Modeling state-related fMRI activity using change-point theory

ADHD diagnosis guided by functional brain networks combined with domain knowledge

Utilizing functional magnetic resonance imaging (fMRI) to model functional brain networks (FBNs) is increasingly prominent in attention-deficit/hyperactivity disorder (ADHD) research, revealing neural impact and mechanisms through the exploration of activated brain regions. However, current FBNs-based methods face two major challenges. The primary challenge stems from the limitations of existing modeling methods in accurately capturing both regional correlations and long-distance dependencies (LDDs) within the dynamic brain, thereby affecting the diagnostic accuracy of FBNs as biomarkers. Additionally, limited sample size and class imbalance also pose a challenge to the learning performance of the model. To address the issues, we propose an automated diagnostic framework, which integrates modeling, multimodal fusion, and classification into a unified process. It aims to extract representative FBNs and efficiently incorporate domain knowledge to guide ADHD classification. Our work mainly includes three-fold: 1) A multi-head attention-based region-enhancement module (MAREM) is designed to simultaneously capture regional correlations and LDDs across the entire sequence of brain activity, which facilitates the construction of representative FBNs. 2) The multimodal supplementary learning module (MSLM) is proposed to integrate domain knowledge from phenotype data with FBNs from neuroimaging data, achieving information complementarity and alleviating the problems of insufficient medical data and unbalanced sample categories. 3) An ADHD automatic diagnosis framework guided by FBNs and domain knowledge (ADF-FAD) is proposed to help doctors make more accurate decisions, which is applied to the ADHD-200 dataset to confirm its effectiveness. The results indicate that the FBNs extracted by MAREM perform well in modeling and classification. After with MSLM, the model achieves accuracy of 92.4%, 74.4%, and 80% at NYU, PU, and KKI, respectively, demonstrating its ability to effectively capture crucial information related to ADHD diagnosis. Codes are available at https://github.com/zhuimengxuebao/ADF-FAD.

An Explainable and Generalizable Recurrent Neural Network Approach for Differentiating Human Brain States on EEG Dataset

Electroencephalogram (EEG) is one of the most widely used brain computer interface (BCI) approaches. Despite the success of existing EEG approaches in brain state recognition studies, it is still challenging to differentiate brain states via explainable and generalizable deep learning approaches. In other words, how to explore meaningful and distinguishing features and how to overcome the huge variability and overfitting problem still need to be further studied. To alleviate these challenges, in this work, a multiple random fragment search-based multilayer recurrent neural network (MRFS-MRNN) is proposed to improve the differentiating performance and explore meaningful patterns. Specifically, an explainable MRNN module is proposed to capture the temporal dependences preserved in EEG time series. Besides, a MRFS module is designed to cut multiple random fragments from the entire EEG signal time course to improve the effectiveness of brain state differentiating ability. MRFS-MRNN is concatenatedto effectively overcome the huge variabilities and overfitting problems. Experiment results demonstrate that the proposed MRFS-MRNN model not only has excellent differentiating performance, but also has good explanation and generalization ability. The classification accuracies reach as high as 95.18% for binary classification and 89.19% for four-category classification on the individual level. Similarly, 95.53% and 85.84% classification accuracies are obtained for the binary and four-category classification on the group level. What's more, 94.28% and 85.43% classification accuracies of binary and four-category classifications are achieved for predicting brand new subjects. The experiment results showed that the proposed method outperformed other state-of-the-art (SOTA) models on the same underlying data and improved the explanation and generalization ability.

Task sub-type states decoding via group deep bidirectional recurrent neural network

Decoding brain states under different cognitive tasks from functional magnetic resonance imaging (fMRI) data has attracted great attention in the neuroimaging filed. However, the well-known temporal dependency in fMRI sequences has not been fully exploited in existing studies, due to the limited temporal-modeling capacity of the backbone machine learning algorithms and rigid training sample organization strategies upon which the brain decoding methods are built. To address these limitations, we propose a novel method for fine-grain brain state decoding, namely, group deep bidirectional recurrent neural network (Group-DBRNN) model. We first propose a training sample organization strategy that consists of a group-task sample generation module and a multiple-scale random fragment strategy (MRFS) module to collect training samples that contain rich task-relevant brain activity contrast (i.e., the comparison of neural activity patterns between different tasks) and maintain the temporal dependency. We then develop a novel decoding model by replacing the unidirectional RNNs that are widely used in existing brain state decoding studies with bidirectional stacked RNNs to better capture the temporal dependency, and by introducing a multi-task interaction layer (MTIL) module to effectively model the task-relevant brain activity contrast. Our experimental results on the Human Connectome Project task fMRI dataset (7 tasks consisting of 23 task sub-type states) show that the proposed model achieves an average decoding accuracy of 94.7% over the 23 fine-grain sub-type states. Meanwhile, our extensive interpretations of the intermediate features learned in the proposed model via visualizations and quantitative assessments of their discriminability and inter-subject alignment evidence that the proposed model can effectively capture the temporal dependency and task-relevant contrast.

Mapping dynamic spatial patterns of brain function with spatial-wise attention

Objective: Using functional magnetic resonance imaging (fMRI) and deep learning to discover the spatial pattern of brain function, or functional brain networks (FBNs) has been attracted many reseachers. Most existing works focus on static FBNs or dynamic functional connectivity among fixed spatial network nodes, but ignore the potential dynamic/time-varying characteristics of the spatial networks themselves. And most of works based on the assumption of linearity and independence, that oversimplify the relationship between blood-oxygen level dependence signal changes and the heterogeneity of neuronal activity within voxels.Approach: To overcome these problems, we proposed a novel spatial-wise attention (SA) based method called Spatial and Channel-wise Attention Autoencoder (SCAAE) to discover the dynamic FBNs without the assumptions of linearity or independence. The core idea of SCAAE is to apply the SA to generate FBNs directly, relying solely on the spatial information present in fMRI volumes. Specifically, we trained the SCAAE in a self-supervised manner, using the autoencoder to guide the SA to focus on the activation regions. Experimental results show that the SA can generate multiple meaningful FBNs at each fMRI time point, which spatial similarity are close to the FBNs derived by known classical methods, such as independent component analysis.Main results: To validate the generalization of the method, we evaluate the approach on HCP-rest, HCP-task and ADHD-200 dataset. The results demonstrate that SA mechanism can be used to discover time-varying FBNs, and the identified dynamic FBNs over time clearly show the process of time-varying spatial patterns fading in and out.Significance: Thus we provide a novel method to understand human brain better. Code is available athttps://github.com/WhatAboutMyStar/SCAAE.

Locus coeruleus integrity predicts ease of attaining and maintaining neural states of high attentiveness

The locus coeruleus (LC), a small subcortical structure in the brainstem, is the brain's principal source of norepinephrine. It plays a primary role in regulating stress, the sleep-wake cycle, and attention, and its degradation is associated with aging and neurodegenerative diseases associated with cognitive deficits (e.g., Parkinson's, Alzheimer's). Yet precisely how norepinephrine drives brain networks to support healthy cognitive function remains poorly understood - partly because LC's small size makes it difficult to study noninvasively in humans. Here, we characterized LC's influence on brain dynamics using a hidden Markov model fitted to functional neuroimaging data from healthy young adults across four attention-related brain networks and LC. We modulated LC activity using a behavioral paradigm and measured individual differences in LC magnetization transfer contrast. The model revealed five hidden states, including a stable state dominated by salience-network activity that occurred when subjects actively engaged with the task. LC magnetization transfer contrast correlated with this state's stability across experimental manipulations and with subjects' propensity to enter into and remain in this state. These results provide new insight into LC's role in driving spatiotemporal neural patterns associated with attention, and demonstrate that variation in LC integrity can explain individual differences in these patterns even in healthy young adults.

Differentiating brain states via multi-clip random fragment strategy-based interactive bidirectional recurrent neural network

EEG is widely adopted to study the brain and brain computer interface (BCI) for its non-invasiveness and low costs. Specifically EEG can be applied to differentiate brain states, which is important for better understanding the working mechanisms of the brain. Recurrent neural network (RNN)-based learning strategy has been widely utilized to differentiate brain states, because its optimization architectures improve the classification performance for differentiating brain states at the group level. However, present classification performance is still far from satisfactory. We have identified two major focal points for improvements: one is about organizing the input EEG signals, and the other is related to the design of the RNN architecture. To optimize the above-mentioned issues and achieve better brain state classification performance, we propose a novel multi-clip random fragment strategy-based interactive bidirectional recurrent neural network (McRFS-IBiRNN) model in this work. This model has two advantages over previous methods. First, the McRFS component is designed to re-organize the input EEG signals to make them more suitable for the RNN architecture. Second, the IBiRNN component is an innovative design to model the RNN layers with interaction connections to enhance the fusion of bidirectional features. By adopting the proposed model, promising brain states classification performances are obtained. For example, 96.97% and 99.34% of individual and group level four-category classification accuracies are successfully obtained on the EEG motor/imagery dataset, respectively. A 99.01% accuracy can be observed for four-category classification tasks with new subjects not seen before, which demonstrates the generalization of our proposed method. Compared with existing methods, our model outperforms them with superior results. Overall, the proposed McRFS-IBiRNN model demonstrates great superiority in differentiating brain states on EEG signals.

Revisiting Nonlinear Functional Brain Co-activations: Directed, Dynamic, and Delayed

The center stage of neuro-imaging is currently occupied by studies of functional correlations between brain regions. These correlations define the brain functional networks, which are the most frequently used framework to represent and interpret a variety of experimental findings. In the previous study, we first demonstrated that the relatively stronger blood oxygenated level dependent (BOLD) activations contain most of the information relevant to understand functional connectivity, and subsequent work confirmed that a large compression of the original signals can be obtained without significant loss of information. In this study, we revisit the correlation properties of these epochs to define a measure of nonlinear dynamic directed functional connectivity (nldFC) across regions of interest. We show that the proposed metric provides at once, without extensive numerical complications, directed information of the functional correlations, as well as a measure of temporal lags across regions, overall offering a different and complementary perspective in the analysis of brain co-activation patterns. In this study, we provide further details for the computations of these measures and for a proof of concept based on replicating existing results from an Autistic Syndrome database, and discuss the main features and advantages of the proposed strategy for the study of brain functional correlations.

Modeling and augmenting of fMRI data using deep recurrent variational auto-encoder

Objective. Recently, deep learning models have been successfully applied in functional magnetic resonance imaging (fMRI) modeling and associated applications. However, there still exist at least two challenges. Firstly, due to the lack of sufficient data, deep learning models tend to suffer from overfitting in the training process. Secondly, it is still challenging to model the temporal dynamics from fMRI, due to that the brain state is continuously changing over scan time. In addition, existing methods rarely studied and applied fMRI data augmentation.Approach. In this work, we construct a deep recurrent variational auto-encoder (DRVAE) that combined variational auto-encoder and recurrent neural network, aiming to address all of the above mentioned challenges. The encoder of DRVAE can extract more generalized temporal features from assumed Gaussian distribution of input data, and the decoder of DRVAE can generate new data to increase training samples and thus partially relieve the overfitting issue. The recurrent layers in DRVAE are designed to effectively model the temporal dynamics of functional brain activities. LASSO (least absolute shrinkage and selection operator) regression is applied on the temporal features and input fMRI data to estimate the corresponding spatial networks.Main results. Extensive experimental results on seven tasks from HCP dataset showed that the DRVAE and LASSO framework can learn meaningful temporal patterns and spatial networks from both real data and generated data. The results on group-wise data and single subject suggest that the brain activities may follow certain distribution. Moreover, we applied DRVAE on four resting state fMRI datasets from ADHD-200 for data augmentation, and the results showed that the classification performances on augmented datasets have been considerably improved.Significance. The proposed method can not only derive meaningful temporal features and spatial networks from fMRI, but also generate high-quality new data for fMRI data augmentation and associated applications.

Dynamic Functional Connectivity Change-Point Detection With Random Matrix Theory Inference

To study the dynamic nature of brain activity, functional magnetic resonance imaging (fMRI) data is useful including some temporal dependencies between the corresponding neural activity estimates. Recent studies have shown that the functional connectivity (FC) varies according to time and location which should be incorporated into the model. Modeling this dynamic FC (DFC) requires time-varying measures of spatial region of interest (ROI) sets. To know about the DFC, change-point detection in FC is of particular interest. In this paper, we propose a method of detecting a change-point based on the maximum of eigenvalues via random matrix theory (RMT). From covariance matrices for FC of all ROI's, the temporal change-point of FC is decided by an RMT approach. Simulation results show that our proposed method can detect meaningful FC change-points. We also illustrate the effectiveness of our FC detection approach by applying our method to epilepsy data where change-points detected are explained by the changes in memory capacity. Our study shows the possibility of RMT based approach in DFC change-point problem and in studying the complex dynamic pattern of functional brain interactions.

The development of an fMRI protocol to investigate vmPFC network functioning underlying the generalization of behavioral control

Experiencing behavioral control over stress can have long-lasting and generalizing effects. Animal research has shown that vmPFC-subcortical interactions are critical for behavioral control; however, research in humans is sparse. Therefore a paradigm was developed in which participants (n = 18) were first assigned to a controllable or uncontrollable version of a signal detection task associated with mild shocks. Subsequently, subjects underwent an fMRI task on the anticipation of speaking in public while measuring self-reported stress, heart rate, and vmPFC network topology. The signal detection task results revealed faster responses to potential shock trials and a trend difference between the controllable and uncontrollable group. The speech anticipation procedure did not show significant between-group differences on self-reported stress or heart rate. fMRI results indicated higher vmPFC efficiency in the controllable threat group at baseline and recovery but similar to the uncontrollable group during speech anticipation. The current report establishes the feasibility of the protocol. However, to evaluate the generalization effect of controllability on the behavioral, physiological, and neural levels further, adequately-powered follow-up research is needed.

Episode detection based on personalized intensity of care thresholds: a schizophrenia case study

BACKGROUND

Schizophrenia Spectrum Disorder (SSD) is characterized by its chronic, episodic nature. The clear definition of such episodes is essential for various clinical and research purposes. Most current definitions of episodes in SSD are based on either hospitalizations or on symptom scales. Both have drawbacks; symptom scales are measured infrequently, while hospitalization rates are often affected by policy. This study presents an approach for defining episodes in healthcare data that does not suffer such drawbacks.

METHODS

Healthcare use of 13,155 SSD patients in the Northern Netherlands with up to 12 years of follow-up was available. Patient-level structural changes in the trend of healthcare use costs were determined using Exponentially Weighted Moving Average (EWMA) control charts. Control charts restart with updated parameters after a detected structural change. Episodes were defined using these structural changes. The resulting episodes were validated by investigating their association with the Global Assessment of Functioning (GAF) scale.

RESULTS

The mean number of episodes was 0.61 (sd: 0.60) per patient per year. For the sub-group without hospitalizations this was 0.51 (sd: 0.71). Average episode duration of the sub-group (147 days, sd: 309.4) was similar to that of the full sample (150 days, sd: 305.5). A significant inverse association was identified between GAF scores and the episode-state indicator.

CONCLUSIONS

The repeated application of EWMA control charts based on healthcare-intensity is a feasible and promising tool for quantifying patient-level healthcare episodes. The validation using GAF scores indicates that our episode indicator is associated with lower levels of global functioning. Results for individuals without hospitalizations indicate that the method is robust with regard to changes in healthcare policy.

Personalized Connectome Mapping to Guide Targeted Therapy and Promote Recovery of Consciousness in the Intensive Care Unit

There are currently no therapies proven to promote early recovery of consciousness in patients with severe brain injuries in the intensive care unit (ICU). For patients whose families face time-sensitive, life-or-death decisions, treatments that promote recovery of consciousness are needed to reduce the likelihood of premature withdrawal of life-sustaining therapy, facilitate autonomous self-expression, and increase access to rehabilitative care. Here, we present the Connectome-based Clinical Trial Platform (CCTP), a new paradigm for developing and testing targeted therapies that promote early recovery of consciousness in the ICU. We report the protocol for STIMPACT (Stimulant Therapy Targeted to Individualized Connectivity Maps to Promote ReACTivation of Consciousness), a CCTP-based trial in which intravenous methylphenidate will be used for targeted stimulation of dopaminergic circuits within the subcortical ascending arousal network (ClinicalTrials.gov NCT03814356). The scientific premise of the CCTP and the STIMPACT trial is that personalized brain network mapping in the ICU can identify patients whose connectomes are amenable to neuromodulation. Phase 1 of the STIMPACT trial is an open-label, safety and dose-finding study in 22 patients with disorders of consciousness caused by acute severe traumatic brain injury. Patients in Phase 1 will receive escalating daily doses (0.5-2.0 mg/kg) of intravenous methylphenidate over a 4-day period and will undergo resting-state functional magnetic resonance imaging and electroencephalography to evaluate the drug's pharmacodynamic properties. The primary outcome measure for Phase 1 relates to safety: the number of drug-related adverse events at each dose. Secondary outcome measures pertain to pharmacokinetics and pharmacodynamics: (1) time to maximal serum concentration; (2) serum half-life; (3) effect of the highest tolerated dose on resting-state functional MRI biomarkers of connectivity; and (4) effect of each dose on EEG biomarkers of cerebral cortical function. Predetermined safety and pharmacodynamic criteria must be fulfilled in Phase 1 to proceed to Phase 2A. Pharmacokinetic data from Phase 1 will also inform the study design of Phase 2A, where we will test the hypothesis that personalized connectome maps predict therapeutic responses to intravenous methylphenidate. Likewise, findings from Phase 2A will inform the design of Phase 2B, where we plan to enroll patients based on their personalized connectome maps. By selecting patients for clinical trials based on a principled, mechanistic assessment of their neuroanatomic potential for a therapeutic response, the CCTP paradigm and the STIMPACT trial have the potential to transform the therapeutic landscape in the ICU and improve outcomes for patients with severe brain injuries.

Recognizing Brain States Using Deep Sparse Recurrent Neural Network

Brain activity is a dynamic combination of different sensory responses and thus brain activity/state is continuously changing over time. However, the brain's dynamical functional states recognition at fast time-scales in task fMRI data have been rarely explored. In this paper, we propose a novel 5-layer deep sparse recurrent neural network (DSRNN) model to accurately recognize the brain states across the whole scan session. Specifically, the DSRNN model includes an input layer, one fully-connected layer, two recurrent layers, and a softmax output layer. The proposed framework has been tested on seven task fMRI data sets of Human Connectome Project. Extensive experiment results demonstrate that the proposed DSRNN model can accurately identify the brain's state in different task fMRI data sets and significantly outperforms other auto-correlation methods or non-temporal approaches in the dynamic brain state recognition accuracy. In general, the proposed DSRNN offers a new methodology for basic neuroscience and clinical research.

Improved state change estimation in dynamic functional connectivity using hidden semi-Markov models

The study of functional brain networks has grown rapidly over the past decade. While most functional connectivity (FC) analyses estimate one static network structure for the entire length of the functional magnetic resonance imaging (fMRI) time series, recently there has been increased interest in studying time-varying changes in FC. Hidden Markov models (HMMs) have proven to be a useful modeling approach for discovering repeating graphs of interacting brain regions (brain states). However, a limitation lies in HMMs assuming that the sojourn time, the number of consecutive time points in a state, is geometrically distributed. This may encourage inaccurate estimation of the time spent in a state before switching to another state. We propose a hidden semi-Markov model (HSMM) approach for inferring time-varying brain networks from fMRI data, which explicitly models the sojourn distribution. Specifically, we propose using HSMMs to find each subject's most probable series of network states and the graphs associated with each state, while properly estimating and modeling the sojourn distribution for each state. We perform a simulation study, as well as an analysis on both task-based fMRI data from an anxiety-inducing experiment and resting-state fMRI data from the Human Connectome Project. Our results demonstrate the importance of model choice when estimating sojourn times and reveal their potential for understanding healthy and diseased brain mechanisms.

Large-Scale Circuitry Interactions Upon Earthquake Experiences Revealed by Recurrent Neural Networks

Brain dynamics has recently received increasing interest due to its significant importance in basic and clinical neurosciences. However, due to inherent difficulties in both data acquisition and data analysis methods, studies on large-scale brain dynamics of mouse with local field potential (LFP) recording are very rare. In this paper, we did a series of works on modeling large-scale mouse brain dynamic activities responding to fearful earthquake. Based on LFP recording data from 13 brain regions that are closely related to fear learning and memory and the effective Bayesian connectivity change point model, we divided the response time series into four stages: "Before," "Earthquake," "Recovery," and "After." We first reported the changes in power and theta-gamma coupling during stage transitions. Then, a recurrent neural network model was designed to model the functional dynamics in these thirteen brain regions and six frequency bands in response to the fear stimulus. Interestingly, our results showed that the functional brain connectivities in theta and gamma bands exhibited distinct response processes: in theta band, there is a separated-united-separated alternation in whole-brain connectivity and a low-high-low change in connectivity strength; however, gamma bands have a united-separated-united transition and a high-low-high alternation in connectivity pattern and strength. In general, our results offer a novel perspective in studying functional brain dynamics under fearful stimulus and reveal its relationship to the brain's structural connectivity substrates.

Modeling and interpreting mesoscale network dynamics

Recent advances in brain imaging techniques, measurement approaches, and storage capacities have provided an unprecedented supply of high temporal resolution neural data. These data present a remarkable opportunity to gain a mechanistic understanding not just of circuit structure, but also of circuit dynamics, and its role in cognition and disease. Such understanding necessitates a description of the raw observations, and a delineation of computational models and mathematical theories that accurately capture fundamental principles behind the observations. Here we review recent advances in a range of modeling approaches that embrace the temporally-evolving interconnected structure of the brain and summarize that structure in a dynamic graph. We describe recent efforts to model dynamic patterns of connectivity, dynamic patterns of activity, and patterns of activity atop connectivity. In the context of these models, we review important considerations in statistical testing, including parametric and non-parametric approaches. Finally, we offer thoughts on careful and accurate interpretation of dynamic graph architecture, and outline important future directions for method development.

People are better at maintaining positive than negative emotional states

Determining how people maintain positive and negative emotional states is critical to understanding emotional dynamics, individual differences in emotion, and the instrumental value of emotions. There has been a surge in interest in tasks assessing affective working memory that can examine how people maintain stimulus-independent positive and negative emotional states. In these tasks, people are asked to maintain their emotional state that was induced by an initial stimulus in order to compare that state with the state induced by a subsequent stimulus. It is unclear, however, whether measures of accuracy in this task actually reflect the success of maintaining the initial emotional state. In a series of studies, we introduce an idiographic metric of accuracy that reflects the success of emotional maintenance and use that metric to examine whether people are better at maintaining positive or negative emotional states. We demonstrate that people are generally better at maintaining positive emotional states than they are at maintaining negative emotional states (Studies 1-3). We also show that this effect is not due to decay or to spontaneous interference processes (Studies 2-3), retroactive interference processes (Studies 4-5), or reduced engagement with the initial emotional state (Study 5). Although the mechanism underlying this effect is not yet clear, our results have important implications for understanding emotional maintenance and the possible functions of positive and negative emotions. (PsycINFO Database Record (c) 2019 APA, all rights reserved).

vmPFC activation during a stressor predicts positive emotions during stress recovery

Despite accruing evidence showing that positive emotions facilitate stress recovery, the neural basis for this effect remains unclear. To identify the underlying mechanism, we compared stress recovery for people reflecting on a stressor while in a positive emotional context with that for people in a neutral context. While blood-oxygen-level dependent data were being collected, participants (N = 43) performed a stressful anagram task, which was followed by a recovery period during which they reflected on the stressor while watching a positive or neutral video. Participants also reported positive and negative emotions throughout the task as well as retrospective thoughts about the task. Although there was no effect of experimental context on emotional recovery, we found that ventromedial prefrontal cortex (vmPFC) activation during the stressor predicted more positive emotions during recovery, which in turn predicted less negative emotions during recovery. In addition, the relationship between vmPFC activation and positive emotions during recovery was mediated by decentering-the meta-cognitive detachment of oneself from one's feelings. In sum, successful recovery from a stressor seems to be due to activation of positive emotion-related regions during the stressor itself as well as to their downstream effects on certain cognitive forms of emotion regulation.

Detecting correlation changes in multivariate time series: A comparison of four non-parametric change point detection methods

Change point detection in multivariate time series is a complex task since next to the mean, the correlation structure of the monitored variables may also alter when change occurs. DeCon was recently developed to detect such changes in mean and\or correlation by combining a moving windows approach and robust PCA. However, in the literature, several other methods have been proposed that employ other non-parametric tools: E-divisive, Multirank, and KCP. Since these methods use different statistical approaches, two issues need to be tackled. First, applied researchers may find it hard to appraise the differences between the methods. Second, a direct comparison of the relative performance of all these methods for capturing change points signaling correlation changes is still lacking. Therefore, we present the basic principles behind DeCon, E-divisive, Multirank, and KCP and the corresponding algorithms, to make them more accessible to readers. We further compared their performance through extensive simulations using the settings of Bulteel et al. (Biological Psychology, 98 (1), 29-42, 2014) implying changes in mean and in correlation structure and those of Matteson and James (Journal of the American Statistical Association, 109 (505), 334-345, 2014) implying different numbers of (noise) variables. KCP emerged as the best method in almost all settings. However, in case of more than two noise variables, only DeCon performed adequately in detecting correlation changes.

Adapted estimate of neural activity based on blood-oxygen-level dependent signal by a model-free spatio-temporal clustering analysis

In this study, we detected brain activity by comparing the overall temporal response of the blood oxygen level referring to hemodynamic response with a modeled hemodynamic response (MHR). However, in a conventional analysis by statistical parametric mapping (SPM) method, the MHR is assumed to be a fixed-response function, which may bias the conclusions about brain activation, such as the shapes of the response curve or the different response delays to stimuli. Therefore, to improve detection efficacy, we applied a spatio-temporal clustering analysis (sTCA) to determine the MHR, which is calculated from the prospective voxels with no a priori information about the experiment design. With the sTCA method, these prospective voxels are detected by the feature with the largest temporal clustering within which these voxels react simultaneously, irrespective of where the variant hemodynamic response occurs. This estimated MHR (eMHR) is then applied to search for brain activation. Preliminary results show that the eMHR signal response closely resembles the real signal response of the target area. Moreover, the activation detection using eMHR method is more sensitive for the human visual and motor tasks than that with the canonical hemodynamic response embedded in the SPM analysis as the default MHR (dMHR). The more precise location of brain activation made possible by the improved sensitivity should provide helpful information about the stimulation of neuron activity.

Big Data and Neuroimaging

Big Data are of increasing importance in a variety of areas, especially in the biosciences. There is an emerging critical need for Big Data tools and methods, because of the potential impact of advancements in these areas. Importantly, statisticians and statistical thinking have a major role to play in creating meaningful progress in this arena. We would like to emphasize this point in this special issue, as it highlights both the dramatic need for statistical input for Big Data analysis and for a greater number of statisticians working on Big Data problems. We use the field of statistical neuroimaging to demonstrate these points. As such, this paper covers several applications and novel methodological developments of Big Data tools applied to neuroimaging data.

The neural basis of emotions varies over time: different regions go with onset- and offset-bound processes underlying emotion intensity

According to theories of emotion dynamics, emotions unfold across two phases in which different types of processes come to the fore: emotion onset and emotion offset. Differences in onset-bound processes are reflected by the degree of explosiveness or steepness of the response at onset, and differences in offset-bound processes by the degree of accumulation or intensification of the subsequent response. Whether onset- and offset-bound processes have distinctive neural correlates and, hence, whether the neural basis of emotions varies over time, still remains unknown. In the present fMRI study, we address this question using a recently developed paradigm that allows to disentangle explosiveness and accumulation. Thirty-one participants were exposed to neutral and negative social feedback, and asked to reflect on its contents. Emotional intensity while reading and thinking about the feedback was measured with an intensity profile tracking approach. Using non-negative matrix factorization, the resulting profile data were decomposed in explosiveness and accumulation components, which were subsequently entered as continuous regressors of the BOLD response. It was found that the neural basis of emotion intensity shifts as emotions unfold over time with emotion explosiveness and accumulation having distinctive neural correlates.

Detection of timescales in evolving complex systems

Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system's configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system.

Real-time estimation of dynamic functional connectivity networks

Two novel and exciting avenues of neuroscientific research involve the study of task-driven dynamic reconfigurations of functional connectivity networks and the study of functional connectivity in real-time. While the former is a well-established field within neuroscience and has received considerable attention in recent years, the latter remains in its infancy. To date, the vast majority of real-time fMRI studies have focused on a single brain region at a time. This is due in part to the many challenges faced when estimating dynamic functional connectivity networks in real-time. In this work, we propose a novel methodology with which to accurately track changes in time-varying functional connectivity networks in real-time. The proposed method is shown to perform competitively when compared to state-of-the-art offline algorithms using both synthetic as well as real-time fMRI data. The proposed method is applied to motor task data from the Human Connectome Project as well as to data obtained from a visuospatial attention task. We demonstrate that the algorithm is able to accurately estimate task-related changes in network structure in real-time. Hum Brain Mapp 38:202-220, 2017. © 2016 Wiley Periodicals, Inc.

Bayesian Inference for Functional Dynamics Exploring in fMRI Data

This paper aims to review state-of-the-art Bayesian-inference-based methods applied to functional magnetic resonance imaging (fMRI) data. Particularly, we focus on one specific long-standing challenge in the computational modeling of fMRI datasets: how to effectively explore typical functional interactions from fMRI time series and the corresponding boundaries of temporal segments. Bayesian inference is a method of statistical inference which has been shown to be a powerful tool to encode dependence relationships among the variables with uncertainty. Here we provide an introduction to a group of Bayesian-inference-based methods for fMRI data analysis, which were designed to detect magnitude or functional connectivity change points and to infer their functional interaction patterns based on corresponding temporal boundaries. We also provide a comparison of three popular Bayesian models, that is, Bayesian Magnitude Change Point Model (BMCPM), Bayesian Connectivity Change Point Model (BCCPM), and Dynamic Bayesian Variable Partition Model (DBVPM), and give a summary of their applications. We envision that more delicate Bayesian inference models will be emerging and play increasingly important roles in modeling brain functions in the years to come.

Change Point Detection in Correlation Networks

Many systems of interacting elements can be conceptualized as networks, where network nodes represent the elements and network ties represent interactions between the elements. In systems where the underlying network evolves, it is useful to determine the points in time where the network structure changes significantly as these may correspond to functional change points. We propose a method for detecting change points in correlation networks that, unlike previous change point detection methods designed for time series data, requires minimal distributional assumptions. We investigate the difficulty of change point detection near the boundaries of the time series in correlation networks and study the power of our method and competing methods through simulation. We also show the generalizable nature of the method by applying it to stock price data as well as fMRI data.

Dynamic connectivity detection: an algorithm for determining functional connectivity change points in fMRI data

Recently there has been an increased interest in using fMRI data to study the dynamic nature of brain connectivity. In this setting, the activity in a set of regions of interest (ROIs) is often modeled using a multivariate Gaussian distribution, with a mean vector and covariance matrix that are allowed to vary as the experiment progresses, representing changing brain states. In this work, we introduce the Dynamic Connectivity Detection (DCD) algorithm, which is a data-driven technique to detect temporal change points in functional connectivity, and estimate a graph between ROIs for data within each segment defined by the change points. DCD builds upon the framework of the recently developed Dynamic Connectivity Regression (DCR) algorithm, which has proven efficient at detecting changes in connectivity for problems consisting of a small to medium (< 50) number of regions, but which runs into computational problems as the number of regions becomes large (>100). The newly proposed DCD method is faster, requires less user input, and is better able to handle high-dimensional data. It overcomes the shortcomings of DCR by adopting a simplified sparse matrix estimation approach and a different hypothesis testing procedure to determine change points. The application of DCD to simulated data, as well as fMRI data, illustrates the efficacy of the proposed method.

Temporal Dynamics of Emotional Processing in the Brain

Emotion theorists have long held that a fundamental characteristic of an emotion is how its constituent processes change and interact over time. Assessing these temporal dynamics of emotion in the brain is critical for understanding the neural representation of emotions as well as advancing theories of emotional processing. We review the neuroimaging research on three temporal dynamic features of emotion: time of onset, duration, and resurgence and show how assessing these temporal dynamics in the brain have led to improved understanding of the structure and function of emotional processes such as revealing which appraisals come first, how emotional processing endures both explicitly and implicitly, and that the resurgence of emotional processing may consist of either single or multiple processes.

A sticky weighted regression model for time-varying resting-state brain connectivity estimation

Despite recent progress on brain connectivity modeling using neuroimaging data such as fMRI, most current approaches assume that brain connectivity networks have time-invariant topology/coefficients. This is clearly problematic as the brain is inherently nonstationary. Here, we present a time-varying model to investigate the temporal dynamics of brain connectivity networks. The proposed method allows for abrupt changes in network structure via a fused least absolute shrinkage and selection operator (LASSO) scheme, as well as recovery of time-varying networks with smoothly changing coefficients via a weighted regression technique. Simulations demonstrate that the proposed method yields improved accuracy on estimating time-dependent connectivity patterns when compared to a static sparse regression model or a weighted time-varying regression model. When applied to real resting-state fMRI datasets from Parkinson's disease (PD) and control subjects, significantly different temporal and spatial patterns were found to be associated with PD. Specifically, PD subjects demonstrated reduced network variability over time, which may be related to impaired cognitive flexibility previously reported in PD. The temporal dynamic properties of brain connectivity in PD subjects may provide insights into brain dynamics associated with PD and may serve as a potential biomarker in future studies.

Evaluating dynamic bivariate correlations in resting-state fMRI: a comparison study and a new approach

To date, most functional Magnetic Resonance Imaging (fMRI) studies have assumed that the functional connectivity (FC) between time series from distinct brain regions is constant across time. However, recently, there has been an increased interest in quantifying possible dynamic changes in FC during fMRI experiments, as it is thought that this may provide insight into the fundamental workings of brain networks. In this work we focus on the specific problem of estimating the dynamic behavior of pair-wise correlations between time courses extracted from two different regions of the brain. We critique the commonly used sliding-window technique, and discuss some alternative methods used to model volatility in the finance literature that could also prove to be useful in the neuroimaging setting. In particular, we focus on the Dynamic Conditional Correlation (DCC) model, which provides a model-based approach towards estimating dynamic correlations. We investigate the properties of several techniques in a series of simulation studies and find that DCC achieves the best overall balance between sensitivity and specificity in detecting dynamic changes in correlations. We also investigate its scalability beyond the bivariate case to demonstrate its utility for studying dynamic correlations between more than two brain regions. Finally, we illustrate its performance in an application to test-retest resting state fMRI data.

Atomic dynamic functional interaction patterns for characterization of ADHD

Modeling abnormal temporal dynamics of functional interactions in psychiatric disorders has been of great interest in the neuroimaging field, and thus a variety of methods have been proposed so far. However, the temporal dynamics and disease-related abnormalities of functional interactions within specific data-driven discovered subnetworks have been rarely explored yet. In this work, we propose a novel computational framework composed of an effective Bayesian connectivity change point model for modeling functional brain interactions and their dynamics simultaneously and an effective variant of nonnegative matrix factorization for assessing the functional interaction abnormalities within subnetworks. This framework has been applied on the resting state fmagnetic resonance imaging (fMRI) datasets of 23 children with attention-deficit/hyperactivity disorder (ADHD) and 45 normal control (NC) children, and has revealed two atomic functional interaction patterns (AFIPs) discovered for ADHD and another two AFIPs derived for NC. Together, these four AFIPs could be grouped into two pairs, one common pair representing the common AFIPs in ADHD and NC, and the other abnormal pair representing the abnormal AFIPs in ADHD. Interestingly, by comparing the abnormal AFIP pair, two data-driven abnormal functional subnetworks are derived. Strikingly, by evaluating the approximation based on the four AFIPs, all of the ADHD children were successfully differentiated from NCs without any false positive.

DeCon: a tool to detect emotional concordance in multivariate time series data of emotional responding

The occurrence of concordance among different response components during an emotional episode is a key feature of several contemporary accounts and definitions of emotion. Yet, capturing such response concordance in empirical data has proven to be elusive, in large part because of a lack of appropriate statistical tools that are tailored to measure the intricacies of response concordance in the context of data on emotional responding. In this article, we present a tool we developed to detect two different forms of response concordance-response patterning and synchronization-in multivariate time series data of emotional responding, and apply this tool to data concerning physiological responding to emotional stimuli. While the findings provide partial evidence for both response patterning and synchronization, they also show that the presence and nature of such patterning and synchronization is strongly person-dependent.

Inferring functional interaction and transition patterns via dynamic Bayesian variable partition models

Multivariate connectivity and functional dynamics have been of wide interest in the neuroimaging field, and a variety of methods have been developed to study functional interactions and dynamics. In contrast, the temporal dynamic transitions of multivariate functional interactions among brain networks, in particular, in resting state, have been much less explored. This article presents a novel dynamic Bayesian variable partition model (DBVPM) that simultaneously considers and models multivariate functional interactions and their dynamics via a unified Bayesian framework. The basic idea is to detect the temporal boundaries of piecewise quasi-stable functional interaction patterns, which are then modeled by representative signature patterns and whose temporal transitions are characterized by finite-state transition machines. Results on both simulated and experimental datasets demonstrated the effectiveness and accuracy of the DBVPM in dividing temporally transiting functional interaction patterns. The application of DBVPM on a post-traumatic stress disorder (PTSD) dataset revealed substantially different multivariate functional interaction signatures and temporal transitions in the default mode and emotion networks of PTSD patients, in comparison with those in healthy controls. This result demonstrated the utility of DBVPM in elucidating salient features that cannot be revealed by static pair-wise functional connectivity analysis.

Detecting brain state changes via fiber-centered functional connectivity analysis

Diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) have been widely used to study structural and functional brain connectivity in recent years. A common assumption used in many previous functional brain connectivity studies is the temporal stationarity. However, accumulating literature evidence has suggested that functional brain connectivity is under temporal dynamic changes in different time scales. In this paper, a novel and intuitive approach is proposed to model and detect dynamic changes of functional brain states based on multimodal fMRI/DTI data. The basic idea is that functional connectivity patterns of all fiber-connected cortical voxels are concatenated into a descriptive functional feature vector to represent the brain's state, and the temporal change points of brain states are decided by detecting the abrupt changes of the functional vector patterns via the sliding window approach. Our extensive experimental results have shown that meaningful brain state change points can be detected in task-based fMRI/DTI, resting state fMRI/DTI, and natural stimulus fMRI/DTI data sets. Particularly, the detected change points of functional brain states in task-based fMRI corresponded well to the external stimulus paradigm administered to the participating subjects, thus partially validating the proposed brain state change detection approach. The work in this paper provides novel perspective on the dynamic behaviors of functional brain connectivity and offers a starting point for future elucidation of the complex patterns of functional brain interactions and dynamics.

Additional evidence for the sustained effect of acupuncture at the vision-related acupuncture point, GB37

OBJECTIVE

To investigate the dynamics underlying the sustained effect of acupuncture as a possible explanation of earlier findings that acupuncture stimulation at the vision-related acupuncture point, GB37, cannot specifically change the functional MRI (fMRI) signals of the visual cortex compared with stimulation at an adjacent non-meridian point.

METHODS

The 'on-off' experimental design was separated into four series conditions: 1 min of baseline scanning at the beginning, then two stimulation epochs separated by a 50 s 'rest' period, and then a 1 min 'rest' epoch. The standard General Linear Model (GLM) approach and multi-conditions analysis were used.

RESULTS

Results from the multi-conditions analysis were different from those from the standard GLM analysis. We found that the neural signal of the limbic-paralimbic-neocortical system after acupuncture stimulus lasted longer than the putative period. Furthermore, the fMRI signal changes in the occipital cortex showed different temporal patterns between GB37 and the non-meridian point.

CONCLUSIONS

Owing to the sustained effect of acupuncture, standard GLM analysis may be unsuitable for 'on-off' design acupuncture studies and lead to uncertain and contradictory results. The findings from this study suggest that acupuncture at GB37 can induce complex brain activity in the vision cortex. The state-related neural signal may reflect one of the significant characteristics underlying acupuncture.

Weed or wheel! FMRI, behavioural, and toxicological investigations of how cannabis smoking affects skills necessary for driving

Marijuana is the most widely used illicit drug, however its effects on cognitive functions underlying safe driving remain mostly unexplored. Our goal was to evaluate the impact of cannabis on the driving ability of occasional smokers, by investigating changes in the brain network involved in a tracking task. The subject characteristics, the percentage of Δ(9)-Tetrahydrocannabinol in the joint, and the inhaled dose were in accordance with real-life conditions. Thirty-one male volunteers were enrolled in this study that includes clinical and toxicological aspects together with functional magnetic resonance imaging of the brain and measurements of psychomotor skills. The fMRI paradigm was based on a visuo-motor tracking task, alternating active tracking blocks with passive tracking viewing and rest condition. We show that cannabis smoking, even at low Δ(9)-Tetrahydrocannabinol blood concentrations, decreases psychomotor skills and alters the activity of the brain networks involved in cognition. The relative decrease of Blood Oxygen Level Dependent response (BOLD) after cannabis smoking in the anterior insula, dorsomedial thalamus, and striatum compared to placebo smoking suggests an alteration of the network involved in saliency detection. In addition, the decrease of BOLD response in the right superior parietal cortex and in the dorsolateral prefrontal cortex indicates the involvement of the Control Executive network known to operate once the saliencies are identified. Furthermore, cannabis increases activity in the rostral anterior cingulate cortex and ventromedial prefrontal cortices, suggesting an increase in self-oriented mental activity. Subjects are more attracted by intrapersonal stimuli ("self") and fail to attend to task performance, leading to an insufficient allocation of task-oriented resources and to sub-optimal performance. These effects correlate with the subjective feeling of confusion rather than with the blood level of Δ(9)-Tetrahydrocannabinol. These findings bolster the zero-tolerance policy adopted in several countries that prohibits the presence of any amount of drugs in blood while driving.

Neurophysiological studies of auditory verbal hallucinations

We discuss 3 neurophysiological approaches to study auditory verbal hallucinations (AVH). First, we describe "state" (or symptom capture) studies where periods with and without hallucinations are compared "within" a patient. These studies take 2 forms: passive studies, where brain activity during these states is compared, and probe studies, where brain responses to sounds during these states are compared. EEG (electroencephalography) and MEG (magnetoencephalography) data point to frontal and temporal lobe activity, the latter resulting in competition with external sounds for auditory resources. Second, we discuss "trait" studies where EEG and MEG responses to sounds are recorded from patients who hallucinate and those who do not. They suggest a tendency to hallucinate is associated with competition for auditory processing resources. Third, we discuss studies addressing possible mechanisms of AVH, including spontaneous neural activity, abnormal self-monitoring, and dysfunctional interregional communication. While most studies show differences in EEG and MEG responses between patients and controls, far fewer show symptom relationships. We conclude that efforts to understand the pathophysiology of AVH using EEG and MEG have been hindered by poor anatomical resolution of the EEG and MEG measures, poor assessment of symptoms, poor understanding of the phenomenon, poor models of the phenomenon, decoupling of the symptoms from the neurophysiology due to medications and comorbidites, and the possibility that the schizophrenia diagnosis breeds truer than the symptoms it comprises. These problems are common to studies of other psychiatric symptoms and should be considered when attempting to understand the basic neural mechanisms responsible for them.

Neural temporal dynamics of stress in comorbid major depressive disorder and social anxiety disorder

Background

Despite advances in neurobiological research on Major Depressive Disorder and Social Anxiety Disorder, little is known about the neural functioning of individuals with comorbid depression/social anxiety. We examined the timing of neural responses to social stress in individuals with major depression and/or social anxiety. We hypothesized that having social anxiety would be associated with earlier responses to stress, having major depression would be associated with sustained responses to stress, and that comorbid participants would exhibit both of these response patterns.

Methods

Participants were females diagnosed with pure depression (n = 12), pure social anxiety (n = 16), comorbid depression/social anxiety (n = 17), or as never having had any Axis-I disorder (control; n = 17). Blood oxygenation-level dependent activity (BOLD) was assessed with functional magnetic resonance imaging (fMRI). To induce social stress, participants prepared a speech that was ostensibly to be evaluated by a third party.

Results

Whereas being diagnosed with depression was associated with a resurgence of activation in the medial frontal cortex late in the stressor, having social anxiety was associated with a vigilance-avoidance activation pattern in the occipital cortex and insula. Comorbid participants exhibited activation patterns that generally overlapped with the non-comorbid groups, with the exception of an intermediate level of activation, between the level of activation of the pure depression and social anxiety groups, in the middle and posterior cingulate cortex.

Conclusions

These findings advance our understanding of the neural underpinnings of major depression and social anxiety, and of their comorbidity. Future research should elucidate more precisely the behavioral correlates of these patterns of brain activation.

Dynamic connectivity regression: determining state-related changes in brain connectivity

Most statistical analyses of fMRI data assume that the nature, timing and duration of the psychological processes being studied are known. However, often it is hard to specify this information a priori. In this work we introduce a data-driven technique for partitioning the experimental time course into distinct temporal intervals with different multivariate functional connectivity patterns between a set of regions of interest (ROIs). The technique, called Dynamic Connectivity Regression (DCR), detects temporal change points in functional connectivity and estimates a graph, or set of relationships between ROIs, for data in the temporal partition that falls between pairs of change points. Hence, DCR allows for estimation of both the time of change in connectivity and the connectivity graph for each partition, without requiring prior knowledge of the nature of the experimental design. Permutation and bootstrapping methods are used to perform inference on the change points. The method is applied to various simulated data sets as well as to an fMRI data set from a study (N=26) of a state anxiety induction using a socially evaluative threat challenge. The results illustrate the method's ability to observe how the networks between different brain regions changed with subjects' emotional state.

Do unexpected panic attacks occur spontaneously?

BACKGROUND

Spontaneous or unexpected panic attacks, per definition, occur "out of the blue," in the absence of cues or triggers. Accordingly, physiological arousal or instability should occur at the onset of, or during, the attack, but not preceding it. To test this hypothesis, we examined if points of significant autonomic changes preceded the onset of spontaneous panic attacks.

METHODS

Forty-three panic disorder patients underwent repeated 24-hour ambulatory monitoring. Thirteen natural panic attacks were recorded during 1960 hours of monitoring. Minute-by-minute epochs beginning 60 minutes before and continuing to 10 minutes after the onset of individual attacks were examined for respiration, heart rate, and skin conductance level. Measures were controlled for physical activity and vocalization and compared with time matched control periods within the same person.

RESULTS

Significant patterns of instability across a number of autonomic and respiratory variables were detected as early as 47 minutes before panic onset. The final minutes before onset were dominated by respiratory changes, with significant decreases in tidal volume followed by abrupt carbon dioxide partial pressure increases. Panic attack onset was characterized by heart rate and tidal volume increases and a drop in carbon dioxide partial pressure. Symptom report was consistent with these changes. Skin conductance levels were generally elevated in the hour before, and during, the attacks. Changes in the matched control periods were largely absent.

CONCLUSIONS

Significant autonomic irregularities preceded the onset of attacks that were reported as abrupt and unexpected. The findings invite reconsideration of the current diagnostic distinction between uncued and cued panic attacks.