Modeling the outcome of structural disconnection on resting-state functional connectivity

Metastability in the wild: A scoping review of empirical neuroimaging studies in humans

Metastability is proposed as the mechanism supporting our adaptive responses to the environment. While extensive research has characterized brain metastability during rest and task performance, prior studies have mainly focused on understanding underlying mechanisms, with limited exploration of its application in mental processes and behaviors. This scoping review offers an overview of the existing empirical literature in this area. Through a systematic search that included 36 articles, our results reveal a predominance of resting-state fMRI studies, variability in how metastability is defined, and a lack of consideration for common confounds in neuroimaging data. The review concludes with suggestions for future research directions to address crucial unresolved issues in the field.

Adaptive Whole-Brain Dynamics Predictive Method: Relevancy to Mental Disorders

The Hopf whole-brain model, based on structural connectivity, overcomes limitations of traditional structural or functional connectivity-focused methods by incorporating heterogeneity parameters, quantifying dynamic brain characteristics in healthy and diseased states. Traditional parameter fitting techniques lack precision, restricting broader use. To address this, we validated parameter fitting methods using simulated networks and synthetic models, introducing improvements such as individual-specific initialization and optimized gradient descent, which reduced individual data loss. We also developed an approximate loss function and gradient adjustment mechanism, enhancing parameter fitting accuracy and stability. Applying this refined method to datasets for major depressive disorder (MDD) and autism spectrum disorder (ASD), we identified differences in brain regions between patients and healthy controls, explaining related anomalies. This rigorous validation is crucial for clinical application, paving the way for precise neuropathological identification and novel treatments in neuropsychiatric research, demonstrating substantial potential in clinical neurology.

Neural mass modeling for the masses: Democratizing access to whole-brain biophysical modeling with FastDMF

Different whole-brain computational models have been recently developed to investigate hypotheses related to brain mechanisms. Among these, the Dynamic Mean Field (DMF) model is particularly attractive, combining a biophysically realistic model that is scaled up via a mean-field approach and multimodal imaging data. However, an important barrier to the widespread usage of the DMF model is that current implementations are computationally expensive, supporting only simulations on brain parcellations that consider less than 100 brain regions. Here, we introduce an efficient and accessible implementation of the DMF model: the FastDMF. By leveraging analytical and numerical advances-including a novel estimation of the feedback inhibition control parameter and a Bayesian optimization algorithm-the FastDMF circumvents various computational bottlenecks of previous implementations, improving interpretability, performance, and memory use. Furthermore, these advances allow the FastDMF to increase the number of simulated regions by one order of magnitude, as confirmed by the good fit to fMRI data parcellated at 90 and 1,000 regions. These advances open the way to the widespread use of biophysically grounded whole-brain models for investigating the interplay between anatomy, function, and brain dynamics and to identify mechanistic explanations of recent results obtained from fine-grained neuroimaging recordings.

Beyond Focal Lesions: Dynamical Network Effects of White Matter Hyperintensities

White matter (WM) tracts shape the brain's dynamical activity and their damage (e.g., white matter hyperintensities, WMH) yields relevant functional alterations, ultimately leading to cognitive symptoms. The mechanisms linking the structural damage caused by WMH to the arising alterations of brain dynamics is currently unknown. To estimate the impact of WMH on brain dynamics, we combine neural-mass whole-brain modeling with a virtual-lesioning (disconnectome) approach informed by empirical data. We account for the heterogeneous effects of WMH either on inter-regional communication (i.e., edges) or on dynamics (i.e., nodes) and create models of their local versus global, and edge versus nodal effects using a large fMRI dataset comprising 188 non-demented individuals (120 cognitively normal, 68 with mild cognitive impairment) with varying degrees of WMH. We show that, although WMH mainly determine local damage to specific WM tracts, these lesions yield relevant global dynamical effects by reducing the overall synchronization of the brain through a reduction of global coupling. Alterations of local nodal dynamics through disconnections are less relevant and present only at later stages of WMH damage. Exploratory analyses suggest that education might play a beneficial role in counteracting the reduction in global coupling associated with WMH. This study provides generative models linking the structural damage caused by WMH to alterations in brain dynamics. These models might be used to evaluate the detrimental effects of WMH on brain dynamics in a subject-specific manner. Furthermore, it validates the use of whole-brain modeling for hypothesis-testing of structure-function relationships in diseased states characterized by empirical disconnections.

Comparison of whole-brain task-modulated functional connectivity methods for fMRI task connectomics

Higher brain functions require flexible integration of information across widely distributed brain regions depending on the task context. Resting-state functional magnetic resonance imaging (fMRI) has provided substantial insight into large-scale intrinsic brain network organisation, yet the principles of rapid context-dependent reconfiguration of that intrinsic network organisation are much less understood. A major challenge for task connectome mapping is the absence of a gold standard for deriving whole-brain task-modulated functional connectivity matrices. Here, we perform biophysically realistic simulations to control the ground-truth task-modulated functional connectivity over a wide range of experimental settings. We reveal the best-performing methods for different types of task designs and their fundamental limitations. Importantly, we demonstrate that rapid (100 ms) modulations of oscillatory neuronal synchronisation can be recovered from sluggish haemodynamic fluctuations even at typically low fMRI temporal resolution (2 s). Finally, we provide practical recommendations on task design and statistical analysis to foster task connectome mapping.

Comparison of whole-brain task-modulated functional connectivity methods for fMRI task connectomics

Higher brain functions require flexible integration of information across widely distributed brain regions depending on the task context. Resting-state functional magnetic resonance imaging (fMRI) has provided substantial insight into large-scale intrinsic brain network organisation, yet the principles of rapid context-dependent reconfiguration of that intrinsic network organisation are much less understood. A major challenge for task connectome mapping is the absence of a gold standard for deriving whole-brain task-modulated functional connectivity matrices. Here, we perform biophysically realistic simulations to control the ground-truth task-modulated functional connectivity over a wide range of experimental settings. We reveal the best-performing methods for different types of task designs and their fundamental limitations. Importantly, we demonstrate that rapid (100 ms) modulations of oscillatory neuronal synchronisation can be recovered from sluggish haemodynamic fluctuations even at typically low fMRI temporal resolution (2 s). Finally, we provide practical recommendations on task design and statistical analysis to foster task connectome mapping.

A Dynamic Entropy Approach Reveals Reduced Functional Network Connectivity Trajectory Complexity in Schizophrenia

Over the past decade and a half, dynamic functional imaging has revealed low-dimensional brain connectivity measures, identified potential common human spatial connectivity states, tracked the transition patterns of these states, and demonstrated meaningful transition alterations in disorders and over the course of development. Recently, researchers have begun to analyze these data from the perspective of dynamic systems and information theory in the hopes of understanding how these dynamics support less easily quantified processes, such as information processing, cortical hierarchy, and consciousness. Little attention has been paid to the effects of psychiatric disease on these measures, however. We begin to rectify this by examining the complexity of subject trajectories in state space through the lens of information theory. Specifically, we identify a basis for the dynamic functional connectivity state space and track subject trajectories through this space over the course of the scan. The dynamic complexity of these trajectories is assessed along each dimension of the proposed basis space. Using these estimates, we demonstrate that schizophrenia patients display substantially simpler trajectories than demographically matched healthy controls and that this drop in complexity concentrates along specific dimensions. We also demonstrate that entropy generation in at least one of these dimensions is linked to cognitive performance. Overall, the results suggest great value in applying dynamic systems theory to problems of neuroimaging and reveal a substantial drop in the complexity of schizophrenia patients' brain function.

Disruption of alpha oscillation propagation in patients with schizophrenia

OBJECTIVE

Propagation of electroencephalogram (EEG) oscillations, often referred to as traveling waves, reflects the role of brain oscillations in neural information transmission. This propagation can be distorted by brain disorders such as schizophrenia that features disconnection of neural information transmission (i.e., disconnection syndrome). However, this possibility of the disruption of EEG oscillation propagation in patients with schizophrenia remains largely unexplored.

METHODS

Using a publicly shared dataset (N = 19 and 24; patients with schizophrenia and healthy controls, respectively), we investigated EEG oscillation propagation by analyzing the local phase gradients (LPG) of alpha (8-12 Hz) oscillations in both healthy participants and patients with schizophrenia.

RESULTS

Our results showed significant directionality in the propagation of alpha oscillations in healthy participants. Specifically, alpha oscillations propagated in an anterior-to-posterior direction along mid-line and a posterior-to-anterior direction laterally. In patients with schizophrenia, some of alpha oscillation propagation were notably disrupted, particularly in the central midline area where alpha oscillations propagated from anterior to posterior areas.

CONCLUSION

Our finding lends support to the hypothesis of a disconnection syndrome in schizophrenia, underscoring a disruption in the anterior-to-posterior propagation of alpha oscillations.

SIGNIFICANCE

This study identified disruption of alpha oscillation propagation observed in scalp EEG as a biomarker for schizophrenia.

Brain dynamics predictive of response to psilocybin for treatment-resistant depression

Psilocybin therapy for depression has started to show promise, yet the underlying causal mechanisms are not currently known. Here, we leveraged the differential outcome in responders and non-responders to psilocybin (10 and 25 mg, 7 days apart) therapy for depression-to gain new insights into regions and networks implicated in the restoration of healthy brain dynamics. We used large-scale brain modelling to fit the spatiotemporal brain dynamics at rest in both responders and non-responders before treatment. Dynamic sensitivity analysis of systematic perturbation of these models enabled us to identify specific brain regions implicated in a transition from a depressive brain state to a healthy one. Binarizing the sample into treatment responders (>50% reduction in depressive symptoms) versus non-responders enabled us to identify a subset of regions implicated in this change. Interestingly, these regions correlate with in vivo density maps of serotonin receptors 5-hydroxytryptamine 2a and 5-hydroxytryptamine 1a, which psilocin, the active metabolite of psilocybin, has an appreciable affinity for, and where it acts as a full-to-partial agonist. Serotonergic transmission has long been associated with depression, and our findings provide causal mechanistic evidence for the role of brain regions in the recovery from depression via psilocybin.

Exploring global and local processes underlying alterations in resting-state functional connectivity and dynamics in schizophrenia

Introduction

We examined changes in large-scale functional connectivity and temporal dynamics and their underlying mechanisms in schizophrenia (ScZ) through measurements of resting-state functional magnetic resonance imaging (rs-fMRI) data and computational modelling.

Methods

The rs-fMRI measurements from patients with chronic ScZ (n=38) and matched healthy controls (n=43), were obtained through the public schizConnect repository. Computational models were constructed based on diffusion-weighted MRI scans and fit to the experimental rs-fMRI data.

Results

We found decreased large-scale functional connectivity across sensory and association areas and for all functional subnetworks for the ScZ group. Additionally global synchrony was reduced in patients while metastability was unaltered. Perturbations of the computational model revealed that decreased global coupling and increased background noise levels both explained the experimentally found deficits better than local changes to the GABAergic or glutamatergic system.

Discussion

The current study suggests that large-scale alterations in ScZ are more likely the result of global rather than local network changes.

Patient-specific modeling for guided rehabilitation of stroke patients: the BrainX3 use-case

BrainX3 is an interactive neuroinformatics platform that has been thoughtfully designed to support neuroscientists and clinicians with the visualization, analysis, and simulation of human neuroimaging, electrophysiological data, and brain models. The platform is intended to facilitate research and clinical use cases, with a focus on personalized medicine diagnostics, prognostics, and intervention decisions. BrainX3 is designed to provide an intuitive user experience and is equipped to handle different data types and 3D visualizations. To enhance patient-based analysis, and in keeping with the principles of personalized medicine, we propose a framework that can assist clinicians in identifying lesions and making patient-specific intervention decisions. To this end, we are developing an AI-based model for lesion identification, along with a mapping of tract information. By leveraging the patient's lesion information, we can gain valuable insights into the structural damage caused by the lesion. Furthermore, constraining whole-brain models with patient-specific disconnection masks can allow for the detection of mesoscale excitatory-inhibitory imbalances that cause disruptions in macroscale network properties. Finally, such information has the potential to guide neuromodulation approaches, assisting in the choice of candidate targets for stimulation techniques such as Transcranial Ultrasound Stimulation (TUS), which modulate E-I balance, potentiating cortical reorganization and the restoration of the dynamics and functionality disrupted due to the lesion.

A phenomenological model of whole brain dynamics using a network of neural oscillators with power-coupling

We present a general, trainable oscillatory neural network as a large-scale model of brain dynamics. The model has a cascade of two stages - an oscillatory stage and a complex-valued feedforward stage - for modelling the relationship between structural connectivity and functional connectivity from neuroimaging data under resting brain conditions. Earlier works of large-scale brain dynamics that used Hopf oscillators used linear coupling of oscillators. A distinctive feature of the proposed model employs a novel form of coupling known as power coupling. Oscillatory networks based on power coupling can accurately model arbitrary multi-dimensional signals. Training the lateral connections in the oscillator layer is done by a modified form of Hebbian learning, whereas a variation of the complex backpropagation algorithm does training in the second stage. The proposed model can not only model the empirical functional connectivity with remarkable accuracy (correlation coefficient between simulated and empirical functional connectivity- 0.99) but also identify default mode network regions. In addition, we also inspected how structural loss in the brain can cause significant aberration in simulated functional connectivity and functional connectivity dynamics; and how it can be restored with optimized model parameters by an in silico perturbational study.

A deep learning approach to estimating initial conditions of Brain Network Models in reference to measured fMRI data

Introduction

Brain Network Models (BNMs) are mathematical models that simulate the activity of the entire brain. These models use neural mass models to represent local activity in different brain regions that interact with each other via a global structural network. Researchers have been interested in using these models to explain measured brain activity, particularly resting state functional magnetic resonance imaging (rs-fMRI). BNMs have shown to produce similar properties as measured data computed over longer periods of time such as average functional connectivity (FC), but it is unclear how well simulated trajectories compare to empirical trajectories on a timepoint-by-timepoint basis. During task fMRI, the relevant processes pertaining to task occur over the time frame of the hemodynamic response function, and thus it is important to understand how BNMs capture these dynamics over these short periods.

Methods

To test the nature of BNMs' short-term trajectories, we used a deep learning technique called Neural ODE to simulate short trajectories from estimated initial conditions based on observed fMRI measurements. To compare to previous methods, we solved for the parameterization of a specific BNM, the Firing Rate Model, using these short-term trajectories as a metric.

Results

Our results show an agreement between parameterization of using previous long-term metrics with the novel short term metrics exists if also considering other factors such as the sensitivity in accuracy with relative to changes in structural connectivity, and the presence of noise.

Discussion

Therefore, we conclude that there is evidence that by using Neural ODE, BNMs can be simulated in a meaningful way when comparing against measured data trajectories, although future studies are necessary to establish how BNM activity relate to behavioral variables or to faster neural processes during this time period.

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.

Computational modelling in disorders of consciousness: Closing the gap towards personalised models for restoring consciousness

Disorders of consciousness are complex conditions characterised by persistent loss of responsiveness due to brain injury. They present diagnostic challenges and limited options for treatment, and highlight the urgent need for a more thorough understanding of how human consciousness arises from coordinated neural activity. The increasing availability of multimodal neuroimaging data has given rise to a wide range of clinically- and scientifically-motivated modelling efforts, seeking to improve data-driven stratification of patients, to identify causal mechanisms for patient pathophysiology and loss of consciousness more broadly, and to develop simulations as a means of testing in silico potential treatment avenues to restore consciousness. As a dedicated Working Group of clinicians and neuroscientists of the international Curing Coma Campaign, here we provide our framework and vision to understand the diverse statistical and generative computational modelling approaches that are being employed in this fast-growing field. We identify the gaps that exist between the current state-of-the-art in statistical and biophysical computational modelling in human neuroscience, and the aspirational goal of a mature field of modelling disorders of consciousness; which might drive improved treatments and outcomes in the clinic. Finally, we make several recommendations for how the field as a whole can work together to address these challenges.

From neurotransmitters to networks: Transcending organisational hierarchies with molecular-informed functional imaging

The human brain exhibits complex interactions across micro, meso-, and macro-scale organisational principles. Recent synergistic multi-modal approaches have begun to link micro-scale information to systems level dynamics, transcending organisational hierarchies and offering novel perspectives into the brain's function and dysfunction. Specifically, the distribution of micro-scale properties (such as receptor density or gene expression) can be mapped onto macro-scale measures from functional MRI to provide novel neurobiological insights. Methodological approaches to enrich functional imaging analyses with molecular information are rapidly evolving, with several streams of research having developed relatively independently, each offering unique potential to explore the trans-hierarchical functioning of the brain. Here, we address the three principal streams of research - spatial correlation, molecular-enriched network, and in-silico whole brain modelling analyses - to provide a critical overview of the different sources of molecular information, how this information can be utilised within analyses of fMRI data, the merits and pitfalls of each methodology, and, through the use of key examples, highlight their promise to shed new light on key domains of neuroscientific inquiry.

Inferring the dynamical effects of stroke lesions through whole-brain modeling

Understanding the effect of focal lesions (stroke) on brain structure-function traditionally relies on behavioral analyses and correlation with neuroimaging data. Here we use structural disconnection maps from individual lesions to derive a causal mechanistic generative whole-brain model able to explain both functional connectivity alterations and behavioral deficits induced by stroke. As compared to other models that use only the local lesion information, the similarity to the empirical fMRI connectivity increases when the widespread structural disconnection information is considered. The presented model classifies behavioral impairment severity with higher accuracy than other types of information (e.g.: functional connectivity). We assessed topological measures that characterize the functional effects of damage. With the obtained results, we were able to understand how network dynamics change emerge, in a nontrivial way, after a stroke injury of the underlying complex brain system. This type of modeling, including structural disconnection information, helps to deepen our understanding of the underlying mechanisms of stroke lesions.

Homeostatic coordination and up-regulation of neural activity by activity-dependent myelination

Activity-dependent myelination (ADM) is a fundamental dimension of brain plasticity through which myelin changes as a function of neural activity. Mediated by structural changes in glia, ADM notably regulates axonal conduction velocity. Yet, it remains unclear how neural activity impacts myelination to orchestrate the timing of neural signalling, and how ADM shapes neural activity. We developed a model of spiking neurons enhanced with neuron-oligodendrocyte feedback and examined the relationship between ADM and neural activity. We found that ADM implements a homeostatic gain control mechanism that enhances neural firing rates and correlations through the temporal coordination of action potentials as axon lengths increase. Stimuli engage ADM plasticity to trigger bidirectional and reversible changes in conduction delays, as may occur during learning. Furthermore, ADM was found to enhance information transmission under various types of time-varying stimuli. These results highlight the role of ADM in shaping neural activity and communication.

Concussion Prone Scenarios: A Multi-Dimensional Exploration in Impact Directions, Brain Morphology, and Network Architectures Using Computational Models

While individual susceptibility to traumatic brain injury (TBI) has been speculated, past work does not provide an analysis considering how physical features of an individual's brain (e.g., brain size, shape), impact direction, and brain network features can holistically contribute to the risk of suffering a TBI from an impact. This work investigated each of these features simultaneously using computational modeling and analyses of simulated functional connectivity. Unlike the past studies that assess the severity of TBI based on the quantification of brain tissue damage (e.g., principal strain), we approached the brain as a complex network in which neuronal oscillations orchestrate to produce normal brain function (estimated by functional connectivity) and, to this end, both the anatomical damage location and its topological characteristics within the brain network contribute to the severity of brain function disruption and injury. To represent the variations in the population, we analyzed a publicly available database of brain imaging data and selected five distinct network architectures, seven different brain sizes, and three uniaxial head rotational conditions to study the consequences of 74 virtual impact scenarios. Results show impact direction produces the most significant change in connections across brain areas (structural connectome) and the functional coupling of activity across these brain areas (functional connectivity). Axial rotations were more injurious than those with sagittal and coronal rotations when the head kinematics were the same for each condition. When the impact direction was held constant, brain network architecture showed a significantly different vulnerability across axial and sagittal, but not coronal rotations. As expected, brain size significantly affected the expected change in structural and functional connectivity after impact. Together, these results provided groupings of predicted vulnerability to impact-a subgroup of male brain architectures exposed to axial impacts were most vulnerable, while a subgroup of female brain architectures was the most tolerant to the sagittal impacts studied. These findings lay essential groundwork for subject-specific analyses of concussion and provide invaluable guidance for designing personalized protection equipment.

Metastable oscillatory modes emerge from synchronization in the brain spacetime connectome

A rich repertoire of oscillatory signals is detected from human brains with electro- and magnetoencephalography (EEG/MEG). However, the principles underwriting coherent oscillations and their link with neural activity remain under debate. Here, we revisit the mechanistic hypothesis that transient brain rhythms are a signature of metastable synchronization, occurring at reduced collective frequencies due to delays between brain areas. We consider a system of damped oscillators in the presence of background noise - approximating the short-lived gamma-frequency oscillations generated within neuronal circuits - coupled according to the diffusion weighted tractography between brain areas. Varying the global coupling strength and conduction speed, we identify a critical regime where spatially and spectrally resolved metastable oscillatory modes (MOMs) emerge at sub-gamma frequencies, approximating the MEG power spectra from 89 healthy individuals at rest. Further, we demonstrate that the frequency, duration, and scale of MOMs - as well as the frequency-specific envelope functional connectivity - can be controlled by global parameters, while the connectome structure remains unchanged. Grounded in the physics of delay-coupled oscillators, these numerical analyses demonstrate how interactions between locally generated fast oscillations in the connectome spacetime structure can lead to the emergence of collective brain rhythms organized in space and time.

Understanding brain states across spacetime informed by whole-brain modelling

In order to survive in a complex environment, the human brain relies on the ability to flexibly adapt ongoing behaviour according to intrinsic and extrinsic signals. This capability has been linked to specific whole-brain activity patterns whose relative stability (order) allows for consistent functioning, supported by sufficient intrinsic instability needed for optimal adaptability. The emergent, spontaneous balance between order and disorder in brain activity over spacetime underpins distinct brain states. For example, depression is characterized by excessively rigid, highly ordered states, while psychedelics can bring about more disordered, sometimes overly flexible states. Recent developments in systems, computational and theoretical neuroscience have started to make inroads into the characterization of such complex dynamics over space and time. Here, we review recent insights drawn from neuroimaging and whole-brain modelling motivating using mechanistic principles from dynamical system theory to study and characterize brain states. We show how different healthy and altered brain states are associated to characteristic spacetime dynamics which in turn may offer insights that in time can inspire new treatments for rebalancing brain states in disease. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Recovery of neural dynamics criticality in personalized whole-brain models of stroke

The critical brain hypothesis states that biological neuronal networks, because of their structural and functional architecture, work near phase transitions for optimal response to internal and external inputs. Criticality thus provides optimal function and behavioral capabilities. We test this hypothesis by examining the influence of brain injury (strokes) on the criticality of neural dynamics estimated at the level of single participants using directly measured individual structural connectomes and whole-brain models. Lesions engender a sub-critical state that recovers over time in parallel with behavior. The improvement of criticality is associated with the re-modeling of specific white-matter connections. We show that personalized whole-brain dynamical models poised at criticality track neural dynamics, alteration post-stroke, and behavior at the level of single participants.

Systematic perturbation of an artificial neural network: A step towards quantifying causal contributions in the brain

Lesion inference analysis is a fundamental approach for characterizing the causal contributions of neural elements to brain function. This approach has gained new prominence through the arrival of modern perturbation techniques with unprecedented levels of spatiotemporal precision. While inferences drawn from brain perturbations are conceptually powerful, they face methodological difficulties. Particularly, they are challenged to disentangle the true causal contributions of the involved elements, since often functions arise from coalitions of distributed, interacting elements, and localized perturbations have unknown global consequences. To elucidate these limitations, we systematically and exhaustively lesioned a small artificial neural network (ANN) playing a classic arcade game. We determined the functional contributions of all nodes and links, contrasting results from sequential single-element perturbations with simultaneous perturbations of multiple elements. We found that lesioning individual elements, one at a time, produced biased results. By contrast, multi-site lesion analysis captured crucial details that were missed by single-site lesions. We conclude that even small and seemingly simple ANNs show surprising complexity that needs to be addressed by multi-lesioning for a coherent causal characterization.

Preparing for a Second Attack: A Lesion Simulation Study on Network Resilience After Stroke

Background:

Does the brain become more resilient after a first stroke to reduce the consequences of a new lesion? Although recurrent strokes are a major clinical issue, whether and how the brain prepares for a second attack is unknown. This is due to the difficulties to obtain an appropriate dataset of stroke patients with comparable lesions, imaged at the same interval after onset. Furthermore, timing of the recurrent event remains unpredictable.

Methods:

Here, we used a novel clinical lesion simulation approach to test the hypothesis that resilience in brain networks increases during stroke recovery. Sixteen highly selected patients with a lesion restricted to the primary motor cortex were recruited. At 3 time points of the index event (10 days, 3 weeks, 3 months), we mimicked recurrent infarcts by deletion of nodes in brain networks (resting-state functional magnetic resonance imaging). Graph measures were applied to determine resilience (global efficiency after attack) and wiring cost (mean degree) of the network.

Results:

At 10 days and 3 weeks after stroke, resilience was similar in patients and controls. However, at 3 months, although motor function had fully recovered, resilience to clinically representative simulated lesions was higher compared to controls (cortical lesion P =0.012; subcortical: P =0.009; cortico-subcortical: P =0.009). Similar results were found after random ( P =0.012) and targeted ( P =0.015) attacks.

Conclusions:

Our results suggest that, in this highly selected cohort of patients with lesions restricted to the primary motor cortex, brain networks reconfigure to increase resilience to future insults. Lesion simulation is an innovative approach, which may have major implications for stroke therapy. Individualized neuromodulation strategies could be developed to foster resilient network reconfigurations after a first stroke to limit the consequences of future attacks.

Effects of virtual lesions on temporal dynamics in cortical networks based on personalized dynamic models

The human brain dynamically shifts between a predominantly integrated state and a predominantly segregated state, each with different roles in supporting cognition and behavior. However, no studies to date have investigated lesions placed in different regions of the cerebral cortex to determine the effects on the temporal balance of integration and segregation. Here, we used the integrated state occurrence rate to measure the temporal balance of integration and segregation in the resting brain. Based on dynamic mean-field models coupled through the individual's structural white matter connections, neural activity was modeled. By lesioning different individual nodes from the model, our results implied that the impact of lesions reaches far beyond focal damage and could impair cognition by affecting system-level dynamics. Lesions in a portion of the nodes in the visual, somatomotor, limbic, and default networks significantly compromised the temporal balance of integration and segregation. Crucially, the effects of lesions in different regions could be predicted based on the hierarchical axis inferred from the T1w/T2w map and specific graph measures of structural brain networks. Taken together, our findings indicate the possibility of significant contributions of anatomical heterogeneity to the dynamics of functional network topology. Although still in its infancy, computational modeling may provide an entry point for understanding brain disorders at a causal mechanistic level, possibly leading to novel, more effective therapeutic interventions.

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.

An interdisciplinary computational model for predicting traumatic brain injury: Linking biomechanics and functional neural networks

The brain is a complex network consisting of neuron cell bodies in the gray matter and their axonal projections, forming the white matter tracts. These neurons are supported by an equally complex vascular network as well as glial cells. Traumatic brain injury (TBI) can lead to the disruption of the structural and functional brain networks due to disruption of both neuronal cell bodies in the gray matter as well as their projections and supporting cells. To explore how an impact can alter the function of brain networks, we integrated a finite element (FE) brain mechanics model with linked models of brain dynamics (Kuramoto oscillator) and vascular perfusion (Balloon-Windkessel) in this study. We used empirical resting-state functional magnetic resonance imaging (MRI) data to optimize the fit of our brain dynamics and perfusion models to clinical data. Results from the FE model were used to mimic injury in these optimized brain dynamics models: injury to the nodes (gray matter) led to a decrease in the nodal oscillation frequency, while damage to the edges (axonal connections/white matter) progressively decreased coupling among connected nodes. A total of 53 cases, including 33 non-injurious and 20 concussive head impacts experienced by professional American football players were simulated using this integrated model. We examined the correlation of injury outcomes with global measures of structural connectivity, neural dynamics, and functional connectivity of the brain networks when using different lesion methods. Results show that injurious head impacts cause significant alterations in global network topology regardless of lesion methods. Changes between the disrupted and healthy functional connectivity (measured by Pearson correlation) consistently correlated well with injury outcomes (AUC≥0.75), although the predictive performance is not significantly different (p>0.05) to that of traditional kinematic measures (angular acceleration). Intriguingly, our lesion model for gray matter damage predicted increases in global efficiency and clustering coefficient with increases in injury risk, while disrupting axonal connections led to lower network efficiency and clustering. When both injury mechanisms were combined into a single injury prediction model, the injury prediction performance depended on the thresholds used to determine neurodegeneration and mechanical tolerance for axonal injury. Together, these results point towards complex effects of mechanical trauma to the brain and provide a new framework for understanding brain injury at a causal mechanistic level and developing more effective diagnostic methods and therapeutic interventions.

Excitatory-Inhibitory Homeostasis and Diaschisis: Tying the Local and Global Scales in the Post-stroke Cortex

Maintaining a balance between excitatory and inhibitory activity is an essential feature of neural networks of the neocortex. In the face of perturbations in the levels of excitation to cortical neurons, synapses adjust to maintain excitatory-inhibitory (EI) balance. In this review, we summarize research on this EI homeostasis in the neocortex, using stroke as our case study, and in particular the loss of excitation to distant cortical regions after focal lesions. Widespread changes following a localized lesion, a phenomenon known as diaschisis, are not only related to excitability, but also observed with respect to functional connectivity. Here, we highlight the main findings regarding the evolution of excitability and functional cortical networks during the process of post-stroke recovery, and how both are related to functional recovery. We show that cortical reorganization at a global scale can be explained from the perspective of EI homeostasis. Indeed, recovery of functional networks is paralleled by increases in excitability across the cortex. These adaptive changes likely result from plasticity mechanisms such as synaptic scaling and are linked to EI homeostasis, providing a possible target for future therapeutic strategies in the process of rehabilitation. In addition, we address the difficulty of simultaneously studying these multiscale processes by presenting recent advances in large-scale modeling of the human cortex in the contexts of stroke and EI homeostasis, suggesting computational modeling as a powerful tool to tie the meso- and macro-scale processes of recovery in stroke patients.

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.

Parcellation-induced variation of empirical and simulated brain connectomes at group and subject levels

Recent developments of whole-brain models have demonstrated their potential when investigating resting-state brain activity. However, it has not been systematically investigated how alternating derivations of the empirical structural and functional connectivity, serving as the model input, from MRI data influence modeling results. Here, we study the influence from one major element: the brain parcellation scheme that reduces the dimensionality of brain networks by grouping thousands of voxels into a few hundred brain regions. We show graph-theoretical statistics derived from the empirical data and modeling results exhibiting a high heterogeneity across parcellations. Furthermore, the network properties of empirical brain connectomes explain the lion’s share of the variance in the modeling results with respect to the parcellation variation. Such a clear-cut relationship is not observed at the subject-resolved level per parcellation. Finally, the graph-theoretical statistics of the simulated connectome correlate with those of the empirical functional connectivity across parcellations. However, this relation is not one-to-one, and its precision can vary between models. Our results imply that network properties of both empirical connectomes can explain the goodness-of-fit of whole-brain models to empirical data at a global group level but not at a single-subject level, which provides further insights into the personalization of whole-brain models.

The structural and functional connectivities of the brain, which reflect the anatomical connections of axonal bundles and the amount of coactivation between brain regions, respectively, only weakly correlate with each other. In order to enhance and investigate this relationship, large-scale whole-brain dynamical models were involved in this branch of research. However, how the definitions of the brain regions parcellated according to a so-called brain atlas influence these models has so far not been systematically assessed. In this article, we show that this influence can be large, and link group-averaged, atlas-induced deviations to network properties extracted from both types of connectivity. Additionally, we demonstrate that the same association does not apply to subject-specific variations. These results may contribute to the further personalization of the whole-brain models.

On a Quantitative Approach to Clinical Neuroscience in Psychiatry: Lessons from the Kuramoto Model

The human brain is a complex system comprising subregions that dynamically exchange information between its various parts through synchronization. These dynamic, complex interactions ultimately play a role in perception, emotion, cognition, and behavior, as well as in various maladaptive neurologic and psychiatric processes. It is therefore important to understand how brain dynamics might be implicated in these processes. Over the past few years, network neuroscience and computational neuroscience have highlighted the importance of measures such as metastability (a property whereby members of an oscillating system tend to linger at the edge of synchronicity without permanently becoming synchronized) in quantifying brain dynamics. Altered metastability has been implicated in various psychiatric illnesses, such as traumatic brain injury and Alzheimer's disease. Computational models, which range in complexity, have been used to assess how various parameters affect metastability, synchronization, and functional connectivity. These models, though limited, can act as heuristics in understanding brain dynamics. This article (aimed at the clinical psychiatrist who might not possess an extensive mathematical background) is intended to provide a brief and qualitative summary of studies that have used a specific, highly simplified computational model of coupled oscillators (Kuramoto model) for understanding brain dynamics-which might bear some relevance to clinical psychiatry.

Emergence of canonical functional networks from the structural connectome

How do functional brain networks emerge from the underlying wiring of the brain? We examine how resting-state functional activation patterns emerge from the underlying connectivity and length of white matter fibers that constitute its “structural connectome”. By introducing realistic signal transmission delays along fiber projections, we obtain a complex-valued graph Laplacian matrix that depends on two parameters: coupling strength and oscillation frequency. This complex Laplacian admits a complex-valued eigen-basis in the frequency domain that is highly tunable and capable of reproducing the spatial patterns of canonical functional networks without requiring any detailed neural activity modeling. Specific canonical functional networks can be predicted using linear superposition of small subsets of complex eigenmodes. Using a novel parameter inference procedure we show that the complex Laplacian outperforms the real-valued Laplacian in predicting functional networks. The complex Laplacian eigenmodes therefore constitute a tunable yet parsimonious substrate on which a rich repertoire of realistic functional patterns can emerge. Although brain activity is governed by highly complex nonlinear processes and dense connections, our work suggests that simple extensions of linear models to the complex domain effectively approximate rich macroscopic spatial patterns observable on BOLD fMRI.

Tractography density affects whole-brain structural architecture and resting-state dynamical modeling

Dynamical modeling of the resting-state brain dynamics essentially relies on the empirical neuroimaging data utilized for the model derivation and validation. There is however still no standardized data processing for magnetic resonance imaging pipelines and the structural and functional connectomes involved in the models. In this study, we thus address how the parameters of diffusion-weighted data processing for structural connectivity (SC) can influence the validation results of the whole-brain mathematical models informed by SC. For this, we introduce a set of simulation conditions including the varying number of total streamlines of the whole-brain tractography (WBT) used for extraction of SC, cortical parcellations based on functional and anatomical brain properties and distinct model fitting modalities. The main objective of this study is to explore how the quality of the model validation can vary across the considered simulation conditions. We observed that the graph-theoretical network properties of structural connectome can be affected by varying tractography density and strongly relate to the model performance. We also found that the optimal number of the total streamlines of WBT can vary for different brain atlases. Consequently, we suggest a way how to improve the model performance based on the network properties and the optimal parameter configurations from multiple WBT conditions. Furthermore, the population of subjects can be stratified into subgroups with divergent behaviors induced by the varying WBT density such that different recommendations can be made with respect to the data processing for individual subjects and brain parcellations.

Computational Models in Electroencephalography

Computational models lie at the intersection of basic neuroscience and healthcare applications because they allow researchers to test hypotheses in silico and predict the outcome of experiments and interactions that are very hard to test in reality. Yet, what is meant by “computational model” is understood in many different ways by researchers in different fields of neuroscience and psychology, hindering communication and collaboration. In this review, we point out the state of the art of computational modeling in Electroencephalography (EEG) and outline how these models can be used to integrate findings from electrophysiology, network-level models, and behavior. On the one hand, computational models serve to investigate the mechanisms that generate brain activity, for example measured with EEG, such as the transient emergence of oscillations at different frequency bands and/or with different spatial topographies. On the other hand, computational models serve to design experiments and test hypotheses in silico. The final purpose of computational models of EEG is to obtain a comprehensive understanding of the mechanisms that underlie the EEG signal. This is crucial for an accurate interpretation of EEG measurements that may ultimately serve in the development of novel clinical applications.

Frequency-Resolved Functional Connectivity: Role of Delay and the Strength of Connections

The brain functional network extracted from the BOLD signals reveals the correlated activity of the different brain regions, which is hypothesized to underlie the integration of the information across functionally specialized areas. Functional networks are not static and change over time and in different brain states, enabling the nervous system to engage and disengage different local areas in specific tasks on demand. Due to the low temporal resolution, however, BOLD signals do not allow the exploration of spectral properties of the brain dynamics over different frequency bands which are known to be important in cognitive processes. Recent studies using imaging tools with a high temporal resolution has made it possible to explore the correlation between the regions at multiple frequency bands. These studies introduce the frequency as a new dimension over which the functional networks change, enabling brain networks to transmit multiplex of information at any time. In this computational study, we explore the functional connectivity at different frequency ranges and highlight the role of the distance between the nodes in their correlation. We run the generalized Kuramoto model with delayed interactions on top of the brain's connectome and show that how the transmission delay and the strength of the connections, affect the correlation between the pair of nodes over different frequency bands.

Lesion Quantification Toolkit: A MATLAB software tool for estimating grey matter damage and white matter disconnections in patients with focal brain lesions

Lesion studies are an important tool for cognitive neuroscientists and neurologists. However, while brain lesion studies have traditionally aimed to localize neurological symptoms to specific anatomical loci, a growing body of evidence indicates that neurological diseases such as stroke are best conceptualized as brain network disorders. While researchers in the fields of neuroscience and neurology are therefore increasingly interested in quantifying the effects of focal brain lesions on the white matter connections that form the brain's structural connectome, few dedicated tools exist to facilitate this endeavor. Here, we present the Lesion Quantification Toolkit, a publicly available MATLAB software package for quantifying the structural impacts of focal brain lesions. The Lesion Quantification Toolkit uses atlas-based approaches to estimate parcel-level grey matter lesion loads and multiple measures of white matter disconnection severity that include tract-level disconnection measures, voxel-wise disconnection maps, and parcel-wise disconnection matrices. The toolkit also estimates lesion-induced increases in the lengths of the shortest structural paths between parcel pairs, which provide information about changes in higher-order structural network topology. We describe in detail each of the different measures produced by the toolkit, discuss their applications and considerations relevant to their use, and perform example analyses using real behavioral data collected from sub-acute stroke patients. We show that analyses performed using the different measures produced by the toolkit produce results that are highly consistent with results that have been reported in the prior literature, and we demonstrate the consistency of results obtained from analyses conducted using the different disconnection measures produced by the toolkit. We anticipate that the Lesion Quantification Toolkit will empower researchers to address research questions that would be difficult or impossible to address using traditional lesion analyses alone, and ultimately, lead to advances in our understanding of how white matter disconnections contribute to the cognitive, behavioral, and physiological consequences of focal brain lesions.

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.

Investigating the network consequences of focal brain lesions through comparisons of real and simulated lesions

Given the increased interest in the functional human connectome, a number of computer simulation studies have sought to develop a better quantitative understanding of the effects of focal lesions on the brain’s functional network organization. However, there has been little work evaluating the predictions of this simulation work vis a vis real lesioned connectomes. One of the few relevant studies reported findings from real chronic focal lesions that only partially confirmed simulation predictions. We hypothesize that these discrepancies arose because although the effects of focal lesions likely consist of two components: short-term node subtraction and long-term network re-organization, previous simulation studies have primarily modeled only the short-term consequences of the subtraction of lesioned nodes and their connections. To evaluate this hypothesis, we compared network properties (modularity, participation coefficient, within-module degree) between real functional connectomes obtained from chronic stroke participants and “pseudo-lesioned” functional connectomes generated by subtracting the same sets of lesioned nodes/connections from healthy control connectomes. We found that, as we hypothesized, the network properties of real-lesioned connectomes in chronic stroke differed from those of the pseudo-lesioned connectomes which instantiated only the short-term consequences of node subtraction. Reflecting the long-term consequences of focal lesions, we found re-organization of the neurotopography of global and local hubs in the real but not the pseudo-lesioned connectomes. We conclude that the long-term network re-organization that occurs in response to focal lesions involves changes in functional connectivity within the remaining intact neural tissue that go well beyond the short-term consequences of node subtraction.

Damage to the structural connectome reflected in resting-state fMRI functional connectivity

The relationship between structural and functional connectivity has been mostly examined in intact brains. Fewer studies have examined how differences in structure as a result of injury alters function. In this study we analyzed the relationship of structure to function across patients with stroke among whom infarcts caused heterogenous structural damage. We estimated relationships between distinct brain regions of interest (ROIs) from functional MRI in two pipelines. In one analysis pipeline, we measured functional connectivity by using correlation and partial correlation between 114 cortical ROIs. We found fMRI-BOLD partial correlation was altered at more edges as a function of the structural connectome (SC) damage, relative to the correlation. In a second analysis pipeline, we limited our analysis to fMRI correlations between pairs of voxels for which we possess SC information. We found that voxel-level functional connectivity showed the effect of structural damage that we could not see when examining correlations between ROIs. Further, the effects of structural damage on functional connectivity are consistent with a model of functional connectivity, diffusion, which expects functional connectivity to result from activity spreading over multiple edge anatomical paths.

White Matter-Based Structural Brain Network of Major Depression

Major depressive disorder (MDD) is frequently characterized as a disorder of the disconnection syndrome. Diffusion tensor imaging (DTI) has played a critical role in supporting this view, with much investigation providing a large amount of evidence of structural connectivity abnormalities in the disorder. Recent research on the human connectome combined neuroimaging techniques with graph theoretic methods to highlight the disrupted topological properties of large-scale structural brain networks under depression, involving global metrics (e.g., global and local efficiencies), and local nodal properties (e.g., degree and betweenness), as well as other related metrics, including a modular structure, assortativity, and (rich) hubs. Here, we review the studies of white matter networks in the case of MDD with the application of these techniques, focusing principally on the consistent findings and the clinical significance of DTI-based network research, while discussing the key methodological issues that frequently arise in the field. The already published literature shows that MDD is associated with a widespread structural connectivity deficit. Topological alteration of structural brain networks in the case of MDD points to decreased overall connectivity strength and reduced global efficiency as well as decreased small-worldness and network resilience. These structural connectivity disturbances entail potential functional consequences, although the relationship between the two is very sophisticated and requires further investigation. In summary, the present study comprehensively maps the structural connectomic disturbances in patients with MDD across the entire brain, which adds important weight to the view suggesting connectivity abnormalities of this disorder and highlights the potential of network properties as diagnostic biomarkers in the psychoradiology field. Several common methodological issues of the study of DTI-based networks are discussed, involving sample heterogeneity and fiber crossing problems and the tractography algorithms. Finally, suggestions for future perspectives, including imaging multimodality, a longitudinal study and computational connectomics, in the further study of white matter networks under depression are given. Surmounting these challenges and advancing the research methods will be required to surpass the simple mapping of connectivity changes to illuminate the underlying psychiatric pathological mechanism.

A multi-scale cortical wiring space links cellular architecture and functional dynamics in the human brain

The vast net of fibres within and underneath the cortex is optimised to support the convergence of different levels of brain organisation. Here, we propose a novel coordinate system of the human cortex based on an advanced model of its connectivity. Our approach is inspired by seminal, but so far largely neglected models of cortico-cortical wiring established by postmortem anatomical studies and capitalises on cutting-edge in vivo neuroimaging and machine learning. The new model expands the currently prevailing diffusion magnetic resonance imaging (MRI) tractography approach by incorporation of additional features of cortical microstructure and cortico-cortical proximity. Studying several datasets and different parcellation schemes, we could show that our coordinate system robustly recapitulates established sensory-limbic and anterior-posterior dimensions of brain organisation. A series of validation experiments showed that the new wiring space reflects cortical microcircuit features (including pyramidal neuron depth and glial expression) and allowed for competitive simulations of functional connectivity and dynamics based on resting-state functional magnetic resonance imaging (rs-fMRI) and human intracranial electroencephalography (EEG) coherence. Our results advance our understanding of how cell-specific neurobiological gradients produce a hierarchical cortical wiring scheme that is concordant with increasing functional sophistication of human brain organisation. Our evaluations demonstrate the cortical wiring space bridges across scales of neural organisation and can be easily translated to single individuals.

Structural Disconnections Explain Brain Network Dysfunction after Stroke

Stroke causes focal brain lesions that disrupt functional connectivity (FC), a measure of activity synchronization, throughout distributed brain networks. It is often assumed that FC disruptions reflect damage to specific cortical regions. However, an alternative explanation is that they reflect the structural disconnection (SDC) of white matter pathways. Here, we compare these explanations using data from 114 stroke patients. Across multiple analyses, we find that SDC measures outperform focal damage measures, including damage to putative critical cortical regions, for explaining FC disruptions associated with stroke. We also identify a core mode of structure-function covariation that links the severity of interhemispheric SDCs to widespread FC disruptions across patients and that correlates with deficits in multiple behavioral domains. We conclude that a lesion's impact on the structural connectome is what determines its impact on FC and that interhemispheric SDCs may play a particularly important role in mediating FC disruptions after stroke.

Experimental and Computational Study on Motor Control and Recovery After Stroke: Toward a Constructive Loop Between Experimental and Virtual Embodied Neuroscience

Being able to replicate real experiments with computational simulations is a unique opportunity to refine and validate models with experimental data and redesign the experiments based on simulations. However, since it is technically demanding to model all components of an experiment, traditional approaches to modeling reduce the experimental setups as much as possible. In this study, our goal is to replicate all the relevant features of an experiment on motor control and motor rehabilitation after stroke. To this aim, we propose an approach that allows continuous integration of new experimental data into a computational modeling framework. First, results show that we could reproduce experimental object displacement with high accuracy via the simulated embodiment in the virtual world by feeding a spinal cord model with experimental registration of the cortical activity. Second, by using computational models of multiple granularities, our preliminary results show the possibility of simulating several features of the brain after stroke, from the local alteration in neuronal activity to long-range connectivity remodeling. Finally, strategies are proposed to merge the two pipelines. We further suggest that additional models could be integrated into the framework thanks to the versatility of the proposed approach, thus allowing many researchers to achieve continuously improved experimental design.

Activity-dependent myelination: A glial mechanism of oscillatory self-organization in large-scale brain networks

Communication and oscillatory synchrony between distributed neural populations are believed to play a key role in multiple cognitive and neural functions. These interactions are mediated by long-range myelinated axonal fiber bundles, collectively termed as white matter. While traditionally considered to be static after development, white matter properties have been shown to change in an activity-dependent way through learning and behavior-a phenomenon known as white matter plasticity. In the central nervous system, this plasticity stems from oligodendroglia, which form myelin sheaths to regulate the conduction of nerve impulses across the brain, hence critically impacting neural communication. We here shift the focus from neural to glial contribution to brain synchronization and examine the impact of adaptive, activity-dependent changes in conduction velocity on the large-scale phase synchronization of neural oscillators. Using a network model based on primate large-scale white matter neuroanatomy, our computational and mathematical results show that such plasticity endows white matter with self-organizing properties, where conduction delay statistics are autonomously adjusted to ensure efficient neural communication. Our analysis shows that this mechanism stabilizes oscillatory neural activity across a wide range of connectivity gain and frequency bands, making phase-locked states more resilient to damage as reflected by diffuse decreases in connectivity. Critically, our work suggests that adaptive myelination may be a mechanism that enables brain networks with a means of temporal self-organization, resilience, and homeostasis.

Brain network constraints and recurrent neural networks reproduce unique trajectories and state transitions seen over the span of minutes in resting-state fMRI

Large-scale patterns of spontaneous whole-brain activity seen in resting-state functional magnetic resonance imaging (rs-fMRI) are in part believed to arise from neural populations interacting through the structural network (Honey, Kötter, Breakspear, & Sporns, 2007). Generative models that simulate this network activity, called brain network models (BNM), are able to reproduce global averaged properties of empirical rs-fMRI activity such as functional connectivity (FC) but perform poorly in reproducing unique trajectories and state transitions that are observed over the span of minutes in whole-brain data (Cabral, Kringelbach, & Deco, 2017; Kashyap & Keilholz, 2019). The manuscript demonstrates that by using recurrent neural networks, it can fit the BNM in a novel way to the rs-fMRI data and predict large amounts of variance between subsequent measures of rs-fMRI data. Simulated data also contain unique repeating trajectories observed in rs-fMRI, called quasiperiodic patterns (QPP), that span 20 s and complex state transitions observed using k-means analysis on windowed FC matrices (Allen et al., 2012; Majeed et al., 2011). Our approach is able to estimate the manifold of rs-fMRI dynamics by training on generating subsequent time points, and it can simulate complex resting-state trajectories better than the traditional generative approaches.

Brain network models have become a promising theoretical framework for simulating signals that are representative of whole-brain activity such as resting-state fMRI. However, it has been difficult to compare the complex brain activity obtained from simulations with empirical data. Previous studies have used simple metrics to characterize coordination between regions such as functional connectivity. In this manuscript, we extend this work by utilizing modern machine learning techniques to fit the brain network models to observed data and train on the mismatch between the model and observed signal. Our results show that our system training on these new metrics generalizes to a system that is able to reproduce trajectories and complex state transitions seen in rs-fMRI over the span of minutes. Our results will be useful in constraining and developing more realistic simulations of whole-brain activity.

Connections, Tracts, Fractals, and the Rest: A Working Guide to Network and Connectivity Studies in Neurosurgery

Brain mapping and connectomics can probe networks that span the entire brain, producing a diverse range of outputs for probing specific clinically relevant questions. The potential for understanding the effect of focal lesions on brain function, cognition, and plasticity abounds, any one of which would likely yield more effective and safer neurosurgical strategies. However, the possibilities of advanced magnetic resonance imaging and connectomics have been somewhat underused in neurosurgery, arising from actual or perceived difficulties in either application or analysis. The present review builds on previous work describing the theoretical attractions of connectomics to deliberate on the practical details of performing high-quality connectomics studies in neurosurgery. First, the data and methods involved in deriving connectomics models will be considered, specifically for the purpose of determining the nature of inferences that can be made subsequently. Next, a selection of key analysis methods will be explored using practical examples that illustrate their effective implementation and the insights that can be gleaned. The principles of study design will be introduced, including analysis tips and methods for making efficient use of available resources. Finally, a review of the best research practices for neuroimaging studies will be discussed, including principles of open access data sharing, study preregistration, and methods for improving replicability. Ultimately, we hope readers will be better placed to appraise the current connectomics studies in neurosurgery and empowered to develop their own high-quality studies, both of which are key steps in realizing the true potential of connectomics and advanced neuroimaging analyses in general.

Predisposition for delirium and EEG characteristics

OBJECTIVE

Delirium is associated with increased electroencephalography (EEG) delta activity, decreased connectivity strength and decreased network integration. To improve our understanding of development of delirium, we studied whether non-delirious individuals with a predisposition for delirium also show these EEG abnormalities.

METHODS

Elderly subjects (N = 206) underwent resting-state EEG measurements and were assessed on predisposing delirium risk factors, i.e. older age, alcohol misuse, cognitive impairment, depression, functional impairment, history of stroke and physical status. Delirium-related EEG characteristics of interest were relative delta power, alpha connectivity strength (phase lag index) and network integration (minimum spanning tree leaf fraction). Linear regression analyses were used to investigate the relation between predisposing delirium risk factors and EEG characteristics that are associated with delirium, adjusting for confounding and multiple testing.

RESULTS

Functional impairment was related to a decrease in connectivity strength (adjusted R² = 0.071, β = 0.201, p < 0.05). None of the other risk factors had significant influence on EEG delta power, connectivity strength or network integration.

CONCLUSIONS

Functional impairment seems to be associated with decreased alpha connectivity strength. Other predisposing risk factors for delirium had no effect on the studied EEG characteristics.

SIGNIFICANCE

Predisposition for delirium is not consistently related to EEG characteristics that can be found during delirium.

Oscillotherapeutics - Time-targeted interventions in epilepsy and beyond

Oscillatory brain activities support many physiological functions from motor control to cognition. Disruptions of the normal oscillatory brain activities are commonly observed in neurological and psychiatric disorders including epilepsy, Parkinson's disease, Alzheimer's disease, schizophrenia, anxiety/trauma-related disorders, major depressive disorders, and drug addiction. Therefore, these disorders can be considered as common oscillation defects despite having distinct behavioral manifestations and genetic causes. Recent technical advances of neuronal activity recording and analysis have allowed us to study the pathological oscillations of each disorder as a possible biomarker of symptoms. Furthermore, recent advances in brain stimulation technologies enable time- and space-targeted interventions of the pathological oscillations of both neurological disorders and psychiatric disorders as possible targets for regulating their symptoms.