Exploration of distance metrics in consensus clustering analysis of FMRI data

Clustering techniques have gained great popularity in neuroscience data analysis especially in analysing data from complex experiment paradigm where it is hard to apply traditional model-based method. However, when employing clustering analysis, many clustering algorithms are available nowadays and even with an individual clustering algorithm, choices like parameter settings and distance metrics are very likely to have impacts on the final clustering results. In our previous work, we have demonstrated the benefits of integrating clustering results from multiple clustering algorithms, which provides more stable, reproducible, and complete clustering solutions. In this paper, we aim to further inspect the possible influences from the choices of distance metrics in clustering analysis

Brain networks under attack : robustness properties and the impact of lesions

A growing number of studies approach the brain as a complex network, the so-called ‘connectome’. Adopting this framework, we examine what types or extent of damage the brain can withstand—referred to as network ‘robustness’—and conversely, which kind of distortions can be expected after brain lesions. To this end, we review computational lesion studies and empirical studies investigating network alterations in brain tumour, stroke and traumatic brain injury patients. Common to these three types of focal injury is that there is no unequivocal relationship between the anatomical lesion site and its topological characteristics within the brain network. Furthermore, large-scale network effects of these focal lesions are compared to those of a widely studied multifocal neurodegenerative disorder, Alzheimer’s disease, in which central parts of the connectome are preferentially affected. Results indicate that human brain networks are remarkably resilient to different types of lesions, compared to other types of complex networks such as random or scale-free networks. However, lesion effects have been found to depend critically on the topological position of the lesion. In particular, damage to network hub regions—and especially those connecting different subnetworks—was found to cause the largest disturbances in network organization. Regardless of lesion location, evidence from empirical and computational lesion studies shows that lesions cause significant alterations in global network topology. The direction of these changes though remains to be elucidated. Encouragingly, both empirical and modelling studies have indicated that after focal damage, the connectome carries the potential to recover at least to some extent, with normalization of graph metrics being related to improved behavioural and cognitive functioning. To conclude, we highlight possible clinical implications of these findings, point out several methodological limitations that pertain to the study of brain diseases adopting a network approach, and provide suggestions for future research

Factorized Binary Search: change point detection in the network structure of multivariate high-dimensional time series

Functional magnetic resonance imaging (fMRI) time series data presents a unique opportunity to understand temporal brain connectivity, and models that uncover the complex dynamic workings of this organ are of keen interest in neuroscience. Change point models can capture and reflect the dynamic nature of brain connectivity, however methods that translate well into a high-dimensional context (where $p>>n$) are scarce. To this end, we introduce $\textit{factorized binary search}$ (FaBiSearch), a novel change point detection method in the network structure of multivariate high-dimensional time series. FaBiSearch uses non-negative matrix factorization, an unsupervised dimension reduction technique, and a new binary search algorithm to identify multiple change points. In addition, we propose a new method for network estimation for data between change points. We show that FaBiSearch outperforms another state-of-the-art method on simulated data sets and we apply FaBiSearch to a resting-state and to a task-based fMRI data set. In particular, for the task-based data set, we explore network dynamics during the reading of Chapter 9 in $\textit{Harry Potter and the Sorcerer's Stone}$ and find that change points across subjects coincide with key plot twists. Further, we find that the density of networks was positively related to the frequency of speech between characters in the story. Finally, we make all the methods discussed available in the R package $\textbf{fabisearch}$ on CRAN

Towards a consensus regarding global signal regression for resting state functional connectivity MRI

The number of resting state functional connectivity MRI studies continues to expand at a rapid rate along with the options for data processing. Of the processing options, few have generated as much controversy as global signal regression and the subsequent observation of negative correlations (anti-correlations). This debate has motivated new processing strategies and advancement in the field, but has also generated significant confusion and contradictory guidelines. In this article, we work towards a consensus regarding global signal regression. We highlight several points of agreement including the fact that there is not a single “right” way to process resting state data that reveals the “true” nature of the brain. Although further work is needed, different processing approaches likely reveal complementary insights about the brain's functional organisation

Dynamic Reorganization of Functional Connectivity Reveals Abnormal Temporal Efficiency in Schizophrenia.

Emerging evidence suggests that schizophrenia is associated with brain dysconnectivity. Nonetheless, the implicit assumption of stationary functional connectivity (FC) adopted in most previous resting-state functional magnetic resonance imaging (fMRI) studies raises an open question of schizophrenia-related aberrations in dynamic properties of resting-state FC. This study introduces an empirical method to examine the dynamic functional dysconnectivity in patients with schizophrenia. Temporal brain networks were estimated from resting-state fMRI of 2 independent datasets (patients/controls = 18/19 and 53/57 for self-recorded dataset and a publicly available replication dataset, respectively) by the correlation of sliding time-windowed time courses among regions of a predefined atlas. Through the newly introduced temporal efficiency approach and temporal random network models, we examined, for the first time, the 3D spatiotemporal architecture of the temporal brain network. We found that although prominent temporal small-world properties were revealed in both groups, temporal brain networks of patients with schizophrenia in both datasets showed a significantly higher temporal global efficiency, which cannot be simply attributable to head motion and sampling error. Specifically, we found localized changes of temporal nodal properties in the left frontal, right medial parietal, and subcortical areas that were associated with clinical features of schizophrenia. Our findings demonstrate that altered dynamic FC may underlie abnormal brain function and clinical symptoms observed in schizophrenia. Moreover, we provide new evidence to extend the dysconnectivity hypothesis in schizophrenia from static to dynamic brain network and highlight the potential of aberrant brain dynamic FC in unraveling the pathophysiologic mechanisms of the disease

An Invitation to the Study of Brain Networks, with Some Statistical Analysis of Thresholding Techniques

We provide a brief introduction to the nascent application of network theory to mesoscale networks in the human brain. Following an overview of the typical data-gathering, processing, and analysis methods employed in this field, we describe the process for inferring a graph from neural time series. A crucial step in the construction of a graph from time series is the thresholding of graph edges to ensure that the graphs represent physiological relationships rather than artifactual noise. We discuss the most popular currently employed methodologies and then introduce one of our own, based on the theory of random matrices. Finally, we provide a comparison of our random-matrix-theory thresholding approach with two dominant approaches on a data set of 1,000 real resting-state functional magnetic resonance imaging scans

Trait self-reflectiveness relates to time-varying dynamics of resting state functional connectivity and underlying structural connectomes:Role of the default mode network

BACKGROUND: Cognitive insight is defined as the ability to reflect upon oneself (i.e. self-reflectiveness), and to not be overly confident of one's own (incorrect) beliefs (i.e. self-certainty). These abilities are impaired in several disorders, while they are essential for the evaluation and regulation of one's behavior. We hypothesized that cognitive insight is a dynamic process, and therefore examined how it relates to temporal dynamics of resting state functional connectivity (FC) and underlying structural network characteristics in 58 healthy individuals. METHODS: Cognitive insight was measured with the Beck Cognitive Insight Scale. FC characteristics were calculated after obtaining four FC states with leading eigenvector dynamics analysis. Gray matter (GM) and DTI connectomes were based on GM similarity and probabilistic tractography. Structural graph characteristics, such as path length, clustering coefficient, and small-world coefficient, were calculated with the Brain Connectivity Toolbox. FC and structural graph characteristics were correlated with cognitive insight. RESULTS: Individuals with lower cognitive insight switched more and spent less time in a globally synchronized state. Additionally, individuals with lower self-reflectiveness spent more time in, had a higher probability of, and had a higher chance of switching to a state entailing default mode network (DMN) areas. With lower self-reflectiveness, DTI-connectomes were segregated less (i.e. lower global clustering coefficient) with lower embeddedness of the left angular gyrus specifically (i.e. lower local clustering coefficient). CONCLUSIONS: Our results suggest less stable functional and structural networks in individuals with poorer cognitive insight, specifically self-reflectiveness. An overly present DMN appears to play a key role in poorer self-reflectiveness

A transdiagnostic data-driven study of children's behaviour and the functional connectome.

Behavioural difficulties are seen as hallmarks of many neurodevelopmental conditions. Differences in functional brain organisation have been observed in these conditions, but little is known about how they are related to a child's profile of behavioural difficulties. We investigated whether behavioural difficulties are associated with how the brain is functionally organised in an intentionally heterogeneous and transdiagnostic sample of 957 children aged 5-15. We used consensus community detection to derive data-driven profiles of behavioural difficulties and constructed functional connectomes from a subset of 238 children with resting-state functional Magnetic Resonance Imaging (fMRI) data. We identified three distinct profiles of behaviour that were characterised by principal difficulties with hot executive function, cool executive function, and learning. Global organisation of the functional connectome did not differ between the groups, but multivariate patterns of connectivity at the level of Intrinsic Connectivity Networks (ICNs), nodes, and hubs significantly predicted group membership in held-out data. Fronto-parietal connector hubs were under-connected in all groups relative to a comparison sample and children with hot vs cool executive function difficulties were distinguished by connectivity in ICNs associated with cognitive control, emotion processing, and social cognition. This demonstrates both general and specific neurodevelopmental risk factors in the functional connectome

Networks in cognitive science

Networks of interconnected nodes have long played a key role in Cognitive Science, from artificial neural networks to spreading activation models of semantic memory. Recently, however, a new Network Science has been developed, providing insights into the emergence of global, system-scale properties in contexts as diverse as the Internet, metabolic reactions, and collaborations among scientists. Today, the inclusion of network theory into Cognitive Sciences, and the expansion of complex-systems science, promises to significantly change the way in which the organization and dynamics of cognitive and behavioral processes are understood. In this paper, we review recent contributions of network theory at different levels and domains within the Cognitive Sciences.Postprint (author's final draft