Dynamical Mechanisms of Interictal Resting-State Functional Connectivity in Epilepsy

Microstate-based brain network dynamics distinguishing temporal lobe epilepsy patients: A machine learning approach

Temporal lobe epilepsy (TLE) stands as the predominant adult focal epilepsy syndrome, characterized by dysfunctional intrinsic brain dynamics. However, the precise mechanisms underlying seizures in these patients remain elusive. Our study encompassed 116 TLE patients compared with 51 healthy controls. Employing microstate analysis, we assessed brain dynamic disparities between TLE patients and healthy controls, as well as between drug-resistant epilepsy (DRE) and drug-sensitive epilepsy (DSE) patients. We constructed dynamic functional connectivity networks based on microstates and quantified their spatial and temporal variability. Utilizing these brain network features, we developed machine learning models to discriminate between TLE patients and healthy controls, and between DRE and DSE patients. Temporal dynamics in TLE patients exhibited significant acceleration compared to healthy controls, along with heightened synchronization and instability in brain networks. Moreover, DRE patients displayed notably lower spatial variability in certain parts of microstate B, E and F dynamic functional connectivity networks, while temporal variability in certain parts of microstate E and G dynamic functional connectivity networks was markedly higher in DRE patients compared to DSE patients. The machine learning model based on these spatiotemporal metrics effectively differentiated TLE patients from healthy controls and discerned DRE from DSE patients. The accelerated microstate dynamics and disrupted microstate sequences observed in TLE patients mirror highly unstable intrinsic brain dynamics, potentially underlying abnormal discharges. Additionally, the presence of highly synchronized and unstable activities in brain networks of DRE patients signifies the establishment of stable epileptogenic networks, contributing to the poor responsiveness to antiseizure medications. The model based on spatiotemporal metrics demonstrated robust predictive performance, accurately distinguishing both TLE patients from healthy controls and DRE patients from DSE patients.

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.

Linking fast and slow: The case for generative models

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.

An exploratory computational analysis in mice brain networks of widespread epileptic seizure onset locations along with potential strategies for effective intervention and propagation control

Mean-field models have been developed to replicate key features of epileptic seizure dynamics. However, the precise mechanisms and the role of the brain area responsible for seizure onset and propagation remain incompletely understood. In this study, we employ computational methods within The Virtual Brain framework and the Epileptor model to explore how the location and connectivity of an Epileptogenic Zone (EZ) in a mouse brain are related to focal seizures (seizures that start in one brain area and may or may not remain localized), with a specific focus on the hippocampal region known for its association with epileptic seizures. We then devise computational strategies to confine seizures (prevent widespread propagation), simulating medical-like treatments such as tissue resection and the application of an anti-seizure drugs or neurostimulation to suppress hyperexcitability. Through selectively removing (blocking) specific connections informed by the structural connectome and graph network measurements or by locally reducing outgoing connection weights of EZ areas, we demonstrate that seizures can be kept constrained around the EZ region. We successfully identified the minimal connections necessary to prevent widespread seizures, with a particular focus on minimizing surgical or medical intervention while simultaneously preserving the original structural connectivity and maximizing brain functionality.

Macroscale intrinsic dynamics are associated with microcircuit function in focal and generalized epilepsies

Epilepsies are a group of neurological disorders characterized by abnormal spontaneous brain activity, involving multiscale changes in brain functional organizations. However, it is not clear to what extent the epilepsy-related perturbations of spontaneous brain activity affect macroscale intrinsic dynamics and microcircuit organizations, that supports their pathological relevance. We collect a sample of patients with temporal lobe epilepsy (TLE) and genetic generalized epilepsy with tonic-clonic seizure (GTCS), as well as healthy controls. We extract massive temporal features of fMRI BOLD time-series to characterize macroscale intrinsic dynamics, and simulate microcircuit neuronal dynamics used a large-scale biological model. Here we show whether macroscale intrinsic dynamics and microcircuit dysfunction are differed in epilepsies, and how these changes are linked. Differences in macroscale gradient of time-series features are prominent in the primary network and default mode network in TLE and GTCS. Biophysical simulations indicate reduced recurrent connection within somatomotor microcircuits in both subtypes, and even more reduced in GTCS. We further demonstrate strong spatial correlations between differences in the gradient of macroscale intrinsic dynamics and microcircuit dysfunction in epilepsies. These results emphasize the impact of abnormal neuronal activity on primary network and high-order networks, suggesting a systematic abnormality of brain hierarchical organization.

Altered spread of waves of activities at large scale is influenced by cortical thickness organization in temporal lobe epilepsy: a magnetic resonance imaging-high-density electroencephalography study

Temporal lobe epilepsy is a brain network disorder characterized by alterations at both the structural and the functional levels. It remains unclear how structure and function are related and whether this has any clinical relevance. In the present work, we adopted a novel methodological approach investigating how network structural features influence the large-scale dynamics. The functional network was defined by the spatio-temporal spreading of aperiodic bursts of activations (neuronal avalanches), as observed utilizing high-density electroencephalography in patients with temporal lobe epilepsy. The structural network was modelled as the region-based thickness covariance. Loosely speaking, we quantified the similarity of the cortical thickness of any two brain regions, both across groups and at the individual level, the latter utilizing a novel approach to define the subject-wise structural covariance network. In order to compare the structural and functional networks (at the nodal level), we studied the correlation between the probability that a wave of activity would propagate from a source to a target region and the similarity of the source region thickness as compared with other target brain regions. Building on the recent evidence that large-waves of activities pathologically spread through the epileptogenic network in temporal lobe epilepsy, also during resting state, we hypothesize that the structural cortical organization might influence such altered spatio-temporal dynamics. We observed a stable cluster of structure-function correlation in the bilateral limbic areas across subjects, highlighting group-specific features for left, right and bilateral temporal epilepsy. The involvement of contralateral areas was observed in unilateral temporal lobe epilepsy. We showed that in temporal lobe epilepsy, alterations of structural and functional networks pair in the regions where seizures propagate and are linked to disease severity. In this study, we leveraged on a well-defined model of neurological disease and pushed forward personalization approaches potentially useful in clinical practice. Finally, the methods developed here could be exploited to investigate the relationship between structure-function networks at subject level in other neurological conditions.

The virtual aging brain: Causal inference supports interhemispheric dedifferentiation in healthy aging

The mechanisms of cognitive decline and its variability during healthy aging are not fully understood, but have been associated with reorganization of white matter tracts and functional brain networks. Here, we built a brain network modeling framework to infer the causal link between structural connectivity and functional architecture and the consequent cognitive decline in aging. By applying in-silico interhemispheric degradation of structural connectivity, we reproduced the process of functional dedifferentiation during aging. Thereby, we found the global modulation of brain dynamics by structural connectivity to increase with age, which was steeper in older adults with poor cognitive performance. We validated our causal hypothesis via a deep-learning Bayesian approach. Our results might be the first mechanistic demonstration of dedifferentiation during aging leading to cognitive decline.

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.

Atypical functional connectivity hierarchy in Rolandic epilepsy

Functional connectivity hierarchy is an important principle in the process of brain functional organization and an important feature reflecting brain development. However, atypical brain network hierarchy organization in Rolandic epilepsy have not been systematically investigated. We examined connectivity alteration with age and its relation to epileptic incidence, cognition, or underlying genetic factors in 162 cases of Rolandic epilepsy and 117 typically developing children, by measuring fMRI multi-axis functional connectivity gradients. Rolandic epilepsy is characterized by contracting and slowing expansion of the functional connectivity gradients, highlighting the atypical age-related change of the connectivity hierarchy in segregation properties. The gradient alterations are relevant to seizure incidence, cognition, and connectivity deficit, and development-associated genetic basis. Collectively, our approach provides converging evidence for atypical connectivity hierarchy as a system-level substrate of Rolandic epilepsy, suggesting this is a disorder of information processing across multiple functional domains, and established a framework for large-scale brain hierarchical research.

Functional connectivity discriminates epileptogenic states and predicts surgical outcome in children with drug resistant epilepsy

Normal brain functioning emerges from a complex interplay among regions forming networks. In epilepsy, these networks are disrupted causing seizures. Highly connected nodes in these networks are epilepsy surgery targets. Here, we assess whether functional connectivity (FC) using intracranial electroencephalography can quantify brain regions epileptogenicity and predict surgical outcome in children with drug resistant epilepsy (DRE). We computed FC between electrodes on different states (i.e. interictal without spikes, interictal with spikes, pre-ictal, ictal, and post-ictal) and frequency bands. We then estimated the electrodes' nodal strength. We compared nodal strength between states, inside and outside resection for good- (n = 22, Engel I) and poor-outcome (n = 9, Engel II-IV) patients, respectively, and tested their utility to predict the epileptogenic zone and outcome. We observed a hierarchical epileptogenic organization among states for nodal strength: lower FC during interictal and pre-ictal states followed by higher FC during ictal and post-ictal states (p < 0.05). We further observed higher FC inside resection (p < 0.05) for good-outcome patients on different states and bands, and no differences for poor-outcome patients. Resection of nodes with high FC was predictive of outcome (positive and negative predictive values: 47-100%). Our findings suggest that FC can discriminate epileptogenic states and predict outcome in patients with DRE.

Resting-state SEEG-based brain network analysis for the detection of epileptic area

BACKGROUND

Most epilepsy research is based on interictal or ictal functional connectivity. However, prolonged electrode implantation may affect patients' health and the accuracy of epileptic zone identification. Brief resting-state SEEG recordings reduce the observation of epileptic discharges by reducing electrode implantation and other seizure-inducing interventions.

NEW METHOD

The location coordinates of SEEG in the brain were identified using CT and MRI. Based on undirected brain network connectivity, five functional connectivity measures and data feature vector centrality were calculated. Network connectivity was calculated from multiple perspectives of linear correlation, information theory, phase, and frequency, and the relative influence of nodes on network connectivity was considered. We investigated the potential value of resting-state SEEG for epileptic zone identification by comparing the differences between epileptic and non-epileptic zones, as well as the differences between patients with different surgical outcomes.

RESULTS

By comparing the centrality of brain network connectivity between epileptic and non-epileptic zones, we found significant differences in the distribution of brain networks between the two zones. There was a significant difference in brain network between patients with good surgical outcomes and those with poor surgical outcomes (p < 0.01). By combining support vector machines with static node importance, we predicted an AUC of 0.94 ± 0.08 for the epilepsy zone.

CONCLUSIONS AND SIGNIFICANCE

The results illustrated that nodes in epileptic zones are distinct from those in non-epileptic zones. Analysis of resting-state SEEG data and the importance of nodes in the brain network may contribute to identifying the epileptic zone and predicting the outcome.

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.

Noise-modulated multistable synapses in a Wilson-Cowan-based model of plasticity

Frequency-dependent plasticity refers to changes in synaptic strength in response to different stimulation frequencies. Resonance is a factor known to be of importance in such frequency dependence, however, the role of neural noise in the process remains elusive. Considering the brain is an inherently noisy system, understanding its effects may prove beneficial in shaping therapeutic interventions based on non-invasive brain stimulation protocols. The Wilson-Cowan (WC) model is a well-established model to describe the average dynamics of neural populations and has been shown to exhibit bistability in the presence of noise. However, the important question of how the different stable regimes in the WC model can affect synaptic plasticity when cortical populations interact has not yet been addressed. Therefore, we investigated plasticity dynamics in a WC-based model of interacting neural populations coupled with activity-dependent synapses in which a periodic stimulation was applied in the presence of noise of controlled intensity. The results indicate that for a narrow range of the noise variance, synaptic strength can be optimized. In particular, there is a regime of noise intensity for which synaptic strength presents a triple-stable state. Regulating noise intensity affects the probability that the system chooses one of the stable states, thereby controlling plasticity. These results suggest that noise is a highly influential factor in determining the outcome of plasticity induced by stimulation.

Graph-generative neural network for EEG-based epileptic seizure detection via discovery of dynamic brain functional connectivity

Dynamic complexity in brain functional connectivity has hindered the effective use of signal processing or machine learning methods to diagnose neurological disorders such as epilepsy. This paper proposed a new graph-generative neural network (GGN) model for the dynamic discovery of brain functional connectivity via deep analysis of scalp electroencephalogram (EEG) signals recorded from various regions of a patient's scalp. Brain functional connectivity graphs are generated for the extraction of spatial-temporal resolution of various onset epilepsy seizure patterns. Our supervised GGN model was substantiated by seizure detection and classification experiments. We train the GGN model using a clinically proven dataset of over 3047 epileptic seizure cases. The GGN model achieved a 91% accuracy in classifying seven types of epileptic seizure attacks, which outperformed the 65%, 74%, and 82% accuracy in using the convolutional neural network (CNN), graph neural networks (GNN), and transformer models, respectively. We present the GGN model architecture and operational steps to assist neuroscientists or brain specialists in using dynamic functional connectivity information to detect neurological disorders. Furthermore, we suggest to merge our spatial-temporal graph generator design in upgrading the conventional CNN and GNN models with dynamic convolutional kernels for accuracy enhancement.

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.

Interictal dynamic network transitions in mesial temporal lobe epilepsy

OBJECTIVE

To reveal the possible routine of brain network dynamic alterations in patients with mesial temporal lobe epilepsy (mTLE) and to establish a predicted model of seizure recurrence during interictal periods.

METHODS

Seventy-nine unilateral mTLE patients with hippocampal sclerosis and 97 healthy controls from two centers were retrospectively enrolled. Dynamic brain configuration analyses were performed with resting-state functional magnetic resonance imaging (MRI) data to quantify the functional stability over time and the dynamic interactions between brain regions. Relationships between seizure frequency and ipsilateral hippocampal module allegiance were evaluated using a machine learning predictive model.

RESULTS

Compared to the healthy controls, patients with mTLE displayed an overall higher dynamic network, switching mainly in the epileptogenic regions (false discovery rate [FDR] corrected p-FDR < .05). Moreover, the dynamic network configuration in mTLE was characterized by decreased recruitment (intra-network communication), and increased integration (inter-network communication) among hippocampal systems and large-scale higher-order brain networks (p-FDR < .05). We further found that the dynamic interactions between the hippocampal system and the default-mode network (DMN) or control networks exhibited an opposite distribution pattern (p-FDR < .05). Strikingly, we showed that there was a robust association between predicted seizure frequency based on the ipsilateral hippocampal-DMN dynamics model and actual seizure frequency (p-perm < .001).

SIGNIFICANCE

These findings suggest that the interictal brain of mTLE is characterized by dynamical shifts toward unstable state. Our study provides novel insights into the brain dynamic network alterations and supports the potential use of DMN dynamic parameters as candidate neuroimaging markers in monitoring the seizure frequency clinically during interictal periods.

Extracting Dynamical Understanding From Neural-Mass Models of Mouse Cortex

New brain atlases with high spatial resolution and whole-brain coverage have rapidly advanced our knowledge of the brain's neural architecture, including the systematic variation of excitatory and inhibitory cell densities across the mammalian cortex. But understanding how the brain's microscale physiology shapes brain dynamics at the macroscale has remained a challenge. While physiologically based mathematical models of brain dynamics are well placed to bridge this explanatory gap, their complexity can form a barrier to providing clear mechanistic interpretation of the dynamics they generate. In this work, we develop a neural-mass model of the mouse cortex and show how bifurcation diagrams, which capture local dynamical responses to inputs and their variation across brain regions, can be used to understand the resulting whole-brain dynamics. We show that strong fits to resting-state functional magnetic resonance imaging (fMRI) data can be found in surprisingly simple dynamical regimes-including where all brain regions are confined to a stable fixed point-in which regions are able to respond strongly to variations in their inputs, consistent with direct structural connections providing a strong constraint on functional connectivity in the anesthetized mouse. We also use bifurcation diagrams to show how perturbations to local excitatory and inhibitory coupling strengths across the cortex, constrained by cell-density data, provide spatially dependent constraints on resulting cortical activity, and support a greater diversity of coincident dynamical regimes. Our work illustrates methods for visualizing and interpreting model performance in terms of underlying dynamical mechanisms, an approach that is crucial for building explanatory and physiologically grounded models of the dynamical principles that underpin large-scale brain activity.

Multimodal Presurgical Evaluation of Medically Refractory Focal Epilepsy in Adults: An Update for Radiologists

Surgery is a potentially curative treatment option for patients with medically refractory focal epilepsy. Advanced neuroimaging modalities often improve surgical outcomes by contributing key information during the highly individualized surgical planning process and intraoperative localization. Hence, neuroradiologists play an integral role as part of the multidisciplinary management team. In this review, we initially present the conceptual background and practical framework of the presurgical evaluation process, including a description of the surgical treatment approaches in medically refractory focal epilepsy in adults. This background is followed by an overview of the advanced modalities commonly used during the presurgical workup at level IV epilepsy centers including diffusion imaging techniques, blood oxygen level dependent (BOLD) functional MRI (fMRI), PET, SPECT, and subtraction ictal SPECT, as well as by introductions to 7-T MRI and electrophysiologic techniques including electroencephalography (EEG) and magnetoencephalography (MEG). We also provide illustrative case examples of multimodal neuroimaging including PET/MRI, PET/MRI-DTI, subtraction ictal SPECT, and image-guided stereotactic planning with fMRI-DTI.

Towards an efficient validation of dynamical whole-brain models

Simulating the resting-state brain dynamics via mathematical whole-brain models requires an optimal selection of parameters, which determine the model’s capability to replicate empirical data. Since the parameter optimization via a grid search (GS) becomes unfeasible for high-dimensional models, we evaluate several alternative approaches to maximize the correspondence between simulated and empirical functional connectivity. A dense GS serves as a benchmark to assess the performance of four optimization schemes: Nelder-Mead Algorithm (NMA), Particle Swarm Optimization (PSO), Covariance Matrix Adaptation Evolution Strategy (CMAES) and Bayesian Optimization (BO). To compare them, we employ an ensemble of coupled phase oscillators built upon individual empirical structural connectivity of 105 healthy subjects. We determine optimal model parameters from two- and three-dimensional parameter spaces and show that the overall fitting quality of the tested methods can compete with the GS. There are, however, marked differences in the required computational resources and stability properties, which we also investigate before proposing CMAES and BO as efficient alternatives to a high-dimensional GS. For the three-dimensional case, these methods generated similar results as the GS, but within less than 6% of the computation time. Our results contribute to an efficient validation of models for personalized simulations of brain dynamics.

Increased Excursions to Functional Networks in Schizophrenia in the Absence of Task

Schizophrenia is a chronic psychotic disorder characterized by the disruption of thought processes, perception, cognition, and behaviors, for which there is still a lack of objective and quantitative biomarkers in brain activity. Using functional magnetic resonance imaging (fMRI) data from an open-source database, this study investigated differences between the dynamic exploration of resting-state networks in 71 schizophrenia patients and 74 healthy controls. Focusing on recurrent states of phase coherence in fMRI signals, brain activity was examined for intergroup differences through the lens of dynamical systems theory. Results showed reduced fractional occupancy and dwell time of a globally synchronized state in schizophrenia. Conversely, patients exhibited increased fractional occupancy, dwell time and limiting probability of being in states during which canonical functional networks—i.e., Limbic, Dorsal Attention and Somatomotor—synchronized in anti-phase with respect to the rest of the brain. In terms of state-to-state transitions, patients exhibited increased probability of switching to Limbic, Somatomotor and Visual networks, and reduced probability of remaining in states related to the Default Mode network, the Orbitofrontal network and the globally synchronized state. All results revealed medium to large effect sizes. Combined, these findings expose pronounced differences in the temporal expression of resting-state networks in schizophrenia patients, which may relate to the pathophysiology of this disorder. Overall, these results reinforce the utility of dynamical systems theory to extend current knowledge regarding disrupted brain dynamics in psychiatric disorders.

Epidemic models characterize seizure propagation and the effects of epilepsy surgery in individualized brain networks based on MEG and invasive EEG recordings

Epilepsy surgery is the treatment of choice for drug-resistant epilepsy patients. However, seizure-freedom is currently achieved in only 2/3 of the patients after surgery. In this study we have developed an individualized computational model based on MEG brain networks to explore seizure propagation and the efficacy of different virtual resections. Eventually, the goal is to obtain individualized models to optimize resection strategy and outcome. We have modelled seizure propagation as an epidemic process using the susceptible-infected (SI) model on individual brain networks derived from presurgical MEG. We included 10 patients who had received epilepsy surgery and for whom the surgery outcome at least one year after surgery was known. The model parameters were tuned in in order to reproduce the patient-specific seizure propagation patterns as recorded with invasive EEG. We defined a personalized search algorithm that combined structural and dynamical information to find resections that maximally decreased seizure propagation for a given resection size. The optimal resection for each patient was defined as the smallest resection leading to at least a 90% reduction in seizure propagation. The individualized model reproduced the basic aspects of seizure propagation for 9 out of 10 patients when using the resection area as the origin of epidemic spreading, and for 10 out of 10 patients with an alternative definition of the seed region. We found that, for 7 patients, the optimal resection was smaller than the resection area, and for 4 patients we also found that a resection smaller than the resection area could lead to a 100% decrease in propagation. Moreover, for two cases these alternative resections included nodes outside the resection area. Epidemic spreading models fitted with patient specific data can capture the fundamental aspects of clinically observed seizure propagation, and can be used to test virtual resections in silico. Combined with optimization algorithms, smaller or alternative resection strategies, that are individually targeted for each patient, can be determined with the ultimate goal to improve surgery outcome. MEG-based networks can provide a good approximation of structural connectivity for computational models of seizure propagation, and facilitate their clinical use.

Linking Brain Structure, Activity, and Cognitive Function through Computation

Understanding the human brain is a "Grand Challenge" for 21st century research. Computational approaches enable large and complex datasets to be addressed efficiently, supported by artificial neural networks, modeling and simulation. Dynamic generative multiscale models, which enable the investigation of causation across scales and are guided by principles and theories of brain function, are instrumental for linking brain structure and function. An example of a resource enabling such an integrated approach to neuroscientific discovery is the BigBrain, which spatially anchors tissue models and data across different scales and ensures that multiscale models are supported by the data, making the bridge to both basic neuroscience and medicine. Research at the intersection of neuroscience, computing and robotics has the potential to advance neuro-inspired technologies by taking advantage of a growing body of insights into perception, plasticity and learning. To render data, tools and methods, theories, basic principles and concepts interoperable, the Human Brain Project (HBP) has launched EBRAINS, a digital neuroscience research infrastructure, which brings together a transdisciplinary community of researchers united by the quest to understand the brain, with fascinating insights and perspectives for societal benefits.

High-resolution Virtual Brain Modeling Personalizes Deep Brain Stimulation for Treatment-Resistant Depression: Spatiotemporal Response Characteristics Following Stimulation of Neural Fiber Pathways

Over the past 15 years, deep brain stimulation (DBS) has been actively investigated as a groundbreaking therapy for patients with treatment-resistant depression (TRD); nevertheless, outcomes have varied from patient to patient, with an average response rate of ∼50%. The engagement of specific fiber tracts at the stimulation site has been hypothesized to be an important factor in determining outcomes, however, the resulting individual network effects at the whole-brain scale remain largely unknown. Here we provide a computational framework that can explore each individual's brain response characteristics elicited by selective stimulation of fiber tracts. We use a novel personalized in-silico approach, the Virtual Big Brain, which makes use of high-resolution virtual brain models at a mm-scale and explicitly reconstructs more than 100 000 fiber tracts for each individual. Each fiber tract is active and can be selectively stimulated. Simulation results demonstrate distinct stimulus-induced event-related potentials as a function of stimulation location, parametrized by the contact positions of the electrodes implanted in each patient, even though validation against empirical patient data reveals some limitations (i.e., the need for individual parameter adjustment, and differential accuracy across stimulation locations). This study provides evidence for the capacity of personalized high-resolution virtual brain models to investigate individual network effects in DBS for patients with TRD and opens up novel avenues in the personalized optimization of brain stimulation.

Multitier Network Analysis Using Resting-State Functional MRI for Epilepsy Surgery

Resting-state functional MRI (rs-fMRI) has been utilized to visualize large-scale brain networks. We evaluated the usefulness of multitier network analysis using rs-fMRI in patients with focal epilepsy. Structural and rs-fMRI data were retrospectively evaluated in 20 cases with medically refractory focal epilepsy, who subsequently underwent surgery. First, structural changes were examined using voxel-based morphometry analysis. Second, alterations in large-scale networks were evaluated using dual-regression analysis. Third, changes in cortical hubs were analyzed and the relationship between aberrant hubs and the epileptogenic zone (EZ) was evaluated. Finally, the relationship between the hubs and the default mode network (DMN) was examined using spectral dynamic causal modeling (spDCM). Dual-regression analysis revealed significant decrease in functional connectivity in several networks including DMN in patients, although no structural difference was seen between groups. Aberrant cortical hubs were observed in and around the EZ (EZ hubs) in 85% of the patients, and a strong degree of EZ hubs correlated to good seizure outcomes postoperatively. In spDCM analysis, facilitation was often seen from the EZ hub to the contralateral side, while inhibition was seen from the EZ hub to nodes of the DMN. Some cognition-related networks were impaired in patients with focal epilepsy. The EZ hub appeared in the vicinity of EZ facilitating connections to distant regions in the early phase, which may eventually generate secondary focus, while inhibiting connections to the DMN, which may cause cognitive deterioration. Our results demonstrate pathological network alterations in epilepsy and suggest that earlier surgical intervention may be more effective.

Discrete spectral eigenmode-resonance network of brain dynamics and connectivity

The problem of finding a compact natural representation of brain dynamics and connectivity is addressed using an expansion in terms of physical spatial eigenmodes and their frequency resonances. It is demonstrated that this discrete expansion via the system transfer function enables linear and nonlinear dynamics to be analyzed in compact form in terms of natural dynamic "atoms," each of which is a frequency resonance of an eigenmode. Because these modal resonances are determined by the system dynamics, not the investigator, they are privileged over widely used phenomenological patterns, and obviate the need for artificial discretizations and thresholding in coordinate space. It is shown that modal resonances participate as nodes of a discrete spectral network, are noninteracting in the linear regime, but are linked nonlinearly by wave-wave coalescence and decay processes. The modal resonance formulation is shown to be capable of speeding numerical calculations of strongly nonlinear interactions. Recent work in brain dynamics, especially based on neural field theory (NFT) approaches, allows eigenmodes and their resonances to be estimated from data without assuming a specific brain model. This means that dynamic equations can be inferred using system identification methods from control theory, rather than being assumed, and resonances can be interpreted as control-systems data filters. The results link brain activity and connectivity with control-systems functions such as prediction and attention via gain control and can also be linked to specific NFT predictions if desired, thereby providing a convenient bridge between physiologically based theories and experiment. Amplitudes of modes and resonances can also be tracked to provide a more direct and temporally localized representation of the dynamics than correlations and covariances, which are widely used in the field. By synthesizing many different lines of research, this work provides a way to link quantitative electrophysiological and imaging measurements, connectivity, brain dynamics, and function. This underlines the need to move between coordinate and spectral representations as required. Moreover, standard theoretical-physics approaches and mathematical methods can be used in place of ad hoc statistical measures such as those based on graph theory of artificially discretized and decimated networks, which are highly prone to selection effects and artifacts.

Atypical functional connectome hierarchy impacts cognition in temporal lobe epilepsy

OBJECTIVE

Drug-resistant temporal lobe epilepsy (TLE) is typically associated with hippocampal pathology. However, widespread network alterations are increasingly recognized and suggested to perturb cognitive function in multiple domains. Here we tested (1) whether TLE shows atypical cortical hierarchical organization, differentiating sensory and higher order systems; and (2) whether atypical hierarchy predicts cognitive impairment.

METHODS

We studied 72 well-characterized drug-resistant TLE patients and 41 healthy controls, statistically matched for age and sex, using multimodal magnetic resonance imaging analysis and cognitive testing. To model cortical hierarchical organization in vivo, we used a bidirectional stepwise functional connectivity analysis tapping into the differentiation between sensory/unimodal and paralimbic/transmodal cortices. Linear models compared patients to controls. Finally, we assessed associations of functional anomalies to cortical atrophy and microstructural anomalies, as well as clinical and cognitive parameters.

RESULTS

Compared to controls, TLE presented with bidirectional disruptions of sensory-paralimbic functional organization. Stepwise connectivity remained segregated within paralimbic and salience networks at the top of the hierarchy, and sensorimotor and dorsal attention at the bottom. Whereas paralimbic segregation was associated with atypical cortical myeloarchitecture and hippocampal atrophy, dysconnectivity of sensorimotor cortices reflected diffuse cortical thinning. The degree of abnormal hierarchical organization in sensory-petal streams covaried, with broad cognitive impairments spanning sensorimotor, attention, fluency, and visuoconstructional ability and memory, and was more marked in patients with longer disease duration and Engel I outcome.

SIGNIFICANCE

Our findings show atypical functional integration between paralimbic/transmodal and sensory/unimodal systems in TLE. Differential associations with paralimbic microstructure and sensorimotor atrophy suggest that system-level imbalance likely reflects complementary structural processes, but ultimately accounts for a broad spectrum of cognitive impairments. Hierarchical contextualization of cognitive deficits promises to open new avenues for personalized counseling in TLE.

A Transcriptome Community-and-Module Approach of the Human Mesoconnectome

Graph analysis allows exploring transcriptome compartments such as communities and modules for brain mesostructures. In this work, we proposed a bottom-up model of a gene regulatory network to brain-wise connectome workflow. We estimated the gene communities across all brain regions from the Allen Brain Atlas transcriptome database. We selected the communities method to yield the highest number of functional mesostructures in the network hierarchy organization, which allowed us to identify specific brain cell functions (e.g., neuroplasticity, axonogenesis and dendritogenesis communities). With these communities, we built brain-wise region modules that represent the connectome. Our findings match with previously described anatomical and functional brain circuits, such the default mode network and the default visual network, supporting the notion that the brain dynamics that carry out low- and higher-order functions originate from the modular composition of a GRN complex network.

Presurgical Evaluation of Epilepsy Using Resting-State MEG Functional Connectivity

Epilepsy is caused by abnormal electrical discharges (clinically identified by electrophysiological recording) in a specific part of the brain [originating in only one part of the brain, namely, the epileptogenic zone (EZ)]. Epilepsy is now defined as an archetypical hyperexcited neural network disorder. It can be investigated through the network analysis of interictal discharges, ictal discharges, and resting-state functional connectivity. Currently, there is an increasing interest in embedding resting-state connectivity analysis into the preoperative evaluation of epilepsy. Among the various neuroimaging technologies employed to achieve brain functional networks, magnetoencephalography (MEG) with the excellent temporal resolution is an ideal tool for estimating the resting-state connectivity between brain regions, which can reveal network abnormalities in epilepsy. What value does MEG resting-state functional connectivity offer for epileptic presurgical evaluation? Regarding this topic, this paper introduced the origin of MEG and the workflow of constructing source-space functional connectivity based on MEG signals. Resting-state functional connectivity abnormalities correlate with epileptogenic networks, which are defined by the brain regions involved in the production and propagation of epileptic activities. This paper reviewed the evidence of altered epileptic connectivity based on low- or high-frequency oscillations (HFOs) and the evidence of the advantage of using simultaneous MEG and intracranial electroencephalography (iEEG) recordings. More importantly, this review highlighted that MEG-based resting-state functional connectivity has the potential to predict postsurgical outcomes. In conclusion, resting-state MEG functional connectivity has made a substantial progress toward serving as a candidate biomarker included in epileptic presurgical evaluations.

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.

Cross-Scale Causality and Information Transfer in Simulated Epileptic Seizures

An information-theoretic approach for detecting causality and information transfer was applied to phases and amplitudes of oscillatory components related to different time scales and obtained using the wavelet transform from a time series generated by the Epileptor model. Three main time scales and their causal interactions were identified in the simulated epileptic seizures, in agreement with the interactions of the model variables. An approach consisting of wavelet transform, conditional mutual information estimation, and surrogate data testing applied to a single time series generated by the model was demonstrated to be successful in the identification of all directional (causal) interactions between the three different time scales described in the model. Thus, the methodology was prepared for the identification of causal cross-frequency phase–phase and phase–amplitude interactions in experimental and clinical neural data.

Topographical reorganization of brain functional connectivity during an early period of epileptogenesis

OBJECTIVE

The current study aims to investigate functional brain network representations during the early period of epileptogenesis.

METHODS

Eighteen rats with the intrahippocampal kainate model of mesial temporal lobe epilepsy were used for this experiment. Functional magnetic resonance imaging (fMRI) measurements were made 1 week after status epilepticus, followed by 2-4-month electrophysiological and video monitoring. Animals were identified as having (1) developed epilepsy (E+, n = 9) or (2) not developed epilepsy (E-, n = 6). Nine additional animals served as controls. Graph theory analysis was performed on the fMRI data to quantify the functional brain networks in all animals prior to the development of epilepsy. Spectrum clustering with the network features was performed to estimate their predictability in epileptogenesis.

RESULTS

Our data indicated that E+ animals showed an overall increase in functional connectivity strength compared to E- and control animals. Global network features and small-worldness of E- rats were similar to controls, whereas E+ rats demonstrated increased small-worldness, including increased reorganization degree, clustering coefficient, and global efficiency, with reduced shortest pathlength. A notable classification of the combined brain network parameters was found in E+ and E- animals. For the local network parameters, the E- rats showed increased hubs in sensorimotor cortex, and decreased hubness in hippocampus. The E+ rats showed a complete loss of hippocampal hubs, and the appearance of new hubs in the prefrontal cortex. We also observed that lesion severity was not related to epileptogenesis.

SIGNIFICANCE

Our data provide a view of the reorganization of topographical functional brain networks in the early period of epileptogenesis and how it can significantly predict the development of epilepsy. The differences from E- animals offer a potential means for applying noninvasive neuroimaging tools for the early prediction of epilepsy.

Noise-driven multistability vs deterministic chaos in phenomenological semi-empirical models of whole-brain activity

An outstanding open problem in neuroscience is to understand how neural systems are capable of producing and sustaining complex spatiotemporal dynamics. Computational models that combine local dynamics with in vivo measurements of anatomical and functional connectivity can be used to test potential mechanisms underlying this complexity. We compared two conceptually different mechanisms: noise-driven switching between equilibrium solutions (modeled by coupled Stuart-Landau oscillators) and deterministic chaos (modeled by coupled Rossler oscillators). We found that both models struggled to simultaneously reproduce multiple observables computed from the empirical data. This issue was especially manifested in the case of noise-driven dynamics close to a bifurcation, which imposed overly strong constraints on the optimal model parameters. In contrast, the chaotic model could produce complex behavior over a range of parameters, thus being capable of capturing multiple observables at the same time with good performance. Our observations support the view of the brain as a non-equilibrium system able to produce endogenous variability. We presented a simple model capable of jointly reproducing functional connectivity computed at different temporal scales. Besides adding to our conceptual understanding of brain complexity, our results inform and constrain the future development of biophysically realistic large-scale models.

Temporal variability profiling of the default mode across epilepsy subtypes

OBJECTIVE

Epilepsies are a group of neurological disorders sharing certain core features, but also demonstrate remarkable pathogenic and symptomatic heterogeneities. Various subtypes of epilepsy have been identified with abnormal shift in the brain default mode network (DMN). This study aims to evaluate the fine details of shared and distinct alterations in the DMN among epileptic subtypes.

METHODS

We collected resting-state functional magnetic resonance imaging (MRI) data from a large epilepsy sample (n = 371) at a single center, including temporal lobe epilepsy (TLE), frontal lobe epilepsy (FLE), and genetic generalized epilepsy with generalized tonic-clonic seizures (GGE-GTCS), as well as healthy controls (HC, n = 150). We analyzed temporal dynamics profiling of the DMN, including edge-wise and node-wise temporal variabilities, and recurrent dynamic states of functional connectivity, to identify abnormalities common to epilepsies as well as those specific to each subtype.

RESULTS

The analyses revealed that hypervariable edges within the specific DMN subsystem were shared by all subtypes (all P_NBS  < .005), and deficits in node-wise temporal variability were prominent in TLE (all t₍₂₄₃₎ ≤ 2.51, P_FDR  < .05) and FLE (all t₍₃₀₂₎ ≤ -2.65, P_FDR  < .05) but relatively weak in GGE-GTCS. Moreover, dynamic states were generally less stable in patients than controls (all P's < .001).

SIGNIFICANCE

Collectively, these findings demonstrated general DMN abnormalities common to different epilepsies as well as distinct dysfunctions to subtypes, and provided insights into understanding the relationship of pathophysiological mechanisms and brain connectivity.