Subject identification using edge-centric functional connectivity

A survey of brain functional network extraction methods using fMRI data

Functional network (FN) analyses play a pivotal role in uncovering insights into brain function and understanding the pathophysiology of various brain disorders. This paper focuses on classical and advanced methods for deriving brain FNs from functional magnetic resonance imaging (fMRI) data. We systematically review their foundational principles, advantages, shortcomings, and interrelations, encompassing both static and dynamic FN extraction approaches. In the context of static FN extraction, we present hypothesis-driven methods such as region of interest (ROI)-based approaches as well as data-driven methods including matrix decomposition, clustering, and deep learning. For dynamic FN extraction, both window-based and windowless methods are surveyed with respect to the estimation of time-varying FN and the subsequent computation of FN states. We also discuss the scope of application of the various methods and avenues for future improvements.

Multimodal identification of the mouse brain using simultaneous Ca 2+ imaging and fMRI

Individual differences in neuroimaging are of interest to clinical and cognitive neuroscientists based on their potential for guiding the personalized treatment of various heterogeneous neurological conditions and diseases. Despite many advantages, the workhorse in this arena, BOLD (blood-oxygen-level-dependent) functional magnetic resonance imaging (fMRI) suffers from low spatiotemporal resolution and specificity as well as a propensity for noise and spurious signal corruption. To better understand individual differences in BOLD-fMRI data, we can use animal models where fMRI, alongside complementary but more invasive contrasts, can be accessed. Here, we apply simultaneous wide-field fluorescence calcium imaging and BOLD-fMRI in mice to interrogate individual differences using a connectome-based identification framework adopted from the human fMRI literature. This approach yields high spatiotemporal resolution cell-type specific signals (here, from glia, excitatory, as well as inhibitory interneurons) from the whole cortex. We found mouse multimodal connectome- based identification to be successful and explored various features of these data.

Diagnostically distinct resting state fMRI energy distributions: A subject-specific maximum entropy modeling study

Objective

Existing neuroimaging studies of psychotic and mood disorders have reported brain activation differences (first-order properties) and altered pairwise correlation-based functional connectivity (second-order properties). However, both approaches have certain limitations that can be overcome by integrating them in a pairwise maximum entropy model (MEM) that better represents a comprehensive picture of fMRI signal patterns and provides a system-wide summary measure called energy. This study examines the applicability of individual-level MEM for psychiatry and identifies image-derived model coefficients related to model parameters.

Method

MEMs are fit to resting state fMRI data from each individual with schizophrenia/schizoaffective disorder, bipolar disorder, and major depression (n=132) and demographically matched healthy controls (n=132) from the UK Biobank to different subsets of the default mode network (DMN) regions.

Results

The model satisfactorily explained observed brain energy state occurrence probabilities across all participants, and model parameters were significantly correlated with image-derived coefficients for all groups. Within clinical groups, averaged energy level distributions were higher in schizophrenia/schizoaffective disorder but lower in bipolar disorder compared to controls for both bilateral and unilateral DMN. Major depression energy distributions were higher compared to controls only in the right hemisphere DMN.

Conclusions

Diagnostically distinct energy states suggest that probability distributions of temporal changes in synchronously active nodes may underlie each diagnostic entity. Subject-specific MEMs allow for factoring in the individual variations compared to traditional group-level inferences, offering an improved measure of biologically meaningful correlates of brain activity that may have potential clinical utility.

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.

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.

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.

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.

Strong intercorrelations among global graph-theoretic indices of structural connectivity in the human brain

Graph-theoretic metrics derived from neuroimaging data have been heralded as powerful tools for uncovering neural mechanisms of psychological traits, psychiatric disorders, and neurodegenerative diseases. In N = 8,185 human structural connectomes from UK Biobank, we examined the extent to which 11 commonly-used global graph-theoretic metrics index distinct versus overlapping information with respect to interindividual differences in brain organization. Using unthresholded, FA-weighted networks we found that all metrics other than Participation Coefficient were highly intercorrelated, both with each other (mean |r| = 0.788) and with a topologically-naïve summary index of brain structure (mean edge weight; mean |r| = 0.873). In a series of sensitivity analyses, we found that overlap between metrics is influenced by the sparseness of the network and the magnitude of variation in edge weights. Simulation analyses representing a range of population network structures indicated that individual differences in global graph metrics may be intrinsically difficult to separate from mean edge weight. In particular, Closeness, Characteristic Path Length, Global Efficiency, Clustering Coefficient, and Small Worldness were nearly perfectly collinear with one another (mean |r| = 0.939) and with mean edge weight (mean |r| = 0.952) across all observed and simulated conditions. Global graph-theoretic measures are valuable for their ability to distill a high-dimensional system of neural connections into summary indices of brain organization, but they may be of more limited utility when the goal is to index separable components of interindividual variation in specific properties of the human structural connectome.

Hierarchical overlapping modular structure in the human cerebral cortex improves individual identification

The idea that brain networks have a hierarchical modular organization is pervasive. Increasing evidence suggests that brain modules overlap. However, little is known about the hierarchical overlapping modular structure in the brain. In this study, we developed a framework to uncover brain hierarchical overlapping modular structures based on a nested-spectral partition algorithm and an edge-centric network model. Overlap degree between brain modules is symmetrical across hemispheres, with highest overlap observed in the control and salience/ventral attention networks. Furthermore, brain edges are clustered into two groups: intrasystem and intersystem edges, to form hierarchical overlapping modules. At different levels, modules are self-similar in the degree of overlap. Additionally, the brain's hierarchical structure contains more individual identifiable information than a single-level structure, particularly in the control and salience/ventral attention networks. Our results offer pathways for future studies aimed at relating the organization of hierarchical overlapping modules to brain cognitive behavior and disorders.

Edge-centric functional network predicts risk propensity in economic decision-making: evidence from a resting-state fMRI study

Despite node-centric studies revealing an association between resting-state functional connectivity and individual risk propensity, the prediction of future risk decisions remains undetermined. Herein, we applied a recently emerging edge-centric method, the edge community similarity network (ECSN), to alternatively describe the community structure of resting-state brain activity and to probe its contribution to predicting risk propensity during gambling. Results demonstrated that inter-individual variability of risk decisions correlates with the inter-subnetwork couplings spanning the visual network (VN) and default mode network (DMN), cingulo-opercular task control network, and sensory/somatomotor hand network (SSHN). Particularly, participants who have higher community similarity of these subnetworks during the resting state tend to choose riskier and higher yielding bets. And in contrast to low-risk propensity participants, those who behave high-risky show stronger couplings spanning the VN and SSHN/DMN. Eventually, based on the resting-state ECSN properties, the risk rate during the gambling task is effectively predicted by the multivariable linear regression model at the individual level. These findings provide new insights into the neural substrates of the inter-individual variability in risk propensity and new neuroimaging metrics to predict individual risk decisions in advance.

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.

Leveraging edge-centric networks complements existing network-level inference for functional connectomes

The human connectome is modular with distinct brain regions clustering together to form large-scale communities, or networks. This concept has recently been leveraged in novel inferencing procedures by averaging the edge-level statistics within networks to induce more powerful inferencing at the network level. However, these networks are constructed based on the similarity between pairs of nodes. Emerging work has described novel edge-centric networks, which instead use the similarity between pairs of edges to construct networks. In this work, we use these edge-centric networks in a network-level inferencing procedure and compare this novel method to traditional inferential procedures and the network-level procedure using node-centric networks. We use data from the Human Connectome Project, the Healthy Brain Network, and the Philadelphia Neurodevelopmental Cohort and use a resampling technique with various sample sizes (n=40, 80, 120) to probe the power and specificity of each method. Across datasets and sample sizes, using the edge-centric networks outperforms using node-centric networks for inference as well as edge-level FDR correction and NBS. Additionally, the edge-centric networks were found to be more consistent in clustering effect sizes of similar values as compared to node-centric networks, although node-centric networks often had a lower average within-network effect size variability. Together, these findings suggest that using edge-centric networks for network-level inference can procure relatively powerful results while remaining similarly accurate to the underlying edge-level effects across networks, complementing previous inferential methods.

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.

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.

Neural connectome features of procrastination: Current progress and future direction

Procrastination refers to an irrationally delay for intended courses of action despite of anticipating a negative consequence due to this delay. Previous studies tried to reveal the neural substrates of procrastination in terms of connectome-based biomarkers. Based on this, we proposed a unified triple brain network model for procrastination and pinpointed out what challenges we are facing in understanding neural mechanism of procrastination. Specifically, based on neuroanatomical features, the unified triple brain network model proposed that connectome-based underpinning of procrastination could be ascribed to the abnormalities of self-control network (i.e., dorsolateral prefrontal cortex, DLPFC), emotion-regulation network (i.e., orbital frontal cortex, OFC), and episodic prospection network (i.e., para-hippocampus cortex, PHC). Moreover, based on the brain functional features, procrastination had been attributed to disruptive neural circuits on FPN (frontoparietal network)-SCN (subcortical network) and FPN-SAN (salience network), which led us to hypothesize the crucial roles of interplay between these networks on procrastination in unified triple brain network model. Despite of these findings, poor interpretability and computational model limited further understanding for procrastination from theoretical and neural perspectives. On balance, the current study provided an overview to show current progress on the connectome-based biomarkers for procrastination, and proposed the integrative neurocognitive model of procrastination.

Time-resolved structure-function coupling in brain networks

The relationship between structural and functional connectivity in the brain is a key question in systems neuroscience. Modern accounts assume a single global structure-function relationship that persists over time. Here we study structure-function coupling from a dynamic perspective, and show that it is regionally heterogeneous. We use a temporal unwrapping procedure to identify moment-to-moment co-fluctuations in neural activity, and reconstruct time-resolved structure-function coupling patterns. We find that patterns of dynamic structure-function coupling are region-specific. We observe stable coupling in unimodal and transmodal cortex, and dynamic coupling in intermediate regions, particularly in insular cortex (salience network) and frontal eye fields (dorsal attention network). Finally, we show that the variability of a region’s structure-function coupling is related to the distribution of its connection lengths. Collectively, our findings provide a way to study structure-function relationships from a dynamic perspective.

Temporal unwrapping analysis of diffusion weighted MRI connectivity and functional MRI scans reveals that the coupling between structure and function in the human brain is regionally heterogeneous and provides a framework to evaluate these relationships from a dynamic perspective.

Edge-centric analysis of stroke patients: An alternative approach for biomarkers of lesion recovery

Most neuroimaging studies of post-stroke recovery rely on analyses derived from standard node-centric functional connectivity to map the distributed effects in stroke patients. Here, given the importance of nonlocal and diffuse damage, we use an edge-centric approach to functional connectivity in order to provide an alternative description of the effects of this disorder. These techniques allow for the rendering of metrics such as normalized entropy, which describes the diversity of edge communities at each node. Moreover, the approach enables the identification of high amplitude co-fluctuations in fMRI time series. We found that normalized entropy is associated with stroke lesion severity and continually increases across the time of patients' recovery. Furthermore, high amplitude co-fluctuations not only relate to the lesion severity but are also associated with patients' level of recovery. The current study is the first edge-centric application for a clinical population in a longitudinal dataset and demonstrates how a different perspective for functional data analysis can further characterize topographic modulations of brain dynamics.

Neural alterations in opioid-exposed infants revealed by edge-centric brain functional networks

Prenatal opioid exposure has been linked to adverse effects spanning multiple neurodevelopmental domains, including cognition, motor development, attention, and vision. However, the neural basis of these abnormalities is largely unknown. A total of 49 infants, including 21 opioid-exposed and 28 controls, were enrolled and underwent MRI (43 ± 6 days old) after birth, including resting state functional MRI. Edge-centric functional networks based on dynamic functional connections were constructed, and machine-learning methods were employed to identify neural features distinguishing opioid-exposed infants from unexposed controls. An accuracy of 73.6% (sensitivity 76.25% and specificity 69.33%) was achieved using 10 times 10-fold cross-validation, which substantially outperformed those obtained using conventional static functional connections (accuracy 56.9%). More importantly, we identified that prenatal opioid exposure preferentially affects inter- rather than intra-network dynamic functional connections, particularly with the visual, subcortical, and default mode networks. Consistent results at the brain regional and connection levels were also observed, where the brain regions and connections associated with visual and higher order cognitive functions played pivotal roles in distinguishing opioid-exposed infants from controls. Our findings support the clinical phenotype of infants exposed to opioids in utero and may potentially explain the higher rates of visual and emotional problems observed in this population. Finally, our findings suggested that edge-centric networks could better capture the neural differences between opioid-exposed infants and controls by abstracting the intrinsic co-fluctuation along edges, which may provide a promising tool for future studies focusing on investigating the effects of prenatal opioid exposure on neurodevelopment.

Dynamic expression of brain functional systems disclosed by fine-scale analysis of edge time series

Functional connectivity (FC) describes the statistical dependence between neuronal populations or brain regions in resting-state fMRI studies and is commonly estimated as the Pearson correlation of time courses. Clustering or community detection reveals densely coupled sets of regions constituting resting-state networks or functional systems. These systems manifest most clearly when FC is sampled over longer epochs but appear to fluctuate on shorter timescales. Here, we propose a new approach to reveal temporal fluctuations in neuronal time series. Unwrapping FC signal correlations yields pairwise co-fluctuation time series, one for each node pair or edge, and allows tracking of fine-scale dynamics across the network. Co-fluctuations partition the network, at each time step, into exactly two communities. Sampled over time, the overlay of these bipartitions, a binary decomposition of the original time series, very closely approximates functional connectivity. Bipartitions exhibit characteristic spatiotemporal patterns that are reproducible across participants and imaging runs, capture individual differences, and disclose fine-scale temporal expression of functional systems. Our findings document that functional systems appear transiently and intermittently, and that FC results from the overlay of many variable instances of system expression. Potential applications of this decomposition of functional connectivity into a set of binary patterns are discussed.