A Robust Modular Automated Neuroimaging Pipeline for Model Inputs to TheVirtualBrain.

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

Exploration of salient risk factors involved in mild cognitive impairment.

Mild cognitive impairment (MCI) is a prevalent and complex condition among older adults that often progresses into Alzheimer's disease (AD). Although MCI affects individuals differently, there are specific indicators of risk commonly associated with the development of MCI. The present study explored the prevalence of seven established MCI risk categories within a large sample of older adults with and without MCI. We explored trends across the different diagnostic groups and extracted the most salient risk factors related to MCI using partial least squares. Neuropsychological risk categories showed the largest differences across groups, with the cognitively unimpaired groups outperforming the MCI groups on all measures. Apolipoprotein E4 (ApoE4) carriers were significantly more common among the more severe MCI group, whereas ApoE4 non-carriers were more common in the healthy controls. Participants with subjective and objective cognitive impairment were trending towards AD-like cerebral spinal fluid (CSF) biomarker levels. Increased age, being male and having fewer years of education were identified as important risk factors of MCI. Higher CSF tau levels were correlated with ApoE4 carrier status, age and a decrease in the ability to carry out daily activities across all diagnostic groups. Amyloid beta1-42 CSF concentration was positively correlated with cognitive and memory performance and non-ApoE4 carrier status regardless of diagnostic status. Unlike previous research, poor cardiovascular health or being female had no relation to MCI. Altogether, the results highlighted risk factors that were specific to persons with MCI, findings that will inform future research in healthy aging, MCI and AD.

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

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

Aging changes the interactions between the oculomotor and memory systems.

The use of multi-modal approaches, particularly in conjunction with multivariate analytic techniques, can enrich models of cognition, brain function, and how they change with age. Recently, multivariate approaches have been applied to the study of eye movements in a manner akin to that of neural activity (i.e., pattern similarity). Here, we review the literature regarding multi-modal and/or multivariate approaches, with specific reference to the use of eyetracking to characterize age-related changes in memory. By applying multi-modal and multivariate approaches to the study of aging, research has shown that aging is characterized by moment-to-moment alterations in the amount and pattern of visual exploration, and by extension, alterations in the activity and function of the hippocampus and broader medial temporal lobe (MTL). These methodological advances suggest that age-related declines in the integrity of the memory system has consequences for oculomotor behavior in the moment, in a reciprocal fashion. Age-related changes in hippocampal and MTL structure and function may lead to an increase in, and change in the patterns of, visual exploration in an effort to upregulate the encoding of information. However, such visual exploration patterns may be non-optimal and actually reduce the amount and/or type of incoming information that is bound into a lasting memory representation. This research indicates that age-related cognitive impairments are considerably broader in scope than previously realized.

Integrating psychosocial variables and societal diversity in epidemic models for predicting COVID-19 transmission dynamics.

During the current COVID-19 pandemic, governments must make decisions based on a variety of information including estimations of infection spread, health care capacity, economic and psychosocial considerations. The disparate validity of current short-term forecasts of these factors is a major challenge to governments. By causally linking an established epidemiological spread model with dynamically evolving psychosocial variables, using Bayesian inference we estimate the strength and direction of these interactions for German and Danish data of disease spread, human mobility, and psychosocial factors based on the serial cross-sectional COVID-19 Snapshot Monitoring (COSMO; N = 16,981). We demonstrate that the strength of cumulative influence of psychosocial variables on infection rates is of a similar magnitude as the influence of physical distancing. We further show that the efficacy of political interventions to contain the disease strongly depends on societal diversity, in particular group-specific sensitivity to affective risk perception. As a consequence, the model may assist in quantifying the effect and timing of interventions, forecasting future scenarios, and differentiating the impact on diverse groups as a function of their societal organization. Importantly, the careful handling of societal factors, including support to the more vulnerable groups, adds another direct instrument to the battery of political interventions fighting epidemic spread.

Signal complexity indicators of health status in clinical EEG.

Brain signal variability changes across the lifespan in both health and disease, likely reflecting changes in information processing capacity related to development, aging and neurological disorders. While signal complexity, and multiscale entropy (MSE) in particular, has been proposed as a biomarker for neurological disorders, most observations of altered signal complexity have come from studies comparing patients with few to no comorbidities against healthy controls. In this study, we examined whether MSE of brain signals was distinguishable across patient groups in a large and heterogeneous set of clinical-EEG data. Using a multivariate analysis, we found unique timescale-dependent differences in MSE across various neurological disorders. We also found MSE to differentiate individuals with non-brain comorbidities, suggesting that MSE is sensitive to brain signal changes brought about by metabolic and other non-brain disorders. Such changes were not detectable in the spectral power density of brain signals. Our findings suggest that brain signal complexity may offer complementary information to spectral power about an individual's health status and is a promising avenue for clinical biomarker development.

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.

Modeling the influence of the hippocampal memory system on the oculomotor system.

Visual exploration is related to activity in the hippocampus (HC) and/or extended medial temporal lobe system (MTL), is influenced by stored memories, and is altered in amnesic cases. An extensive set of polysynaptic connections exists both within and between the HC and oculomotor systems such that investigating how HC responses ultimately influence neural activity in the oculomotor system, and the timing by which such neural modulation could occur, is not trivial. We leveraged TheVirtualBrain, a software platform for large-scale network simulations, to model the functional dynamics that govern the interactions between the two systems in the macaque cortex. Evoked responses following the stimulation of the MTL and some, but not all, subfields of the HC resulted in observable responses in oculomotor regions, including the frontal eye fields, within the time of a gaze fixation. Modeled lesions to some MTL regions slowed the dissipation of HC signal to oculomotor regions, whereas HC lesions generally did not affect the rapid MTL activity propagation to oculomotor regions. These findings provide a framework for investigating how information represented by the HC/MTL may influence the oculomotor system during a fixation and predict how HC lesions may affect visual exploration.

Complexity Matching: Brain Signals Mirror Environment Information Patterns during Music Listening and Reward.

Understanding how the human brain integrates information from the environment with intrinsic brain signals to produce individual perspectives is an essential element of understanding the human mind. Brain signal complexity, measured with multiscale entropy, has been employed as a measure of information processing in the brain, and we propose that it can also be used to measure the information available from a stimulus. We can directly assess the correspondence between brain signal complexity and stimulus complexity as an indication of how well the brain reflects the content of the environment in an analysis that we term "complexity matching." Music is an ideal stimulus because it is a multidimensional signal with a rich temporal evolution and because of its emotion- and reward-inducing potential. When participants focused on acoustic features of music, we found that EEG complexity was lower and more closely resembled the musical complexity compared to an emotional task that asked them to monitor how the music made them feel. Music-derived reward scores on the Barcelona Music Reward Questionnaire correlated with less complexity matching but higher EEG complexity. Compared with perceptual-level processing, emotional and reward responses are associated with additional internal information processes above and beyond those linked to the external stimulus. In other words, the brain adds something when judging the emotional valence of music.

The intersection between the oculomotor and hippocampal memory systems: empirical developments and clinical implications.

Decades of cognitive neuroscience research has shown that where we look is intimately connected to what we remember. In this article, we review findings from human and nonhuman animals, using behavioral, neuropsychological, neuroimaging, and computational modeling methods, to show that the oculomotor and hippocampal memory systems interact in a reciprocal manner, on a moment-to-moment basis, mediated by a vast structural and functional network. Visual exploration serves to efficiently gather information from the environment for the purpose of creating new memories, updating existing memories, and reconstructing the rich, vivid details from memory. Conversely, memory increases the efficiency of visual exploration. We call for models of oculomotor control to consider the influence of the hippocampal memory system on the cognitive control of eye movements, and for models of hippocampal and broader medial temporal lobe function to consider the influence of the oculomotor system on the development and expression of memory. We describe eye movement-based applications for the detection of neurodegeneration and delivery of therapeutic interventions for mental health disorders for which the hippocampus is implicated and memory dysfunctions are at the forefront.

Eye Movements Actively Reinstate Spatiotemporal Mnemonic Content.

Eye movements support memory encoding by binding distinct elements of the visual world into coherent representations. However, the role of eye movements in memory retrieval is less clear. We propose that eye movements play a functional role in retrieval by reinstating the encoding context. By overtly shifting attention in a manner that broadly recapitulates the spatial locations and temporal order of encoded content, eye movements facilitate access to, and reactivation of, associated details. Such mnemonic gaze reinstatement may be obligatorily recruited when task demands exceed cognitive resources, as is often observed in older adults. We review research linking gaze reinstatement to retrieval, describe the neural integration between the oculomotor and memory systems, and discuss implications for models of oculomotor control, memory, and aging.

A macaque connectome for large-scale network simulations in TheVirtualBrain.

Models of large-scale brain networks that are informed by the underlying anatomical connectivity contribute to our understanding of the mapping between the structure of the brain and its dynamical function. Connectome-based modelling is a promising approach to a more comprehensive understanding of brain function across spatial and temporal scales, but it must be constrained by multi-scale empirical data from animal models. Here we describe the construction of a macaque (Macaca mulatta and Macaca fascicularis) connectome for whole-cortex simulations in TheVirtualBrain, an open-source simulation platform. We take advantage of available axonal tract-tracing datasets and enhance the existing connectome data using diffusion-based tractography in macaques. We illustrate the utility of the connectome as an extension of TheVirtualBrain by simulating resting-state BOLD-fMRI data and fitting it to empirical resting-state data.

Exploring the limits of network topology estimation using diffusion-based tractography and tracer studies in the macaque cortex.

Reconstructing the anatomical pathways of the brain to study the human connectome has become an important endeavour for understanding brain function and dynamics. Reconstruction of the cortico-cortical connectivity matrix in vivo often relies on noninvasive diffusion-weighted imaging (DWI) techniques but the extent to which they can accurately represent the topological characteristics of structural connectomes remains unknown. We addressed this question by constructing connectomes using DWI data collected from macaque monkeys in vivo and with data from published invasive tracer studies. We found the strength of fiber tracts was well estimated from DWI and topological properties like degree and modularity were captured by tractography-based connectomes. Rich-club/core-periphery type architecture could also be detected but the classification of hubs using betweenness centrality, participation coefficient and core-periphery identification techniques was inaccurate. Our findings indicate that certain aspects of cortical topology can be faithfully represented in noninvasively-obtained connectomes while other network analytic measures warrant cautionary interpretations.

A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas.

Cortical activity has distinct features across scales, from the spiking statistics of individual cells to global resting-state networks. We here describe the first full-density multi-area spiking network model of cortex, using macaque visual cortex as a test system. The model represents each area by a microcircuit with area-specific architecture and features layer- and population-resolved connectivity between areas. Simulations reveal a structured asynchronous irregular ground state. In a metastable regime, the network reproduces spiking statistics from electrophysiological recordings and cortico-cortical interaction patterns in fMRI functional connectivity under resting-state conditions. Stable inter-area propagation is supported by cortico-cortical synapses that are moderately strong onto excitatory neurons and stronger onto inhibitory neurons. Causal interactions depend on both cortical structure and the dynamical state of populations. Activity propagates mainly in the feedback direction, similar to experimental results associated with visual imagery and sleep. The model unifies local and large-scale accounts of cortex, and clarifies how the detailed connectivity of cortex shapes its dynamics on multiple scales. Based on our simulations, we hypothesize that in the spontaneous condition the brain operates in a metastable regime where cortico-cortical projections target excitatory and inhibitory populations in a balanced manner that produces substantial inter-area interactions while maintaining global stability.

Age-related changes in the relationship between visual exploration and hippocampal activity.

Deciphering the mechanisms underlying age-related memory declines remains an important goal in cognitive neuroscience. Recently, we observed that visual sampling behavior predicted activity within the hippocampus, a region critical for memory. In younger adults, increases in the number of gaze fixations were associated with increases in hippocampal activity (Liu et al., 2017). This finding suggests a close coupling between the oculomotor and memory system. However, the extent to which this coupling is altered with aging has not been investigated. In this study, we gave older adults the same face processing task used in Liu et al. (2017) and compared their visual exploration behavior and neural activation in the hippocampus and the fusiform face area (FFA) to those of younger adults. Compared to younger adults, older adults showed an increase in visual exploration as indexed by the number of gaze fixations. However, the relationship between visual exploration and neural responses in the hippocampus and FFA was weaker than that of younger adults. Older adults also showed weaker responses to novel faces and a smaller repetition suppression effect in the hippocampus and FFA compared to younger adults. All together, this study provides novel evidence that the capacity to bind visually sampled information, in real-time, into coherent representations along the ventral visual stream and the medial temporal lobe declines with aging.

Visual Sampling Predicts Hippocampal Activity.

Eye movements serve to accumulate information from the visual world, contributing to the formation of coherent memory representations that support cognition and behavior. The hippocampus and the oculomotor network are well connected anatomically through an extensive set of polysynaptic pathways. However, the extent to which visual sampling behavior is related to functional responses in the hippocampus during encoding has not been studied directly in human neuroimaging. In the current study, participants engaged in a face processing task while brain responses were recorded with fMRI and eye movements were monitored simultaneously. The number of gaze fixations that a participant made on a given trial was correlated significantly with hippocampal activation such that more fixations were associated with stronger hippocampal activation. Similar results were also found in the fusiform face area, a face-selective perceptual processing region. Notably, the number of fixations was associated with stronger hippocampal activation when the presented faces were novel, but not when the faces were repeated. Increases in fixations during viewing of novel faces also led to larger repetition-related suppression in the hippocampus, indicating that this fixation-hippocampal relationship may reflect the ongoing development of lasting representations. Together, these results provide novel empirical support for the idea that visual exploration and hippocampal binding processes are inherently linked. SIGNIFICANCE STATEMENT: The hippocampal and oculomotor networks have each been studied extensively for their roles in the binding of information and gaze function, respectively. Despite the evidence that individuals with amnesia whose damage includes the hippocampus show alterations in their eye movement patterns and recent findings that the two systems are anatomically connected, it has not been demonstrated whether visual exploration is related to hippocampal activity in neurologically intact adults. In this combined fMRI-eye-tracking study, we show how hippocampal responses scale with the number of gaze fixations made during viewing of novel, but not repeated, faces. These findings provide new evidence suggesting that the hippocampus plays an important role in the binding of information, as sampled by gaze fixations, during visual exploration.

The Rhesus Monkey Connectome Predicts Disrupted Functional Networks Resulting from Pharmacogenetic Inactivation of the Amygdala.

Contemporary research suggests that the mammalian brain is a complex system, implying that damage to even a single functional area could have widespread consequences across the system. To test this hypothesis, we pharmacogenetically inactivated the rhesus monkey amygdala, a subcortical region with distributed and well-defined cortical connectivity. We then examined the impact of that perturbation on global network organization using resting-state functional connectivity MRI. Amygdala inactivation disrupted amygdalocortical communication and distributed corticocortical coupling across multiple functional brain systems. Altered coupling was explained using a graph-based analysis of experimentally established structural connectivity to simulate disconnection of the amygdala. Communication capacity via monosynaptic and polysynaptic pathways, in aggregate, largely accounted for the correlational structure of endogenous brain activity and many of the non-local changes that resulted from amygdala inactivation. These results highlight the structural basis of distributed neural activity and suggest a strategy for linking focal neuropathology to remote neurophysiological changes.

An Anatomical Interface between Memory and Oculomotor Systems.

Visual behavior is guided by memories from prior experience and knowledge of the visual scene. The hippocampal system (HC), in particular, has been implicated in the guidance of saccades: Amnesic patients, following damage to the HC, exhibit selective deficits in their gaze patterns. However, the neural circuitry by which mnemonic representations influence the oculomotor system remains unknown. We used a data-driven, network-based approach on directed anatomical connectivity from the macaque brain to reveal an extensive set of polysnaptic pathways spanning the extrastriate, posterior parietal and prefrontal cortices that potentially mediate the exchange of information between the memory and visuo-oculomotor systems. We additionally show how the potential for directed information flow from the hippocampus to oculomotor control areas is exceptionally high. In particular, the dorsolateral pFC and FEF-regions known to be responsible for the cognitive control of saccades-are topologically well positioned to receive information from the hippocampus. Together with neuropsychological evidence of altered gaze patterns following damage to the hippocampus, our findings suggest that a reconsideration of hippocampal involvement in oculomotor guidance is needed.