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About the Authors: Veronika Cheplygina Affiliation: Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands Felienne Hermans * E-mail: felienne@gmail.com Affiliations Leiden Institute of Advanced Computer Science, Leiden University, Leiden, The Netherlands, Software Engineering Research Group, Delft University of Technology, Delft, The Netherlands ORCID logo http://orcid.org/0000-0003-0722-0156 Casper Albers Affiliation: Heymans Institute for Psychological Research, University of Groningen, Groningen, The Netherlands ORCID logo http://orcid.org/0000-0002-9213-6743 Natalia Bielczyk Affiliation: Stichting Solaris Onderzoek en Ontwikkeling, Nijmegen, the Netherlands ORCID logo http://orcid.org/0000-0003-1604-9143 Ionica Smeets Affiliation: Science Communication and Society, Institute of Biology, Leiden University, Leiden, The Netherlands ORCID logo http://orcid.org/0000-0003-1743-9493 Introduction Twitter is one of the most popular social media platforms, with over 320 million active users as of February 2019. By default, regular Twitter messages are visible to the whole world, including (via search engines such as Google) people who do not have a Twitter account. * Hashtag (#)—used to make it easier to find tweets with a common theme by defining ad hoc keywords, for instance tweets about a conference (#ICA19) or career talks (#PhDChat). * List—a list of Twitter users that can be public (followed by anyone) or private. Senior researchers openly share ideas through Twitter and this can lead to the development of new concepts which often move on to become fully-fledged research projects. For ECRs, starting Twitter activity may be hard. [...]we recommend joining a peer group, together with members of your local research group, together with other collaborators or friends in the research community.

The brain is a complex, multiscale dynamical system composed of many interacting regions. Knowledge of the spatiotemporal organization of these interactions is critical for establishing a solid understanding of the brain’s functional architecture and the relationship between neural dynamics and cognition in health and disease. The possibility of studying these dynamics through careful analysis of neuroimaging data has catalyzed substantial interest in methods that estimate time-resolved fluctuations in functional connectivity (often referred to as “dynamic” or time-varying functional connectivity; TVFC). At the same time, debates have emerged regarding the application of TVFC analyses to resting fMRI data, and about the statistical validity, physiological origins, and cognitive and behavioral relevance of resting TVFC. These and other unresolved issues complicate interpretation of resting TVFC findings and limit the insights that can be gained from this promising new research area. This article brings together scientists with a variety of perspectives on resting TVFC to review the current literature in light of these issues. We introduce core concepts, define key terms, summarize controversies and open questions, and present a forward-looking perspective on how resting TVFC analyses can be rigorously and productively applied to investigate a wide range of questions in cognitive and systems neuroscience.

It is known that cortical networks operate on the edge of instability, in which oscillations can appear. However, the influence of this dynamic regime on performance in decision making, is not well understood. In this work, we propose a population model of decision making based on a winner-take-all mechanism. Using this model, we demonstrate that local slow inhibition within the competing neuronal populations can lead to Hopf bifurcation. At the edge of instability, the system exhibits ambiguity in the decision making, which can account for the perceptual switches observed in human experiments. We further validate this model with fMRI datasets from an experiment on semantic priming in perception of ambivalent (male versus female) faces. We demonstrate that the model can correctly predict the drop in the variance of the BOLD within the Superior Parietal Area and Inferior Parietal Area while watching ambiguous visual stimuli.

In the past two decades, functional Magnetic Resonance Imaging (fMRI) has been used to relate neuronal network activity to cognitive processing and behavior. Recently this approach has been augmented by algorithms that allow us to infer causal links between component populations of neuronal networks. Multiple inference procedures have been proposed to approach this research question but so far, each method has limitations when it comes to establishing whole-brain connectivity patterns. In this paper, we discuss eight ways to infer causality in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality, Likelihood Ratios, Linear Non-Gaussian Acyclic Models, Patel’s Tau, Structural Equation Modelling, and Transfer Entropy. We finish with formulating some recommendations for the future directions in this area.

Functional connectivity has been shown to be a very promising tool for studying the large-scale functional architecture of the human brain. In network research in fMRI, functional connectivity is considered as a set of pair-wise interactions between the nodes of the network. These interactions are typically operationalized through the full or partial correlation between all pairs of regional time series. Estimating the structure of the latent underlying functional connectome from the set of pair-wise partial correlations remains an open research problem though. Typically, this thresholding problem is approached by proportional thresholding, or by means of parametric or non-parametric permutation testing across a cohort of subjects at each possible connection. As an alternative, we propose a data-driven thresholding approach for network matrices on the basis of mixture modeling. This approach allows for creating subject-specific sparse connectomes by modeling the full set of partial correlations as a mixture of low correlation values associated with weak or unreliable edges in the connectome and a sparse set of reliable connections. Consequently, we propose to use alternative thresholding strategy based on the model fit using pseudo-False Discovery Rates derived on the basis of the empirical null estimated as part of the mixture distribution. We evaluate the method on synthetic benchmark fMRI datasets where the underlying network structure is known, and demonstrate that it gives improved performance with respect to the alternative methods for thresholding connectomes, given the canonical thresholding levels. We also demonstrate that mixture modeling gives highly reproducible results when applied to the functional connectomes of the visual system derived from the n-back Working Memory task in the Human Connectome Project. The sparse connectomes obtained from mixture modeling are further discussed in the light of the previous knowledge of the functional architecture of the visual system in humans. We also demonstrate that with use of our method, we are able to extract similar information on the group level as can be achieved with permutation testing even though these two methods are not equivalent. We demonstrate that with both of these methods, we obtain functional decoupling between the two hemispheres in the higher order areas of the visual cortex during visual stimulation as compared to the resting state, which is in line with previous studies suggesting lateralization in the visual processing. However, as opposed to permutation testing, our approach does not require inference at the cohort level and can be used for creating sparse connectomes at the level of a single subject. •Sparse functional connectomes are useful in analyzing and interpreting fMRI data.•We propose thresholding by means of mixture modeling and control of FDR.•We benchmark the approach on synthetic fMRI data against established methods.•We apply the method to the resting state and working memory task datasets from HCP500.•Results are reproducible on synthetic data and interpretable on experimental data.

Quantification and parametrisation of movement are widely used in animal behavioural paradigms. In particular, free movement in controlled conditions (e.g., open field paradigm) is used as a “proxy for indices of baseline and drug-induced behavioural changes. However, the analysis of this is often time- and labour-intensive and existing algorithms do not always classify the behaviour correctly. Here, we propose a new approach to quantify behaviour in an unconstrained environment: searching for frequent patterns (k-motifs) in the time series representing the position of the subject over time. Validation of this method was performed using subchronic quinpirole-induced changes in open field experiment behaviours in rodents. Analysis of this data was performed using k-motifs as features to better classify subjects into experimental groups on the basis of behaviour in the open field. Our classifier using k-motifs gives as high as 94% accuracy in classifying repetitive behaviour versus controls which is a substantial improvement compared to currently available methods including using standard feature definitions (depending on the choice of feature set and classification strategy, accuracy up to 88%). Furthermore, visualisation of the movement/time patterns is highly predictive of these behaviours. By using machine learning, this can be applied to behavioural analysis across experimental paradigms.

Impairments in decision-making are frequently observed in neurodegenerative diseases, but the mechanisms underlying such pathologies remain elusive. In this work, we study, on the basis of novel time-delayed neuronal population model, if the delay in self-inhibition terms can explain those impairments. Analysis of proposed system reveals that there can be up to three positive steady states, with the one having the lowest neuronal activity being always locally stable in nondelayed case. We show, however, that this steady state becomes unstable above a critical delay value for which, in certain parameter ranges, a subcritical Hopf bifurcation occurs. We then apply psychometric function to translate model-predicted ring rates into probabilities that a decision is being made. Using numerical simulations, we demonstrate that for small synaptic delays the decision-making process depends directly on the strength of supplied stimulus and the system correctly identifies to which population the stimulus was applied. However, for delays above the Hopf bifurcation threshold we observe complex impairments in the decision-making process; that is, increasing the strength of the stimulus may lead to the change in the neuronal decision into a wrong one. Furthermore, above critical delay threshold, the system exhibits ambiguity in the decision-making.

Estimating causal interactions in the brain from functional magnetic resonance imaging (fMRI) data remains a challenging task. Multiple studies have demonstrated that all current approaches to determine direction of connectivity perform poorly when applied to synthetic fMRI datasets. Recent advances in this field include methods for pairwise inference, which involve creating a sparse connectome in the first step, and then using a classifier in order to determine the directionality of connection between every pair of nodes in the second step. In this work, we introduce an advance to the second step of this procedure, by building a classifier based on fractional moments of the BOLD distribution combined into cumulants. The classifier is trained on datasets generated under the dynamic causal modeling (DCM) generative model. The directionality is inferred based on statistical dependencies between the two-node time series, for example, by assigning a causal link from time series of low variance to time series of high variance. Our approach outperforms or performs as well as other methods for effective connectivity when applied to the benchmark datasets. Crucially, it is also more resilient to confounding effects such as differential noise level across different areas of the connectome. Estimating causal interactions from functional magnetic resonance imaging (fMRI) data is a formidable task. Recent advances in this field include methods for pairwise inference. In the first step of this procedure, connections are revealed by means of functional connectivity. In the second step, every detected connection is analyzed separately to reveal the direction of the causal links. We introduce an advance to the second step of this procedure by building a classifier based on the novel concept of fractional moments of the BOLD distribution combined into cumulants. The classifier is trained on datasets generated under the dynamic causal modeling (DCM) generative model. Using fractional cumulants gives a measure resilient to confounding effects such as differential noise levels across different areas of the connectome.

Purpose Multiple computational studies have demonstrated that essentially all current analytical approaches to determine effective connectivity perform poorly when applied to synthetic functional Magnetic Resonance Imaging (fMRI) datasets. In this study, we take a theoretical approach to investigate the potential factors facilitating and hindering effective connectivity research in fMRI. Materials and Methods In this work, we perform a simulation study with use of Dynamic Causal Modeling generative model in order to gain new insights on the influence of factors such as the slow hemodynamic response, mixed signals in the network and short time series, on the effective connectivity estimation in fMRI studies. Results First, we perform a Linear Discriminant Analysis study and find that not the hemodynamics itself but mixed signals in the neuronal networks are detrimental to the signatures of distinct connectivity patterns. This result suggests that for statistical methods (which do not involve lagged signals), deconvolving the BOLD responses is not necessary, but at the same time, functional parcellation into Regions of Interest (ROIs) is essential. Second, we study the impact of hemodynamic variability on the inference with use of lagged methods. We find that the local hemodynamic variability provide with an upper bound on the success rate of the lagged methods. Furthermore, we demonstrate that upsampling the data to TRs lower than the TRs in state‐of‐the‐art datasets does not influence the performance of the lagged methods. Conclusions Factors such as background scale‐free noise and hemodynamic variability have a major impact on the performance of methods for effective connectivity research in functional Magnetic Resonance Imaging. In this work, we perform a simulation study in order to gain new insights on the influence of potential confounders on the effective connectivity estimation in functional Magnetic Resonance Imaging studies. We find that factors such as the magnitude of the background scale‐free noise and a local hemodynamic variability have a major influence on the performance of methods for effective connectivity research in fMRI.

Doc number: P26