An automated pipeline for constructing personalized virtual brains from multimodal neuroimaging data

Precision data-driven modeling of cortical dynamics reveals person-specific mechanisms underpinning brain electrophysiology

Task-free brain activity affords unique insight into the functional structure of brain network dynamics and has been used to identify neural markers of individual differences. In this work, we present an algorithmic optimization framework that directly inverts and parameterizes brain-wide dynamical-systems models involving hundreds of interacting neural populations, from single-subject M/EEG time-series recordings. This technique provides a powerful neurocomputational tool for interrogating mechanisms underlying individual brain dynamics ("precision brain models") and making quantitative predictions. We extensively validate the models' performance in forecasting future brain activity and predicting individual variability in key M/EEG metrics. Last, we demonstrate the power of our technique in resolving individual differences in the generation of alpha and beta-frequency oscillations. We characterize subjects based upon model attractor topology and a dynamical-systems mechanism by which these topologies generate individual variation in the expression of alpha vs. beta rhythms. We trace these phenomena back to global variation in excitatory-inhibitory balance, highlighting the explanatory power of our framework to generate mechanistic insights.

Contributions of short- and long-range white matter tracts in dynamic compensation with aging

Optimal brain function is shaped by a combination of global information integration, facilitated by long-range connections, and local processing, which relies on short-range connections and underlying biological factors. With aging, anatomical connectivity undergoes significant deterioration, which affects the brain's overall function. Despite the structural loss, previous research has shown that normative patterns of functions remain intact across the lifespan, defined as the compensatory mechanism of the aging brain. However, the crucial components in guiding the compensatory preservation of the dynamical complexity and the underlying mechanisms remain uncovered. Moreover, it remains largely unknown how the brain readjusts its biological parameters to maintain optimal brain dynamics with age; in this work, we provide a parsimonious mechanism using a whole-brain generative model to uncover the role of sub-communities comprised of short-range and long-range connectivity in driving the dynamic compensation process in the aging brain. We utilize two neuroimaging datasets to demonstrate how short- and long-range white matter tracts affect compensatory mechanisms. We unveil their modulation of intrinsic global scaling parameters, such as global coupling strength and conduction delay, via a personalized large-scale brain model. Our key finding suggests that short-range tracts predominantly amplify global coupling strength with age, potentially representing an epiphenomenon of the compensatory mechanism. This mechanistically explains the significance of short-range connections in compensating for the major loss of long-range connections during aging. This insight could help identify alternative avenues to address aging-related diseases where long-range connections are significantly deteriorated.

Homeodynamic feedback inhibition control in whole-brain simulations

Simulations of large-scale brain dynamics are often impacted by overexcitation resulting from heavy-tailed structural network distributions, leading to biologically implausible simulation results. We implement a homeodynamic plasticity mechanism, known from other modeling work, in the widely used Jansen-Rit neural mass model for The Virtual Brain (TVB) simulation framework. We aim at heterogeneously adjusting the inhibitory coupling weights to reach desired dynamic regimes in each brain region. We show that, by using this dynamic approach, we can control the target activity level to obtain biologically plausible brain simulations, including post-synaptic potentials and blood-oxygen-level-dependent functional magnetic resonance imaging (fMRI) activity. We demonstrate that the derived dynamic Feedback Inhibitory Control (dFIC) can be used to enable increased variability of model dynamics. We derive the conditions under which the simulated brain activity converges to a predefined target level analytically and via simulations. We highlight the benefits of dFIC in the context of fitting the TVB model to static and dynamic measures of fMRI empirical data, accounting for global synchronization across the whole brain. The proposed novel method helps computational neuroscientists, especially TVB users, to easily "tune" brain models to desired dynamical regimes depending on the specific requirements of each study. The presented method is a steppingstone towards increased biological realism in brain network models and a valuable tool to better understand their underlying behavior.

Epileptic network identification: insights from dynamic mode decomposition of sEEG data

Objective.For medically-refractory epilepsy patients, stereoelectroencephalography (sEEG) is a surgical method using intracranial electrode recordings to identify brain networks participating in early seizure organization and propagation (i.e. the epileptogenic zone, EZ). If identified, surgical EZ treatment via resection, ablation or neuromodulation can lead to seizure-freedom. To date, quantification of sEEG data, including its visualization and interpretation, remains a clinical and computational challenge. Given elusiveness of physical laws or governing equations modelling complex brain dynamics, data science offers unique insight into identifying unknown patterns within high-dimensional sEEG data. We apply here an unsupervised data-driven algorithm, dynamic mode decomposition (DMD), to sEEG recordings from five focal epilepsy patients (three with temporal lobe, and two with cingulate epilepsy), who underwent subsequent resective or ablative surgery and became seizure free.Approach.DMD obtains a linear approximation of nonlinear data dynamics, generating coherent structures ('modes') defining important signal features, used to extract frequencies, growth rates and spatial structures. DMD was adapted to produce dynamic modal maps (DMMs) across frequency sub-bands, capturing onset and evolution of epileptiform dynamics in sEEG data. Additionally, we developed a static estimate of EZ-localized electrode contacts, termed the higher-frequency mode-based norm index (MNI). DMM and MNI maps for representative patient seizures were validated against clinical sEEG results and seizure-free outcomes following surgery.Main results.DMD was most informative at higher frequencies, i.e. gamma (including high-gamma) and beta range, successfully identifying EZ contacts. Combined interpretation of DMM/MNI plots best identified spatiotemporal evolution of mode-specific network changes, with strong concordance to sEEG results and outcomes across all five patients. The method identified network attenuation in other contacts not implicated in the EZ.Significance.This is the first application of DMD to sEEG data analysis, supporting integration of neuroengineering, mathematical and machine learning methods into traditional workflows for sEEG review and epilepsy surgical decision-making.

Recent Progress in Brain Network Models for Medical Applications: A Review

Importance: Pathological perturbations of the brain often spread via connectome to fundamentally alter functional consequences. By integrating multimodal neuroimaging data with mathematical neural mass modeling, brain network models (BNMs) enable to quantitatively characterize aberrant network dynamics underlying multiple neurological and psychiatric disorders. We delved into the advancements of BNM-based medical applications, discussed the prevalent challenges within this field, and provided possible solutions and future directions. Highlights: This paper reviewed the theoretical foundations and current medical applications of computational BNMs. Composed of neural mass models, the BNM framework allows to investigate large-scale brain dynamics behind brain diseases by linking the simulated functional signals to the empirical neurophysiological data, and has shown promise in exploring neuropathological mechanisms, elucidating therapeutic effects, and predicting disease outcome. Despite that several limitations existed, one promising trend of this research field is to precisely guide clinical neuromodulation treatment based on individual BNM simulation. Conclusion: BNM carries the potential to help understand the mechanism underlying how neuropathology affects brain network dynamics, further contributing to decision-making in clinical diagnosis and treatment. Several constraints must be addressed and surmounted to pave the way for its utilization in the clinic.

Parameter estimation in a whole-brain network model of epilepsy: Comparison of parallel global optimization solvers

The Virtual Epileptic Patient (VEP) refers to a computer-based representation of a patient with epilepsy that combines personalized anatomical data with dynamical models of abnormal brain activities. It is capable of generating spatio-temporal seizure patterns that resemble those recorded with invasive methods such as stereoelectro EEG data, allowing for the evaluation of clinical hypotheses before planning surgery. This study highlights the effectiveness of calibrating VEP models using a global optimization approach. The approach utilizes SaCeSS, a cooperative metaheuristic algorithm capable of parallel computation, to yield high-quality solutions without requiring excessive computational time. Through extensive benchmarking on synthetic data, our proposal successfully solved a set of different configurations of VEP models, demonstrating better scalability and superior performance against other parallel solvers. These results were further enhanced using a Bayesian optimization framework for hyperparameter tuning, with significant gains in terms of both accuracy and computational cost. Additionally, we added a scalable uncertainty quantification phase after model calibration, and used it to assess the variability in estimated parameters across different problems. Overall, this study has the potential to improve the estimation of pathological brain areas in drug-resistant epilepsy, thereby to inform the clinical decision-making process.

Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression

Brain activity during the resting state is widely used to examine brain organization, cognition and alterations in disease states. While it is known that neuromodulation and the state of alertness impact resting-state activity, neural mechanisms behind such modulation of resting-state activity are unknown. In this work, we used a computational model to demonstrate that change in excitability and recurrent connections, due to cholinergic modulation, impacts resting-state activity. The results of such modulation in the model match closely with experimental work on direct cholinergic modulation of Default Mode Network (DMN) in rodents. We further extended our study to the human connectome derived from diffusion-weighted MRI. In human resting-state simulations, an increase in cholinergic input resulted in a brain-wide reduction of functional connectivity. Furthermore, selective cholinergic modulation of DMN closely captured experimentally observed transitions between the baseline resting state and states with suppressed DMN fluctuations associated with attention to external tasks. Our study thus provides insight into potential neural mechanisms for the effects of cholinergic neuromodulation on resting-state activity and its dynamics.

MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline

Large-scale diffusion MRI tractography remains a significant challenge. Users must orchestrate a complex sequence of instructions that requires many software packages with complex dependencies and high computational costs. We developed MaPPeRTrac, an edge-centric tractography pipeline that simplifies and accelerates this process in a wide range of high-performance computing (HPC) environments. It fully automates either probabilistic or deterministic tractography, starting from a subject's magnetic resonance imaging (MRI) data, including structural and diffusion MRI images, to the edge density image (EDI) of their structural connectomes. Dependencies are containerized with Singularity (now called Apptainer) and decoupled from code to enable rapid prototyping and modification. Data derivatives are organized with the Brain Imaging Data Structure (BIDS) to ensure that they are findable, accessible, interoperable, and reusable following FAIR principles. The pipeline takes full advantage of HPC resources using the Parsl parallel programming framework, resulting in the creation of connectome datasets of unprecedented size. MaPPeRTrac is publicly available and tested on commercial and scientific hardware, so it can accelerate brain connectome research for a broader user community. MaPPeRTrac is available at: https://github.com/LLNL/mappertrac .

High-Density Exploration of Activity States in a Multi-Area Brain Model

To simulate whole brain dynamics with only a few equations, biophysical, mesoscopic models of local neuron populations can be connected using empirical tractography data. The development of mesoscopic mean-field models of neural populations, in particular, the Adaptive Exponential (AdEx mean-field model), has successfully summarized neuron-scale phenomena leading to the emergence of global brain dynamics associated with conscious (asynchronous and rapid dynamics) and unconscious (synchronized slow-waves, with Up-and-Down state dynamics) brain states, based on biophysical mechanisms operating at cellular scales (e.g. neuromodulatory regulation of spike-frequency adaptation during sleep-wake cycles or anesthetics). Using the Virtual Brain (TVB) environment to connect mean-field AdEx models, we have previously simulated the general properties of brain states, playing on spike-frequency adaptation, but have not yet performed detailed analyses of other parameters possibly also regulating transitions in brain-scale dynamics between different brain states. We performed a dense grid parameter exploration of the TVB-AdEx model, making use of High Performance Computing. We report a remarkable robustness of the effect of adaptation to induce synchronized slow-wave activity. Moreover, the occurrence of slow waves is often paralleled with a closer relation between functional and structural connectivity. We find that hyperpolarization can also generate unconscious-like synchronized Up and Down states, which may be a mechanism underlying the action of anesthetics. We conclude that the TVB-AdEx model reveals large-scale properties identified experimentally in sleep and anesthesia.

Macroscopic resting-state brain dynamics are best described by linear models

It is typically assumed that large networks of neurons exhibit a large repertoire of nonlinear behaviours. Here we challenge this assumption by leveraging mathematical models derived from measurements of local field potentials via intracranial electroencephalography and of whole-brain blood-oxygen-level-dependent brain activity via functional magnetic resonance imaging. We used state-of-the-art linear and nonlinear families of models to describe spontaneous resting-state activity of 700 participants in the Human Connectome Project and 122 participants in the Restoring Active Memory project. We found that linear autoregressive models provide the best fit across both data types and three performance metrics: predictive power, computational complexity and the extent of the residual dynamics unexplained by the model. To explain this observation, we show that microscopic nonlinear dynamics can be counteracted or masked by four factors associated with macroscopic dynamics: averaging over space and over time, which are inherent to aggregated macroscopic brain activity, and observation noise and limited data samples, which stem from technological limitations. We therefore argue that easier-to-interpret linear models can faithfully describe macroscopic brain dynamics during resting-state conditions.

A multi-layer mean-field model of the cerebellum embedding microstructure and population-specific dynamics

Mean-field (MF) models are computational formalism used to summarize in a few statistical parameters the salient biophysical properties of an inter-wired neuronal network. Their formalism normally incorporates different types of neurons and synapses along with their topological organization. MFs are crucial to efficiently implement the computational modules of large-scale models of brain function, maintaining the specificity of local cortical microcircuits. While MFs have been generated for the isocortex, they are still missing for other parts of the brain. Here we have designed and simulated a multi-layer MF of the cerebellar microcircuit (including Granule Cells, Golgi Cells, Molecular Layer Interneurons, and Purkinje Cells) and validated it against experimental data and the corresponding spiking neural network (SNN) microcircuit model. The cerebellar MF was built using a system of equations, where properties of neuronal populations and topological parameters are embedded in inter-dependent transfer functions. The model time constant was optimised using local field potentials recorded experimentally from acute mouse cerebellar slices as a template. The MF reproduced the average dynamics of different neuronal populations in response to various input patterns and predicted the modulation of the Purkinje Cells firing depending on cortical plasticity, which drives learning in associative tasks, and the level of feedforward inhibition. The cerebellar MF provides a computationally efficient tool for future investigations of the causal relationship between microscopic neuronal properties and ensemble brain activity in virtual brain models addressing both physiological and pathological conditions.

Modeling the role of the thalamus in resting-state functional connectivity: Nature or structure

The thalamus is a central brain structure that serves as a relay station for sensory inputs from the periphery to the cortex and regulates cortical arousal. Traditionally, it has been regarded as a passive relay that transmits information between brain regions. However, recent studies have suggested that the thalamus may also play a role in shaping functional connectivity (FC) in a task-based context. Based on this idea, we hypothesized that due to its centrality in the network and its involvement in cortical activation, the thalamus may also contribute to resting-state FC, a key neurological biomarker widely used to characterize brain function in health and disease. To investigate this hypothesis, we constructed ten in-silico brain network models based on neuroimaging data (MEG, MRI, and dwMRI), and simulated them including and excluding the thalamus, and raising the noise into thalamus to represent the afferences related to the reticular activating system (RAS) and the relay of peripheral sensory inputs. We simulated brain activity and compared the resulting FC to their empirical MEG counterparts to evaluate model's performance. Results showed that a parceled version of the thalamus with higher noise, able to drive damped cortical oscillators, enhanced the match to empirical FC. However, with an already active self-oscillatory cortex, no impact on the dynamics was observed when introducing the thalamus. We also demonstrated that the enhanced performance was not related to the structural connectivity of the thalamus, but to its higher noisy inputs. Additionally, we highlighted the relevance of a balanced signal-to-noise ratio in thalamus to allow it to propagate its own dynamics. In conclusion, our study sheds light on the role of the thalamus in shaping brain dynamics and FC in resting-state and allowed us to discuss the general role of criticality in the brain at the mesoscale level.

Structural-and-dynamical similarity predicts compensatory brain areas driving the post-lesion functional recovery mechanism

The focal lesion alters the excitation-inhibition (E-I) balance and healthy functional connectivity patterns, which may recover over time. One possible mechanism for the brain to counter the insult is global reshaping functional connectivity alterations. However, the operational principles by which this can be achieved remain unknown. We propose a novel equivalence principle based on structural and dynamic similarity analysis to predict whether specific compensatory areas initiate lost E-I regulation after lesion. We hypothesize that similar structural areas (SSAs) and dynamically similar areas (DSAs) corresponding to a lesioned site are the crucial dynamical units to restore lost homeostatic balance within the surviving cortical brain regions. SSAs and DSAs are independent measures, one based on structural similarity properties measured by Jaccard Index and the other based on post-lesion recovery time. We unravel the relationship between SSA and DSA by simulating a whole brain mean field model deployed on top of a virtually lesioned structural connectome from human neuroimaging data to characterize global brain dynamics and functional connectivity at the level of individual subjects. Our results suggest that wiring proximity and similarity are the 2 major guiding principles of compensation-related utilization of hemisphere in the post-lesion functional connectivity re-organization process.

Learning how network structure shapes decision-making for bio-inspired computing

To better understand how network structure shapes intelligent behavior, we developed a learning algorithm that we used to build personalized brain network models for 650 Human Connectome Project participants. We found that participants with higher intelligence scores took more time to solve difficult problems, and that slower solvers had higher average functional connectivity. With simulations we identified a mechanistic link between functional connectivity, intelligence, processing speed and brain synchrony for trading accuracy with speed in dependence of excitation-inhibition balance. Reduced synchrony led decision-making circuits to quickly jump to conclusions, while higher synchrony allowed for better integration of evidence and more robust working memory. Strict tests were applied to ensure reproducibility and generality of the obtained results. Here, we identify links between brain structure and function that enable to learn connectome topology from noninvasive recordings and map it to inter-individual differences in behavior, suggesting broad utility for research and clinical applications.

Accurate and Efficient Simulation of Very High-Dimensional Neural Mass Models with Distributed-Delay Connectome Tensors

This paper introduces methods and a novel toolbox that efficiently integrates high-dimensional Neural Mass Models (NMMs) specified by two essential components. The first is the set of nonlinear Random Differential Equations (RDEs) of the dynamics of each neural mass. The second is the highly sparse three-dimensional Connectome Tensor (CT) that encodes the strength of the connections and the delays of information transfer along the axons of each connection. To date, simplistic assumptions prevail about delays in the CT, often assumed to be Dirac-delta functions. In reality, delays are distributed due to heterogeneous conduction velocities of the axons connecting neural masses. These distributed-delay CTs are challenging to model. Our approach implements these models by leveraging several innovations. Semi-analytical integration of RDEs is done with the Local Linearization (LL) scheme for each neural mass model, ensuring dynamical fidelity to the original continuous-time nonlinear dynamic. This semi-analytic LL integration is highly computationally-efficient. In addition, a tensor representation of the CT facilitates parallel computation. It also seamlessly allows modeling distributed delays CT with any level of complexity or realism. This ease of implementation includes models with distributed-delay CTs. Consequently, our algorithm scales linearly with the number of neural masses and the number of equations they are represented with, contrasting with more traditional methods that scale quadratically at best. To illustrate the toolbox's usefulness, we simulate a single Zetterberg-Jansen-Rit (ZJR) cortical column, a single thalmo-cortical unit, and a toy example comprising 1000 interconnected ZJR columns. These simulations demonstrate the consequences of modifying the CT, especially by introducing distributed delays. The examples illustrate the complexity of explaining EEG oscillations, e.g., split alpha peaks, since they only appear for distinct neural masses. We provide an open-source Script for the toolbox.

Automatic Quality Control of the numerical accuracy of EEG Lead fields

Precise individualized EEG source localization is predicated on having accurate subject-specific Lead Fields (LFs) obtained from their Magnetic Resonance Images (MRI). LF calculation is a complex process involving several error-prone steps that start with obtaining a realistic head model from the MRI and finalizing with computationally expensive solvers such as the Boundary Element Method (BEM) or Finite Element Method (FEM). Current Big-Data applications require the calculation of batches of hundreds or thousands of LFs. LF. Quality Control is conventionally checked subjectively by experts, a procedure not feasible in practice for larger batches. To facilitate this step, we introduce the Lead Field Automatic-Quality Control Index (LF-AQI) that flags LF with potential errors. We base our LF-AQI on the assumption that LFs obtained from simpler head models, i.e., the homogeneous head model LF (HHM-LF) or spherical head model LF (SHM-LF), deviate only moderately from a "good" realistic test LF. Since these simpler LFs are easier to compute and check for errors, they may serve as "reference LF" to detect anomalous realistic test LF. We investigated this assumption by comparing correlation-based channel ρ_min(ref,test)and source τ_min(ref,test) similarity indices (SI) between "gold standards," i.e., very accurate FEM and BEM LFs, and the proposed references (HHM-LF and SHM-LF). Surprisingly we found that the most uncomplicated possible reference, HHM-LF had high SI values with the gold standards-leading us to explore further use of the channel ρ_min(HHM-LF,test)and source τ_min(HHM-LF,test)_{SI as a basis for} our LF-AQI. Indeed, these SI successfully detected five simulated scenarios of LFs artifacts. This result encouraged us to evaluate the SI on a large dataset and thus define our LF-AQI. We thus computed the SI of 1251 LFs obtained from the Child Mind Institute (CMI) MRI dataset. When ρ_min(HHM-LF,test)and source τ_min(HHM-LF,test) were plotted for all test subjects on a 2D space, most were tightly clustered around the median of a high similarity centroid (HSC), except for a smaller proportion of outliers. We define the LF-AQI for a given LF as the log Euclidean distance between its SI and the HSC median. To automatically detect outliers, the threshold is at the 90^th percentile of the CMI LF-AQIs (-0.9755). LF-AQI greater than this threshold flag individual LF to be checked. The robustness of this LF-AQI screening was checked by repeated out-of-sample validation. Strikingly, minor corrections in re-processing the flagged cases eliminated their status as outliers. Furthermore, the "doubtful" labels assigned by LF-AQI were validated by neuroscience students using a Likert scale questionnaire designed to manually check the LF's quality. Item Response Theory (IRT) analysis was applied to the questionnaire results to compute an optimized model and a latent variable θ for that model. A linear mixed model (LMM) between the θ and LF-AQI resulted in an effect with a Cohen's d value of 1.3 and a p-value <0.001, thus validating the correspondence of LF-AQI with the visual quality control. We provide an open-source pipeline to implement both LF calculation and its quality control to allow further evaluation of our index.

Amortized Bayesian inference on generative dynamical network models of epilepsy using deep neural density estimators

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.

A comprehensive neural simulation of slow-wave sleep and highly responsive wakefulness dynamics

Hallmarks of neural dynamics during healthy human brain states span spatial scales from neuromodulators acting on microscopic ion channels to macroscopic changes in communication between brain regions. Developing a scale-integrated understanding of neural dynamics has therefore remained challenging. Here, we perform the integration across scales using mean-field modeling of Adaptive Exponential (AdEx) neurons, explicitly incorporating intrinsic properties of excitatory and inhibitory neurons. The model was run using The Virtual Brain (TVB) simulator, and is open-access in EBRAINS. We report that when AdEx mean-field neural populations are connected via structural tracts defined by the human connectome, macroscopic dynamics resembling human brain activity emerge. Importantly, the model can qualitatively and quantitatively account for properties of empirically observed spontaneous and stimulus-evoked dynamics in space, time, phase, and frequency domains. Large-scale properties of cortical dynamics are shown to emerge from both microscopic-scale adaptation that control transitions between wake-like to sleep-like activity, and the organization of the human structural connectome; together, they shape the spatial extent of synchrony and phase coherence across brain regions consistent with the propagation of sleep-like spontaneous traveling waves at intermediate scales. Remarkably, the model also reproduces brain-wide, enhanced responsiveness and capacity to encode information particularly during wake-like states, as quantified using the perturbational complexity index. The model was run using The Virtual Brain (TVB) simulator, and is open-access in EBRAINS. This approach not only provides a scale-integrated understanding of brain states and their underlying mechanisms, but also open access tools to investigate brain responsiveness, toward producing a more unified, formal understanding of experimental data from conscious and unconscious states, as well as their associated pathologies.

White-matter degradation and dynamical compensation support age-related functional alterations in human brain

Structural connectivity of the brain at different ages is analyzed using diffusion-weighted magnetic resonance imaging (MRI) data. The largest decrease of streamlines is found in frontal regions and for long inter-hemispheric links. The average length of the tracts also decreases, but the clustering is unaffected. From functional MRI we identify age-related changes of dynamic functional connectivity (dFC) and spatial covariation features of functional connectivity (FC) links captured by metaconnectivity. They indicate more stable dFC, but wider range and variance of MC, whereas static features of FC did not show any significant differences with age. We implement individual connectivity in whole-brain models and test several hypotheses for the mechanisms of operation among underlying neural system. We demonstrate that age-related functional fingerprints are only supported if the model accounts for: (i) compensation of the individual brains for the overall loss of structural connectivity and (ii) decrease of propagation velocity due to the loss of myelination. We also show that with these 2 conditions, it is sufficient to decompose the time-delays as bimodal distribution that only distinguishes between intra- and inter-hemispheric delays, and that the same working point also captures the static FC the best, and produces the largest variability at slow time-scales.

Exploring personalized structural connectomics for moderate to severe traumatic brain injury

Graph theoretical analysis of the structural connectome has been employed successfully to characterize brain network alterations in patients with traumatic brain injury (TBI). However, heterogeneity in neuropathology is a well-known issue in the TBI population, such that group comparisons of patients against controls are confounded by within-group variability. Recently, novel single-subject profiling approaches have been developed to capture inter-patient heterogeneity. We present a personalized connectomics approach that examines structural brain alterations in five chronic patients with moderate to severe TBI who underwent anatomical and diffusion magnetic resonance imaging. We generated individualized profiles of lesion characteristics and network measures (including personalized graph metric GraphMe plots, and nodal and edge-based brain network alterations) and compared them against healthy reference cases (N = 12) to assess brain damage qualitatively and quantitatively at the individual level. Our findings revealed alterations of brain networks with high variability between patients. With validation and comparison to stratified, normative healthy control comparison cohorts, this approach could be used by clinicians to formulate a neuroscience-guided integrative rehabilitation program for TBI patients, and for designing personalized rehabilitation protocols based on their unique lesion load and connectome.

Pre- and post-surgery brain tumor multimodal magnetic resonance imaging data optimized for large scale computational modelling

We present a dataset of magnetic resonance imaging (MRI) data (T1, diffusion, BOLD) acquired in 25 brain tumor patients before the tumor resection surgery, and six months after the surgery, together with the tumor masks, and in 11 controls (recruited among the patients’ caregivers). The dataset also contains behavioral and emotional scores obtained with standardized questionnaires. To simulate personalized computational models of the brain, we also provide structural connectivity matrices, necessary to perform whole-brain modelling with tools such as The Virtual Brain. In addition, we provide blood-oxygen-level-dependent imaging time series averaged across regions of interest for comparison with simulation results. An average resting state hemodynamic response function for each region of interest, as well as shape maps for each voxel, are also contributed.

Measurement(s)	BOLD signal • Diffusion Anisotropy
Technology Type(s)	Functional Magnetic Resonance Imaging • Diffusion Weighted Imaging
Factor Type(s)	Surgery
Sample Characteristic - Organism	Homo sapiens

Mean-field based framework for forward modeling of LFP and MEG signals

The use of mean-field models to describe the activity of large neuronal populations has become a very powerful tool for large-scale or whole brain simulations. However, the calculation of brain signals from mean-field models, such as the electric and magnetic fields, is still under development. Thus, the emergence of new methods for an accurate and efficient calculation of such brain signals is currently of great relevance. In this paper we propose a novel method to calculate the local field potentials (LFP) and magnetic fields from mean-field models. The calculation of LFP is done via a kernel method based on unitary LFP's (the LFP generated by a single axon) that was recently introduced for spiking-networks simulations and that we adapt here for mean-field models. The calculation of the magnetic field is based on current-dipole and volume-conductor models, where the secondary currents (due to the conducting extracellular medium) are estimated using the LFP calculated via the kernel method and the effects of medium-inhomogeneities are incorporated. We provide an example of the application of our method for the calculation of LFP and MEG under slow-waves of neuronal activity generated by a mean-field model of a network of Adaptive-Exponential Integrate-and-Fire (AdEx) neurons. We validate our method via comparison with results obtained from the corresponding spiking neuronal networks. Finally we provide an example of our method for whole brain simulations performed with The Virtual Brain (TVB), a recently developed tool for large scale simulations of the brain. Our method provides an efficient way of calculating electric and magnetic fields from mean-field models. This method exhibits a great potential for its application in large-scale or whole-brain simulations, where calculations via detailed biological models are not feasible.

A perturbative approach to study information communication in brain networks

How communication among neuronal ensembles shapes functional brain dynamics is a question of fundamental importance to neuroscience. Communication in the brain can be viewed as a product of the interaction of node activities with the structural network over which these activities flow. The study of these interactions is, however, restricted by the difficulties in describing the complex dynamics of the brain. There is thus a need to develop methods to study these network-dynamical interactions and how they impact information flow, without having to ascertain dynamics a priori or resort to restrictive analytical approaches. Here, we adapt a recently established network analysis method based on perturbations, it to a neuroscientific setting to study how information flow in the brain can raise from properties of underlying structure. For proof-of-concept, we apply the approach on in silico whole-brain models. We expound on the functional implications of the distributions of metrics that capture network-dynamical interactions, termed net influence and flow. We also study the network-dynamical interactions at the level of resting-state networks. An attractive feature of this method is its simplicity, which allows a direct translation to an experimental or clinical setting, such as for identifying targets for stimulation studies or therapeutic interventions.

Developing control-theoretic objectives for large-scale brain dynamics and cognitive enhancement

The development of technologies for brain stimulation provides a means for scientists and clinicians to directly actuate the brain and nervous system. Brain stimulation has shown intriguing potential in terms of modifying particular symptom clusters in patients and behavioral characteristics of subjects. The stage is thus set for optimization of these techniques and the pursuit of more nuanced stimulation objectives, including the modification of complex cognitive functions such as memory and attention. Control theory and engineering will play a key role in the development of these methods, guiding computational and algorithmic strategies for stimulation. In particular, realizing this goal will require new development of frameworks that allow for controlling not only brain activity, but also latent dynamics that underlie neural computation and information processing. In the current opinion, we review recent progress in brain stimulation and outline challenges and potential research pathways associated with exogenous control of cognitive function.

Normalizing the brain connectome for communication through synchronization

Networks in neuroscience determine how brain function unfolds, and their perturbations lead to psychiatric disorders and brain disease. Brain networks are characterized by their connectomes, which comprise the totality of all connections, and are commonly described by graph theory. This approach is deeply rooted in a particle view of information processing, based on the quantification of informational bits such as firing rates. Oscillations and brain rhythms demand, however, a wave perspective of information processing based on synchronization. We extend traditional graph theory to a dual, particle-wave, perspective, integrate time delays due to finite transmission speeds, and derive a normalization of the connectome. When applied to the database of the Human Connectome Project, it explains the emergence of frequency-specific network cores including the visual and default mode networks. These findings are robust across human subjects (N = 100) and are a fundamental network property within the wave picture. The normalized connectome comprises the particle view in the limit of infinite transmission speeds and opens the applicability of graph theory to a wide range of novel network phenomena, including physiological and pathological brain rhythms. These two perspectives are orthogonal, but not incommensurable, when understood within the novel, here-proposed, generalized framework of structural connectivity.

Personalized Connectome-Based Modeling in Patients with Semi-Acute Phase TBI: Relationship to Acute Neuroimaging and 6 Month Follow-Up

Following traumatic brain injury (TBI), cognitive impairments manifest through interactions between microscopic and macroscopic changes. On the microscale, a neurometabolic cascade alters neurotransmission, while on the macroscale diffuse axonal injury impacts the integrity of long-range connections. Large-scale brain network modeling allows us to make predictions across these spatial scales by integrating neuroimaging data with biophysically based models to investigate how microscale changes invisible to conventional neuroimaging influence large-scale brain dynamics. To this end, we analyzed structural and functional neuroimaging data from a well characterized sample of 44 adult TBI patients recruited from a regional trauma center, scanned at 1–2 weeks postinjury, and with follow-up behavioral outcome assessed 6 months later. Thirty-six age-matched healthy adults served as comparison participants. Using The Virtual Brain, we fit simulations of whole-brain resting-state functional MRI to the empirical static and dynamic functional connectivity of each participant. Multivariate partial least squares (PLS) analysis showed that patients with acute traumatic intracranial lesions had lower cortical regional inhibitory connection strengths than comparison participants, while patients without acute lesions did not differ from the comparison group. Further multivariate PLS analyses found correlations between lower semiacute regional inhibitory connection strengths and more symptoms and lower cognitive performance at a 6 month follow-up. Critically, patients without acute lesions drove this relationship, suggesting clinical relevance of regional inhibitory connection strengths even when traumatic intracranial lesions were not present. Our results suggest that large-scale connectome-based models may be sensitive to pathophysiological changes in semi-acute phase TBI patients and predictive of their chronic outcomes.

A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain

TheVirtualBrain, an open-source platform for large-scale network modeling, can be personalized to an individual using a wide range of neuroimaging modalities. With the growing number and scale of neuroimaging data sharing initiatives of both healthy and clinical populations comes an opportunity to create large and heterogeneous sets of dynamic network models to better understand individual differences in network dynamics and their impact on brain health. Here we present TheVirtualBrain-UK Biobank pipeline, a robust, automated and open-source brain image processing solution to address the expanding scope of TheVirtualBrain project. Our pipeline generates connectome-based modeling inputs compatible for use with TheVirtualBrain. We leverage the existing multimodal MRI processing pipeline from the UK Biobank made for use with a variety of brain imaging modalities. We add various features and changes to the original UK Biobank implementation specifically for informing large-scale network models, including user-defined parcellations for the construction of matching whole-brain functional and structural connectomes. Changes also include detailed reports for quality control of all modalities, a streamlined installation process, modular software packaging, updated software versions, and support for various publicly available datasets. The pipeline has been tested on various datasets from both healthy and clinical populations and is robust to the morphological changes observed in aging and dementia. In this paper, we describe these and other pipeline additions and modifications in detail, as well as how this pipeline fits into the TheVirtualBrain ecosystem.

Multiscale dynamic mean field (MDMF) model relates resting-state brain dynamics with local cortical excitatory-inhibitory neurotransmitter homeostasis

Previous computational models have related spontaneous resting-state brain activity with local excitatory–inhibitory balance in neuronal populations. However, how underlying neurotransmitter kinetics associated with E–I balance govern resting-state spontaneous brain dynamics remains unknown. Understanding the mechanisms by virtue of which fluctuations in neurotransmitter concentrations, a hallmark of a variety of clinical conditions, relate to functional brain activity is of critical importance. We propose a multiscale dynamic mean field (MDMF) model—a system of coupled differential equations for capturing the synaptic gating dynamics in excitatory and inhibitory neural populations as a function of neurotransmitter kinetics. Individual brain regions are modeled as population of MDMF and are connected by realistic connection topologies estimated from diffusion tensor imaging data. First, MDMF successfully predicts resting-state functional connectivity. Second, our results show that optimal range of glutamate and GABA neurotransmitter concentrations subserve as the dynamic working point of the brain, that is, the state of heightened metastability observed in empirical blood-oxygen-level-dependent signals. Third, for predictive validity the network measures of segregation (modularity and clustering coefficient) and integration (global efficiency and characteristic path length) from existing healthy and pathological brain network studies could be captured by simulated functional connectivity from an MDMF model.

How changes in neurotransmitter kinetics impact the organization of large-scale neurocognitive networks is an open question in neuroscience. Here, we propose a multiscale dynamic mean field (MDMF) model that incorporates biophysically realistic kinetic parameters of receptor binding in a dynamic mean field model and captures brain dynamics from the “whole brain.” MDMF could reliably reproduce the resting-state brain functional connectivity patterns. Further employing graph theoretic methods, MDMF could qualitatively explain the idiosyncrasies of network integration and segregation measures reported by previous clinical studies.

Neuronal Cascades Shape Whole-Brain Functional Dynamics at Rest

At rest, mammalian brains display remarkable spatiotemporal complexity, evolving through recurrent functional connectivity (FC) states on a slow timescale of the order of tens of seconds. While the phenomenology of the resting state dynamics is valuable in distinguishing healthy and pathologic brains, little is known about its underlying mechanisms. Here, we identify neuronal cascades as a potential mechanism. Using full-brain network modeling, we show that neuronal populations, coupled via a detailed structural connectome, give rise to large-scale cascades of firing rate fluctuations evolving at the same time scale of resting-state networks (RSNs). The ignition and subsequent propagation of cascades depend on the brain state and connectivity of each region. The largest cascades produce bursts of blood oxygen level-dependent (BOLD) co-fluctuations at pairs of regions across the brain, which shape the simulated RSN dynamics. We experimentally confirm these theoretical predictions. We demonstrate the existence and stability of intermittent epochs of FC comprising BOLD co-activation (CA) bursts in mice and human functional magnetic resonance imaging (fMRI). We then provide evidence for the existence and leading role of the neuronal cascades in humans with simultaneous EEG/fMRI recordings. These results show that neuronal cascades are a major determinant of spontaneous fluctuations in brain dynamics at rest.

Patient-Specific Network Connectivity Combined With a Next Generation Neural Mass Model to Test Clinical Hypothesis of Seizure Propagation

Dynamics underlying epileptic seizures span multiple scales in space and time, therefore, understanding seizure mechanisms requires identifying the relations between seizure components within and across these scales, together with the analysis of their dynamical repertoire. In this view, mathematical models have been developed, ranging from single neuron to neural population. In this study, we consider a neural mass model able to exactly reproduce the dynamics of heterogeneous spiking neural networks. We combine mathematical modeling with structural information from non invasive brain imaging, thus building large-scale brain network models to explore emergent dynamics and test the clinical hypothesis. We provide a comprehensive study on the effect of external drives on neuronal networks exhibiting multistability, in order to investigate the role played by the neuroanatomical connectivity matrices in shaping the emergent dynamics. In particular, we systematically investigate the conditions under which the network displays a transition from a low activity regime to a high activity state, which we identify with a seizure-like event. This approach allows us to study the biophysical parameters and variables leading to multiple recruitment events at the network level. We further exploit topological network measures in order to explain the differences and the analogies among the subjects and their brain regions, in showing recruitment events at different parameter values. We demonstrate, along with the example of diffusion-weighted magnetic resonance imaging (dMRI) connectomes of 20 healthy subjects and 15 epileptic patients, that individual variations in structural connectivity, when linked with mathematical dynamic models, have the capacity to explain changes in spatiotemporal organization of brain dynamics, as observed in network-based brain disorders. In particular, for epileptic patients, by means of the integration of the clinical hypotheses on the epileptogenic zone (EZ), i.e., the local network where highly synchronous seizures originate, we have identified the sequence of recruitment events and discussed their links with the topological properties of the specific connectomes. The predictions made on the basis of the implemented set of exact mean-field equations turn out to be in line with the clinical pre-surgical evaluation on recruited secondary networks.

Virtual Connectomic Datasets in Alzheimer's Disease and Aging Using Whole-Brain Network Dynamics Modelling

Large neuroimaging datasets, including information about structural connectivity (SC) and functional connectivity (FC), play an increasingly important role in clinical research, where they guide the design of algorithms for automated stratification, diagnosis or prediction. A major obstacle is, however, the problem of missing features [e.g., lack of concurrent DTI SC and resting-state functional magnetic resonance imaging (rsfMRI) FC measurements for many of the subjects]. We propose here to address the missing connectivity features problem by introducing strategies based on computational whole-brain network modeling. Using two datasets, the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset and a healthy aging dataset, for proof-of-concept, we demonstrate the feasibility of virtual data completion (i.e., inferring “virtual FC” from empirical SC or “virtual SC” from empirical FC), by using self-consistent simulations of linear and nonlinear brain network models. Furthermore, by performing machine learning classification (to separate age classes or control from patient subjects), we show that algorithms trained on virtual connectomes achieve discrimination performance comparable to when trained on actual empirical data; similarly, algorithms trained on virtual connectomes can be used to successfully classify novel empirical connectomes. Completion algorithms can be combined and reiterated to generate realistic surrogate connectivity matrices in arbitrarily large number, opening the way to the generation of virtual connectomic datasets with network connectivity information comparable to the one of the original data.

On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread

Individualized anatomical information has been used as prior knowledge in Bayesian inference paradigms of whole-brain network models. However, the actual sensitivity to such personalized information in priors is still unknown. In this study, we introduce the use of fully Bayesian information criteria and leave-one-out cross-validation technique on the subject-specific information to assess different epileptogenicity hypotheses regarding the location of pathological brain areas based on a priori knowledge from dynamical system properties. The Bayesian Virtual Epileptic Patient (BVEP) model, which relies on the fusion of structural data of individuals, a generative model of epileptiform discharges, and a self-tuning Monte Carlo sampling algorithm, is used to infer the spatial map of epileptogenicity across different brain areas. Our results indicate that measuring the out-of-sample prediction accuracy of the BVEP model with informative priors enables reliable and efficient evaluation of potential hypotheses regarding the degree of epileptogenicity across different brain regions. In contrast, while using uninformative priors, the information criteria are unable to provide strong evidence about the epileptogenicity of brain areas. We also show that the fully Bayesian criteria correctly assess different hypotheses about both structural and functional components of whole-brain models that differ across individuals. The fully Bayesian information-theory based approach used in this study suggests a patient-specific strategy for epileptogenicity hypothesis testing in generative brain network models of epilepsy to improve surgical outcomes.

Modeling seizures: From single neurons to networks

Dynamical system tools offer a complementary approach to detailed biophysical seizure modeling, with a high potential for clinical applications. This review describes the theoretical framework that provides a basis for theorizing certain properties of seizures and for their classification according to their dynamical properties at onset and offset. We describe various modeling approaches spanning different scales, from single neurons to large-scale networks. This narrative review provides an accessible overview of this field, including non-exhaustive examples of key recent works.

Reconfiguration of Directed Functional Connectivity Among Neurocognitive Networks with Aging: Considering the Role of Thalamo-Cortical Interactions

A complete picture of how subcortical nodes, such as the thalamus, exert directional influence on large-scale brain network interactions across age remains elusive. Using directed functional connectivity and weighted net causal outflow on resting-state fMRI data, we provide evidence of a comprehensive reorganization within and between neurocognitive networks (default mode: DMN, salience: SN, and central executive: CEN) associated with age and thalamocortical interactions. We hypothesize that thalamus subserves both modality-specific and integrative hub role in organizing causal weighted outflow among large-scale neurocognitive networks. To this end, we observe that within-network directed functional connectivity is driven by thalamus and progressively weakens with age. Secondly, we find that age-associated increase in between CEN- and DMN-directed functional connectivity is driven by both the SN and the thalamus. Furthermore, left and right thalami act as a causal integrative hub exhibiting substantial interactions with neurocognitive networks with aging and play a crucial role in reconfiguring network outflow. Notably, these results were largely replicated on an independent dataset of matched young and old individuals. Our findings strengthen the hypothesis that the thalamus is a key causal hub balancing both within- and between-network connectivity associated with age and maintenance of cognitive functioning with aging.

Brain Network Simulations Indicate Effects of Neuregulin-1 Genotype on Excitation-Inhibition Balance in Cortical Dynamics

Neuregulin-1 (NRG1) represents an important factor for multiple processes including neurodevelopment, brain functioning or cognitive functions. Evidence from animal research suggests an effect of NRG1 on the excitation-inhibition (E/I) balance in cortical circuits. However, direct evidence for the importance of NRG1 in E/I balance in humans is still lacking. In this work, we demonstrate the application of computational, biophysical network models to advance our understanding of the interaction between cortical activity observed in neuroimaging and the underlying neurobiology. We employed a biophysical neuronal model to simulate large-scale brain dynamics and to investigate the role of polymorphisms in the NRG1 gene (rs35753505, rs3924999) in n = 96 healthy adults. Our results show that G/G-carriers (rs3924999) exhibit a significant difference in global coupling (P = 0.048) and multiple parameters determining E/I-balance such as excitatory synaptic coupling (P = 0.047), local excitatory recurrence (P = 0.032) and inhibitory synaptic coupling (P = 0.028). This indicates that NRG1 may be related to excitatory recurrence or excitatory synaptic coupling potentially resulting in altered E/I-balance. Moreover, we suggest that computational modeling is a suitable tool to investigate specific biological mechanisms in health and disease.

The relationship between EEG and fMRI connectomes is reproducible across simultaneous EEG-fMRI studies from 1.5T to 7T

Both electroencephalography (EEG) and functional Magnetic Resonance Imaging (fMRI) are non-invasive methods that show complementary aspects of human brain activity. Despite measuring different proxies of brain activity, both the measured blood-oxygenation (fMRI) and neurophysiological recordings (EEG) are indirectly coupled. The electrophysiological and BOLD signal can map the underlying functional connectivity structure at the whole brain scale at different timescales. Previous work demonstrated a moderate but significant correlation between resting-state functional connectivity of both modalities, however there is a wide range of technical setups to measure simultaneous EEG-fMRI and the reliability of those measures between different setups remains unknown. This is true notably with respect to different magnetic field strengths (low and high field) and different spatial sampling of EEG (medium to high-density electrode coverage). Here, we investigated the reproducibility of the bimodal EEG-fMRI functional connectome in the most comprehensive resting-state simultaneous EEG-fMRI dataset compiled to date including a total of 72 subjects from four different imaging centers. Data was acquired from 1.5T, 3T and 7T scanners with simultaneously recorded EEG using 64 or 256 electrodes. We demonstrate that the whole-brain monomodal connectivity reproducibly correlates across different datasets and that a moderate crossmodal correlation between EEG and fMRI connectivity of r ≈ 0.3 can be reproducibly extracted in low- and high-field scanners. The crossmodal correlation was strongest in the EEG-β frequency band but exists across all frequency bands. Both homotopic and within intrinsic connectivity network (ICN) connections contributed the most to the crossmodal relationship. This study confirms, using a considerably diverse range of recording setups, that simultaneous EEG-fMRI offers a consistent estimate of multimodal functional connectomes in healthy subjects that are dominantly linked through a functional core of ICNs across spanning across the different timescales measured by EEG and fMRI. This opens new avenues for estimating the dynamics of brain function and provides a better understanding of interactions between EEG and fMRI measures. This observed level of reproducibility also defines a baseline for the study of alterations of this coupling in pathological conditions and their role as potential clinical markers.

Estimation and validation of individualized dynamic brain models with resting state fMRI

A key challenge for neuroscience is to develop generative, causal models of the human nervous system in an individualized, data-driven manner. Previous initiatives have either constructed biologically-plausible models that are not constrained by individual-level human brain activity or used data-driven statistical characterizations of individuals that are not mechanistic. We aim to bridge this gap through the development of a new modeling approach termed Mesoscale Individualized Neurodynamic (MINDy) modeling, wherein we fit nonlinear dynamical systems models directly to human brain imaging data. The MINDy framework is able to produce these data-driven network models for hundreds to thousands of interacting brain regions in just 1-3 ​min per subject. We demonstrate that the models are valid, reliable, and robust. We show that MINDy models are predictive of individualized patterns of resting-state brain dynamical activity. Furthermore, MINDy is better able to uncover the mechanisms underlying individual differences in resting state activity than functional connectivity methods.

The Importance of Cerebellar Connectivity on Simulated Brain Dynamics

The brain shows a complex multiscale organization that prevents a direct understanding of how structure, function and dynamics are correlated. To date, advances in neural modeling offer a unique opportunity for simulating global brain dynamics by embedding empirical data on different scales in a mathematical framework. The Virtual Brain (TVB) is an advanced data-driven model allowing to simulate brain dynamics starting from individual subjects' structural and functional connectivity obtained, for example, from magnetic resonance imaging (MRI). The use of TVB has been limited so far to cerebral connectivity but here, for the first time, we have introduced cerebellar nodes and interconnecting tracts to demonstrate the impact of cerebro-cerebellar loops on brain dynamics. Indeed, the matching between the empirical and simulated functional connectome was significantly improved when including the cerebro-cerebellar loops. This positive result should be considered as a first step, since issues remain open about the best strategy to reconstruct effective structural connectivity and the nature of the neural mass or mean-field models generating local activity in the nodes. For example, signal processing is known to differ remarkably between cortical and cerebellar microcircuits. Tackling these challenges is expected to further improve the predictive power of functional brain activity simulations, using TVB or other similar tools, in explaining not just global brain dynamics but also the role of cerebellum in determining brain states in physiological conditions and in the numerous pathologies affecting the cerebro-cerebellar loops.

Dynamic Functional Connectivity between order and randomness and its evolution across the human adult lifespan

Functional Connectivity (FC) during resting-state or task conditions is not static but inherently dynamic. Yet, there is no consensus on whether fluctuations in FC may resemble isolated transitions between discrete FC states rather than continuous changes. This quarrel hampers advancing the study of dynamic FC. This is unfortunate as the structure of fluctuations in FC can certainly provide more information about developmental changes, aging, and progression of pathologies. We merge the two perspectives and consider dynamic FC as an ongoing network reconfiguration, including a stochastic exploration of the space of possible steady FC states. The statistical properties of this random walk deviate both from a purely "order-driven" dynamics, in which the mean FC is preserved, and from a purely "randomness-driven" scenario, in which fluctuations of FC remain uncorrelated over time. Instead, dynamic FC has a complex structure endowed with long-range sequential correlations that give rise to transient slowing and acceleration epochs in the continuous flow of reconfiguration. Our analysis for fMRI data in healthy elderly revealed that dynamic FC tends to slow down and becomes less complex as well as more random with increasing age. These effects appear to be strongly associated with age-related changes in behavioural and cognitive performance.

Dynamical Mechanisms of Interictal Resting-State Functional Connectivity in Epilepsy

Drug-resistant focal epilepsy is a large-scale brain networks disorder characterized by altered spatiotemporal patterns of functional connectivity (FC), even during interictal resting state (RS). Although RS-FC-based metrics can detect these changes, results from RS functional magnetic resonance imaging (RS-fMRI) studies are unclear and difficult to interpret, and the underlying dynamical mechanisms are still largely unknown. To better capture the RS dynamics, we phenomenologically extended the neural mass model of partial seizures, the Epileptor, by including two neuron subpopulations of epileptogenic and nonepileptogenic type, making it capable of producing physiological oscillations in addition to the epileptiform activity. Using the neuroinformatics platform The Virtual Brain, we reconstructed 14 epileptic and 5 healthy human (of either sex) brain network models (BNMs), based on individual anatomical connectivity and clinically defined epileptogenic heatmaps. Through systematic parameter exploration and fitting to neuroimaging data, we demonstrated that epileptic brains during interictal RS are associated with lower global excitability induced by a shift in the working point of the model, indicating that epileptic brains operate closer to a stable equilibrium point than healthy brains. Moreover, we showed that functional networks are unaffected by interictal spikes, corroborating previous experimental findings; additionally, we observed higher excitability in epileptogenic regions, in agreement with the data. We shed light on new dynamical mechanisms responsible for altered RS-FC in epilepsy, involving the following two key factors: (1) a shift of excitability of the whole brain leading to increased stability; and (2) a locally increased excitability in the epileptogenic regions supporting the mixture of hyperconnectivity and hypoconnectivity in these areas.

SIGNIFICANCE STATEMENT Advances in functional neuroimaging provide compelling evidence for epilepsy-related brain network alterations, even during the interictal resting state (RS). However, the dynamical mechanisms underlying these changes are still elusive. To identify local and network processes behind the RS-functional connectivity (FC) spatiotemporal patterns, we systematically manipulated the local excitability and the global coupling in the virtual human epileptic patient brain network models (BNMs), complemented by the analysis of the impact of interictal spikes and fitting to the neuroimaging data. Our results suggest that a global shift of the dynamic working point of the brain model, coupled with locally hyperexcitable node dynamics of the epileptogenic networks, provides a mechanistic explanation of the epileptic processes during the interictal RS period. These, in turn, are associated with the changes in FC.

Control of brain network dynamics across diverse scales of space and time

The human brain is composed of distinct regions that are each associated with particular functions and distinct propensities for the control of neural dynamics. However, the relation between these functions and control profiles is poorly understood, as is the variation in this relation across diverse scales of space and time. Here we probe the relation between control and dynamics in brain networks constructed from diffusion tensor imaging data in a large community sample of young adults. Specifically, we probe the control properties of each brain region and investigate their relationship with dynamics across various spatial scales using the Laplacian eigenspectrum. In addition, through analysis of regional modal controllability and partitioning of modes, we determine whether the associated dynamics are fast or slow, as well as whether they are alternating or monotone. We find that brain regions that facilitate the control of energetically easy transitions are associated with activity on short length scales and slow timescales. Conversely, brain regions that facilitate control of difficult transitions are associated with activity on long length scales and fast timescales. Built on linear dynamical models, our results offer parsimonious explanations for the activity propagation and network control profiles supported by regions of differing neuroanatomical structure.

White Matter Brain Network Research in Alzheimer's Disease Using Persistent Features

Despite the severe social burden caused by Alzheimer’s disease (AD), no drug than can change the disease progression has been identified yet. The structural brain network research provides an opportunity to understand physiological deterioration caused by AD and its precursor, mild cognitive impairment (MCI). Recently, persistent homology has been used to study brain network dynamics and characterize the global network organization. However, it is unclear how these parameters reflect changes in structural brain networks of patients with AD or MCI. In this study, our previously proposed persistent features and various traditional graph-theoretical measures are used to quantify the topological property of white matter (WM) network in 150 subjects with diffusion tensor imaging (DTI). We found significant differences in these measures among AD, MCI, and normal controls (NC) under different brain parcellation schemes. The decreased network integration and increased network segregation are presented in AD and MCI. Moreover, the persistent homology-based measures demonstrated stronger statistical capability and robustness than traditional graph-theoretic measures, suggesting that they represent a more sensitive approach to detect altered brain structures and to better understand AD symptomology at the network level. These findings contribute to an increased understanding of structural connectome in AD and provide a novel approach to potentially track the progression of AD.

Transmission time delays organize the brain network synchronization

The timing of activity across brain regions can be described by its phases for oscillatory processes, and is of crucial importance for brain functioning. The structure of the brain constrains its dynamics through the delays due to propagation and the strengths of the white matter tracts. We use self-sustained delay-coupled, non-isochronous, nonlinearly damped and chaotic oscillators to study how spatio-temporal organization of the brain governs phase lags between the coherent activity of its regions. In silico results for the brain network model demonstrate a robust switching from in- to anti-phase synchronization by increasing the frequency, with a consistent lagging of the stronger connected regions. Relative phases are well predicted by an earlier analysis of Kuramoto oscillators, confirming the spatial heterogeneity of time delays as a crucial mechanism in shaping the functional brain architecture. Increased frequency and coupling are also shown to distort the oscillators by decreasing their amplitude, and stronger regions have lower, but more synchronized activity. These results indicate specific features in the phase relationships within the brain that need to hold for a wide range of local oscillatory dynamics, given that the time delays of the connectome are proportional to the lengths of the structural pathways. This article is part of the theme issue 'Nonlinear dynamics of delay systems'.

Linking Molecular Pathways and Large-Scale Computational Modeling to Assess Candidate Disease Mechanisms and Pharmacodynamics in Alzheimer's Disease

Introduction: While the prevalence of neurodegenerative diseases associated with dementia such as Alzheimer's disease (AD) increases, our knowledge on the underlying mechanisms, outcome predictors, or therapeutic targets is limited. In this work, we demonstrate how computational multi-scale brain modeling links phenomena of different scales and therefore identifies potential disease mechanisms leading the way to improved diagnostics and treatment. Methods: The Virtual Brain (TVB; thevirtualbrain.org) neuroinformatics platform allows standardized large-scale structural connectivity-based simulations of whole brain dynamics. We provide proof of concept for a novel approach that quantitatively links the effects of altered molecular pathways onto neuronal population dynamics. As a novelty, we connect chemical compounds measured with positron emission tomography (PET) with neural function in TVB addressing the phenomenon of hyperexcitability in AD related to the protein amyloid beta (Abeta). We construct personalized virtual brains based on an averaged healthy connectome and individual PET derived distributions of Abeta in patients with mild cognitive impairment (MCI, N = 8) and Alzheimer's Disease (AD, N = 10) and in age-matched healthy controls (HC, N = 15) using data from ADNI-3 data base (http://adni.loni.usc.edu). In the personalized virtual brains, individual Abeta burden modulates regional Excitation-Inhibition balance, leading to local hyperexcitation with high Abeta loads. We analyze simulated regional neural activity and electroencephalograms (EEG). Results: Known empirical alterations of EEG in patients with AD compared to HCs were reproduced by simulations. The virtual AD group showed slower frequencies in simulated local field potentials and EEG compared to MCI and HC groups. The heterogeneity of the Abeta load is crucial for the virtual EEG slowing which is absent for control models with homogeneous Abeta distributions. Slowing phenomena primarily affect the network hubs, independent of the spatial distribution of Abeta. Modeling the N-methyl-D-aspartate (NMDA) receptor antagonism of memantine in local population models, reveals potential functional reversibility of the observed large-scale alterations (reflected by EEG slowing) in virtual AD brains. Discussion: We demonstrate how TVB enables the simulation of systems effects caused by pathogenetic molecular candidate mechanisms in human virtual brains.

Quantitative System Pharmacology (QSP): An Integrative Framework for paradigm change in the treatment of the first-episode schizophrenia

Despite the lack of progress in the curative treatment of mental illness, especially schizophrenia, the accumulation of neuroscience data over the past decade suggests the re-conceptualization of schizophrenia. With the advent of new biomarkers and cognitive tools, new neuroscience technologies such as functional dynamic connectivity and the identification of subtle clinical features; it is now possible to detect early stages at risk or prodromes of a first psychotic episode. Current concepts reconceptualizes schizophrenia as a neurodevelopmental disorder at early onset, with polygenic risk and only symptomatic treatment for positive symptoms at this time. The use of such technologies in the future suggests new diagnostic and therapeutic options. Next steps include new pharmacological perspectives and potential contributions of new technologies such as quantitative system pharmacology brain computational modeling approach.

Metastable neural dynamics in Alzheimer's disease are disrupted by lesions to the structural connectome

Current theory suggests brain regions interact to reconcile the competing demands of integration and segregation by leveraging metastable dynamics. An emerging consensus recognises the importance of metastability in healthy neural dynamics where the transition between network states over time is dependent upon the structural connectivity between brain regions. In Alzheimer's disease (AD) - the most common form of dementia - these couplings are progressively weakened, metastability of neural dynamics are reduced and cognitive ability is impaired. Accordingly, we use a joint empirical and computational approach to reveal how behaviourally relevant changes in neural metastability are contingent on the structural integrity of the anatomical connectome. We estimate the metastability of fMRI BOLD signal in subjects from across the AD spectrum and in healthy controls and demonstrate the dissociable effects of structural disconnection on synchrony versus metastability. In addition, we reveal the critical role of metastability in general cognition by demonstrating the link between an individuals cognitive performance and their metastable neural dynamic. Finally, using whole-brain computer modelling, we demonstrate how a healthy neural dynamic is conditioned upon the topological integrity of the structural connectome. Overall, the results of our joint computational and empirical analysis suggest an important causal relationship between metastable neural dynamics, cognition, and the structural efficiency of the anatomical connectome.

Subject specificity of the correlation between large-scale structural and functional connectivity

Structural connectivity (SC), the physical pathways connecting regions in the brain, and functional connectivity (FC), the temporal coactivations, are known to be tightly linked. However, the nature of this relationship is still not understood. In the present study, we examined this relation more closely in six separate human neuroimaging datasets with different acquisition and preprocessing methods. We show that using simple linear associations, the relation between an individual's SC and FC is not subject specific for five of the datasets. Subject specificity of SC-FC fit is achieved only for one of the six datasets, the multimodal Glasser Human Connectome Project (HCP) parcellated dataset. We show that subject specificity of SC-FC correspondence is limited across datasets due to relatively small variability between subjects in SC compared with the larger variability in FC.