Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches

In the past two decades, functional Magnetic Resonance Imaging has been used to relate neuronal network activity to cognitive processing and behaviour. 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 work, we discuss eight ways to infer causality in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality, Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and Transfer Entropy. We finish with formulating some recommendations for the future directions in this area

Advancing functional connectivity research from association to causation

Cognition and behavior emerge from brain network interactions, such that investigating causal interactions should be central to the study of brain function. Approaches that characterize statistical associations among neural time series-functional connectivity (FC) methods-are likely a good starting point for estimating brain network interactions. Yet only a subset of FC methods ('effective connectivity') is explicitly designed to infer causal interactions from statistical associations. Here we incorporate best practices from diverse areas of FC research to illustrate how FC methods can be refined to improve inferences about neural mechanisms, with properties of causal neural interactions as a common ontology to facilitate cumulative progress across FC approaches. We further demonstrate how the most common FC measures (correlation and coherence) reduce the set of likely causal models, facilitating causal inferences despite major limitations. Alternative FC measures are suggested to immediately start improving causal inferences beyond these common FC measures

Combining optogenetic stimulation and fMRI to validate a multivariate dynamical systems model for estimating causal brain interactions

State-space multivariate dynamical systems (MDS) (Ryali et al., 2011) and other causal estimation models are being increasingly used to identify directed functional interactions between brain regions. However, the validity and accuracy of such methods is poorly understood. Performance evaluation based on computer simulations of small artificial causal networks can address this problem to some extent, but they often involve simplifying assumptions that reduce biological validity of the resulting data. Here, we use a novel approach taking advantage of recently developed optogenetic fMRI (ofMRI) techniques to selectively stimulate brain regions while simultaneously recording high-resolution whole-brain fMRI data. ofMRI allows for a more direct investigation of causal influences from the stimulated site to brain regions activated downstream and is therefore ideal for evaluating causal estimation methods in vivo. We used ofMRI to investigate whether MDS models for fMRI can accurately estimate causal functional interactions between brain regions. Two cohorts of ofMRI data were acquired, one at Stanford University and the University of California Los Angeles (Cohort 1) and the other at the University of North Carolina Chapel Hill (Cohort 2). In each cohort optical stimulation was delivered to the right primary motor cortex (M1). General linear model analysis revealed prominent downstream thalamic activation in Cohort 1, and caudate-putamen (CPu) activation in Cohort 2. MDS accurately estimated causal interactions from M1 to thalamus and from M1 to CPu in Cohort 1 and Cohort 2, respectively. As predicted, no causal influences were found in the reverse direction. Additional control analyses demonstrated the specificity of causal interactions between stimulated and target sites. Our findings suggest that MDS state-space models can accurately and reliably estimate causal interactions in ofMRI data and further validate their use for estimating causal interactions in fMRI. More generally, our study demonstrates that the combined use of optogenetics and fMRI provides a powerful new tool for evaluating computational methods designed to estimate causal interactions between distributed brain regions

Effective connectivity among the working memory regions during preparation for and during performance of the n-back task

Recent neuroimaging studies have shown that working memory (WM) task difficulty can be decoded from patterns of brain activation in the WM network during preparation to perform those tasks. The inter-regional connectivity among the WM regions during task preparation has not yet been investigated. We examined this question using the graph modeling methods IMaGES and LOFS, applied to the previously published fMRI data of Manelis and Reder (2013). In that study, subjects performed 1-, 2-, and 3-back tasks. Each block of n-back was preceded by a preparation period and followed by a rest period. The analyses of task-related brain activity identified a network of 18 regions that increased in activation from 1to 3-back (Increase network) and a network of 17 regions that decreased in activation from 1to 3-back (Decrease network). The graph analyses revealed two types of connectivity sub-networks within the Increase and Decrease networks: "default" and "preparation-related." The "default" connectivity was present not only during task performance, but also during task preparation and during rest. We propose that this sub-network may serve as a core system that allows one to quickly activate cognitive, perceptual and motor systems in response to the relevant stimuli. The "preparation-related" connectivity was present during task preparation and task performance, but not at rest, and depended on the n-back condition. The role of this sub-network may be to pre-activate a connectivity "road map" in order to establish a top-down and bottom-up regulation of attention prior to performance on WM tasks. © 2014 Manelis and Reder

Dynamic effective connectivity

Metastability is a key source of itinerant dynamics in the brain; namely, spontaneous spatiotemporal reorganization of neuronal activity. This itinerancy has been the focus of numerous dynamic functional connectivity (DFC) analyses - developed to characterize the formation and dissolution of distributed functional patterns over time, using resting state fMRI. However, aside from technical and practical controversies, these approaches cannot recover the neuronal mechanisms that underwrite itinerant (e.g., metastable) dynamics-due to their descriptive, model-free nature. We argue that effective connectivity (EC) analyses are more apt for investigating the neuronal basis of metastability. To this end, we appeal to biologically-grounded models (i.e., dynamic causal modelling, DCM) and dynamical systems theory (i.e., heteroclinic sequential dynamics) to create a probabilistic, generative model of haemodynamic fluctuations. This model generates trajectories in the parametric space of EC modes (i.e., states of connectivity) that characterize functional brain architectures. In brief, it extends an established spectral DCM, to generate functional connectivity data features that change over time. This foundational paper tries to establish the model's face validity by simulating non-stationary fMRI time series and recovering key model parameters (i.e., transition probabilities among connectivity states and the parametric nature of these states) using variational Bayes. These data are further characterized using Bayesian model comparison (within and between subjects). Finally, we consider practical issues that attend applications and extensions of this scheme. Importantly, the scheme operates within a generic Bayesian framework - that can be adapted to study metastability and itinerant dynamics in any non-stationary time series

Altered structural and effective connectivity in anorexia and bulimia nervosa in circuits that regulate energy and reward homeostasis.

Anorexia and bulimia nervosa are severe eating disorders that share many behaviors. Structural and functional brain circuits could provide biological links that those disorders have in common. We recruited 77 young adult women, 26 healthy controls, 26 women with anorexia and 25 women with bulimia nervosa. Probabilistic tractography was used to map white matter connectivity strength across taste and food intake regulating brain circuits. An independent multisample greedy equivalence search algorithm tested effective connectivity between those regions during sucrose tasting. Anorexia and bulimia nervosa had greater structural connectivity in pathways between insula, orbitofrontal cortex and ventral striatum, but lower connectivity from orbitofrontal cortex and amygdala to the hypothalamus (P<0.05, corrected for comorbidity, medication and multiple comparisons). Functionally, in controls the hypothalamus drove ventral striatal activity, but in anorexia and bulimia nervosa effective connectivity was directed from anterior cingulate via ventral striatum to the hypothalamus. Across all groups, sweetness perception was predicted by connectivity strength in pathways connecting to the middle orbitofrontal cortex. This study provides evidence that white matter structural as well as effective connectivity within the energy-homeostasis and food reward-regulating circuitry is fundamentally different in anorexia and bulimia nervosa compared with that in controls. In eating disorders, anterior cingulate cognitive-emotional top down control could affect food reward and eating drive, override hypothalamic inputs to the ventral striatum and enable prolonged food restriction

Characterizing Network Search Algorithms Developed for Dynamic Causal Modeling

Dynamic causal modeling (DCM) is a widely used tool to estimate the effective connectivity of specified models of a brain network. Finding the model explaining measured data is one of the most important outstanding problems in Bayesian modeling. Using heuristic model search algorithms enables us to find an optimal model without having to define a model set a priori. However, the development of such methods is cumbersome in the case of large model-spaces. We aimed to utilize commonly used graph theoretical search algorithms for DCM to create a framework for characterizing them, and to investigate relevance of such methods for single-subject and group-level studies. Because of the enormous computational demand of DCM calculations, we separated the model estimation procedure from the search algorithm by providing a database containing the parameters of all models in a full model-space. For test data a publicly available fMRI dataset of 60 subjects was used. First, we reimplemented the deterministic bilinear DCM algorithm in the ReDCM R package, increasing computational speed during model estimation. Then, three network search algorithms have been adapted for DCM, and we demonstrated how modifications to these methods, based on DCM posterior parameter estimates, can enhance search performance. Comparison of the results are based on model evidence, structural similarities and the number of model estimations needed during search. An analytical approach using Bayesian model reduction (BMR) for efficient network discovery is already available for DCM. Comparing model search methods we found that topological algorithms often outperform analytical methods for single-subject analysis and achieve similar results for recovering common network properties of the winning model family, or set of models, obtained by multi-subject family-wise analysis. However, network search methods show their limitations in higher level statistical analysis of parametric empirical Bayes. Optimizing such linear modeling schemes the BMR methods are still considered the recommended approach. We envision the freely available database of estimated model-spaces to help further studies of the DCM model-space, and the ReDCM package to be a useful contribution for Bayesian inference within and beyond the field of neuroscience

Contributions to the Modelling of Auditory Hallucinations, Social robotics, and Multiagent Systems

165 p.The Thesis covers three diverse lines of work that have been tackled with the central endeavor of modeling and understanding the phenomena under consideration. Firstly, the Thesis works on the problem of finding brain connectivity biomarkers of auditory hallucinations, a rather frequent phenomena that can be related some pathologies, but which is also present in healthy population. We apply machine learning techniques to assess the significance of effective brain connections extracted by either dynamical causal modeling or Granger causality. Secondly, the Thesis deals with the usefulness of social robotics strorytelling as a therapeutic tools for children at risk of exclussion. The Thesis reports on the observations gathered in several therapeutic sessions carried out in Spain and Bulgaria, under the supervision of tutors and caregivers. Thirdly, the Thesis deals with the spatio-temporal dynamic modeling of social agents trying to explain the phenomena of opinion survival of the social minorities. The Thesis proposes a eco-social model endowed with spatial mobility of the agents. Such mobility and the spatial perception of the agents are found to be strong mechanisms explaining opinion propagation and survival

Contributions to the Modelling of Auditory Hallucinations, Social robotics, and Multiagent Systems

165 p.The Thesis covers three diverse lines of work that have been tackled with the central endeavor of modeling and understanding the phenomena under consideration. Firstly, the Thesis works on the problem of finding brain connectivity biomarkers of auditory hallucinations, a rather frequent phenomena that can be related some pathologies, but which is also present in healthy population. We apply machine learning techniques to assess the significance of effective brain connections extracted by either dynamical causal modeling or Granger causality. Secondly, the Thesis deals with the usefulness of social robotics strorytelling as a therapeutic tools for children at risk of exclussion. The Thesis reports on the observations gathered in several therapeutic sessions carried out in Spain and Bulgaria, under the supervision of tutors and caregivers. Thirdly, the Thesis deals with the spatio-temporal dynamic modeling of social agents trying to explain the phenomena of opinion survival of the social minorities. The Thesis proposes a eco-social model endowed with spatial mobility of the agents. Such mobility and the spatial perception of the agents are found to be strong mechanisms explaining opinion propagation and survival