenced those of left orbital frontal and right cuneus (CUN), as well as the affective symptoms and BART behaviors in patients with BD-I. Our results suggested that the altered temporal dynamics of brain connectivity might contribute to the impulsivity of BD-I during resting and task states. More importantly, the left SMG might be a therapeutic target to reduce the risk behavior in BD-I patients.
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Affiliation(s)
- Shanling Ji
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, China
| | - Hongxia Ma
- School of Clinical Medicine, Jining Medical University, Jining, Shandong Province, China
| | - Mengyuan Yao
- Department of Psychiatry, Jining Psychiatric Hospital, Jining, Shandong Province, China
| | - Man Guo
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, China
| | - Shan Li
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, China
| | - Nan Chen
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, China
| | - Xia Liu
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, China
| | - Xuexiao Shao
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, China
| | - Zhijun Yao
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, China.
| | - Bin Hu
- Gansu Provincial Key Laboratory of Wearable Computing, School of Information Science and Engineering, Lanzhou University, China; School of Computer Science, Qinghai Normal University, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China; Joint Research Center for Cognitive Neurosensor Technology of Lanzhou University & Institute of Semiconductors, Chinese Academy of Sciences, China; Engineering Research Center of Open Source Software and Real-Time System (Lanzhou University), Ministry of Education, Lanzhou, China.
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30
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Frässle S, Aponte EA, Bollmann S, Brodersen KH, Do CT, Harrison OK, Harrison SJ, Heinzle J, Iglesias S, Kasper L, Lomakina EI, Mathys C, Müller-Schrader M, Pereira I, Petzschner FH, Raman S, Schöbi D, Toussaint B, Weber LA, Yao Y, Stephan KE. TAPAS: An Open-Source Software Package for Translational Neuromodeling and Computational Psychiatry. Front Psychiatry 2021; 12:680811. [PMID: 34149484 PMCID: PMC8206497 DOI: 10.3389/fpsyt.2021.680811] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/10/2021] [Indexed: 12/26/2022] Open
Abstract
Psychiatry faces fundamental challenges with regard to mechanistically guided differential diagnosis, as well as prediction of clinical trajectories and treatment response of individual patients. This has motivated the genesis of two closely intertwined fields: (i) Translational Neuromodeling (TN), which develops "computational assays" for inferring patient-specific disease processes from neuroimaging, electrophysiological, and behavioral data; and (ii) Computational Psychiatry (CP), with the goal of incorporating computational assays into clinical decision making in everyday practice. In order to serve as objective and reliable tools for clinical routine, computational assays require end-to-end pipelines from raw data (input) to clinically useful information (output). While these are yet to be established in clinical practice, individual components of this general end-to-end pipeline are being developed and made openly available for community use. In this paper, we present the Translational Algorithms for Psychiatry-Advancing Science (TAPAS) software package, an open-source collection of building blocks for computational assays in psychiatry. Collectively, the tools in TAPAS presently cover several important aspects of the desired end-to-end pipeline, including: (i) tailored experimental designs and optimization of measurement strategy prior to data acquisition, (ii) quality control during data acquisition, and (iii) artifact correction, statistical inference, and clinical application after data acquisition. Here, we review the different tools within TAPAS and illustrate how these may help provide a deeper understanding of neural and cognitive mechanisms of disease, with the ultimate goal of establishing automatized pipelines for predictions about individual patients. We hope that the openly available tools in TAPAS will contribute to the further development of TN/CP and facilitate the translation of advances in computational neuroscience into clinically relevant computational assays.
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Affiliation(s)
- Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Eduardo A. Aponte
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Saskia Bollmann
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, United States
- Department of Radiology, Harvard Medical School, Charlestown, MA, United States
| | - Kay H. Brodersen
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Cao T. Do
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Olivia K. Harrison
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- School of Pharmacy, University of Otago, Dunedin, New Zealand
| | - Samuel J. Harrison
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Jakob Heinzle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Sandra Iglesias
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Lars Kasper
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Techna Institute, University Health Network, Toronto, ON, Canada
| | - Ekaterina I. Lomakina
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Christoph Mathys
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
- Interacting Minds Center, Aarhus University, Aarhus, Denmark
| | - Matthias Müller-Schrader
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Inês Pereira
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Frederike H. Petzschner
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Sudhir Raman
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Dario Schöbi
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Birte Toussaint
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Lilian A. Weber
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Yu Yao
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Klaas E. Stephan
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
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31
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Xie X, Cai C, Damasceno PF, Nagarajan SS, Raj A. Emergence of canonical functional networks from the structural connectome. Neuroimage 2021; 237:118190. [PMID: 34022382 PMCID: PMC8451304 DOI: 10.1016/j.neuroimage.2021.118190] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/05/2021] [Accepted: 05/18/2021] [Indexed: 01/21/2023] Open
Abstract
How do functional brain networks emerge from the underlying wiring of the brain? We examine how resting-state functional activation patterns emerge from the underlying connectivity and length of white matter fibers that constitute its “structural connectome”. By introducing realistic signal transmission delays along fiber projections, we obtain a complex-valued graph Laplacian matrix that depends on two parameters: coupling strength and oscillation frequency. This complex Laplacian admits a complex-valued eigen-basis in the frequency domain that is highly tunable and capable of reproducing the spatial patterns of canonical functional networks without requiring any detailed neural activity modeling. Specific canonical functional networks can be predicted using linear superposition of small subsets of complex eigenmodes. Using a novel parameter inference procedure we show that the complex Laplacian outperforms the real-valued Laplacian in predicting functional networks. The complex Laplacian eigenmodes therefore constitute a tunable yet parsimonious substrate on which a rich repertoire of realistic functional patterns can emerge. Although brain activity is governed by highly complex nonlinear processes and dense connections, our work suggests that simple extensions of linear models to the complex domain effectively approximate rich macroscopic spatial patterns observable on BOLD fMRI.
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Affiliation(s)
- Xihe Xie
- Department of Neuroscience, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10028, United States.
| | - Chang Cai
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 505 Parnassus Avenue, San Francisco, CA 94143, United States
| | - Pablo F Damasceno
- Center for Intelligent Imaging, University of California San Francisco, 505 Parnassus Avenue, San Francisco, CA, United States
| | - Srikantan S Nagarajan
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 505 Parnassus Avenue, San Francisco, CA 94143, United States.
| | - Ashish Raj
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 505 Parnassus Avenue, San Francisco, CA 94143, United States.
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32
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Adams NE, Hughes LE, Rouse MA, Phillips HN, Shaw AD, Murley AG, Cope TE, Bevan-Jones WR, Passamonti L, Street D, Holland N, Nesbitt D, Friston K, Rowe JB. GABAergic cortical network physiology in frontotemporal lobar degeneration. Brain 2021; 144:2135-2145. [PMID: 33710299 PMCID: PMC8370432 DOI: 10.1093/brain/awab097] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 11/23/2022] Open
Abstract
The clinical syndromes caused by frontotemporal lobar degeneration are heterogeneous, including the behavioural variant frontotemporal dementia (bvFTD) and progressive supranuclear palsy. Although pathologically distinct, they share many behavioural, cognitive and physiological features, which may in part arise from common deficits of major neurotransmitters such as γ-aminobutyric acid (GABA). Here, we quantify the GABAergic impairment and its restoration with dynamic causal modelling of a double-blind placebo-controlled crossover pharmaco-magnetoencephalography study. We analysed 17 patients with bvFTD, 15 patients with progressive supranuclear palsy, and 20 healthy age- and gender-matched controls. In addition to neuropsychological assessment and structural MRI, participants undertook two magnetoencephalography sessions using a roving auditory oddball paradigm: once on placebo and once on 10 mg of the oral GABA reuptake inhibitor tiagabine. A subgroup underwent ultrahigh-field magnetic resonance spectroscopy measurement of GABA concentration, which was reduced among patients. We identified deficits in frontotemporal processing using conductance-based biophysical models of local and global neuronal networks. The clinical relevance of this physiological deficit is indicated by the correlation between top-down connectivity from frontal to temporal cortex and clinical measures of cognitive and behavioural change. A critical validation of the biophysical modelling approach was evidence from parametric empirical Bayes analysis that GABA levels in patients, measured by spectroscopy, were related to posterior estimates of patients’ GABAergic synaptic connectivity. Further evidence for the role of GABA in frontotemporal lobar degeneration came from confirmation that the effects of tiagabine on local circuits depended not only on participant group, but also on individual baseline GABA levels. Specifically, the phasic inhibition of deep cortico-cortical pyramidal neurons following tiagabine, but not placebo, was a function of GABA concentration. The study provides proof-of-concept for the potential of dynamic causal modelling to elucidate mechanisms of human neurodegenerative disease, and explains the variation in response to candidate therapies among patients. The laminar- and neurotransmitter-specific features of the modelling framework, can be used to study other treatment approaches and disorders. In the context of frontotemporal lobar degeneration, we suggest that neurophysiological restoration in selected patients, by targeting neurotransmitter deficits, could be used to bridge between clinical and preclinical models of disease, and inform the personalized selection of drugs and stratification of patients for future clinical trials.
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Affiliation(s)
- Natalie E Adams
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Laura E Hughes
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,MMRC Cognition and Brain Sciences Unit, Cambridge CB2 7EF, UK
| | - Matthew A Rouse
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Holly N Phillips
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Alexander G Murley
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - Thomas E Cope
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,MMRC Cognition and Brain Sciences Unit, Cambridge CB2 7EF, UK.,Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - W Richard Bevan-Jones
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - Luca Passamonti
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - Duncan Street
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - Negin Holland
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - David Nesbitt
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,MMRC Cognition and Brain Sciences Unit, Cambridge CB2 7EF, UK.,Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
| | - Karl Friston
- Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3AR, UK
| | - James B Rowe
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0QQ, UK.,MMRC Cognition and Brain Sciences Unit, Cambridge CB2 7EF, UK.,Cambridge University Hospitals, Cambridge, CB2 0QQ, UK
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33
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Tso IF, Angstadt M, Rutherford S, Peltier S, Diwadkar VA, Taylor SF. Dynamic causal modeling of eye gaze processing in schizophrenia. Schizophr Res 2021; 229:112-121. [PMID: 33229223 PMCID: PMC8324063 DOI: 10.1016/j.schres.2020.11.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/16/2020] [Accepted: 11/12/2020] [Indexed: 11/15/2022]
Abstract
BACKGROUND Abnormal eye gaze perception is related to symptoms and social functioning in schizophrenia. However, little is known about the brain network mechanisms underlying these abnormalities. Here, we employed dynamic causal modeling (DCM) of fMRI data to discover aberrant effective connectivity within networks associated with eye gaze processing in schizophrenia. METHODS Twenty-seven patients (schizophrenia/schizoaffective disorder, SZ) and 22 healthy controls (HC) completed an eye gaze processing task during fMRI. Participants viewed faces with different gaze angles and performed explicit gaze discrimination (Gaze: "Looking at you?" yes/no) or implicit gaze processing (Gender: "male or female?"). Four brain regions, the secondary visual cortex (Vis), posterior superior temporal sulcus (pSTS), inferior parietal lobule (IPL), and posterior medial frontal cortex (pMFC) were identified as nodes for subsequent DCM analysis. RESULTS SZ and HC showed similar generative model structure, but SZ showed altered connectivity for specific self-connections, inter-regional connections during all gaze processing (reduced excitatory bottom-up and enhanced inhibitory top-down connections), and modulation by explicit gaze discrimination (increased frontal inhibition of visual cortex). Altered effective connectivity was significantly associated with poorer social cognition and functioning. CONCLUSIONS General gaze processing in SZ is associated with distributed cortical dysfunctions and bidirectional connectivity between regions, while explicit gaze discrimination involves predominantly top-down abnormalities in the visual system. These results suggest plausible neural mechanisms underpinning gaze processing deficits and may serve as bio-markers for intervention.
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Affiliation(s)
- Ivy F. Tso
- Department of Psychiatry, University of Michigan, Ann Arbor,Address correspondence to Ivy Tso, Department of Psychiatry, University of Michigan, 4250 Plymouth Road, Ann Arbor, MI 48109, U.S.A.
| | - Mike Angstadt
- Department of Psychiatry, University of Michigan, Ann Arbor
| | | | - Scott Peltier
- Functional MRI Laboratory, University of Michigan, Ann Arbor
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34
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Frässle S, Harrison SJ, Heinzle J, Clementz BA, Tamminga CA, Sweeney JA, Gershon ES, Keshavan MS, Pearlson GD, Powers A, Stephan KE. Regression dynamic causal modeling for resting-state fMRI. Hum Brain Mapp 2021; 42:2159-2180. [PMID: 33539625 PMCID: PMC8046067 DOI: 10.1002/hbm.25357] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/05/2021] [Accepted: 01/20/2021] [Indexed: 02/03/2023] Open
Abstract
“Resting‐state” functional magnetic resonance imaging (rs‐fMRI) is widely used to study brain connectivity. So far, researchers have been restricted to measures of functional connectivity that are computationally efficient but undirected, or to effective connectivity estimates that are directed but limited to small networks. Here, we show that a method recently developed for task‐fMRI—regression dynamic causal modeling (rDCM)—extends to rs‐fMRI and offers both directional estimates and scalability to whole‐brain networks. First, simulations demonstrate that rDCM faithfully recovers parameter values over a wide range of signal‐to‐noise ratios and repetition times. Second, we test construct validity of rDCM in relation to an established model of effective connectivity, spectral DCM. Using rs‐fMRI data from nearly 200 healthy participants, rDCM produces biologically plausible results consistent with estimates by spectral DCM. Importantly, rDCM is computationally highly efficient, reconstructing whole‐brain networks (>200 areas) within minutes on standard hardware. This opens promising new avenues for connectomics.
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Affiliation(s)
- Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Zurich, Switzerland
| | - Samuel J Harrison
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Zurich, Switzerland
| | - Jakob Heinzle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Zurich, Switzerland
| | - Brett A Clementz
- Department of Psychology and Neuroscience, Bio-Imaging Research Center, University of Georgia, Athens, Georgia, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - John A Sweeney
- Department of Psychiatry, University of Cincinnati, Cincinnati, Ohio, USA
| | - Elliot S Gershon
- Department of Psychiatry, University of Chicago, Chicago, Illinois, USA.,Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Matcheri S Keshavan
- Department of Psychiatry, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Godfrey D Pearlson
- Olin Neuropsychiatry Research Center, Hartford Hospital, Institute of Living, Hartford, Connecticut, USA.,Department of Psychiatry & Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Albert Powers
- Department of Psychiatry & Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Klaas E Stephan
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Zurich, Switzerland.,Max Planck Institute for Metabolism Research, Cologne, Germany
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35
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Huys QJM, Browning M, Paulus MP, Frank MJ. Advances in the computational understanding of mental illness. Neuropsychopharmacology 2021; 46:3-19. [PMID: 32620005 PMCID: PMC7688938 DOI: 10.1038/s41386-020-0746-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/11/2022]
Abstract
Computational psychiatry is a rapidly growing field attempting to translate advances in computational neuroscience and machine learning into improved outcomes for patients suffering from mental illness. It encompasses both data-driven and theory-driven efforts. Here, recent advances in theory-driven work are reviewed. We argue that the brain is a computational organ. As such, an understanding of the illnesses arising from it will require a computational framework. The review divides work up into three theoretical approaches that have deep mathematical connections: dynamical systems, Bayesian inference and reinforcement learning. We discuss both general and specific challenges for the field, and suggest ways forward.
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Affiliation(s)
- Quentin J M Huys
- Division of Psychiatry and Max Planck UCL Centre for Computational Psychiatry and Ageing Research, University College London, London, UK.
- Camden and Islington NHS Trust, London, UK.
| | - Michael Browning
- Computational Psychiatry Lab, Department of Psychiatry, University of Oxford, Oxford, UK
- Oxford Health NHS Trust, Oxford, UK
| | - Martin P Paulus
- Laureate Institute For Brain Research (LIBR), Tulsa, OK, USA
| | - Michael J Frank
- Cognitive, Linguistic & Psychological Sciences, Neuroscience Graduate Program, Brown University, Providence, RI, USA
- Carney Center for Computational Brain Science, Carney Institute for Brain Science Psychiatry and Human Behavior, Brown University, Providence, RI, USA
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36
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Sadeghi S, Mier D, Gerchen MF, Schmidt SNL, Hass J. Dynamic Causal Modeling for fMRI With Wilson-Cowan-Based Neuronal Equations. Front Neurosci 2020; 14:593867. [PMID: 33328865 PMCID: PMC7728993 DOI: 10.3389/fnins.2020.593867] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/29/2020] [Indexed: 01/26/2023] Open
Abstract
Dynamic causal modeling (DCM) is an analysis technique that has been successfully used to infer about directed connectivity between brain regions based on imaging data such as functional magnetic resonance imaging (fMRI). Most variants of DCM for fMRI rely on a simple bilinear differential equation for neural activation, making it difficult to interpret the results in terms of local neural dynamics. In this work, we introduce a modification to DCM for fMRI by replacing the bilinear equation with a non-linear Wilson-Cowan based equation and use Bayesian Model Comparison (BMC) to show that this modification improves the model evidences. Improved model evidence of the non-linear model is shown for our empirical data (imitation of facial expressions) and validated by synthetic data as well as an empirical test dataset (attention to visual motion) used in previous foundational papers. For our empirical data, we conduct the analysis for a group of 42 healthy participants who performed an imitation task, activating regions putatively containing the human mirror neuron system (MNS). In this regard, we build 540 models as one family for comparing the standard bilinear with the modified Wilson-Cowan models on the family-level. Using this modification, we can interpret the sigmoid transfer function as an averaged f-I curve of many neurons in a single region with a sigmoidal format. In this way, we can make a direct inference from the macroscopic model to detailed microscopic models. The new DCM variant shows superior model evidence on all tested data sets.
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Affiliation(s)
- Sadjad Sadeghi
- Department of Theoretical Neuroscience, Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, Mannheim, Germany.,Bernstein Center for Computational Neuroscience (BCCN) Heidelberg/Mannheim, Mannheim, Germany.,Department of Physics and Astronomy, University of Heidelberg, Heidelberg, Germany
| | - Daniela Mier
- Department of Clinical Psychology, Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, Mannheim, Germany.,Department of Psychology, University of Konstanz, Konstanz, Germany
| | - Martin F Gerchen
- Bernstein Center for Computational Neuroscience (BCCN) Heidelberg/Mannheim, Mannheim, Germany.,Department of Clinical Psychology, Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, Mannheim, Germany
| | | | - Joachim Hass
- Department of Theoretical Neuroscience, Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, Mannheim, Germany.,Bernstein Center for Computational Neuroscience (BCCN) Heidelberg/Mannheim, Mannheim, Germany.,Faculty of Applied Psychology, SRH University of Applied Sciences Heidelberg, Heidelberg, Germany
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37
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Engel M, Kasper L, Wilm B, Dietrich B, Vionnet L, Hennel F, Reber J, Pruessmann KP. T-Hex: Tilted hexagonal grids for rapid 3D imaging. Magn Reson Med 2020; 85:2507-2523. [PMID: 33270941 DOI: 10.1002/mrm.28600] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/09/2023]
Abstract
PURPOSE The purpose of this work is to devise and demonstrate an encoding strategy for 3D MRI that reconciles high speed with flexible segmentation, uniform k-space density, and benign T 2 ∗ effects. METHODS Fast sampling of a 3D k-space is typically accomplished by 2D readouts per shot using EPI trains or spiral readouts. Tilted hexagonal (T-Hex) sampling is a way of acquiring more k-space volume per excitation while maintaining uniform sampling density and a smooth T 2 ∗ filter. The k-space volume covered per shot is controlled by the tilting angle. Image reconstruction is performed with a 3D extension of the iterative SENSE approach, incorporating actual field dynamics and static off-resonance. T-Hex imaging is compared with established 3D schemes in terms of speed and noise performance. RESULTS Tilted hexagonal acquisition is found to achieve greater imaging speed than known alternatives, particularly in combination with spiral trajectories. The interplay of the proposed 3D trajectories, array detection, and off-resonance is successfully addressed by iterative inversion of the full signal model. Enhanced coverage per shot is of greatest utility for high speed in an intermediate resolution regime of 1 to 4 mm. T-Hex EPI combines the benefits of extended coverage per shot with increased robustness against off-resonance effects. CONCLUSION Sampling of tilted hexagonal grids is a feasible means of gaining 3D imaging speed with near-optimal SNR efficiency and benign depiction properties. It is a particularly promising technique for time-resolved applications such as fMRI.
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Affiliation(s)
- Maria Engel
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Lars Kasper
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland.,Translational Neuromodeling Unit, IBT, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Bertram Wilm
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Benjamin Dietrich
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Laetitia Vionnet
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Franciszek Hennel
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Jonas Reber
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Klaas P Pruessmann
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
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38
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Whole-brain estimates of directed connectivity for human connectomics. Neuroimage 2020; 225:117491. [PMID: 33115664 DOI: 10.1016/j.neuroimage.2020.117491] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/13/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Connectomics is essential for understanding large-scale brain networks but requires that individual connection estimates are neurobiologically interpretable. In particular, a principle of brain organization is that reciprocal connections between cortical areas are functionally asymmetric. This is a challenge for fMRI-based connectomics in humans where only undirected functional connectivity estimates are routinely available. By contrast, whole-brain estimates of effective (directed) connectivity are computationally challenging, and emerging methods require empirical validation. Here, using a motor task at 7T, we demonstrate that a novel generative model can infer known connectivity features in a whole-brain network (>200 regions, >40,000 connections) highly efficiently. Furthermore, graph-theoretical analyses of directed connectivity estimates identify functional roles of motor areas more accurately than undirected functional connectivity estimates. These results, which can be achieved in an entirely unsupervised manner, demonstrate the feasibility of inferring directed connections in whole-brain networks and open new avenues for human connectomics.
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39
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Sokolov AA, Zeidman P, Razi A, Erb M, Ryvlin P, Pavlova MA, Friston KJ. Asymmetric high-order anatomical brain connectivity sculpts effective connectivity. Netw Neurosci 2020; 4:871-890. [PMID: 33615094 PMCID: PMC7888488 DOI: 10.1162/netn_a_00150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Bridging the gap between symmetric, direct white matter brain connectivity and neural dynamics that are often asymmetric and polysynaptic may offer insights into brain architecture, but this remains an unresolved challenge in neuroscience. Here, we used the graph Laplacian matrix to simulate symmetric and asymmetric high-order diffusion processes akin to particles spreading through white matter pathways. The simulated indirect structural connectivity outperformed direct as well as absent anatomical information in sculpting effective connectivity, a measure of causal and directed brain dynamics. Crucially, an asymmetric diffusion process determined by the sensitivity of the network nodes to their afferents best predicted effective connectivity. The outcome is consistent with brain regions adapting to maintain their sensitivity to inputs within a dynamic range. Asymmetric network communication models offer a promising perspective for understanding the relationship between structural and functional brain connectomes, both in normalcy and neuropsychiatric conditions.
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Affiliation(s)
- Arseny A. Sokolov
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London, United Kingdom
- Department of Neurology, University Neurorehabilitation, University Hospital Inselspital, University of Bern, Bern, Switzerland
- Service de Neurologie and Neuroscape@NeuroTech Platform, Département des Neurosciences Cliniques, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Neuroscape Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Peter Zeidman
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London, United Kingdom
| | - Adeel Razi
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London, United Kingdom
- Monash Institute of Cognitive and Clinical Neurosciences & Monash Biomedical Imaging, Monash University, Clayton, Australia
- Department of Electronic Engineering, NED University of Engineering and Technology, Karachi, Pakistan
| | - Michael Erb
- Department of Biomedical Magnetic Resonance, University of Tübingen Medical School, Tübingen, Germany
| | - Philippe Ryvlin
- Service de Neurologie and Neuroscape@NeuroTech Platform, Département des Neurosciences Cliniques, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Marina A. Pavlova
- Department of Psychiatry and Psychotherapy, University of Tübingen Medical School, Tübingen, Germany
| | - Karl J. Friston
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London, United Kingdom
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40
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Singh MF, Wang A, Braver TS, Ching S. Scalable surrogate deconvolution for identification of partially-observable systems and brain modeling. J Neural Eng 2020; 17:046025. [PMID: 32590377 DOI: 10.1088/1741-2552/aba07d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE For many biophysical systems, direct measurement of all state-variables, in - vivo is not feasible. Thus, a key challenge in biological modeling and signal processing is to reconstruct the activity and structure of interesting biological systems from indirect measurements. These measurements are often generated by approximately linear time-invariant dynamical interactions with the hidden system and may therefore be described as a convolution of hidden state-variables with an unknown kernel. APPROACH In the current work, we present an approach termed surrogate deconvolution, to directly identify such coupled systems (i.e. parameterize models). Surrogate deconvolution reframes certain non linear partially-observable identification problems, which are common in neuroscience/biology, as analytical objectives that are compatible with almost any user-chosen optimization procedure. MAIN RESULTS We show that the proposed technique is highly scalable, low in computational complexity, and performs competitively with the current gold-standard in partially-observable system estimation: the joint Kalman Filters (Unscented and Extended). We show the benefits of surrogate deconvolution for model identification when applied to simulations of the Local Field Potential and blood oxygen level dependent (BOLD) signal. Lastly, we demonstrate the empirical stability of Hemodynamic Response Function (HRF) kernel estimates for Mesoscale Individualized NeuroDynamic (MINDy) models of individual human brains. The recovered HRF parameters demonstrate reliable individual variation as well as a stereotyped spatial distribution, on average. SIGNIFICANCE These results demonstrate that surrogate deconvolution promises to enhance brain-modeling approaches by simultaneously and rapidly fitting large-scale models of brain networks and the physiological processes which generate neuroscientific measurements (e.g. hemodynamics for BOLD fMRI).
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Affiliation(s)
- Matthew F Singh
- Department of Electrical and Systems Engineering, Washington University in St. Louis, St. Louis, MO, United States of America. Department of Psychological and Brain Sciences, Washington University in St. Louis, St. Louis, MO, United States of America. Author to whom any correspondence should be addressed
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41
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Raj A, Cai C, Xie X, Palacios E, Owen J, Mukherjee P, Nagarajan S. Spectral graph theory of brain oscillations. Hum Brain Mapp 2020; 41:2980-2998. [PMID: 32202027 PMCID: PMC7336150 DOI: 10.1002/hbm.24991] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 11/10/2022] Open
Abstract
The relationship between the brain's structural wiring and the functional patterns of neural activity is of fundamental interest in computational neuroscience. We examine a hierarchical, linear graph spectral model of brain activity at mesoscopic and macroscopic scales. The model formulation yields an elegant closed-form solution for the structure-function problem, specified by the graph spectrum of the structural connectome's Laplacian, with simple, universal rules of dynamics specified by a minimal set of global parameters. The resulting parsimonious and analytical solution stands in contrast to complex numerical simulations of high dimensional coupled nonlinear neural field models. This spectral graph model accurately predicts spatial and spectral features of neural oscillatory activity across the brain and was successful in simultaneously reproducing empirically observed spatial and spectral patterns of alpha-band (8-12 Hz) and beta-band (15-30 Hz) activity estimated from source localized magnetoencephalography (MEG). This spectral graph model demonstrates that certain brain oscillations are emergent properties of the graph structure of the structural connectome and provides important insights towards understanding the fundamental relationship between network topology and macroscopic whole-brain dynamics. .
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Affiliation(s)
- Ashish Raj
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCalifornia
- Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Chang Cai
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCalifornia
| | - Xihe Xie
- Department of Neuroscience, Weill Cornell Graduate School of Medical SciencesWeill Cornell MedicineNew YorkNew YorkUSA
| | - Eva Palacios
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCalifornia
| | - Julia Owen
- Department of RadiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Pratik Mukherjee
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCalifornia
- Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Srikantan Nagarajan
- Department of Radiology and Biomedical ImagingUniversity of CaliforniaSan FranciscoCalifornia
- Department of Bioengineering and Therapeutic SciencesUniversity of CaliforniaSan FranciscoCaliforniaUSA
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42
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Hashemi M, Vattikonda AN, Sip V, Guye M, Bartolomei F, Woodman MM, Jirsa VK. The Bayesian Virtual Epileptic Patient: A probabilistic framework designed to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread. Neuroimage 2020; 217:116839. [PMID: 32387625 DOI: 10.1016/j.neuroimage.2020.116839] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 12/28/2022] Open
Abstract
Despite the importance and frequent use of Bayesian frameworks in brain network modeling for parameter inference and model prediction, the advanced sampling algorithms implemented in probabilistic programming languages to overcome the inference difficulties have received relatively little attention in this context. In this technical note, we propose a probabilistic framework, namely the Bayesian Virtual Epileptic Patient (BVEP), which relies on the fusion of structural data of individuals to infer the spatial map of epileptogenicity in a personalized large-scale brain model of epilepsy spread. To invert the individualized whole-brain model employed in this study, we use the recently developed algorithms known as No-U-Turn Sampler (NUTS) as well as Automatic Differentiation Variational Inference (ADVI). Our results indicate that NUTS and ADVI accurately estimate the degree of epileptogenicity of brain regions, therefore, the hypothetical brain areas responsible for the seizure initiation and propagation, while the convergence diagnostics and posterior behavior analysis validate the reliability of the estimations. Moreover, we illustrate the efficiency of the transformed non-centered parameters in comparison to centered form of parameterization. The Bayesian framework used in this work proposes an appropriate patient-specific strategy for estimating the epileptogenicity of the brain regions to improve outcome after epilepsy surgery.
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Affiliation(s)
- M Hashemi
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France.
| | - A N Vattikonda
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - V Sip
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - M Guye
- Aix Marseille Univ, CNRS, CRMBM, Marseille, France
| | - F Bartolomei
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France; Epileptology Department, and Clinical Neurophysiology Department, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - M M Woodman
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France
| | - V K Jirsa
- Aix Marseille Univ, INSERM, INS, Inst Neurosci Syst, Marseille, France.
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43
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Gilson M, Zamora-López G, Pallarés V, Adhikari MH, Senden M, Campo AT, Mantini D, Corbetta M, Deco G, Insabato A. Model-based whole-brain effective connectivity to study distributed cognition in health and disease. Netw Neurosci 2020; 4:338-373. [PMID: 32537531 PMCID: PMC7286310 DOI: 10.1162/netn_a_00117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
Neuroimaging techniques are now widely used to study human cognition. The functional associations between brain areas have become a standard proxy to describe how cognitive processes are distributed across the brain network. Among the many analysis tools available, dynamic models of brain activity have been developed to overcome the limitations of original connectivity measures such as functional connectivity. This goes in line with the many efforts devoted to the assessment of directional interactions between brain areas from the observed neuroimaging activity. This opinion article provides an overview of our model-based whole-brain effective connectivity to analyze fMRI data, while discussing the pros and cons of our approach with respect to other established approaches. Our framework relies on the multivariate Ornstein-Uhlenbeck (MOU) process and is thus referred to as MOU-EC. Once tuned, the model provides a directed connectivity estimate that reflects the dynamical state of BOLD activity, which can be used to explore cognition. We illustrate this approach using two applications on task-evoked fMRI data. First, as a connectivity measure, MOU-EC can be used to extract biomarkers for task-specific brain coordination, understood as the patterns of areas exchanging information. The multivariate nature of connectivity measures raises several challenges for whole-brain analysis, for which machine-learning tools present some advantages over statistical testing. Second, we show how to interpret changes in MOU-EC connections in a collective and model-based manner, bridging with network analysis. Our framework provides a comprehensive set of tools that open exciting perspectives to study distributed cognition, as well as neuropathologies.
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Affiliation(s)
- Matthieu Gilson
- Center for Brain and Cognition and Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Gorka Zamora-López
- Center for Brain and Cognition and Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Vicente Pallarés
- Center for Brain and Cognition and Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mohit H. Adhikari
- Center for Brain and Cognition and Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mario Senden
- Department of Cognitive Neuroscience, University of Maastricht, Maastricht, The Netherlands
| | | | - Dante Mantini
- Neuroplasticity and Motor Control Research Group, KU Leuven, Leuven, Belgium
- Brain Imaging and Neural Dynamics Research Group, IRCCS San Camillo Hospital, Venice, Italy
| | - Maurizio Corbetta
- Department of Neuroscience, Venetian Institute of Molecular Medicine (VIMM) and Padova Neuroscience Center (PNC), University of Padua, Italy
- Department of Neurology, Radiology, and Neuroscience, Washington University School of Medicine, St. Louis, MO, USA
| | - Gustavo Deco
- Center for Brain and Cognition and Department of Information and Communication Technologies, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de la Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Andrea Insabato
- Institut de Neurosciences de la Timone, CNRS, Marseille, France
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44
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Deshpande G, Jia H. Multi-Level Clustering of Dynamic Directional Brain Network Patterns and Their Behavioral Relevance. Front Neurosci 2020; 13:1448. [PMID: 32116487 PMCID: PMC7017718 DOI: 10.3389/fnins.2019.01448] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 12/27/2019] [Indexed: 11/18/2022] Open
Abstract
Dynamic functional connectivity (DFC) obtained from resting state functional magnetic resonance imaging (fMRI) data has been shown to provide novel insights into brain function which may be obscured by static functional connectivity (SFC). Further, DFC, and by implication how different brain regions may engage or disengage with each other over time, has been shown to be behaviorally relevant and more predictive than SFC of behavioral performance and/or diagnostic status. DFC is not a directional entity and may capture neural synchronization. However, directional interactions between different brain regions is another putative mechanism by which neural populations communicate. Accordingly, static effective connectivity (SEC) has been explored as a means of characterizing such directional interactions. But investigation of its dynamic counterpart, i.e., dynamic effective connectivity (DEC), is still in its infancy. Of particular note are methodological insufficiencies in identifying DEC configurations that are reproducible across time and subjects as well as a lack of understanding of the behavioral relevance of DEC obtained from resting state fMRI. In order to address these issues, we employed a dynamic multivariate autoregressive (MVAR) model to estimate DEC. The method was first validated using simulations and then applied to resting state fMRI data obtained in-house (N = 21), wherein we performed dynamic clustering of DEC matrices across multiple levels [using adaptive evolutionary clustering (AEC)] – spatial location, time, and subjects. We observed a small number of directional brain network configurations alternating between each other over time in a quasi-stable manner akin to brain microstates. The dominant and consistent DEC network patterns involved several regions including inferior and mid temporal cortex, motor and parietal cortex, occipital cortex, as well as part of frontal cortex. The functional relevance of these DEC states were determined using meta-analyses and pertained mainly to memory and emotion, but also involved execution and language. Finally, a larger cohort of resting-state fMRI and behavioral data from the Human Connectome Project (HCP) (N = 232, Q1–Q3 release) was used to demonstrate that metrics derived from DEC can explain larger variance in 70 behaviors across different domains (alertness, cognition, emotion, and personality traits) compared to SEC in healthy individuals.
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Affiliation(s)
- Gopikrishna Deshpande
- Department of Electrical and Computer Engineering, AU MRI Research Center, Auburn University, Auburn, AL, United States.,Department of Psychology, Auburn University, Auburn, AL, United States.,Center for Neuroscience, Auburn University, Auburn, AL, United States.,Center for Health Ecology and Equity Research, Auburn, AL, United States.,Alabama Advanced Imaging Consortium, Birmingham, AL, United States.,Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru, India.,School of Psychology, Capital Normal University, Beijing, China.,Key Laboratory for Learning and Cognition, Capital Normal University, Beijing, China
| | - Hao Jia
- Department of Automation, College of Information Engineering, Taiyuan University of Technology, Taiyuan, China
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45
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Frässle S, Marquand AF, Schmaal L, Dinga R, Veltman DJ, van der Wee NJA, van Tol MJ, Schöbi D, Penninx BWJH, Stephan KE. Predicting individual clinical trajectories of depression with generative embedding. NEUROIMAGE-CLINICAL 2020; 26:102213. [PMID: 32197140 PMCID: PMC7082217 DOI: 10.1016/j.nicl.2020.102213] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/27/2020] [Accepted: 02/13/2020] [Indexed: 12/11/2022]
Abstract
Patients with major depressive disorder (MDD) show variable clinical trajectories. Generative embedding (GE) is used to predict clinical trajectories in MDD patients. GE classifies patients with chronic depression vs. fast remission with 79% accuracy. GE provides mechanistic interpretability and outperforms conventional measures. Proof-of-concept that illustrates the potential of GE for clinical prediction.
Patients with major depressive disorder (MDD) show heterogeneous treatment response and highly variable clinical trajectories: while some patients experience swift recovery, others show relapsing-remitting or chronic courses. Predicting individual clinical trajectories at an early stage is a key challenge for psychiatry and might facilitate individually tailored interventions. So far, however, reliable predictors at the single-patient level are absent. Here, we evaluated the utility of a machine learning strategy – generative embedding (GE) – which combines interpretable generative models with discriminative classifiers. Specifically, we used functional magnetic resonance imaging (fMRI) data of emotional face perception in 85 MDD patients from the NEtherlands Study of Depression and Anxiety (NESDA) who had been followed up over two years and classified into three subgroups with distinct clinical trajectories. Combining a generative model of effective (directed) connectivity with support vector machines (SVMs), we could predict whether a given patient would experience chronic depression vs. fast remission with a balanced accuracy of 79%. Gradual improvement vs. fast remission could still be predicted above-chance, but less convincingly, with a balanced accuracy of 61%. Generative embedding outperformed classification based on conventional (descriptive) features, such as functional connectivity or local activation estimates, which were obtained from the same data and did not allow for above-chance classification accuracy. Furthermore, predictive performance of GE could be assigned to a specific network property: the trial-by-trial modulation of connections by emotional content. Given the limited sample size of our study, the present results are preliminary but may serve as proof-of-concept, illustrating the potential of GE for obtaining clinical predictions that are interpretable in terms of network mechanisms. Our findings suggest that abnormal dynamic changes of connections involved in emotional face processing might be associated with higher risk of developing a less favorable clinical course.
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Affiliation(s)
- Stefan Frässle
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Zurich 8032, Switzerland.
| | - Andre F Marquand
- Donders Institute for Brain, Cognition and Behaviour, Radbound University, Nijmegen, The Netherlands; Department of Neuroimaging, Institute of Psychiatry, King's College London, London, United Kingdom
| | - Lianne Schmaal
- Orygen, The National Centre of Excellence in Youth Mental Health, Parkville, Australia; Centre for Youth Mental Health, University of Melbourne, Melbourne, Australia
| | - Richard Dinga
- Department of Psychiatry and Neuroscience Campus Amsterdam, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Dick J Veltman
- Department of Psychiatry and Neuroscience Campus Amsterdam, VU University Medical Center Amsterdam, Amsterdam, The Netherlands
| | - Nic J A van der Wee
- Department of Psychiatry, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Marie-José van Tol
- Cognitive Neuroscience Center, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Dario Schöbi
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Zurich 8032, Switzerland
| | - Brenda W J H Penninx
- Department of Psychiatry and Neuroscience Campus Amsterdam, VU University Medical Center Amsterdam, Amsterdam, The Netherlands; Department of Psychiatry, Amsterdam UMC, VU University, and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Klaas E Stephan
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich & ETH Zurich, Zurich 8032, Switzerland; Wellcome Centre for Human Neuroimaging, University College London, London WC1N 3BG, United Kingdom; Max Planck Institute for Metabolism Research, Cologne, Germany
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46
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Sadaghiani S, Wirsich J. Intrinsic connectome organization across temporal scales: New insights from cross-modal approaches. Netw Neurosci 2020; 4:1-29. [PMID: 32043042 PMCID: PMC7006873 DOI: 10.1162/netn_a_00114] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/11/2019] [Indexed: 12/17/2022] Open
Abstract
The discovery of a stable, whole-brain functional connectivity organization that is largely independent of external events has drastically extended our view of human brain function. However, this discovery has been primarily based on functional magnetic resonance imaging (fMRI). The role of this whole-brain organization in fast oscillation-based connectivity as measured, for example, by electroencephalography (EEG) and magnetoencephalography (MEG) is only beginning to emerge. Here, we review studies of intrinsic connectivity and its whole-brain organization in EEG, MEG, and intracranial electrophysiology with a particular focus on direct comparisons to connectome studies in fMRI. Synthesizing this literature, we conclude that irrespective of temporal scale over four orders of magnitude, intrinsic neurophysiological connectivity shows spatial similarity to the connectivity organization commonly observed in fMRI. A shared structural connectivity basis and cross-frequency coupling are possible mechanisms contributing to this similarity. Acknowledging that a stable whole-brain organization governs long-range coupling across all timescales of neural processing motivates researchers to take "baseline" intrinsic connectivity into account when investigating brain-behavior associations, and further encourages more widespread exploration of functional connectomics approaches beyond fMRI by using EEG and MEG modalities.
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Affiliation(s)
- Sepideh Sadaghiani
- Psychology Department, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan Wirsich
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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47
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Manjaly ZM, Iglesias S. A Computational Theory of Mindfulness Based Cognitive Therapy from the "Bayesian Brain" Perspective. Front Psychiatry 2020; 11:404. [PMID: 32499726 PMCID: PMC7243935 DOI: 10.3389/fpsyt.2020.00404] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/21/2020] [Indexed: 12/21/2022] Open
Abstract
Mindfulness Based Cognitive Therapy (MBCT) was developed to combine methods from cognitive behavioral therapy and meditative techniques, with the specific goal of preventing relapse in recurrent depression. While supported by empirical evidence from multiple clinical trials, the cognitive mechanisms behind the effectiveness of MBCT are not well understood in computational (information processing) or biological terms. This article introduces a testable theory about the computational mechanisms behind MBCT that is grounded in "Bayesian brain" concepts of perception from cognitive neuroscience, such as predictive coding. These concepts regard the brain as embodying a model of its environment (including the external world and the body) which predicts future sensory inputs and is updated by prediction errors, depending on how precise these error signals are. This article offers a concrete proposal how core concepts of MBCT-(i) the being mode (accepting whatever sensations arise, without judging or changing them), (ii) decentering (experiencing thoughts and percepts simply as events in the mind that arise and pass), and (iii) cognitive reactivity (changes in mood reactivate negative beliefs)-could be understood in terms of perceptual and metacognitive processes that draw on specific computational mechanisms of the "Bayesian brain." Importantly, the proposed theory can be tested experimentally, using a combination of behavioral paradigms, computational modelling, and neuroimaging. The novel theoretical perspective on MBCT described in this paper may offer opportunities for finessing the conceptual and practical aspects of MBCT.
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Affiliation(s)
- Zina-Mary Manjaly
- Department of Neurology, Schulthess Clinic, Zurich, Switzerland.,Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Sandra Iglesias
- Translational Neuromodeling Unit (TNU), Institute for Biomedical Engineering, University of Zurich and ETH Zurich, Zurich, Switzerland
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48
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Peraza-Goicolea JA, Martínez-Montes E, Aubert E, Valdés-Hernández PA, Mulet R. Modeling functional resting-state brain networks through neural message passing on the human connectome. Neural Netw 2019; 123:52-69. [PMID: 31830607 DOI: 10.1016/j.neunet.2019.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022]
Abstract
In this work, we propose a natural model for information flow in the brain through a neural message-passing dynamics on a structural network of macroscopic regions, such as the human connectome (HC). In our model, each brain region is assumed to have a binary behavior (active or not), the strengths of interactions among them are encoded in the anatomical connectivity matrix defined by the HC, and the dynamics of the system is defined by the Belief Propagation (BP) algorithm, working near the critical point of the network. We show that in the absence of direct external stimuli the BP algorithm converges to a spatial map of activations that is similar to the Default Mode Network (DMN) of the brain, which has been defined from the analysis of functional MRI data. Moreover, we use Susceptibility Propagation (SP) to compute the matrix of long-range correlations between the different regions and show that the modules defined by a clustering of this matrix resemble several Resting State Networks (RSN) determined experimentally. Both results suggest that the functional DMN and RSNs can be seen as simple consequences of the anatomical structure of the brain and a neural message-passing dynamics between macroscopic regions. With the new model, we explore predictions on how functional maps change when the anatomical brain network suffers structural alterations, like in Alzheimer's disease and in lesions of the Corpus Callosum. The implications and novel interpretations suggested by the model, as well as the role of criticality, are discussed.
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Affiliation(s)
- Julio A Peraza-Goicolea
- Group of Complex Systems and Statistical Physics, Department of Theoretical Physics, University of Havana, Havana, Cuba; Department of Physics, Florida International University, Miami, FL, USA.
| | - Eduardo Martínez-Montes
- Neuroinformatics Department, Cuban Neuroscience Center, Havana, Cuba; Advanced Center for Electrical and Electronic Engineering (AC3E), Universidad Técnica Federico Santa María, Valparaíso, Chile.
| | - Eduardo Aubert
- Neuroinformatics Department, Cuban Neuroscience Center, Havana, Cuba.
| | | | - Roberto Mulet
- Group of Complex Systems and Statistical Physics, Department of Theoretical Physics, University of Havana, Havana, Cuba.
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49
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Reid AT, Headley DB, Mill RD, Sanchez-Romero R, Uddin LQ, Marinazzo D, Lurie DJ, Valdés-Sosa PA, Hanson SJ, Biswal BB, Calhoun V, Poldrack RA, Cole MW. Advancing functional connectivity research from association to causation. Nat Neurosci 2019; 22:1751-1760. [PMID: 31611705 PMCID: PMC7289187 DOI: 10.1038/s41593-019-0510-4] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 09/06/2019] [Indexed: 11/09/2022]
Abstract
Cognition and behavior emerge from brain network interactions, such that investigating causal interactions should be central to the study of brain function. Approaches that characterize statistical associations among neural time series-functional connectivity (FC) methods-are likely a good starting point for estimating brain network interactions. Yet only a subset of FC methods ('effective connectivity') is explicitly designed to infer causal interactions from statistical associations. Here we incorporate best practices from diverse areas of FC research to illustrate how FC methods can be refined to improve inferences about neural mechanisms, with properties of causal neural interactions as a common ontology to facilitate cumulative progress across FC approaches. We further demonstrate how the most common FC measures (correlation and coherence) reduce the set of likely causal models, facilitating causal inferences despite major limitations. Alternative FC measures are suggested to immediately start improving causal inferences beyond these common FC measures.
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Affiliation(s)
- Andrew T Reid
- School of Psychology, University of Nottingham, Nottingham, UK
| | - Drew B Headley
- Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ, USA
| | - Ravi D Mill
- Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ, USA
| | - Ruben Sanchez-Romero
- Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ, USA
| | - Lucina Q Uddin
- Department of Psychology, University of Miami, Coral Gables, FL, USA
- Neuroscience Program, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Daniel J Lurie
- Department of Psychology, University of California, Berkeley, Berkeley, CA, USA
| | - Pedro A Valdés-Sosa
- The Clinical Hospital of Chengdu Brain Science Institute, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
- Cuban Neuroscience Center, La Habana, Cuba
| | | | - Bharat B Biswal
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, USA
| | - Vince Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) [Georgia State University, Georgia Institute of Technology, Emory University], Atlanta, GA, USA
| | | | - Michael W Cole
- Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ, USA.
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50
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Jovellar DB, Doudet DJ. fMRI in Non-human Primate: A Review on Factors That Can Affect Interpretation and Dynamic Causal Modeling Application. Front Neurosci 2019; 13:973. [PMID: 31619951 PMCID: PMC6759819 DOI: 10.3389/fnins.2019.00973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 08/30/2019] [Indexed: 11/13/2022] Open
Abstract
Dynamic causal modeling (DCM)-a framework for inferring hidden neuronal states from brain activity measurements (e. g., fMRI) and their context-dependent modulation-was developed for human neuroimaging, and has not been optimized for non-human primate (NHP) studies, which are usually done under anesthesia. Animal neuroimaging studies offer the potential to improve effective connectivity modeling using DCM through combining functional imaging with invasive procedures such as in vivo optogenetic or electrical stimulation. Employing a Bayesian approach, model parameters are estimated based on prior knowledge of conditions that might be related to neural and BOLD dynamics (e.g., requires empirical knowledge about the range of plausible parameter values). As such, we address the following questions in this review: What factors need to be considered when applying DCM to NHP data? What differences in functional networks, cerebrovascular architecture and physiology exist between human and NHPs that are relevant for DCM application? How do anesthetics affect vascular physiology, BOLD contrast, and neural dynamics-particularly, effective communication within, and between networks? Considering the factors that are relevant for DCM application to NHP neuroimaging, we propose a strategy for modeling effective connectivity under anesthesia using an integrated physiologic-stochastic DCM (IPS-DCM).
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Affiliation(s)
- D Blair Jovellar
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.,Center of Neurology, Hertie Institute for Clinical Brain Research, University Hospital, Tuebingen, Germany
| | - Doris J Doudet
- Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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