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Effective connectivity (EC) refers to directional or causal influences between interacting neuronal populations or brain regions and can be estimated from functional magnetic resonance imaging (fMRI) data via dynamic causal modeling (DCM). In contrast to functional connectivity, the impact of data processing varieties on DCM estimates of task‐evoked EC has hardly ever been addressed. We therefore investigated how task‐evoked EC is affected by choices made for data processing. In particular, we considered the impact of global signal regression (GSR), block/event‐related design of the general linear model (GLM) used for the first‐level task‐evoked fMRI analysis, type of activation contrast, and significance thresholding approach. Using DCM, we estimated individual and group‐averaged task‐evoked EC within a brain network related to spatial conflict processing for all the parameters considered and compared the differences in task‐evoked EC between any two data processing conditions via between‐group parametric empirical Bayes (PEB) analysis and Bayesian data comparison (BDC). We observed strongly varying patterns of the group‐averaged EC depending on the data processing choices. In particular, task‐evoked EC and parameter certainty were strongly impacted by GLM design and type of activation contrast as revealed by PEB and BDC, respectively, whereas they were little affected by GSR and the type of significance thresholding. The event‐related GLM design appears to be more sensitive to task‐evoked modulations of EC, but provides model parameters with lower certainty than the block‐based design, while the latter is more sensitive to the type of activation contrast than is the event‐related design. Our results demonstrate that applying different reasonable data processing choices can substantially alter task‐evoked EC as estimated by DCM. Such choices should be made with care and, whenever possible, varied across parallel analyses to evaluate their impact and identify potential convergence for robust outcomes. This study considered the impact of data processing conditions on the task‐evoked modulatory effective connectivity (EC) using a stimulus–response compatibility task. Our study demonstrated that task‐evoked EC and parameter certainty were significantly impacted by the general linear model design and type of activation contrast as revealed by parametric empirical Bayes and Bayesian data comparison, respectively.

Major depressive disorder (MDD) is a serious and widespread psychiatric disorder. Previous studies mainly focused on cerebrum functional connectivity, and the sample size was relatively small. However, functional connectivity is undirected. And, there is increasing evidence that the cerebellum is also involved in emotion and cognitive processing and makes outstanding contributions to the symptomology and pathology of depression. Therefore, we used a large sample size of resting-state functional magnetic resonance imaging (rs-fMRI) data to investigate the altered effective connectivity (EC) among the cerebellum and other cerebral cortex in patients with MDD. Here, from the perspective of data-driven analysis, we used two different atlases to divide the whole brain into different regions and analyzed the alterations of EC and EC networks in the MDD group compared with healthy controls group (HCs). The results showed that compared with HCs, there were significantly altered EC in the cerebellum-neocortex and cerebellum-basal ganglia circuits in MDD patients, which implied that the cerebellum may be a potential biomarker of depressive disorders. And, the alterations of EC brain networks in MDD patients may provide new insights into the pathophysiological mechanisms of depression.

Gestures and speech, as linked communicative expressions, form an integrated system. Previous functional magnetic resonance imaging studies have suggested that neural networks for gesture and spoken word production share similar brain regions consisting of fronto-temporo-parietal brain regions. However, information flow within the neural network may dynamically change during the planning of two communicative expressions and also differ between them. To investigate dynamic information flow in the neural network during the planning of gesture and spoken word generation in this study, participants were presented with spatial images and were required to plan the generation of gestures or spoken words to represent the same spatial situations. The evoked potentials in response to spatial images were recorded to analyze the effective connectivity within the neural network. An independent component analysis of the evoked potentials indicated 12 clusters of independent components, the dipoles of which were located in the bilateral fronto-temporo-parietal brain regions and on the medial wall of the frontal and parietal lobes. Comparison of effective connectivity indicated that information flow from the right middle cingulate gyrus (MCG) to the left supplementary motor area (SMA) and from the left SMA to the left precentral area increased during gesture planning compared with that of word planning. Furthermore, information flow from the right MCG to the left superior frontal gyrus also increased during gesture planning compared with that of word planning. These results suggest that information flow to the brain regions for hand praxis is more strongly activated during gesture planning than during word planning.

Analysis of the human connectome using functional magnetic resonance imaging (fMRI) started in the mid-1990s and attracted increasing attention in attempts to discover the neural underpinnings of human cognition and neurological disorders. In general, brain connectivity patterns from fMRI data are classified as statistical dependencies (functional connectivity) or causal interactions (effective connectivity) among various neural units. Computational methods, especially graph theory-based methods, have recently played a significant role in understanding brain connectivity architecture. Thanks to the emergence of graph theoretical analysis, the main purpose of the current paper is to systematically review how brain properties can emerge through the interactions of distinct neuronal units in various cognitive and neurological applications using fMRI. Moreover, this article provides an overview of the existing functional and effective connectivity methods used to construct the brain network, along with their advantages and pitfalls. In this systematic review, the databases Science Direct, Scopus, arXiv, Google Scholar, IEEE Xplore, PsycINFO, PubMed, and SpringerLink are employed for exploring the evolution of computational methods in human brain connectivity from 1990 to the present, focusing on graph theory. The Cochrane Collaboration's tool was used to assess the risk of bias in individual studies. Our results show that graph theory and its implications in cognitive neuroscience have attracted the attention of researchers since 2009 (as the Human Connectome Project launched), because of their prominent capability in characterizing the behavior of complex brain systems. Although graph theoretical approach can be generally applied to either functional or effective connectivity patterns during rest or task performance, to date, most articles have focused on the resting-state functional connectivity. This review provides an insight into how to utilize graph theoretical measures to make neurobiological inferences regarding the mechanisms underlying human cognition and behavior as well as different brain disorders.

Functional MRI (fMRI) allows one to study task-related regional responses and task-dependent connectivity analysis using psychophysiological interaction (PPI) methods. The latter affords the additional opportunity to understand how brain regions interact in a task-dependent manner. The current implementation of PPI in Statistical Parametric Mapping (SPM8) is configured primarily to assess connectivity differences between two task conditions, when in practice fMRI tasks frequently employ more than two conditions. Here we evaluate how a generalized form of context-dependent PPI (gPPI; http://www.nitrc.org/projects/gppi), which is configured to automatically accommodate more than two task conditions in the same PPI model by spanning the entire experimental space, compares to the standard implementation in SPM8. These comparisons are made using both simulations and an empirical dataset. In the simulated dataset, we compare the interaction beta estimates to their expected values and model fit using the Akaike information criterion (AIC). We found that interaction beta estimates in gPPI were robust to different simulated data models, were not different from the expected beta value, and had better model fits than when using standard PPI (sPPI) methods. In the empirical dataset, we compare the model fit of the gPPI approach to sPPI. We found that the gPPI approach improved model fit compared to sPPI. There were several regions that became non-significant with gPPI. These regions all showed significantly better model fits with gPPI. Also, there were several regions where task-dependent connectivity was only detected using gPPI methods, also with improved model fit. Regions that were detected with all methods had more similar model fits. These results suggest that gPPI may have greater sensitivity and specificity than standard implementation in SPM. This notion is tempered slightly as there is no gold standard; however, data simulations with a known outcome support our conclusions about gPPI. In sum, the generalized form of context-dependent PPI approach has increased flexibility of statistical modeling, and potentially improves model fit, specificity to true negative findings, and sensitivity to true positive findings.

Functional magnetic resonance imaging (fMRI) studies have converged to reveal the default mode network (DMN), a constellation of regions that display co-activation during resting-state but co-deactivation during attention-demanding tasks in the brain. Here, we employed a Bayesian network (BN) analysis method to construct a directed effective connectivity model of the DMN and compared the organizational architecture and interregional directed connections under both resting-state and task-state. The analysis results indicated that the DMN was consistently organized into two closely interacting subsystems in both resting-state and task-state. The directed connections between DMN regions, however, changed significantly from the resting-state to task-state condition. The results suggest that the DMN intrinsically maintains a relatively stable structure whether at rest or performing tasks but has different information processing mechanisms under varied states.

To advance understanding of brain networks involved in language, the effective connectivity between 26 cortical regions implicated in language by a community analysis and 360 cortical regions was measured in 171 humans from the Human Connectome Project, and complemented with functional connectivity and diffusion tractography, all using the HCP multimodal parcellation atlas. A (semantic) network (Group 1) involving inferior cortical regions of the superior temporal sulcus cortex (STS) with the adjacent inferior temporal visual cortex TE1a and temporal pole TG, and the connected parietal PGi region, has effective connectivity with inferior temporal visual cortex (TE) regions; with parietal PFm which also has visual connectivity; with posterior cingulate cortex memory-related regions; with the frontal pole, orbitofrontal cortex, and medial prefrontal cortex; with the dorsolateral prefrontal cortex; and with 44 and 45 for output regions. It is proposed that this system can build in its temporal lobe (STS and TG) and parietal parts (PGi and PGs) semantic representations of objects incorporating especially their visual and reward properties. Another (semantic) network (Group 3) involving superior regions of the superior temporal sulcus cortex and more superior temporal lobe regions including STGa, auditory A5, TPOJ1, the STV and the Peri-Sylvian Language area (PSL) has effective connectivity with auditory areas (A1, A4, A5, Pbelt); with relatively early visual areas involved in motion, e.g., MT and MST, and faces/words (FFC); with somatosensory regions (frontal opercular FOP, insula and parietal PF); with other TPOJ regions; and with the inferior frontal gyrus regions (IFJa and IFSp). It is proposed that this system builds semantic representations specialising in auditory and related facial motion information useful in theory of mind and somatosensory / body image information, with outputs directed not only to regions 44 and 45, but also to premotor 55b and midcingulate premotor cortex. Both semantic networks (Groups 1 and 3) have access to the hippocampal episodic memory system via parahippocampal TF. A third largely frontal network (Group 2) (44, 45, 47l; 55b; the Superior Frontal Language region SFL; and including temporal pole TGv) receives effective connectivity from the two semantic systems, and is implicated in syntax and speech output.

Over the past 20 years, neuroimaging has become a predominant technique in systems neuroscience. One might envisage that over the next 20 years the neuroimaging of distributed processing and connectivity will play a major role in disclosing the brain's functional architecture and operational principles. The inception of this journal has been foreshadowed by an ever-increasing number of publications on functional connectivity, causal modeling, connectomics, and multivariate analyses of distributed patterns of brain responses. I accepted the invitation to write this review with great pleasure and hope to celebrate and critique the achievements to date, while addressing the challenges ahead.

In order to understand the working brain as a network, it is essential to identify the mechanisms by which information is gated between regions. We here propose that information is gated by inhibiting task-irrelevant regions, thus routing information to task-relevant regions. The functional inhibition is reflected in oscillatory activity in the alpha band (8-13 Hz). From a physiological perspective the alpha activity provides pulsed inhibition reducing the processing capabilities of a given area. Active processing in the engaged areas is reflected by neuronal synchronization in the gamma band (30-100 Hz) accompanied by an alpha band decrease. According to this framework the brain could be studied as a network by investigating cross-frequency interactions between gamma and alpha activity. Specifically the framework predicts that optimal task performance will correlate with alpha activity in task-irrelevant areas. In this review we will discuss the empirical support for this framework. Given that alpha activity is by far the strongest signal recorded by EEG and MEG, we propose that a major part of the electrophysiological activity detected from the working brain reflects gating by inhibition.

This technical note introduces a dynamic causal model (DCM) for resting state fMRI time series based upon observed functional connectivity—as measured by the cross spectra among different brain regions. This DCM is based upon a deterministic model that generates predicted crossed spectra from a biophysically plausible model of coupled neuronal fluctuations in a distributed neuronal network or graph. Effectively, the resulting scheme finds the best effective connectivity among hidden neuronal states that explains the observed functional connectivity among haemodynamic responses. This is because the cross spectra contain all the information about (second order) statistical dependencies among regional dynamics. In this note, we focus on describing the model, its relationship to existing measures of directed and undirected functional connectivity and establishing its face validity using simulations. In subsequent papers, we will evaluate its construct validity in relation to stochastic DCM and its predictive validity in Parkinson's and Huntington's disease. •This paper describes an efficient estimation of resting state connectivity.•The scheme is based on fitting observed complex fMRI cross spectra.•This spectral DCM grandfathers functional connectivity and Granger causality.