scholarly journals Large-scale DCMs for resting-state fMRI

2017 ◽  
Vol 1 (3) ◽  
pp. 222-241 ◽  
Author(s):  
Adeel Razi ◽  
Mohamed L. Seghier ◽  
Yuan Zhou ◽  
Peter McColgan ◽  
Peter Zeidman ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Large Scale ◽  
Effective Connectivity ◽  
Directed Graphs ◽  
Resting State Fmri ◽  
Causal Modeling ◽  
Large Graphs ◽  
Model Inversion ◽  
Graph Theoretic

This paper considers the identification of large directed graphs for resting-state brain networks based on biophysical models of distributed neuronal activity, that is, effective connectivity. This identification can be contrasted with functional connectivity methods based on symmetric correlations that are ubiquitous in resting-state functional MRI (fMRI). We use spectral dynamic causal modeling (DCM) to invert large graphs comprising dozens of nodes or regions. The ensuing graphs are directed and weighted, hence providing a neurobiologically plausible characterization of connectivity in terms of excitatory and inhibitory coupling. Furthermore, we show that the use of Bayesian model reduction to discover the most likely sparse graph (or model) from a parent (e.g., fully connected) graph eschews the arbitrary thresholding often applied to large symmetric (functional connectivity) graphs. Using empirical fMRI data, we show that spectral DCM furnishes connectivity estimates on large graphs that correlate strongly with the estimates provided by stochastic DCM. Furthermore, we increase the efficiency of model inversion using functional connectivity modes to place prior constraints on effective connectivity. In other words, we use a small number of modes to finesse the potentially redundant parameterization of large DCMs. We show that spectral DCM—with functional connectivity priors—is ideally suited for directed graph theoretic analyses of resting-state fMRI. We envision that directed graphs will prove useful in understanding the psychopathology and pathophysiology of neurodegenerative and neurodevelopmental disorders. We will demonstrate the utility of large directed graphs in clinical populations in subsequent reports, using the procedures described in this paper.

scholarly journals Altered hypothalamus functional connectivity with limbic system in fibromyalgia and the modulation effect of intervention

2020 ◽  
Author(s):  
Jian Kong ◽  
Yiting Huang ◽  
Jiao Liu ◽  
Siyi Yu ◽  
Ming Cheng ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Limbic System ◽  
Resting State ◽  
Tai Chi ◽  
Effective Connectivity ◽  
Resting State Fmri ◽  
Trial Registration ◽  
Modulation Effect ◽  
Resting State Functional Connectivity ◽  
Before And After

Abstract Background: This study aims to investigate the resting state functional connectivity (rsFC) changes of the hypothalamus in Fibromyalgia patients and the modulation effect of effective treatments. Methods: Fibromyalgia patients and matched healthy controls (HC’s) were recruited. Resting state fMRI data were collected from fibromyalgia patients before and after a 12-week Tai Chi intervention and once from HC’s. Results: Data analysis showed that fibromyalgia patients displayed significantly decreased medial hypothalamus (MH) rsFC with the thalamus and amygdala when compared to HC’s at baseline. After the intervention, fibromyalgia patients showed increased (normalized) MH rsFC in the thalamus and amygdala. Effective connectivity analysis showed disrupted MH and thalamus interaction in fibromyalgia, which nonetheless could be partially restored by Tai Chi. Conclusions: Elucidating the role of the diencephalon and limbic system in the pathophysiology and development of fibromyalgia may facilitate the development of new treatment methods for this prevalent disorder. Trial registration: Trial registration ClinicalTrials.gov Identifier: NCT02407665. Registered 3 April 2015 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT02407665

scholarly journals The effect of global signal regression on DCM estimates of noise and effective connectivity from resting state fMRI

2019 ◽  
Author(s):  
Hannes Almgren ◽  
Frederik Van de Steen ◽  
Adeel Razi ◽  
Karl Friston ◽  
Daniele Marinazzo
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Effective Connectivity ◽  
Network Connectivity ◽  
Resting State Fmri ◽  
Measurement Noise ◽  
Resting State Networks ◽  
Cross Sectional ◽  
Global Signal ◽  
Leibler Divergence

AbstractThe influence of the global BOLD signal on resting state functional connectivity in fMRI data remains a topic of debate, with little consensus. In this study, we assessed the effects of global signal regression (GSR) on effective connectivity within and between resting-state networks – as estimated with dynamic causal modelling (DCM) for resting state fMRI (rsfMRI). DCM incorporates a forward (generative) model that quantifies the contribution of different types of noise (including global measurement noise), effective connectivity, and (neuro)vascular processes to functional connectivity measurements. DCM analyses were applied to two different designs; namely, longitudinal and cross-sectional designs. In the modelling of longitudinal designs, we included four extensive longitudinal resting state fMRI datasets with a total number of 20 subjects. In the analysis of cross-sectional designs, we used rsfMRI data from 361 subjects from the Human Connectome Project. We hypothesized that (1) GSR would have no discernible impact on effective connectivity estimated with DCM, and (2) GSR would be reflected in the parameters representing global measurement noise. Additionally, we performed comparative analyses of the informative value of data with and without GSR. Our results showed negligible to small effects of GSR on connectivity within small (separately estimated) RSNs. For between-network connectivity, we found two important effects: the effect of GSR on between-network connectivity (averaged over all connections) was negligible to small, while the effect of GSR on individual connections was non-negligible. Contrary to our expectations, we found either no effect (in the longitudinal designs) or a non-specific (cross-sectional design) effect of GSR on parameters representing (global) measurement noise. Data without GSR were found to be more informative than data with GSR; however, in small resting state networks the precision of posterior estimates was greater using data after GSR. In conclusion, GSR is a minor concern in DCM studies; however, individual between-network connections (as opposed to average between-network connectivity) and noise parameters should be interpreted quantitatively with some caution. The Kullback-Leibler divergence of the posterior from the prior, together with the precision of posterior estimates, might offer a useful measure to assess the appropriateness of GSR, when nuancing data features in resting state fMRI.

scholarly journals State-Dependent Effective Connectivity in Resting-State fMRI

2021 ◽  
Vol 15 ◽  
Author(s):  
Hae-Jeong Park ◽  
Jinseok Eo ◽  
Chongwon Pae ◽  
Junho Son ◽  
Sung Min Park ◽  
...  
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Empirical Bayes ◽  
Time Course ◽  
Effective Connectivity ◽  
The State ◽  
Causal Modeling ◽  
Occupation Times ◽  
State Dependent ◽  
Mental Diseases

The human brain at rest exhibits intrinsic dynamics transitioning among the multiple metastable states of the inter-regional functional connectivity. Accordingly, the demand for exploring the state-specific functional connectivity increases for a deeper understanding of mental diseases. Functional connectivity, however, lacks information about the directed causal influences among the brain regions, called effective connectivity. This study presents the dynamic causal modeling (DCM) framework to explore the state-dependent effective connectivity using spectral DCM for the resting-state functional MRI (rsfMRI). We established the sequence of brain states using the hidden Markov model with the multivariate autoregressive coefficients of rsfMRI, summarizing the functional connectivity. We decomposed the state-dependent effective connectivity using a parametric empirical Bayes scheme that models the effective connectivity of consecutive windows with the time course of the discrete states as regressors. We showed the plausibility of the state-dependent effective connectivity analysis in a simulation setting. To test the clinical applicability, we applied the proposed method to characterize the state- and subtype-dependent effective connectivity of the default mode network in children with combined-type attention deficit hyperactivity disorder (ADHD-C) compared with age-matched, typically developed children (TDC). All 88 children were subtyped according to the occupation times (i.e., dwell times) of the three dominant functional connectivity states, independently of clinical diagnosis. The state-dependent effective connectivity differences between ADHD-C and TDC according to the subtypes and those between the subtypes of ADHD-C were expressed mainly in self-inhibition, magnifying the importance of excitation inhibition balance in the subtyping. These findings provide a clear motivation for decomposing the state-dependent dynamic effective connectivity and state-dependent analysis of the directed coupling in exploring mental diseases.

scholarly journals Static and dynamic aspects of cerebro-cerebellar functional connectivity are associated with self-reported measures of impulsivity: A resting-state fMRI study

2020 ◽  
Vol 4 (3) ◽  
pp. 891-909
Author(s):  
Majd Abdallah ◽  
Nicolas Farrugia ◽  
Valentine Chirokoff ◽  
Sandra Chanraud
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Sensation Seeking ◽  
Large Scale ◽  
Resting State Fmri ◽  
Posterior Cingulate Cortex ◽  
Impulsive Behavior ◽  
Dynamic Features ◽  
Behavioral Correlates ◽  
Total Strength

Human and animal brain studies bring converging evidence of a possible role for the cerebellum and the cerebro-cerebellar system in impulsivity. However, the precise nature of the relation between cerebro-cerebellar coupling and impulsivity is far from understood. Characterizing functional connectivity (FC) patterns between large-scale brain networks that mediate different forms of impulsivity, and the cerebellum may improve our understanding of this relation. Here, we analyzed static and dynamic features of cerebro-cerebellar FC using a highly sampled resting-state functional magnetic resonance imaging (rs-fMRI) dataset and tested their association with two widely used self-reports of impulsivity: the UPPS-P impulsive behavior scale and the behavioral inhibition/approach systems (BIS/BAS) in a large group of healthy subjects ( N = 134, ≈ 1 hr of rs-fMRI/subject). We employed robust data-driven techniques to identify cerebral and cerebellar resting-state networks and extract descriptive summary measures of static and dynamic cerebro-cerebellar FC. We observed evidence linking BIS, BAS, sensation seeking, and lack of premeditation to the total strength and temporal variability of FC within networks connecting regions of the prefrontal cortex, precuneus, posterior cingulate cortex, basal ganglia, and thalamus with the cerebellum. Overall, our findings improve the existing knowledge of the neural correlates of impulsivity and the behavioral correlates of the cerebro-cerebellar system.

scholarly journals Effective Connectivity within the Default Mode Network: Dynamic Causal Modeling of Resting-State fMRI Data

2016 ◽  
Vol 10 ◽  
Author(s):  
Maksim G. Sharaev ◽  
Viktoria V. Zavyalova ◽  
Vadim L. Ushakov ◽  
Sergey I. Kartashov ◽  
Boris M. Velichkovsky
Keyword(s):  
Default Mode Network ◽  
Resting State ◽  
Effective Connectivity ◽  
Resting State Fmri ◽  
Causal Modeling ◽  
Fmri Data ◽  
Network Dynamic ◽  
Dynamic Causal Modeling ◽  
Default Mode

scholarly journals Heritability analysis with repeat measurements and its application to resting-state functional connectivity

2017 ◽  
Vol 114 (21) ◽  
pp. 5521-5526 ◽  
Author(s):  
Tian Ge ◽  
Avram J. Holmes ◽  
Randy L. Buckner ◽  
Jordan W. Smoller ◽  
Mert R. Sabuncu
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Large Scale ◽  
Resting State Fmri ◽  
Transient Effects ◽  
Resting State Functional Connectivity ◽  
Linear Mixed Effects ◽  
Heritability Analysis ◽  
Test Retest Reliability ◽  
Different Levels

Heritability, defined as the proportion of phenotypic variation attributable to genetic variation, provides important information about the genetic basis of a trait. Existing heritability analysis methods do not discriminate between stable effects (e.g., due to the subject’s unique environment) and transient effects, such as measurement error. This can lead to misleading assessments, particularly when comparing the heritability of traits that exhibit different levels of reliability. Here, we present a linear mixed effects model to conduct heritability analyses that explicitly accounts for intrasubject fluctuations (e.g., due to measurement noise or biological transients) using repeat measurements. We apply the proposed strategy to the analysis of resting-state fMRI measurements—a prototypic data modality that exhibits variable levels of test–retest reliability across space. Our results reveal that the stable components of functional connectivity within and across well-established large-scale brain networks can be considerably heritable. Furthermore, we demonstrate that dissociating intra- and intersubject variation can reveal genetic influence on a phenotype that is not fully captured by conventional heritability analyses.

scholarly journals Regression dynamic causal modeling for resting-state fMRI

2020 ◽  
Author(s):  
Stefan Frässle ◽  
Samuel J. Harrison ◽  
Jakob Heinzle ◽  
Brett A. Clementz ◽  
Carol A. Tamminga ◽  
...  
Keyword(s):  
Resting State ◽  
Brain Connectivity ◽  
Effective Connectivity ◽  
Brain Networks ◽  
Resting State Fmri ◽  
Causal Modeling ◽  
Computationally Efficient ◽  
Dynamic Causal Modeling ◽  
Whole Brain ◽  
Wide Range

Abstract“Resting-state” functional magnetic resonance imaging (rs-fMRI) is widely used to study brain connectivity. So far, researchers have been restricted to measures of functional connectivity that are computationally efficient but undirected, or to effective connectivity estimates that are directed but limited to small networks.Here, we show that a method recently developed for task-fMRI – regression dynamic causal modeling (rDCM) – extends to rs-fMRI and offers both directional estimates and scalability to whole-brain networks. First, simulations demonstrate that rDCM faithfully recovers parameter values over a wide range of signal-to-noise ratios and repetition times. Second, we test construct validity of rDCM in relation to an established model of effective connectivity, spectral DCM. Using rs-fMRI data from nearly 200 healthy participants, rDCM produces biologically plausible results consistent with estimates by spectral DCM. Importantly, rDCM is computationally highly efficient, reconstructing whole-brain networks (>200 areas) within minutes on standard hardware. This opens promising new avenues for connectomics.

scholarly journals Variability and reliability of effective connectivity within the core default mode network: A longitudinal spectral DCM study

2018 ◽  
Author(s):  
Hannes Almgren ◽  
Frederik Van de Steen ◽  
Simone Kühn ◽  
Adeel Razi ◽  
Karl Friston ◽  
...  
Keyword(s):  
Resting State ◽  
Hemispheric Asymmetry ◽  
Large Scale ◽  
Effective Connectivity ◽  
Brain Networks ◽  
Resting State Fmri ◽  
Global Signal ◽  
Cognitive Behavioural ◽  
Connectivity Patterns ◽  
Within Subjects

AbstractDynamic causal modelling (DCM) for resting state fMRI – namely spectral DCM – is a recently developed and widely adopted method for inferring effective connectivity in intrinsic brain networks. Most research applying spectral DCM has focused on group-averaged connectivity within large-scale intrinsic brain networks; however, the consistency of subject- and session-specific estimates of effective connectivity has not been evaluated. Establishing reliability (within subjects) is crucial for its clinical use; e.g., as a neurophysiological phenotype of disease progression. Effective connectivity during rest is likely to vary due to changes in cognitive, behavioural, and physical states. Determining the sources of fluctuations in effective connectivity may yield greater understanding of brain processes and inform clinical applications about potential confounds. In the present study, we investigated the consistency of effective connectivity within and between subjects, as well as potential sources of variability (e.g., hemispheric asymmetry). We further investigated how standard procedures for data processing and signal extraction affect this consistency. DCM analyses were applied to four longitudinal resting state fMRI datasets. Our sample consisted of 20 subjects with 653 resting state fMRI sessions in total. These data allowed to quantify the robustness of connectivity estimates for each subject, and to draw conclusions beyond specific data features. We found that subjects contributing to all datasets showed systematic and reliable patterns of hemispheric asymmetry. When asymmetry was taken into account, subjects showed very similar connectivity patterns. We also found that various processing procedures (e.g. global signal regression and ROI size) had little effect on inference and reliability of connectivity for the majority of subjects. Bayesian model reduction increased reliability (within-subjects) and stability (between-subjects) of connectivity patterns.

Brain Functional Connectivity in OCD

2017 ◽  
Author(s):  
Carles Soriano-Mas ◽  
Ben J. Harrison
Keyword(s):  
Functional Connectivity ◽  
Resting State ◽  
Large Scale ◽  
Resting State Fmri ◽  
Obsessive Compulsive ◽  
Compulsive Disorder ◽  
Regulatory Systems ◽  
Variable Nature ◽  
Brain Functional Connectivity ◽  
Or Task

This chapter provides an overview of studies assessing alterations in brain functional connectivity in obsessive-compulsive disorder (OCD) as assessed by functional magnetic resonance imaging (fMRI). Although most of the reviewed studies relate to the analysis of resting-state fMRI data, the chapter also reviews studies that have combined resting-state with structural or task-based approaches, as well as task-based studies in which the analysis of functional connectivity was reported. The main conclusions to be drawn from this review are that patients with OCD consistently demonstrate altered patterns of brain functional connectivity in large-scale “frontostriatal” and “default mode” networks, and that the heterogeneity of OCD symptoms is likely to partly arise via distinct modulatory influences on these networks by broader disturbances of affective, motivational, and regulatory systems. The variable nature of some findings across studies as well as the influence of medications on functional connectivity measures is also discussed.

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