Individualized event structure drives individual differences in whole-brain functional connectivity

Disentangle the group and individual components of functional connectome with autoencoders

One of the central goals of neuroscience is to understand the group commonality and individual variability in functional connectome. However, the entangled nature of the group and individual components in functional connectome poses challenges. Some methods have attempted to disentangle these group and individual components, typically using functional connectivity (FC). Among them, some first compute FC from BOLD signals and then disentangle group and individual components with FC; these approaches are termed FC-level methods. In contrast, some methods first disentangle group and individual components at the BOLD level and then compute FC; these techniques are termed BOLD-level methods. BOLD-level research has demonstrated that directly modeling BOLD signals enables the capture of novel aspects of group and individual components and achieves a better disentangling effect. To this end, we propose a novel network framework, termed BRAin Signal DEcoupling (BRASDE), to disentangle group and individual components from BOLD signals, as well as complementary inductive biases that serves as disentangling strategies. Here, we assume that group components are consistent across different subjects and sessions in BOLD signals; individual components are consistent across different sessions within the same subject but variable across different subjects in BOLD signals. Utilizing the multiple sessions of fMRI data from the Human Connectome Project (HCP), we demonstrate that compared to the existing methods, BRASDE yields enhanced consistency across subjects for group components. At the same time, BRASDE amplifies the differentiation among individual components across subjects, and provides enhanced consistency within the same subjects across various sessions. Moreover, the superior performance achieved on novel sessions and subjects demonstrates the excellent generalization of BRASDE. Our methods also reveal significantly higher individual differences in the right hemisphere than in the left hemisphere. In addition, experiments validate the associations between individual components and cognitive behaviors. Overall, we propose an effective approach for disentangling group and individual components, which will facilitate further investigation into the general principles and neural mechanisms underlying individual variability in the human brain. The code can be found at https://github.com/PeiKeepMoving/BRASDE.

The emergence of multiscale connectomics-based approaches in stroke recovery

Stroke is a leading cause of adult disability. Understanding stroke damage and recovery requires deciphering changes in complex brain networks across different spatiotemporal scales. While recent developments in brain readout technologies and progress in complex network modeling have revolutionized current understanding of the effects of stroke on brain networks at a macroscale, reorganization of smaller scale brain networks remains incompletely understood. In this review, we use a conceptual framework of graph theory to define brain networks from nano- to macroscales. Highlighting stroke-related brain connectivity studies at multiple scales, we argue that multiscale connectomics-based approaches may provide new routes to better evaluate brain structural and functional remapping after stroke and during recovery.

Higher-order functional connectivity analysis of resting-state functional magnetic resonance imaging data using multivariate cumulants

Blood-level oxygenation-dependent (BOLD) functional magnetic resonance imaging (fMRI) is the most common modality to study functional connectivity in the human brain. Most research to date has focused on connectivity between pairs of brain regions. However, attention has recently turned towards connectivity involving more than two regions, that is, higher-order connectivity. It is not yet clear how higher-order connectivity can best be quantified. The measures that are currently in use cannot distinguish between pairwise (i.e., second-order) and higher-order connectivity. We show that genuine higher-order connectivity can be quantified by using multivariate cumulants. We explore the use of multivariate cumulants for quantifying higher-order connectivity and the performance of block bootstrapping for statistical inference. In particular, we formulate a generative model for fMRI signals exhibiting higher-order connectivity and use it to assess bias, standard errors, and detection probabilities. Application to resting-state fMRI data from the Human Connectome Project demonstrates that spontaneous fMRI signals are organized into higher-order networks that are distinct from second-order resting-state networks. Application to a clinical cohort of patients with multiple sclerosis further demonstrates that cumulants can be used to classify disease groups and explain behavioral variability. Hence, we present a novel framework to reliably estimate genuine higher-order connectivity in fMRI data which can be used for constructing hyperedges, and finally, which can readily be applied to fMRI data from populations with neuropsychiatric disease or cognitive neuroscientific experiments.

Edge time series components of functional connectivity and cognitive function in Alzheimer's disease

Understanding the interrelationships of brain function as measured by resting-state magnetic resonance imaging and neuropsychological/behavioral measures in Alzheimer's disease is key for advancement of neuroimaging analysis methods in clinical research. The edge time-series framework recently developed in the field of network neuroscience, in combination with other network science methods, allows for investigations of brain-behavior relationships that are not possible with conventional functional connectivity methods. Data from the Indiana Alzheimer's Disease Research Center sample (53 cognitively normal control, 47 subjective cognitive decline, 32 mild cognitive impairment, and 20 Alzheimer's disease participants) were used to investigate relationships between functional connectivity components, each derived from a subset of time points based on co-fluctuation of regional signals, and measures of domain-specific neuropsychological functions. Multiple relationships were identified with the component approach that were not found with conventional functional connectivity. These involved attentional, limbic, frontoparietal, and default mode systems and their interactions, which were shown to couple with cognitive, executive, language, and attention neuropsychological domains. Additionally, overlapping results were obtained with two different statistical strategies (network contingency correlation analysis and network-based statistics correlation). Results demonstrate that connectivity components derived from edge time-series based on co-fluctuation reveal disease-relevant relationships not observed with conventional static functional connectivity.

Modular subgraphs in large-scale connectomes underpin spontaneous co-fluctuation events in mouse and human brains

Previous studies have adopted an edge-centric framework to study fine-scale network dynamics in human fMRI. To date, however, no studies have applied this framework to data collected from model organisms. Here, we analyze structural and functional imaging data from lightly anesthetized mice through an edge-centric lens. We find evidence of "bursty" dynamics and events - brief periods of high-amplitude network connectivity. Further, we show that on a per-frame basis events best explain static FC and can be divided into a series of hierarchically-related clusters. The co-fluctuation patterns associated with each cluster centroid link distinct anatomical areas and largely adhere to the boundaries of algorithmically detected functional brain systems. We then investigate the anatomical connectivity undergirding high-amplitude co-fluctuation patterns. We find that events induce modular bipartitions of the anatomical network of inter-areal axonal projections. Finally, we replicate these same findings in a human imaging dataset. In summary, this report recapitulates in a model organism many of the same phenomena observed in previously edge-centric analyses of human imaging data. However, unlike human subjects, the murine nervous system is amenable to invasive experimental perturbations. Thus, this study sets the stage for future investigation into the causal origins of fine-scale brain dynamics and high-amplitude co-fluctuations. Moreover, the cross-species consistency of the reported findings enhances the likelihood of future translation.

Edge Time Series Components of Functional Connectivity and Cognitive Function in Alzheimer's Disease

Understanding the interrelationships of brain function as measured by resting-state magnetic resonance imaging and neuropsychological/behavioral measures in Alzheimer's disease is key for advancement of neuroimaging analysis methods in clinical research. The edge time-series framework recently developed in the field of network neuroscience, in combination with other network science methods, allows for investigations of brain-behavior relationships that are not possible with conventional functional connectivity methods. Data from the Indiana Alzheimer's Disease Research Center sample (53 cognitively normal control, 47 subjective cognitive decline, 32 mild cognitive impairment, and 20 Alzheimer's disease participants) were used to investigate relationships between functional connectivity components, each derived from a subset of time points based on co-fluctuation of regional signals, and measures of domain-specific neuropsychological functions. Multiple relationships were identified with the component approach that were not found with conventional functional connectivity. These involved attentional, limbic, frontoparietal, and default mode systems and their interactions, which were shown to couple with cognitive, executive, language, and attention neuropsychological domains. Additionally, overlapping results were obtained with two different statistical strategies (network contingency correlation analysis and network-based statistics correlation). Results demonstrate that connectivity components derived from edge time-series based on co-fluctuation reveal disease-relevant relationships not observed with conventional static functional connectivity.

Living on the edge: network neuroscience beyond nodes

Network neuroscience has emphasized the connectional properties of neural elements - cells, populations, and regions. This has come at the expense of the anatomical and functional connections that link these elements to one another. A new perspective - namely one that emphasizes 'edges' - may prove fruitful in addressing outstanding questions in network neuroscience. We highlight one recently proposed 'edge-centric' method and review its current applications, merits, and limitations. We also seek to establish conceptual and mathematical links between this method and previously proposed approaches in the network science and neuroimaging literature. We conclude by presenting several avenues for future work to extend and refine existing edge-centric analysis.

Substructure of the brain's Cingulo-Opercular network

The Cingulo-Opercular network (CON) is an executive network of the human brain that regulates actions. CON is composed of many widely distributed cortical regions that are involved in top-down control over both lower-level (i.e., motor) and higher-level (i.e., cognitive) functions, as well as in processing of painful stimuli. Given the topographical and functional heterogeneity of the CON, we investigated whether subnetworks within the CON support separable aspects of action control. Using precision functional mapping (PFM) in 15 participants with > 5 hours of resting state functional connectivity (RSFC) and task data, we identified three anatomically and functionally distinct CON subnetworks within each individual. These three distinct subnetworks were linked to Decisions, Actions, and Feedback (including pain processing), respectively, in convergence with a meta-analytic task database. These Decision, Action and Feedback subnetworks represent pathways by which the brain establishes top-down goals, transforms those goals into actions, implemented as movements, and processes critical action feedback such as pain.

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.

High-amplitude network co-fluctuations linked to variation in hormone concentrations over the menstrual cycle

Many studies have shown that the human endocrine system modulates brain function, reporting associations between fluctuations in hormone concentrations and brain connectivity. However, how hormonal fluctuations impact fast changes in brain network organization over short timescales remains unknown. Here, we leverage a recently proposed framework for modeling co-fluctuations between the activity of pairs of brain regions at a framewise timescale. In previous studies we showed that time points corresponding to high-amplitude co-fluctuations disproportionately contributed to the time-averaged functional connectivity pattern and that these co-fluctuation patterns could be clustered into a low-dimensional set of recurring "states." Here, we assessed the relationship between these network states and quotidian variation in hormone concentrations. Specifically, we were interested in whether the frequency with which network states occurred was related to hormone concentration. We addressed this question using a dense-sampling dataset (N = 1 brain). In this dataset, a single individual was sampled over the course of two endocrine states: a natural menstrual cycle and while the subject underwent selective progesterone suppression via oral hormonal contraceptives. During each cycle, the subject underwent 30 daily resting-state fMRI scans and blood draws. Our analysis of the imaging data revealed two repeating network states. We found that the frequency with which state 1 occurred in scan sessions was significantly correlated with follicle-stimulating and luteinizing hormone concentrations. We also constructed representative networks for each scan session using only "event frames"-those time points when an event was determined to have occurred. We found that the weights of specific subsets of functional connections were robustly correlated with fluctuations in the concentration of not only luteinizing and follicle-stimulating hormones, but also progesterone and estradiol.

Hierarchical organization of spontaneous co-fluctuations in densely sampled individuals using fMRI

Edge time series decompose functional connectivity into its framewise contributions. Previous studies have focused on characterizing the properties of high-amplitude frames (time points when the global co-fluctuation amplitude takes on its largest value), including their cluster structure. Less is known about middle- and low-amplitude co-fluctuations (peaks in co-fluctuation time series but of lower amplitude). Here, we directly address those questions, using data from two dense-sampling studies: the MyConnectome project and Midnight Scan Club. We develop a hierarchical clustering algorithm to group peak co-fluctuations of all magnitudes into nested and multiscale clusters based on their pairwise concordance. At a coarse scale, we find evidence of three large clusters that, collectively, engage virtually all canonical brain systems. At finer scales, however, each cluster is dissolved, giving way to increasingly refined patterns of co-fluctuations involving specific sets of brain systems. We also find an increase in global co-fluctuation magnitude with hierarchical scale. Finally, we comment on the amount of data needed to estimate co-fluctuation pattern clusters and implications for brain-behavior studies. Collectively, the findings reported here fill several gaps in current knowledge concerning the heterogeneity and richness of co-fluctuation patterns as estimated with edge time series while providing some practical guidance for future studies.

A low dimensional embedding of brain dynamics enhances diagnostic accuracy and behavioral prediction in stroke

Large-scale brain networks reveal structural connections as well as functional synchronization between distinct regions of the brain. The latter, referred to as functional connectivity (FC), can be derived from neuroimaging techniques such as functional magnetic resonance imaging (fMRI). FC studies have shown that brain networks are severely disrupted by stroke. However, since FC data are usually large and high-dimensional, extracting clinically useful information from this vast amount of data is still a great challenge, and our understanding of the functional consequences of stroke remains limited. Here, we propose a dimensionality reduction approach to simplify the analysis of this complex neural data. By using autoencoders, we find a low-dimensional representation encoding the fMRI data which preserves the typical FC anomalies known to be present in stroke patients. By employing the latent representations emerging from the autoencoders, we enhanced patients' diagnostics and severity classification. Furthermore, we showed how low-dimensional representation increased the accuracy of recovery prediction.

Estimating dynamic individual coactivation patterns based on densely sampled resting-state fMRI data and utilizing it for better subject identification

As a complex dynamic system, the brain exhibits spatially organized recurring patterns of activity over time. Coactivation patterns (CAPs), which analyzes data from each single frame, have been utilized to detect transient brain activity states recently. However, previous CAP analyses have been conducted at the group level, which might neglect meaningful individual differences. Here, we estimated individual CAP states at both subject- and scan-level based on a densely sampled dataset: Midnight Scan Club. We used differential identifiability, which measures the gap between intra- and inter-subject similarity, to evaluate individual differences. We found individual CAPs at the subject-level achieved the best fingerprinting ability by maintaining high intra-subject similarity and enlarging inter-subject differences, and brain regions of association networks mainly contributed to the identifiability. On the other hand, scan-level CAP states were unstable across scans for the same participant. Expectedly, we found subject-specific CAPs became more reliable and discriminative with more data (i.e., longer duration). As the acquisition time of each participant is limited in practice, our results recommend a data collection strategy that collects more scans with appropriate duration (e.g., 12 ~ 15 min/scan) to obtain more reliable subject-specific CAPs, when total acquisition time is fixed (e.g., 150 min). In summary, this work has constructed reliable subject-specific CAP states with meaningful individual differences, and recommended an appropriate data collection strategy, which can guide subsequent investigations into individualized brain dynamics.

Leading basic modes of spontaneous activity drive individual functional connectivity organization in the resting human brain

Spontaneous activity of the human brain provides a window to explore intrinsic principles of functional organization. However, most studies have focused on interregional functional connectivity. The principles underlying rich repertoires of instantaneous activity remain largely unknown. We apply a recently proposed eigen-microstate analysis to three resting-state functional MRI datasets to identify basic modes that represent fundamental activity patterns that coexist over time. We identify five leading basic modes that dominate activity fluctuations. Each mode exhibits a distinct functional system-dependent coactivation pattern and corresponds to specific cognitive profiles. In particular, the spatial pattern of the first leading basis mode shows the separation of activity between the default-mode and primary and attention regions. Based on theoretical modelling, we further reconstruct individual functional connectivity as the weighted superposition of coactivation patterns corresponding to these leading basic modes. Moreover, these leading basic modes capture sleep deprivation-induced changes in brain activity and interregional connectivity, primarily involving the default-mode and task-positive regions. Our findings reveal a dominant set of basic modes of spontaneous activity that reflect multiplexed interregional coordination and drive conventional functional connectivity, furthering the understanding of the functional significance of spontaneous brain activity.

Partial entropy decomposition reveals higher-order information structures in human brain activity

The standard approach to modeling the human brain as a complex system is with a network, where the basic unit of interaction is a pairwise link between two brain regions. While powerful, this approach is limited by the inability to assess higher-order interactions involving three or more elements directly. In this work, we explore a method for capturing higher-order dependencies in multivariate data: the partial entropy decomposition (PED). Our approach decomposes the joint entropy of the whole system into a set of nonnegative atoms that describe the redundant, unique, and synergistic interactions that compose the system's structure. PED gives insight into the mathematics of functional connectivity and its limitation. When applied to resting-state fMRI data, we find robust evidence of higher-order synergies that are largely invisible to standard functional connectivity analyses. Our approach can also be localized in time, allowing a frame-by-frame analysis of how the distributions of redundancies and synergies change over the course of a recording. We find that different ensembles of regions can transiently change from being redundancy-dominated to synergy-dominated and that the temporal pattern is structured in time. These results provide strong evidence that there exists a large space of unexplored structures in human brain data that have been largely missed by a focus on bivariate network connectivity models. This synergistic structure is dynamic in time and likely will illuminate interesting links between brain and behavior. Beyond brain-specific application, the PED provides a very general approach for understanding higher-order structures in a variety of complex systems.

Manifold learning for fMRI time-varying functional connectivity

Whole-brain functional connectivity (FC) measured with functional MRI (fMRI) evolves over time in meaningful ways at temporal scales going from years (e.g., development) to seconds [e.g., within-scan time-varying FC (tvFC)]. Yet, our ability to explore tvFC is severely constrained by its large dimensionality (several thousands). To overcome this difficulty, researchers often seek to generate low dimensional representations (e.g., 2D and 3D scatter plots) hoping those will retain important aspects of the data (e.g., relationships to behavior and disease progression). Limited prior empirical work suggests that manifold learning techniques (MLTs)-namely those seeking to infer a low dimensional non-linear surface (i.e., the manifold) where most of the data lies-are good candidates for accomplishing this task. Here we explore this possibility in detail. First, we discuss why one should expect tvFC data to lie on a low dimensional manifold. Second, we estimate what is the intrinsic dimension (ID; i.e., minimum number of latent dimensions) of tvFC data manifolds. Third, we describe the inner workings of three state-of-the-art MLTs: Laplacian Eigenmaps (LEs), T-distributed Stochastic Neighbor Embedding (T-SNE), and Uniform Manifold Approximation and Projection (UMAP). For each method, we empirically evaluate its ability to generate neuro-biologically meaningful representations of tvFC data, as well as their robustness against hyper-parameter selection. Our results show that tvFC data has an ID that ranges between 4 and 26, and that ID varies significantly between rest and task states. We also show how all three methods can effectively capture subject identity and task being performed: UMAP and T-SNE can capture these two levels of detail concurrently, but LE could only capture one at a time. We observed substantial variability in embedding quality across MLTs, and within-MLT as a function of hyper-parameter selection. To help alleviate this issue, we provide heuristics that can inform future studies. Finally, we also demonstrate the importance of feature normalization when combining data across subjects and the role that temporal autocorrelation plays in the application of MLTs to tvFC data. Overall, we conclude that while MLTs can be useful to generate summary views of labeled tvFC data, their application to unlabeled data such as resting-state remains challenging.

Intermediately synchronised brain states optimise trade-off between subject specificity and predictive capacity

Functional connectivity (FC) refers to the statistical dependencies between activity of distinct brain areas. To study temporal fluctuations in FC within the duration of a functional magnetic resonance imaging (fMRI) scanning session, researchers have proposed the computation of an edge time series (ETS) and their derivatives. Evidence suggests that FC is driven by a few time points of high-amplitude co-fluctuation (HACF) in the ETS, which may also contribute disproportionately to interindividual differences. However, it remains unclear to what degree different time points actually contribute to brain-behaviour associations. Here, we systematically evaluate this question by assessing the predictive utility of FC estimates at different levels of co-fluctuation using machine learning (ML) approaches. We demonstrate that time points of lower and intermediate co-fluctuation levels provide overall highest subject specificity as well as highest predictive capacity of individual-level phenotypes.

Exploring neural heterogeneity in inattention and hyperactivity

Inattention and hyperactivity are cardinal symptoms of Attention Deficit Hyperactivity Disorder (ADHD). These characteristics have also been observed across a range of other neurodevelopmental conditions, such as autism and dyspraxia, suggesting that they might best be studied across diagnostic categories. Here, we evaluated the associations between inattention and hyperactivity behaviours and features of the structural brain network (connectome) in a large transdiagnostic sample of children (Centre for Attention, Learning, and Memory; n = 383). In our sample, we found that a single latent factor explains 77.6% of variance in scores across multiple questionnaires measuring inattention and hyperactivity. Partial Least-Squares (PLS) regression revealed that variability in this latent factor could not be explained by a linear component representing nodewise properties of connectomes. We then investigated the type and extent of neural heterogeneity in a subset of our sample with clinically-elevated levels of inattention and hyperactivity. Multidimensional scaling combined with k-means clustering revealed two neural subtypes in children with elevated levels of inattention and hyperactivity (n = 232), differentiated primarily by nodal communicability-a measure which demarcates the extent to which neural signals propagate through specific brain regions. These different clusters had similar behavioural profiles, which included high levels of inattention and hyperactivity. However, one of the clusters scored higher on multiple cognitive assessment measures of executive function. We conclude that inattention and hyperactivity are so common in children with neurodevelopmental difficulties because they emerge through multiple different trajectories of brain development. In our own data, we can identify two of these possible trajectories, which are reflected by measures of structural brain network topology and cognition.

Few temporally distributed brain connectivity states predict human cognitive abilities

Human functional brain connectivity can be temporally decomposed into states of high and low cofluctuation, defined as coactivation of brain regions over time. Rare states of particularly high cofluctuation have been shown to reflect fundamentals of intrinsic functional network architecture and to be highly subject-specific. However, it is unclear whether such network-defining states also contribute to individual variations in cognitive abilities - which strongly rely on the interactions among distributed brain regions. By introducing CMEP, a new eigenvector-based prediction framework, we show that as few as 16 temporally separated time frames (< 1.5% of 10min resting-state fMRI) can significantly predict individual differences in intelligence (N = 263, p < .001). Against previous expectations, individual's network-defining time frames of particularly high cofluctuation do not predict intelligence. Multiple functional brain networks contribute to the prediction, and all results replicate in an independent sample (N = 831). Our results suggest that although fundamentals of person-specific functional connectomes can be derived from few time frames of highest connectivity, temporally distributed information is necessary to extract information about cognitive abilities. This information is not restricted to specific connectivity states, like network-defining high-cofluctuation states, but rather reflected across the entire length of the brain connectivity time series.

Dynamic segregation and integration of brain functional networks associated with emotional arousal

The organization of brain functional networks dynamically changes with emotional stimuli, but its relationship to emotional behaviors is still unclear. In the DEAP dataset, we used the nested-spectral partition approach to identify the hierarchical segregation and integration of functional networks and investigated the dynamic transitions between connectivity states under different arousal conditions. The frontal and right posterior parietal regions were dominant for network integration whereas the bilateral temporal, left posterior parietal, and occipital regions were responsible for segregation and functional flexibility. High emotional arousal behavior was associated with stronger network integration and more stable state transitions. Crucially, the connectivity states of frontal, central, and right parietal regions were closely related to arousal ratings in individuals. Besides, we predicted the individual emotional performance based on functional connectivity activities. Our results demonstrate that brain connectivity states are closely associated with emotional behaviors and could be reliable and robust indicators for emotional arousal.

Multivariate information theory uncovers synergistic subsystems of the human cerebral cortex

One of the most well-established tools for modeling the brain is the functional connectivity network, which is constructed from pairs of interacting brain regions. While powerful, the network model is limited by the restriction that only pairwise dependencies are considered and potentially higher-order structures are missed. Here, we explore how multivariate information theory reveals higher-order dependencies in the human brain. We begin with a mathematical analysis of the O-information, showing analytically and numerically how it is related to previously established information theoretic measures of complexity. We then apply the O-information to brain data, showing that synergistic subsystems are widespread in the human brain. Highly synergistic subsystems typically sit between canonical functional networks, and may serve an integrative role. We then use simulated annealing to find maximally synergistic subsystems, finding that such systems typically comprise ≈10 brain regions, recruited from multiple canonical brain systems. Though ubiquitous, highly synergistic subsystems are invisible when considering pairwise functional connectivity, suggesting that higher-order dependencies form a kind of shadow structure that has been unrecognized by established network-based analyses. We assert that higher-order interactions in the brain represent an under-explored space that, accessible with tools of multivariate information theory, may offer novel scientific insights.

Uncovering individual differences in fine-scale dynamics of functional connectivity

Functional connectivity (FC) profiles contain subject-specific features that are conserved across time and have potential to capture brain-behavior relationships. Most prior work has focused on spatial features (nodes and systems) of these FC fingerprints, computed over entire imaging sessions. We propose a method for temporally filtering FC, which allows selecting specific moments in time while also maintaining the spatial pattern of node-based activity. To this end, we leverage a recently proposed decomposition of FC into edge time series (eTS). We systematically analyze functional magnetic resonance imaging frames to define features that enhance identifiability across multiple fingerprinting metrics, similarity metrics, and data sets. Results show that these metrics characteristically vary with eTS cofluctuation amplitude, similarity of frames within a run, transition velocity, and expression of functional systems. We further show that data-driven optimization of features that maximize fingerprinting metrics isolates multiple spatial patterns of system expression at specific moments in time. Selecting just 10% of the data can yield stronger fingerprints than are obtained from the full data set. Our findings support the idea that FC fingerprints are differentially expressed across time and suggest that multiple distinct fingerprints can be identified when spatial and temporal characteristics are considered simultaneously.

Manifold Learning for fMRI time-varying FC

Whole-brain functional connectivity ( FC ) measured with functional MRI (fMRI) evolve over time in meaningful ways at temporal scales going from years (e.g., development) to seconds (e.g., within-scan time-varying FC ( tvFC )). Yet, our ability to explore tvFC is severely constrained by its large dimensionality (several thousands). To overcome this difficulty, researchers seek to generate low dimensional representations (e.g., 2D and 3D scatter plots) expected to retain its most informative aspects (e.g., relationships to behavior, disease progression). Limited prior empirical work suggests that manifold learning techniques ( MLTs )-namely those seeking to infer a low dimensional non-linear surface (i.e., the manifold) where most of the data lies-are good candidates for accomplishing this task. Here we explore this possibility in detail. First, we discuss why one should expect tv FC data to lie on a low dimensional manifold. Second, we estimate what is the intrinsic dimension (i.e., minimum number of latent dimensions; ID ) of tvFC data manifolds. Third, we describe the inner workings of three state-of-the-art MLTs : Laplacian Eigenmaps ( LE ), T-distributed Stochastic Neighbor Embedding ( T-SNE ), and Uniform Manifold Approximation and Projection ( UMAP ). For each method, we empirically evaluate its ability to generate neuro-biologically meaningful representations of tvFC data, as well as their robustness against hyper-parameter selection. Our results show that tvFC data has an ID that ranges between 4 and 26, and that ID varies significantly between rest and task states. We also show how all three methods can effectively capture subject identity and task being performed: UMAP and T-SNE can capture these two levels of detail concurrently, but L E could only capture one at a time. We observed substantial variability in embedding quality across MLTs , and within- MLT as a function of hyper-parameter selection. To help alleviate this issue, we provide heuristics that can inform future studies. Finally, we also demonstrate the importance of feature normalization when combining data across subjects and the role that temporal autocorrelation plays in the application of MLTs to tvFC data. Overall, we conclude that while MLTs can be useful to generate summary views of labeled tvFC data, their application to unlabeled data such as resting-state remains challenging.

Brain motion networks predict head motion during rest- and task-fMRI

Introduction

The capacity to stay still during scanning, which is necessary to avoid motion confounds while imaging, varies markedly between people.

Methods

Here we investigated the effect of head motion on functional connectivity using connectome-based predictive modeling (CPM) and publicly available brain functional magnetic resonance imaging (fMRI) data from 414 individuals with low frame-to-frame motion (Δd < 0.18 mm). Leave-one-out was used for internal cross-validation of head motion prediction in 207 participants, and twofold cross-validation was used in an independent sample (n = 207).

Results and Discussion

Parametric testing, as well as CPM-based permutations for null hypothesis testing, revealed strong linear associations between observed and predicted values of head motion. Motion prediction accuracy was higher for task- than for rest-fMRI, and for absolute head motion (d) than for Δd. Denoising attenuated the predictability of head motion, but stricter framewise displacement threshold (FD = 0.2 mm) for motion censoring did not alter the accuracy of the predictions obtained with lenient censoring (FD = 0.5 mm). For rest-fMRI, prediction accuracy was lower for individuals with low motion (mean Δd < 0.02 mm; n = 200) than for those with moderate motion (Δd < 0.04 mm; n = 414). The cerebellum and default-mode network (DMN) regions that forecasted individual differences in d and Δd during six different tasks- and two rest-fMRI sessions were consistently prone to the deleterious effect of head motion. However, these findings generalized to a novel group of 1,422 individuals but not to simulated datasets without neurobiological contributions, suggesting that cerebellar and DMN connectivity could partially reflect functional signals pertaining to inhibitory motor control during fMRI.

BOLD cofluctuation 'events' are predicted from static functional connectivity

Recent work identified single time points ("events") of high regional cofluctuation in functional Magnetic Resonance Imaging (fMRI) which contain more large-scale brain network information than other, low cofluctuation time points. This suggested that events might be a discrete, temporally sparse signal which drives functional connectivity (FC) over the timeseries. However, a different, not yet explored possibility is that network information differences between time points are driven by sampling variability on a constant, static, noisy signal. Using a combination of real and simulated data, we examined the relationship between cofluctuation and network structure and asked if this relationship was unique, or if it could arise from sampling variability alone. First, we show that events are not discrete - there is a gradually increasing relationship between network structure and cofluctuation; ∼50% of samples show very strong network structure. Second, using simulations we show that this relationship is predicted from sampling variability on static FC. Finally, we show that randomly selected points can capture network structure about as well as events, largely because of their temporal spacing. Together, these results suggest that, while events exhibit particularly strong representations of static FC, there is little evidence that events are unique timepoints that drive FC structure. Instead, a parsimonious explanation for the data is that events arise from a single static, but noisy, FC structure.

Cofluctuation analysis reveals aberrant default mode network patterns in adolescents and youths with autism spectrum disorder

Resting-state functional connectivity (rsFC) approaches provide informative estimates of the functional architecture of the brain, and recently-proposed cofluctuation analysis temporally unwraps FC at every moment in time, providing refined information for quantifying brain dynamics. As a brain network disorder, autism spectrum disorder (ASD) was characterized by substantial alteration in FC, but the contribution of moment-to-moment-activity cofluctuations to the overall dysfunctional connectivity pattern in ASD remains poorly understood. Here, we used the cofluctuation approach to explore the underlying dynamic properties of FC in ASD, using a large multisite resting-state functional magnetic resonance imaging (rs-fMRI) dataset (ASD = 354, typically developing controls [TD] = 446). Our results verified that the networks estimated using high-amplitude frames were highly correlated with the traditional rsFC. Moreover, these frames showed higher average amplitudes in participants with ASD than those in the TD group. Principal component analysis was performed on the activity patterns in these frames and aggregated over all subjects. The first principal component (PC1) corresponds to the default mode network (DMN), and the PC1 coefficients were greater in participants with ASD than those in the TD group. Additionally, increased ASD symptom severity was associated with the increased coefficients, which may result in excessive internally oriented cognition and social cognition deficits in individuals with ASD. Our finding highlights the utility of cofluctuation approaches in prevalent neurodevelopmental disorders and verifies that the aberrant contribution of DMN to rsFC may underline the symptomatology in adolescents and youths with ASD.

Equalization of Brain State Occupancy Accompanies Cognitive Impairment in Cerebral Small Vessel Disease

BACKGROUND

Cognitive impairment is a hallmark of cerebral small vessel disease (cSVD). Functional magnetic resonance imaging has highlighted connections between patterns of brain activity and variability in behavior. We aimed to characterize the associations between imaging markers of cSVD, dynamic connectivity, and cognitive impairment.

METHODS

We obtained magnetic resonance imaging and clinical data from the population-based Hamburg City Health Study. cSVD was quantified by white matter hyperintensities and peak-width of skeletonized mean diffusivity (PSMD). Resting-state blood oxygen level-dependent signals were clustered into discrete brain states, for which fractional occupancies (%) and dwell times (seconds) were computed. Cognition in multiple domains was assessed using validated tests. Regression analysis was used to quantify associations between white matter damage, spatial coactivation patterns, and cognitive function.

RESULTS

Data were available for 979 participants (ages 45-74 years, median white matter hyperintensity volume 0.96 mL). Clustering identified five brain states with the most time spent in states characterized by activation (+) or suppression (-) of the default mode network (DMN) (fractional occupancy: DMN+ = 25.1 ± 7.2%, DMN- = 25.5 ± 7.2%). Every 4.7-fold increase in white matter hyperintensity volume was associated with a 0.95-times reduction of the odds of occupying DMN+ or DMN-. Time spent in DMN-related brain states was associated with executive function.

CONCLUSIONS

Associations between white matter damage, whole-brain spatial coactivation patterns, and cognition suggest equalization of time spent in different brain states as a marker for cSVD-associated cognitive decline. Reduced gradients between brain states in association with brain damage and cognitive impairment reflect the dedifferentiation hypothesis of neurocognitive aging in a network-theoretical context.

Frontoparietal network activation is associated with motor recovery in ischemic stroke patients

Strokes cause lesions that damage brain tissue, disrupt normal brain activity patterns and can lead to impairments in motor function. Although modulation of cortical activity is central to stimulation-based rehabilitative therapies, aberrant and adaptive patterns of brain activity after stroke have not yet been fully characterized. Here, we apply a brain dynamics analysis approach to study longitudinal brain activity patterns in individuals with ischemic pontine stroke. We first found 4 commonly occurring brain states largely characterized by high amplitude activations in the visual, frontoparietal, default mode, and motor networks. Stroke subjects spent less time in the frontoparietal state compared to controls. For individuals with dominant-hand CST damage, more time spent in the frontoparietal state from 1 week to 3-6 months post-stroke was associated with better motor recovery over the same time period, an association which was independent of baseline impairment. Furthermore, the amount of time spent in brain states was linked empirically to functional connectivity. This work suggests that when the dominant-hand CST is compromised in stroke, resting state configurations may include increased activation of the frontoparietal network, which may facilitate compensatory neural pathways that support recovery of motor function when traditional motor circuits of the dominant-hemisphere are compromised.

Edge-centric analysis of time-varying functional brain networks with applications in autism spectrum disorder

The interaction between brain regions changes over time, which can be characterized using time-varying functional connectivity (tvFC). The common approach to estimate tvFC uses sliding windows and offers limited temporal resolution. An alternative method is to use the recently proposed edge-centric approach, which enables the tracking of moment-to-moment changes in co-fluctuation patterns between pairs of brain regions. Here, we first examined the dynamic features of edge time series and compared them to those in the sliding window tvFC (sw-tvFC). Then, we used edge time series to compare subjects with autism spectrum disorder (ASD) and healthy controls (CN). Our results indicate that relative to sw-tvFC, edge time series captured rapid and bursty network-level fluctuations that synchronize across subjects during movie-watching. The results from the second part of the study suggested that the magnitude of peak amplitude in the collective co-fluctuations of brain regions (estimated as root sum square (RSS) of edge time series) is similar in CN and ASD. However, the trough-to-trough duration in RSS signal is greater in ASD, compared to CN. Furthermore, an edge-wise comparison of high-amplitude co-fluctuations showed that the within-network edges exhibited greater magnitude fluctuations in CN. Our findings suggest that high-amplitude co-fluctuations captured by edge time series provide details about the disruption of functional brain dynamics that could potentially be used in developing new biomarkers of mental disorders.

Precision dynamical mapping using topological data analysis reveals a hub-like transition state at rest

In the absence of external stimuli, neural activity continuously evolves from one configuration to another. Whether these transitions or explorations follow some underlying arrangement or lack a predictable ordered plan remains to be determined. Here, using fMRI data from highly sampled individuals (~5 hours of resting-state data per individual), we aimed to reveal the rules that govern transitions in brain activity at rest. Our Topological Data Analysis based Mapper approach characterized a highly visited transition state of the brain that acts as a switch between different neural configurations to organize the spontaneous brain activity. Further, while the transition state was characterized by a uniform representation of canonical resting-state networks (RSNs), the periphery of the landscape was dominated by a subject-specific combination of RSNs. Altogether, we revealed rules or principles that organize spontaneous brain activity using a precision dynamics approach.

A parsimonious description of global functional brain organization in three spatiotemporal patterns

Resting-state functional magnetic resonance imaging (MRI) has yielded seemingly disparate insights into large-scale organization of the human brain. The brain's large-scale organization can be divided into two broad categories: zero-lag representations of functional connectivity structure and time-lag representations of traveling wave or propagation structure. In this study, we sought to unify observed phenomena across these two categories in the form of three low-frequency spatiotemporal patterns composed of a mixture of standing and traveling wave dynamics. We showed that a range of empirical phenomena, including functional connectivity gradients, the task-positive/task-negative anti-correlation pattern, the global signal, time-lag propagation patterns, the quasiperiodic pattern and the functional connectome network structure, are manifestations of these three spatiotemporal patterns. These patterns account for much of the global spatial structure that underlies functional connectivity analyses and unifies phenomena in resting-state functional MRI previously thought distinct.