Relating structure and function in the human brain: relative contributions of anatomy, stationary dynamics, and non-stationarities

A general framework for characterizing optimal communication in brain networks

Efficient communication in brain networks is foundational for cognitive function and behavior. However, how communication efficiency is defined depends on the assumed model of signaling dynamics, e.g., shortest path signaling, random walker navigation, broadcasting, and diffusive processes. Thus, a general and model-agnostic framework for characterizing optimal neural communication is needed. We address this challenge by assigning communication efficiency through a virtual multi-site lesioning regime combined with game theory, applied to large-scale models of human brain dynamics. Our framework quantifies the exact influence each node exerts over every other, generating optimal influence maps given the underlying model of neural dynamics. These descriptions reveal how communication patterns unfold if regions are set to maximize their influence over one another. Comparing these maps with a variety of brain communication models showed that optimal communication closely resembles a broadcasting regime in which regions leverage multiple parallel channels for information dissemination. Moreover, we found that the brain's most influential regions are its rich-club, exploiting their topological vantage point by broadcasting across numerous pathways that enhance their reach even if the underlying connections are weak. Altogether, our work provides a rigorous and versatile framework for characterizing optimal brain communication, and uncovers the most influential brain regions, and the topological features underlying their influence.

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.

Abnormal Alterations of the White Matter Structural Network in Patients with Herpes Zoster and Postherpetic Neuralgia

PHN is one of the most common clinical complications of herpes zoster (HZ), the pathogenesis of which is unclear and poorly treated clinically, and many studies now suggest that postherpetic neuralgia (PHN) pain may be related to central neurologic mechanisms. This study aimed to investigate the white matter structural networks and changes in the organization of the rich-club in HZ and PHN. Diffusion imaging (DTI) data from 89 PHN patients, 76 HZ patients, and 66 healthy controls (HCs) were used to construct corresponding structural networks. Using graph-theoretic analysis, changes in the overall and local characteristics of the structural networks and rich-club organization were analyzed, and their correlations with clinical scales were analyzed. Compared with HCs, PHN patients had reduced global efficiency (Eg), reduced local efficiency (Eloc), a reduced clustering coefficient (Cp), a longer characteristic path length (Lp), and reduced nodal efficiency (Ne) in several brain regions, including the right posterior cingulate gyrus, the right supraoccipital gyrus, the bilateral postcentral gyrus, and the right precuneus; HZ patients had reduced Eg, a longer Lp, and reduced right orbital frontalis suprachiasmatic Ne. Moreover, HZ and PHN patients showed a significant reduction in the strength of rich-club connections. Compared with HZ patients, the intensities of the rich-club and feeder connections were lower in the PHN patients. Moreover, the changes in the structural networks and rich-club organization topology indices of the patients in the HZ and PHN patients were significantly correlated with disease duration, pain scores, and emotional changes. The structural networks of HZ and PHN patients exhibited reduced network transmission efficiency and rich-club connectivity, possibly due to structural damage to the white matter, and this was more obvious in PHN patients. The rich-club connectivity of HZ patients showed incomplete compensation in the acute pain stage.

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

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

A spatially constrained independent component analysis jointly informed by structural and functional network connectivity

There are a growing number of neuroimaging studies motivating joint structural and functional brain connectivity. The brain connectivity of different modalities provides an insight into brain functional organization by leveraging complementary information, especially for brain disorders such as schizophrenia. In this paper, we propose a multimodal independent component analysis (ICA) model that utilizes information from both structural and functional brain connectivity guided by spatial maps to estimate intrinsic connectivity networks (ICNs). Structural connectivity is estimated through whole-brain tractography on diffusion-weighted MRI (dMRI), while functional connectivity is derived from resting-state functional MRI (rs-fMRI). The proposed structural-functional connectivity and spatially constrained ICA (sfCICA) model estimates ICNs at the subject level using a multiobjective optimization framework. We evaluated our model using synthetic and real datasets (including dMRI and rs-fMRI from 149 schizophrenia patients and 162 controls). Multimodal ICNs revealed enhanced functional coupling between ICNs with higher structural connectivity, improved modularity, and network distinction, particularly in schizophrenia. Statistical analysis of group differences showed more significant differences in the proposed model compared with the unimodal model. In summary, the sfCICA model showed benefits from being jointly informed by structural and functional connectivity. These findings suggest advantages in simultaneously learning effectively and enhancing connectivity estimates using structural connectivity.

Comparing structure-function relationships in brain networks using EEG and fNIRS

Identifying relationships between structural and functional networks is crucial for understanding the large-scale organization of the human brain. The potential contribution of emerging techniques like functional near-infrared spectroscopy to investigate the structure-functional relationship has yet to be explored. In our study, using simultaneous Electroencephalography (EEG) and Functional near-infrared spectroscopy (fNIRS) recordings from 18 subjects, we characterize global and local structure-function coupling using source-reconstructed EEG and fNIRS signals in both resting state and motor imagery tasks, as this relationship during task periods remains underexplored. Employing the mathematical framework of graph signal processing, we investigate how this relationship varies across electrical and hemodynamic networks and different brain states. Results show that fNIRS structure-function coupling resembles slower-frequency EEG coupling at rest, with variations across brain states and oscillations. Locally, the relationship is heterogeneous, with greater coupling in the sensory cortex and increased decoupling in the association cortex, following the unimodal to transmodal gradient. Discrepancies between EEG and fNIRS are noted, particularly in the frontoparietal network. Cross-band representations of neural activity revealed lower correspondence between electrical and hemodynamic activity in the transmodal cortex, irrespective of brain state while showing specificity for the somatomotor network during a motor imagery task. Overall, these findings initiate a multimodal comprehension of structure-function relationship and brain organization when using affordable functional brain imaging.

A within-subject voxel-wise constant-block partial least squares correlation method to explore MRI-based brain structure-function relationship

The brain structure-function relationship is crucial to how the human brain works under normal or diseased conditions. Exploring such a relationship is challenging when using the 3-dimensional magnetic resonance imaging (MRI) functional dataset which is temporal dynamic and the structural MRI which is static. Partial Least Squares Correlation (PLSC) is one of the classical methods for exploring the joint spatial and temporal relationship. The goal of PLSC is to identify covarying patterns via linear voxel-wise combinations in each of the structural and functional data sets to maximize the covariance. However, existing PLSC cannot adequately deal with the unmatched temporal dimensions between structural and functional data sets. We proposed a new alternative variant of the PLSC, termed within-subject, voxel-wise, and constant-block PLSC, to address this problem. To validate our method, we used two data sets with weak and strong relationships in simulated data. Additionally, the analysis of real brain data was carried out based on gray matter volume hubs derived from sMRI and whole-brain voxel-wise measures from resting-state fMRI for aging effect based on healthy subjects aged 16-85 years. Our results showed that our constant-block PLSC can detect weak structure-function relationships and has better robustness to noise. In fact, it adequately unearthed the true simulated number of significant and more accurate latent variables for the simulated data and more meaningful LVs for the real data, with covariance improvement from 16.19 to 41.48% (simulated) and 13.29-53.68% (real data), respectively. More interestingly in the real data analysis, our method identified simultaneously the well-known brain networks such as the default mode, sensorimotor, auditory, and dorsal attention networks both functionally and structurally, implying the hubs we derived from gray matter volumes are the basis of brain function, supporting diverse functions. Constant-block PLSC is a feasible tool for analyzing the brain structure-function relationship.

A spatially constrained independent component analysis jointly informed by structural and functional network connectivity

There are a growing number of neuroimaging studies motivating joint structural and functional brain connectivity. Brain connectivity of different modalities provides insight into brain functional organization by leveraging complementary information, especially for brain disorders such as schizophrenia. In this paper, we propose a multi-modal independent component analysis (ICA) model that utilizes information from both structural and functional brain connectivity guided by spatial maps to estimate intrinsic connectivity networks (ICNs). Structural connectivity is estimated through whole-brain tractography on diffusion-weighted MRI (dMRI), while functional connectivity is derived from resting-state functional MRI (rs-fMRI). The proposed structural-functional connectivity and spatially constrained ICA (sfCICA) model estimates ICNs at the subject level using a multi-objective optimization framework. We evaluated our model using synthetic and real datasets (including dMRI and rs-fMRI from 149 schizophrenia patients and 162 controls). Multi-modal ICNs revealed enhanced functional coupling between ICNs with higher structural connectivity, improved modularity, and network distinction, particularly in schizophrenia. Statistical analysis of group differences showed more significant differences in the proposed model compared to the unimodal model. In summary, the sfCICA model showed benefits from being jointly informed by structural and functional connectivity. These findings suggest advantages in simultaneously learning effectively and enhancing connectivity estimates using structural connectivity.

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

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

Structural-functional brain network coupling predicts human cognitive ability

Individual differences in general cognitive ability (GCA) have a biological basis within the structure and function of the human brain. Network neuroscience investigations revealed neural correlates of GCA in structural as well as in functional brain networks. However, whether the relationship between structural and functional networks, the structural-functional brain network coupling (SC-FC coupling), is related to individual differences in GCA remains an open question. We used data from 1030 adults of the Human Connectome Project, derived structural connectivity from diffusion weighted imaging, functional connectivity from resting-state fMRI, and assessed GCA as a latent g-factor from 12 cognitive tasks. Two similarity measures and six communication measures were used to model possible functional interactions arising from structural brain networks. SC-FC coupling was estimated as the degree to which these measures align with the actual functional connectivity, providing insights into different neural communication strategies. At the whole-brain level, higher GCA was associated with higher SC-FC coupling, but only when considering path transitivity as neural communication strategy. Taking region-specific variations in the SC-FC coupling strategy into account and differentiating between positive and negative associations with GCA, allows for prediction of individual cognitive ability scores in a cross-validated prediction framework (correlation between predicted and observed scores: r = 0.25, p < .001). The same model also predicts GCA scores in a completely independent sample (N = 567, r = 0.19, p < .001). Our results propose structural-functional brain network coupling as a neurobiological correlate of GCA and suggest brain region-specific coupling strategies as neural basis of efficient information processing predictive of cognitive ability.

Brain Anatomy in Boys with Conduct Disorder: Differences Among Aggression Subtypes

Aggression is a core feature of conduct disorder (CD), but the motivation, execution of aggression may vary. A deeper understanding of the neural substrates of aggressive behaviours is critical for effective clinical intervention. Seventy-six Boys with CD (50 with impulsive aggression (I-CD) and 26 with premeditated aggression (P-CD)) and 69 healthy controls (HCs) underwent a structural MRI scan and behavioural assessments. Whole-brain analyses revealed that, compared to HCs, the I-CD group showed significant cortical thinning in the right frontal cortex, while the P-CD group demonstrated significant folding deficits in the bilateral superior parietal cortex. Both types of aggression negatively correlated with the left amygdala volume, albeit in different ways. The present results demonstrated that the complex nature of aggression relies on differentiated anatomical substrates, highlighting the importance of exploring differential circuit-targeted interventions for CD patients.

Enhanced simulations of whole-brain dynamics using hybrid resting-state structural connectomes

The human brain, composed of billions of neurons and synaptic connections, is an intricate network coordinating a sophisticated balance of excitatory and inhibitory activities between brain regions. The dynamical balance between excitation and inhibition is vital for adjusting neural input/output relationships in cortical networks and regulating the dynamic range of their responses to stimuli. To infer this balance using connectomics, we recently introduced a computational framework based on the Ising model, which was first developed to explain phase transitions in ferromagnets, and proposed a novel hybrid resting-state structural connectome (rsSC). Here, we show that a generative model based on the Kuramoto phase oscillator can be used to simulate static and dynamic functional connectomes (FC) with rsSC as the coupling weight coefficients, such that the simulated FC aligns well with the observed FC when compared with that simulated traditional structural connectome.

Mentalizing in individuals with state and trait risk for psychosis: a systematic review

Background

Mentalization is an umbrella concept defined as the ability to interpret one's and others' mental states. Previous studies have hypothesized that mentalization may be a crucial resilience factor that significantly moderates the likelihood of developing psychotic disorders in individuals with both state and trait risk factors for the illness.

Purpose

The study reviews the role of mentalizing abilities (e.g., reflective functioning, Theory of Mind (ToM), and metacognition) in young adults with At-Risk Mental States (ARMS) and schizotypal traits. Specifically, the objective is to include articles that (a) evaluate the links between low mentalizing and both state (ARMS/CHR) and trait (schizotypy) risk for psychosis (b) compare the differences in mentalizing abilities between individuals with ARMS, schizotypy, full-blown psychosis, and healthy controls.

Method

Electronic databases (PsycINFO, PubMed, Scopus, and Google Scholar) were used to search for articles, while Rayyan was employed to facilitate the screening and selection of studies. Eligible studies are original English-language; peer-reviewed research articles on populations that met validated risk diagnostic criteria for psychosis, ARMS, and healthy controls; empirical studies evaluating the association or differences between psychotic risk and mentalizing abilities. Non-English language studies, the ones not considering state or trait risk for psychosis, and qualitative studies were excluded. After the application of the PRISMA checklist and the inclusion and exclusion criteria previously mentioned, 10 articles were extracted. The systematic review has been registered on Prospero (CRD42023397594).

Results

Low levels of reflective functioning and metacognition may predict a transition to psychosis. In addition, reflective functioning and metacognitive impairments are associated with attenuated psychotic symptoms in both state risk groups and in non-clinical individuals with schizotypal traits. Concerning ToM tasks, mixed results emerged.

Conclusion

The results obtained from the review suggest that the application of strategies to attenuate maladaptive metacognitive beliefs and low mentalization may be equally effective in improving psychotic symptoms. The assessment of mentalization and metacognition could potentially provide additional prognostic value over factors predisposing to psychosis. Good mentalization and metacognition functioning should be considered as protective factors able to minimize the transition to psychosis.

Controversies and progress on standardization of large-scale brain network nomenclature

Progress in scientific disciplines is accompanied by standardization of terminology. Network neuroscience, at the level of macroscale organization of the brain, is beginning to confront the challenges associated with developing a taxonomy of its fundamental explanatory constructs. The Workgroup for HArmonized Taxonomy of NETworks (WHATNET) was formed in 2020 as an Organization for Human Brain Mapping (OHBM)-endorsed best practices committee to provide recommendations on points of consensus, identify open questions, and highlight areas of ongoing debate in the service of moving the field toward standardized reporting of network neuroscience results. The committee conducted a survey to catalog current practices in large-scale brain network nomenclature. A few well-known network names (e.g., default mode network) dominated responses to the survey, and a number of illuminating points of disagreement emerged. We summarize survey results and provide initial considerations and recommendations from the workgroup. This perspective piece includes a selective review of challenges to this enterprise, including (1) network scale, resolution, and hierarchies; (2) interindividual variability of networks; (3) dynamics and nonstationarity of networks; (4) consideration of network affiliations of subcortical structures; and (5) consideration of multimodal information. We close with minimal reporting guidelines for the cognitive and network neuroscience communities to adopt.

Light induced spiking of proteinoids

Proteinoids, or thermal proteins, are produced by heating amino acids to their melting point and initiating polymerisation to produce polymeric chains. In aqueous solutions proteinoids swell into hollow microspheres. These microspheres produce endogenous burst of electrical potential spikes and change patterns of their electrical activity in response to illumination. We report results on a detailed investigation on the effects of white cold light on the spiking of proteinoids. We study how different types and intensities of light determine proteinoids' spiking amplitude, period, and pattern. The results of this study will be utilised to evaluate proteinoids for their potential as optical sensors and their application in unconventional computing.

Structural basis of envelope and phase intrinsic coupling modes in the cerebral cortex

Intrinsic coupling modes (ICMs) can be observed in ongoing brain activity at multiple spatial and temporal scales. Two families of ICMs can be distinguished: phase and envelope ICMs. The principles that shape these ICMs remain partly elusive, in particular their relation to the underlying brain structure. Here we explored structure-function relationships in the ferret brain between ICMs quantified from ongoing brain activity recorded with chronically implanted micro-ECoG arrays and structural connectivity (SC) obtained from high-resolution diffusion MRI tractography. Large-scale computational models were used to explore the ability to predict both types of ICMs. Importantly, all investigations were conducted with ICM measures that are sensitive or insensitive to volume conduction effects. The results show that both types of ICMs are significantly related to SC, except for phase ICMs when using measures removing zero-lag coupling. The correlation between SC and ICMs increases with increasing frequency which is accompanied by reduced delays. Computational models produced results that were highly dependent on the specific parameter settings. The most consistent predictions were derived from measures solely based on SC. Overall, the results demonstrate that patterns of cortical functional coupling as reflected in both phase and envelope ICMs are both related, albeit to different degrees, to the underlying structural connectivity in the cerebral cortex.

Estimation of Discriminative Multimodal Brain Network Connectivity Using Message-Passing-Based Nonlinear Network Fusion

Effective estimation of brain network connectivity enables better unraveling of the extraordinary complexity interactions of brain regions and helps in auxiliary diagnosis of psychiatric disorders. Considering different modalities can provide comprehensive characterizations of brain connectivity, we propose the message-passing-based nonlinear network fusion (MP-NNF) algorithm to estimate multimodal brain network connectivity. In the proposed method, the initial functional and structural networks were computed from fMRI and DTI separately. Then, we update every unimodal network iteratively, making it more similar to the others in every iteration, and finally converge to one unified network. The estimated brain connectivities integrate complementary information from multiple modalities while preserving their original structure, by adding the strong connectivities present in unimodal brain networks and eliminating the weak connectivities. The effectiveness of the method was evaluated by applying the learned brain connectivity for the classification of major depressive disorder (MDD). Specifically, 82.18% classification accuracy was achieved even with the simple feature selection and classification pipeline, which significantly outperforms the competing methods. Exploration of brain connectivity contributed to MDD identification suggests that the proposed method not only improves the classification performance but also was sensitive to critical disease-related neuroimaging biomarkers.

Dynamic sensitivity analysis: Defining personalised strategies to drive brain state transitions via whole brain modelling

Traditionally, in neuroimaging, model-free analyses are used to find significant differences between brain states via signal detection theory. Depending on the a priori assumptions about the underlying data, different spatio-temporal features can be analysed. Alternatively, model-based techniques infer features from the data and compare significance from model parameters. However, to assess transitions from one brain state to another remains a challenge in current paradigms. Here, we introduce a "Dynamic Sensitivity Analysis" framework that quantifies transitions between brain states in terms of stimulation ability to rebalance spatio-temporal brain activity towards a target state such as healthy brain dynamics. In practice, it means building a whole-brain model fitted to the spatio-temporal description of brain dynamics, and applying systematic stimulations in-silico to assess the optimal strategy to drive brain dynamics towards a target state. Further, we show how Dynamic Sensitivity Analysis extends to various brain stimulation paradigms, ultimately contributing to improving the efficacy of personalised clinical interventions.

Strength-dependent perturbation of whole-brain model working in different regimes reveals the role of fluctuations in brain dynamics

Despite decades of research, there is still a lack of understanding of the role and generating mechanisms of the ubiquitous fluctuations and oscillations found in recordings of brain dynamics. Here, we used whole-brain computational models capable of presenting different dynamical regimes to reproduce empirical data's turbulence level. We showed that the model's fluctuations regime fitted to turbulence more faithfully reproduces the empirical functional connectivity compared to oscillatory and noise regimes. By applying global and local strength-dependent perturbations and subsequently measuring the responsiveness of the model, we revealed each regime's computational capacity demonstrating that brain dynamics is shifted towards fluctuations to provide much-needed flexibility. Importantly, fluctuation regime stimulation in a brain region within a given resting state network modulates that network, aligned with previous empirical and computational studies. Furthermore, this framework generates specific, testable empirical predictions for human stimulation studies using strength-dependent rather than constant perturbation. Overall, the whole-brain models fitted to the level of empirical turbulence together with functional connectivity unveil that the fluctuation regime best captures empirical data, and the strength-dependent perturbative framework demonstrates how this regime provides maximal flexibility to the human brain.

Structural-Functional Connectivity Bandwidth of the Human Brain

BACKGROUND

The human brain is a complex network that seamlessly manifests behaviour and cognition. This network comprises neurons that directly, or indirectly mediate communication between brain regions. Here, we show how multilayer/multiplex network analysis provides a suitable framework to uncover the throughput of structural connectivity (SC) to mediate information transfer-giving rise to functional connectivity (FC).

METHOD

We implemented a novel method to reconcile SC and FC using diffusion and resting-state functional MRI connectivity data from 484 subjects (272 females, 212 males; age = 29.15 ± 3.47) from the Human Connectome Project. First, we counted the number of direct and indirect structural paths that mediate FC. FC nodes with indirect SC paths were then weighted according to their least restrictive SC path. We refer to this as SC-FC Bandwidth. We then mapped paths with the highest SC-FC Bandwidth across 7 canonical resting-state networks.

FINDINGS

We found that most pairs of FC nodes were connected by SC paths of length two and three (SC paths of length >5 were virtually non-existent). Direct SC-FC connections accounted for only 10% of all SC-FC connections. The majority of FC nodes without a direct SC path were mediated by a proportion of two (44%) or three SC path lengths (39%). Only a small proportion of FC nodes were mediated by SC path lengths of four (5%). We found high-bandwidth direct SC-FC connections show dense intra- and sparse inter-network connectivity, with a bilateral, anteroposterior distribution. High bandwidth SC-FC triangles have a right superomedial distribution within the somatomotor network. High-bandwidth SC-FC quads have a superoposterior distribution within the default mode network.

CONCLUSION

Our method allows the measurement of indirect SC-FC using undirected, weighted graphs derived from multimodal MRI data in order to map the location and throughput of SC to mediate FC. An extension of this work may be to explore how SC-FC Bandwidth changes over time, relates to cognition/behavior, and if this measure reflects a marker of neurological injury or psychiatric disorders.

What lies underneath: Precise classification of brain states using time-dependent topological structure of dynamics

The self-organising global dynamics underlying brain states emerge from complex recursive nonlinear interactions between interconnected brain regions. Until now, most efforts of capturing the causal mechanistic generating principles have supposed underlying stationarity, being unable to describe the non-stationarity of brain dynamics, i.e. time-dependent changes. Here, we present a novel framework able to characterise brain states with high specificity, precisely by modelling the time-dependent dynamics. Through describing a topological structure associated to the brain state at each moment in time (its attractor or ‘information structure’), we are able to classify different brain states by using the statistics across time of these structures hitherto hidden in the neuroimaging dynamics. Proving the strong potential of this framework, we were able to classify resting-state BOLD fMRI signals from two classes of post-comatose patients (minimally conscious state and unresponsive wakefulness syndrome) compared with healthy controls with very high precision.

Brain states emerge through continuously evolving dynamics of brain networks. The usual way of modelling these dynamics is by using stationary systems: there is one structure (attractor) which is responsible of the brain dynamics. We adopt a different approach by characterising the brain activity through a landscape of informational structures (IS) changing in time. We use a model transformation procedure to produce these structures and look at several properties related to how the different brain networks interact not in the observed resting-state fMRI signal but in the information structure underlying it. These properties provide measures strongly related with relevant characteristics of conscious activity, such as metastability, information integration or synchronisation. The distribution of IS measures is studied for healthy controls (HC) and two groups of post-comatose patients with disorders of consciousness (DOC): minimally conscious state (MCS) and unresponsive wakefulness syndrome (UWS). Based on IS measures, machine learners classifiers identify the state of consciousness with an outstanding discrimination (precision of 95.6% por HC/DOC and 86.6% for MCS/UWS).

Reliability and subject specificity of personalized whole-brain dynamical models

Dynamical whole-brain models were developed to link structural (SC) and functional connectivity (FC) together into one framework. Nowadays, they are used to investigate the dynamical regimes of the brain and how these relate to behavioral, clinical and demographic traits. However, there is no comprehensive investigation on how reliable and subject specific the modeling results are given the variability of the empirical FC. In this study, we show that the parameters of these models can be fitted with a "poor" to "good" reliability depending on the exact implementation of the modeling paradigm. We find, as a general rule of thumb, that enhanced model personalization leads to increasingly reliable model parameters. In addition, we observe no clear effect of the model complexity evaluated by separately sampling results for linear, phase oscillator and neural mass network models. In fact, the most complex neural mass model often yields modeling results with "poor" reliability comparable to the simple linear model, but demonstrates an enhanced subject specificity of the model similarity maps. Subsequently, we show that the FC simulated by these models can outperform the empirical FC in terms of both reliability and subject specificity. For the structure-function relationship, simulated FC of individual subjects may be identified from the correlations with the empirical SC with an accuracy up to 70%, but not vice versa for non-linear models. We sample all our findings for 8 distinct brain parcellations and 6 modeling conditions and show that the parcellation-induced effect is much more pronounced for the modeling results than for the empirical data. In sum, this study provides an exploratory account on the reliability and subject specificity of dynamical whole-brain models and may be relevant for their further development and application. In particular, our findings suggest that the application of the dynamical whole-brain modeling should be tightly connected with an estimate of the reliability of the results.

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'.

Dynamic Connectivity Analysis Using Adaptive Window Size

In this paper, we propose a new method to study and evaluate the time-varying brain network dynamics. The proposed RICI-imCPCC method (relative intersection of confidence intervals for the imaginary component of the complex Pearson correlation coefficient) is based on an adaptive window size and the imaginary part of the complex Pearson correlation coefficient. It reduces the weaknesses of the existing method of constant sliding window analysis with narrow and wide windows. These are the low temporal precision and low reliability for short connectivity periods for wide windows, and high susceptibility to noise for narrow windows, all resulting in low estimation accuracy. The proposed method overcomes these shortcomings by dynamically adjusting the window width using the RICI rule, which is based on the statistical properties of the area around the observed sample. In this paper, we compare the RICI-imCPCC with the existing constant sliding window analysis method and describe its advantages. First, the mathematical principles are established. Then, the comparison between the existing and the proposed method using synthetic and real electroencephalography (EEG) data is presented. The results show that the proposed RICI-imCPCC method has improved temporal resolution and estimation accuracy compared to the existing method and is less affected by the noise. The estimation error energy calculated for the RICI-imCPCC method on synthetic signals was lower by a factor of 1.22 compared to the error of the constant sliding window analysis using narrow window size imCPCC, by a factor of 2.87 compared to using wide window size imCPCC, by a factor of 6.69 compared to using narrow window size wPLI, and by a factor of 4.72 compared to using wide window size wPLI. Analysis of the real signals shows the ability of the proposed method to detect a P300 response and to detect a decrease in dynamic connectivity due to desynchronization and blockage of mu-rhythms.

Forecasting brain activity based on models of spatiotemporal brain dynamics: A comparison of graph neural network architectures

Comprehending the interplay between spatial and temporal characteristics of neural dynamics can contribute to our understanding of information processing in the human brain. Graph neural networks (GNNs) provide a new possibility to interpret graph-structured signals like those observed in complex brain networks. In our study we compare different spatiotemporal GNN architectures and study their ability to model neural activity distributions obtained in functional MRI (fMRI) studies. We evaluate the performance of the GNN models on a variety of scenarios in MRI studies and also compare it to a VAR model, which is currently often used for directed functional connectivity analysis. We show that by learning localized functional interactions on the anatomical substrate, GNN-based approaches are able to robustly scale to large network studies, even when available data are scarce. By including anatomical connectivity as the physical substrate for information propagation, such GNNs also provide a multimodal perspective on directed connectivity analysis, offering a novel possibility to investigate the spatiotemporal dynamics in brain networks.

Mindfulness and Nondual Well-Being – What is the Evidence that We Can Stay Happy?

Research into subjective well-being (SWB) focuses on conducive life conditions, healthy cognitive-affective processes and adaptive behaviours, however, in this model, well-being fluctuates based on changing mental and physical phenomena. This inquiry explores the possibility that we can have a nondual experience of well-being that is unaffected by such movements and investigates if the literature supports this. The assertion in traditional mindfulness that the sense of self is constructed and responsible for such fluctuations is explored, along with what evidence there is that mindfulness practices deliver relevant cognitive and behavioural correlates associated with such a way of being. Proposed preconditions include (a) nondual awareness or the perception of no-self; (b) increased positive affect, decreased negative affect, and increased self-lessness; (c) increased capacity to maintain (or protect) well-being including heightened emotional self-regulation and resilience to aversive stimuli. Research findings provide some evidence that the sense of self can be both constructed and deconstructed, and that mindfulness training may target psychological dimensions that could contribute to an experience of well-being that transcends the impact of life conditions. Recommendations are made for a collaborative relationship between SWB research and mindfulness to expand the inquiry into possible causes and conditions of ‘nondual well-being’.

Trajectories of Mini-Mental State Examination Scores over the Lifespan in General Populations: A Systematic Review and Meta-Regression Analysis

Objectives: Over the lifespan cumulative changes to the brain lead to cognitive decline and eventually to dementia in 20-25% of adults 85 years and older. A commonly used screening tool for cognitive function is the Standard 30 point Mini-Mental State Examination (MMSE). Though the MMSE is used to screen for dementia, little is known about the changes in scores over the lifespan in general populations.Method: A systematic search was conducted using Cochrane, EMBASE, MEDLINE and PsycINFO for articles published from January 1, 2007 to May 25, 2017. Articles were included if they had a longitudinal design reporting at least two MMSE scores. A mixed-effect meta-regression analysis was conducted to examine the influence of age on MMSE score followed by a change-point regression analysis determining the age at which MMSE declines.Results: 45 articles including 58,939 individuals (age range 18-108 years, 61.2% female) summarized 222 MMSE point estimates from 35 cohorts. The meta-regression demonstrated a significant decrease in MMSE scores with higher age (regression coefficient of age: -0.10 (Confidence Interval (CI) -0.15, -0.05)). The average annual decline in MMSE scores identified by the change-point analysis at the age of 41 years and 84 years were -0.04 (95% CI: -0.05, -0.03) and -0.53 (95% CI: -0.55, -0.50), respectively.Conclusions: Between the age of 29 and 105 years MMSE scores decline, with the highest decline between age 84 and 105 years.Clinical Implementations: The use of MMSE should be restricted to higher age categories in aging general populations.

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.

On the intersection between data quality and dynamical modelling of large-scale fMRI signals

Large-scale dynamics of the brain are routinely modelled using systems of nonlinear dynamical equations that describe the evolution of population-level activity, with distinct neural populations often coupled according to an empirically measured structural connectivity matrix. This modelling approach has been used to generate insights into the neural underpinnings of spontaneous brain dynamics, as recorded with techniques such as resting state functional MRI (fMRI). In fMRI, researchers have many degrees of freedom in the way that they can process the data and recent evidence indicates that the choice of pre-processing steps can have a major effect on empirical estimates of functional connectivity. However, the potential influence of such variations on modelling results are seldom considered. Here we show, using three popular whole-brain dynamical models, that different choices during fMRI preprocessing can dramatically affect model fits and interpretations of findings. Critically, we show that the ability of these models to accurately capture patterns in fMRI dynamics is mostly driven by the degree to which they fit global signals rather than interesting sources of coordinated neural dynamics. We show that widespread deflections can arise from simple global synchronisation. We introduce a simple two-parameter model that captures these fluctuations and performs just as well as more complex, multi-parameter biophysical models. From our combined analyses of data and simulations, we describe benchmarks to evaluate model fit and validity. Although most models are not resilient to denoising, we show that relaxing the approximation of homogeneous neural populations by more explicitly modelling inter-regional effective connectivity can improve model accuracy at the expense of increased model complexity. Our results suggest that many complex biophysical models may be fitting relatively trivial properties of the data, and underscore a need for tighter integration between data quality assurance and model development.

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.

A Perspective Roadmap for IoMT-Based Early Detection and Care of the Neural Disorder, Dementia

The Internet of Medical Things (IoMT) has emerged as one of the most important key applications of IoT. IoMT makes the diagnosis and care more convenient and reliable with proven results. The paper presents the technology, open issues, and challenges of IoMT-based systems. It explores the various types of sensors and smart equipment based on IoMT and used for diagnosis and patient care. A comprehensive survey of early detection and postdetection care of the neural disorder dementia is conducted. The paper also presents a postdiagnosis dementia care model named “Demencare.” This model incorporates eight sensors capable of tracking the daily routine of dementia patient. The patients can be monitored locally by an edge computing device kept at their premises. The medical experts may also monitor the patients' status for any deviation from normal behavior. IoMT enables better postdiagnosis care for neural disorders, like dementia and Alzheimer's. The patient's behavior and vital parameters are always available despite the remote location of the patients. The data of the patients may be classified, and new insights may be obtained to tackle patients in a better manner.

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.

Two classes of functional connectivity in dynamical processes in networks

The relationship between network structure and dynamics is one of the most extensively investigated problems in the theory of complex systems of recent years. Understanding this relationship is of relevance to a range of disciplines-from neuroscience to geomorphology. A major strategy of investigating this relationship is the quantitative comparison of a representation of network architecture (structural connectivity, SC) with a (network) representation of the dynamics (functional connectivity, FC). Here, we show that one can distinguish two classes of functional connectivity-one based on simultaneous activity (co-activity) of nodes, the other based on sequential activity of nodes. We delineate these two classes in different categories of dynamical processes-excitations, regular and chaotic oscillators-and provide examples for SC/FC correlations of both classes in each of these models. We expand the theoretical view of the SC/FC relationships, with conceptual instances of the SC and the two classes of FC for various application scenarios in geomorphology, ecology, systems biology, neuroscience and socio-ecological systems. Seeing the organisation of dynamical processes in a network either as governed by co-activity or by sequential activity allows us to bring some order in the myriad of observations relating structure and function of complex networks.

Nonequilibrium brain dynamics as a signature of consciousness

The cognitive functions of human and nonhuman primates rely on the dynamic interplay of distributed neural assemblies. As such, it seems unlikely that cognition can be supported by macroscopic brain dynamics at the proximity of equilibrium. We confirmed this hypothesis by investigating electrocorticography data from nonhuman primates undergoing different states of unconsciousness (sleep, and anesthesia with propofol, ketamine, and ketamine plus medetomidine), and functional magnetic resonance imaging data from humans, both during deep sleep and under propofol anesthesia. Systematically, all states of reduced consciousness unfolded at higher proximity to equilibrium compared to conscious wakefulness, as demonstrated by the computation of entropy production and the curl of probability flux in phase space. Our results establish nonequilibrium macroscopic brain dynamics as a robust signature of consciousness, opening the way for the characterization of cognition and awareness using tools from statistical mechanics.

An expression system of channelrhodopsin-2 driven by a minimal Arc/Arg3.1 promoter and Tet system was developed in human neuroblastoma cells

Advances in neuroscience have relied on the development of techniques that examine neuronal cell activities. One major challenge involves the limitations in labeling and controlling neuronal activities relating to the cell's activation state. In this study, the modified human codon-optimized channelrhodopsin-2 photoreceptor hChR2(C128S) was integrated into function with inducible gene expression methods and materials: the Tet system and the highly efficient minimum promoter of Arc/Arg3.1. The system successfully expressed the target fusion gene exclusively in activated SH-SY5Y human neuroblastoma cells while maintaining the essential characteristics of ChR2. The expression of the channelrhodopsin construct was observed, while the expression duration was refined by treatment with doxycycline. The optogenetic construct here tested the application of the minimum Arc/Arg3.1 promoter, an advanced immediate-early gene promoter, for the expression of the channelrhodopsin gene. Along with its noninvasive nature, this expression system promises to serve dual functions as a cell activity indicator and cell actuator, creating the possibility for researchers to precisely label cells according to their activation state and control the activities of specific neuronal cell populations.

Determination of Dynamic Brain Connectivity via Spectral Analysis

Spectral analysis based on neural field theory is used to analyze dynamic connectivity via methods based on the physical eigenmodes that are the building blocks of brain dynamics. These approaches integrate over space instead of averaging over time and thereby greatly reduce or remove the temporal averaging effects, windowing artifacts, and noise at fine spatial scales that have bedeviled the analysis of dynamical functional connectivity (FC). The dependences of FC on dynamics at various timescales, and on windowing, are clarified and the results are demonstrated on simple test cases, demonstrating how modes provide directly interpretable insights that can be related to brain structure and function. It is shown that FC is dynamic even when the brain structure and effective connectivity are fixed, and that the observed patterns of FC are dominated by relatively few eigenmodes. Common artifacts introduced by statistical analyses that do not incorporate the physical nature of the brain are discussed and it is shown that these are avoided by spectral analysis using eigenmodes. Unlike most published artificially discretized “resting state networks” and other statistically-derived patterns, eigenmodes overlap, with every mode extending across the whole brain and every region participating in every mode—just like the vibrations that give rise to notes of a musical instrument. Despite this, modes are independent and do not interact in the linear limit. It is argued that for many purposes the intrinsic limitations of covariance-based FC instead favor the alternative of tracking eigenmode coefficients vs. time, which provide a compact representation that is directly related to biophysical brain dynamics.

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

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

Beyond the disconnectivity hypothesis of schizophrenia

To go beyond the disconnectivity hypothesis of schizophrenia, directed (effective) connectivity was measured between 94 brain regions, to provide evidence on the source of the changes in schizophrenia and a mechanistic model. Effective connectivity (EC) was measured in 180 participants with schizophrenia and 208 controls. For the significantly different effective connectivities in schizophrenia, on average the forward (stronger) effective connectivities were smaller, whereas the backward connectivities tended to be larger. Further, higher EC in schizophrenia was found from the precuneus and posterior cingulate cortex (PCC) to areas such as the parahippocampal, hippocampal, temporal, fusiform, and occipital cortices. These are backward effective connectivities and were positively correlated with the positive symptoms of schizophrenia. Lower effective connectivities were found from temporal and other regions and were negatively correlated with the symptoms, especially the negative and general symptoms. Further, a signal variance parameter was increased for areas that included the parahippocampal gyrus and hippocampus, consistent with the hypothesis that hippocampal overactivity is involved in schizophrenia. This investigation goes beyond the disconnectivity hypothesis by drawing attention to differences in schizophrenia between backprojections and forward connections, with the backward connections from the precuneus and PCC implicated in memory stronger in schizophrenia.

Brain Connectivity Studies on Structure-Function Relationships: A Short Survey with an Emphasis on Machine Learning

This short survey reviews the recent literature on the relationship between the brain structure and its functional dynamics. Imaging techniques such as diffusion tensor imaging (DTI) make it possible to reconstruct axonal fiber tracks and describe the structural connectivity (SC) between brain regions. By measuring fluctuations in neuronal activity, functional magnetic resonance imaging (fMRI) provides insights into the dynamics within this structural network. One key for a better understanding of brain mechanisms is to investigate how these fast dynamics emerge on a relatively stable structural backbone. So far, computational simulations and methods from graph theory have been mainly used for modeling this relationship. Machine learning techniques have already been established in neuroimaging for identifying functionally independent brain networks and classifying pathological brain states. This survey focuses on methods from machine learning, which contribute to our understanding of functional interactions between brain regions and their relation to the underlying anatomical substrate.

Inter-subject and inter-parcellation variability of resting-state whole-brain dynamical modeling

Modern approaches to investigate complex brain dynamics suggest to represent the brain as a functional network of brain regions defined by a brain atlas, while edges represent the structural or functional connectivity among them. This approach is also utilized for mathematical modeling of the resting-state brain dynamics, where the applied brain parcellation plays an essential role in deriving the model network and governing the modeling results. There is however no consensus and empirical evidence on how a given brain atlas affects the model outcome, and the choice of parcellation is still rather arbitrary. Accordingly, we explore the impact of brain parcellation on inter-subject and inter-parcellation variability of model fitting to empirical data. Our objective is to provide a comprehensive empirical evidence of potential influences of parcellation choice on resting-state whole-brain dynamical modeling. We show that brain atlases strongly influence the quality of model validation and propose several variables calculated from empirical data to account for the observed variability. A few classes of such data variables can be distinguished depending on their inter-subject and inter-parcellation explanatory power.

A graph neural network framework for causal inference in brain networks

A central question in neuroscience is how self-organizing dynamic interactions in the brain emerge on their relatively static structural backbone. Due to the complexity of spatial and temporal dependencies between different brain areas, fully comprehending the interplay between structure and function is still challenging and an area of intense research. In this paper we present a graph neural network (GNN) framework, to describe functional interactions based on the structural anatomical layout. A GNN allows us to process graph-structured spatio-temporal signals, providing a possibility to combine structural information derived from diffusion tensor imaging (DTI) with temporal neural activity profiles, like that observed in functional magnetic resonance imaging (fMRI). Moreover, dynamic interactions between different brain regions discovered by this data-driven approach can provide a multi-modal measure of causal connectivity strength. We assess the proposed model's accuracy by evaluating its capabilities to replicate empirically observed neural activation profiles, and compare the performance to those of a vector auto regression (VAR), like that typically used in Granger causality. We show that GNNs are able to capture long-term dependencies in data and also computationally scale up to the analysis of large-scale networks. Finally we confirm that features learned by a GNN can generalize across MRI scanner types and acquisition protocols, by demonstrating that the performance on small datasets can be improved by pre-training the GNN on data from an earlier study. We conclude that the proposed multi-modal GNN framework can provide a novel perspective on the structure-function relationship in the brain. Accordingly this approach appears to be promising for the characterization of the information flow in brain networks.

Structural alterations in cortical and thalamocortical white matter tracts after recovery from prefrontal cortex lesions in macaques

Unilateral damage to the frontoparietal network typically impairs saccade target selection within the contralesional visual hemifield. Severity of deficits and the degree of recovery have been associated with widespread network dysfunction, yet it is not clear how these behavioural and functional brain changes relate with the underlying structural white matter tracts. Here, we investigated whether recovery after unilateral prefrontal cortex (PFC) lesions was associated with changes in white matter microstructure across large-scale frontoparietal cortical and thalamocortical networks. Diffusion-weighted imaging was acquired in four male rhesus macaques at pre-lesion, week 1, and week 8-16 post-lesion when target selection deficits largely recovered. Probabilistic tractography was used to reconstruct cortical frontoparietal fiber tracts, including the superior longitudinal fasciculus (SLF) and transcallosal fibers connecting the PFC or posterior parietal cortex (PPC), as well as thalamocortical fiber tracts connecting the PFC and PPC to thalamic nuclei. We found that the two animals with small PFC lesions showed increased fractional anisotropy in both cortical and thalamocortical fiber tracts when behaviour had recovered. However, we found that fractional anisotropy decreased in cortical frontoparietal tracts after larger PFC lesions yet increased in some thalamocortical tracts at the time of behavioural recovery. These findings indicate that behavioural recovery after small PFC lesions may be supported by both cortical and subcortical areas, whereas larger PFC lesions may have induced widespread structural damage and hindered compensatory remodeling in the cortical frontoparietal network.

Generative Embeddings of Brain Collective Dynamics Using Variational Autoencoders

We consider the problem of encoding pairwise correlations between coupled dynamical systems in a low-dimensional latent space based on few distinct observations. We use variational autoencoders (VAEs) to embed temporal correlations between coupled nonlinear oscillators that model brain states in the wake-sleep cycle into a two-dimensional manifold. Training a VAE with samples generated using two different parameter combinations results in an embedding that encodes the repertoire of collective dynamics, as well as the topology of the underlying connectivity network. We first follow this approach to infer the trajectory of brain states measured from wakefulness to deep sleep from the two end points of this trajectory; then, we show that the same architecture was capable of representing the pairwise correlations of generic Landau-Stuart oscillators coupled by complex network topology.

Structure-function coupling in the human connectome: A machine learning approach

While the function of most biological systems is tightly constrained by their structure, current evidence suggests that coupling between the structure and function of brain networks is relatively modest. We aimed to investigate whether the modest coupling between connectome structure and function is a fundamental property of nervous systems or a limitation of current brain network models. We developed a new deep learning framework to predict an individual's brain function from their structural connectome, achieving prediction accuracies that substantially exceeded state-of-the-art biophysical models (group: R=0.9±0.1, individual: R=0.55±0.1). Crucially, brain function predicted from an individual's structural connectome explained significant inter-individual variation in cognitive performance. Our results suggest that structure-function coupling in human brain networks is substantially tighter than previously suggested. We establish the margin by which current brain network models can be improved and demonstrate how deep learning can facilitate investigation of relations between brain function and behavior.

Network communication models improve the behavioral and functional predictive utility of the human structural connectome

The connectome provides the structural substrate facilitating communication between brain regions. We aimed to establish whether accounting for polysynaptic communication in structural connectomes would improve prediction of interindividual variation in behavior as well as increase structure-function coupling strength. Connectomes were mapped for 889 healthy adults participating in the Human Connectome Project. To account for polysynaptic signaling, connectomes were transformed into communication matrices for each of 15 different network communication models. Communication matrices were (a) used to perform predictions of five data-driven behavioral dimensions and (b) correlated to resting-state functional connectivity (FC). While FC was the most accurate predictor of behavior, communication models, in particular communicability and navigation, improved the performance of structural connectomes. Communication also strengthened structure-function coupling, with the navigation and shortest paths models leading to 35-65% increases in association strength with FC. We combined behavioral and functional results into a single ranking that provides insight into which communication models may more faithfully recapitulate underlying neural signaling patterns. Comparing results across multiple connectome mapping pipelines suggested that modeling polysynaptic communication is particularly beneficial in sparse high-resolution connectomes. We conclude that network communication models can augment the functional and behavioral predictive utility of the human structural connectome.

Signal diffusion along connectome gradients and inter-hub routing differentially contribute to dynamic human brain function

Human cognition is dynamic, alternating over time between externally-focused states and more abstract, often self-generated, patterns of thought. Although cognitive neuroscience has documented how networks anchor particular modes of brain function, mechanisms that describe transitions between distinct functional states remain poorly understood. Here, we examined how time-varying changes in brain function emerge within the constraints imposed by macroscale structural network organization. Studying a large cohort of healthy adults (n = 326), we capitalized on manifold learning techniques that identify low dimensional representations of structural connectome organization and we decomposed neurophysiological activity into distinct functional states and their transition patterns using Hidden Markov Models. Structural connectome organization predicted dynamic transitions anchored in sensorimotor systems and those between sensorimotor and transmodal states. Connectome topology analyses revealed that transitions involving sensorimotor states traversed short and intermediary distances and adhered strongly to communication mechanisms of network diffusion. Conversely, transitions between transmodal states involved spatially distributed hubs and increasingly engaged long-range routing. These findings establish that the structure of the cortex is optimized to allow neural states the freedom to vary between distinct modes of processing, and so provides a key insight into the neural mechanisms that give rise to the flexibility of human cognition.

Impact of Physical Obstacles on the Structural and Effective Connectivity of in silico Neuronal Circuits

Scaffolds and patterned substrates are among the most successful strategies to dictate the connectivity between neurons in culture. Here, we used numerical simulations to investigate the capacity of physical obstacles placed on a flat substrate to shape structural connectivity, and in turn collective dynamics and effective connectivity, in biologically-realistic neuronal networks. We considered μ-sized obstacles placed in mm-sized networks. Three main obstacle shapes were explored, namely crosses, circles and triangles of isosceles profile. They occupied either a small area fraction of the substrate or populated it entirely in a periodic manner. From the point of view of structure, all obstacles promoted short length-scale connections, shifted the in- and out-degree distributions toward lower values, and increased the modularity of the networks. The capacity of obstacles to shape distinct structural traits depended on their density and the ratio between axonal length and substrate diameter. For high densities, different features were triggered depending on obstacle shape, with crosses trapping axons in their vicinity and triangles funneling axons along the reverse direction of their tip. From the point of view of dynamics, obstacles reduced the capacity of networks to spontaneously activate, with triangles in turn strongly dictating the direction of activity propagation. Effective connectivity networks, inferred using transfer entropy, exhibited distinct modular traits, indicating that the presence of obstacles facilitated the formation of local effective microcircuits. Our study illustrates the potential of physical constraints to shape structural blueprints and remodel collective activity, and may guide investigations aimed at mimicking organizational traits of biological neuronal circuits.

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.

Whole-Brain Models to Explore Altered States of Consciousness from the Bottom Up

The scope of human consciousness includes states departing from what most of us experience as ordinary wakefulness. These altered states of consciousness constitute a prime opportunity to study how global changes in brain activity relate to different varieties of subjective experience. We consider the problem of explaining how global signatures of altered consciousness arise from the interplay between large-scale connectivity and local dynamical rules that can be traced to known properties of neural tissue. For this purpose, we advocate a research program aimed at bridging the gap between bottom-up generative models of whole-brain activity and the top-down signatures proposed by theories of consciousness. Throughout this paper, we define altered states of consciousness, discuss relevant signatures of consciousness observed in brain activity, and introduce whole-brain models to explore the biophysics of altered consciousness from the bottom-up. We discuss the potential of our proposal in view of the current state of the art, give specific examples of how this research agenda might play out, and emphasize how a systematic investigation of altered states of consciousness via bottom-up modeling may help us better understand the biophysical, informational, and dynamical underpinnings of consciousness.