A New Constrained Spatiotemporal ICA Method Based on Multi-Objective Optimization for fMRI Data Analysis

Exploring brain effective connectivity of early MCI with GRU_GC model on resting-state fMRI

BACKGROUND

Investigating the functional interactions between different brain regions and revealing the transmission of information by computing brain connectivity have great potential and significance in the diagnosis of early Mild Cognitive Impairment (EMCI).

METHODS

The Granger causality with Gate Recurrent Unit (GRU_GC) model is a suitable method that allows the detection of a nonlinear causal relationship and solves the limitation of fixed time lag, which cannot be detected by the classical Granger method. The model can transmit time series signals with any transmission delay length, and the time series can be screened and learned through the gate model.

RESULTS

The classification experiment of 89 EMCI and 73 neurologically healthy controls (HC) shows that the accuracy reached 87.88%. Compared with multivariate variables GC (MVGC) and Long Short-Term Memory-based GC (LSTM_GC), the GRU_GC significantly improved the estimation of brain connectivity communication. Constructing a difference network to explore the brain effective connectivity between EMCI and HC.

CONCLUSIONS

The GRU_GC can discover the abnormal brain regions, including the parahippocampal gyrus, the posterior cingulate gyrus. The method can be used in clinical applications as an effective brain connectivity analysis tool and provides auxiliary means for the medical diagnosis of EMCI.

Homogeneous-Multiset-CCA-Based Brain Covariation and Contravariance Connectivity Network Modeling

Brain connectivity networks based on functional magnetic resonance imaging (fMRI) have expanded our understanding of brain functions in both healthy and diseased states. However, most current studies construct connectivity networks using averaged regional time courses with the strong assumption that the activities of voxels contained in each brain region are similar, ignoring their possible variations. Additionally, pairwise correlation analysis is often adopted with more attention to positive relationships, while joint interactions at the network level as well as anti-correlations are less investigated. In this paper, to provide a new strategy for regional activity representation and brain connectivity modeling, a novel homogeneous multiset canonical correlation analysis (HMCCA) model is proposed, which enforces sign constraints on the weights of voxels to guarantee homogeneity within each brain region. It is capable of obtaining regional representative signals and constructing covariation and contravariance networks simultaneously, at both group and subject levels. Validations on two sessions of fMRI data verified its reproducibility and reliability when dealing with brain connectivity networks. Further experiments on subjects with and without Parkinson's disease (PD) revealed significant alterations in brain connectivity patterns, which were further associated with clinical scores and demonstrated superior prediction ability, indicating its potential in clinical practice.

Brain Response of Major Depressive Disorder Patients to Emotionally Positive and Negative Music

Depression is characterized by poor emotion regulation that makes it difficult to escape the effects of emotional pain, but the neuromodulation behind these symptoms is still unclear. This study investigated the neural mechanism of emotional state-related responses during music stimuli in participants with major depressive disorder (MDD) compared to never-depressed (ND) controls. A novel two-level feature selection method, integrating recursive feature elimination based on support vector machine (SVM-RFE) and random forest algorithm (RF), was proposed to screen emotional recognition brain regions (ERBRs). On this basis, the differences of functional connectivity (FC) were systematically analyzed by two-sample t-test. The results demonstrate that ND participants show eight pairs of FCs with a significant difference between positive emotional music stimuli (pEMS) versus negative emotional music stimuli (nEMS) in 15 ERBRs of MDD, but the participants with MDD show one pair of significant difference in FC. The decreased number reflects the fuzzy response to positive and negative emotions in MDD, which appears to arise from obstacle to emotional cognition and regulation. Furthermore, there was no significant difference in FC between MDDs and NDs under pEMS, but a significant difference was detected between the two groups under nEMS (p < 0.01), revealing a 'bias' against the negative state in MDD. The current study may help to better comprehend the abnormal evolution from normal to depression and inform the utilization of pEMS in formal treatment for depression.

Dynamical Complexity Fingerprints of Occupation-Dependent Brain Functional Networks in Professional Seafarers

The complexity derived from resting-state functional magnetic resonance imaging (rs-fMRI) data has been applied for exploring cognitive states and occupational neuroplasticity. However, there is little information about the influence of occupational factors on dynamic complexity and topological properties of the connectivity networks. In this paper, we proposed a novel dynamical brain complexity analysis (DBCA) framework to explore the changes in dynamical complexity of brain activity at the voxel level and complexity topology for professional seafarers caused by long-term working experience. The proposed DBCA is made up of dynamical brain entropy mapping analysis and complex network analysis based on brain entropy sequences, which generate the dynamical complexity of local brain areas and the topological complexity across brain areas, respectively. First, the transient complexity of voxel-wise brain map was calculated; compared with non-seafarers, seafarers showed decreased dynamic entropy values in the cerebellum and increased values in the left fusiform gyrus (BA20). Further, the complex network analysis based on brain entropy sequences revealed small-worldness in terms of topological complexity in both seafarers and non-seafarers, indicating that it is an inherent attribute of human the brain. In addition, seafarers showed a higher average path length and lower average clustering coefficient than non-seafarers, suggesting that the information processing ability is reduced in seafarers. Moreover, the reduction in efficiency of seafarers suggests that they have a less efficient processing network. To sum up, the proposed DBCA is effective for exploring the dynamic complexity changes in voxel-wise activity and region-wise connectivity, showing that occupational experience can reshape seafarers’ dynamic brain complexity fingerprints.

Functional Covariance Connectivity of Gray and White Matter in Olfactory-Related Brain Regions in Parkinson’s Disease

Before the onset of motor symptoms, Parkinson’s disease (PD) involves dysfunction of the anterior olfactory nucleus and olfactory bulb, causing olfactory disturbance, commonly resulting in hyposmia in the early stages of PD. Accumulating evidence has shown that blood oxygen level dependent (BOLD) signals in white matter are altered by olfactory disorders and related stimuli, and the signal changes in brain white matter pathways show a certain degree of specificity, which can reflect changes of early olfactory dysfunction in Parkinson’s disease. In this study, we apply the functional covariance connectivity (FCC) method to decode FCC of gray and white matter in olfactory-related brain regions in Parkinson’s disease. Our results show that the dorsolateral prefrontal, anterior entorhinal cortex and fronto-orbital cortices in the gray matter have abnormal connectivity with the posterior corona radiata and superior corona radiata in white matter in patients with Parkinson’s hyposmia. The functional covariance connection strength (FCS) of the right dorsolateral prefrontal cortex and white matter, and the covariance connection strength of the left superior corona radiata and gray matter function have potential diagnostic value. These results demonstrate that alterations in FCC of gray and white matter in olfactory-related brain regions can reflect the change of olfactory function in the early stages of Parkinson’s disease, indicating that it could be a potential neuroimaging marker for early diagnosis.

A Novel Constrained Non-negative Matrix Factorization Method for Group Functional Magnetic Resonance Imaging Data Analysis of Adult Attention-Deficit/Hyperactivity Disorder

Attention-deficit/hyperactivity disorder (ADHD) is a common childhood psychiatric disorder that often persists into adulthood. Extracting brain networks from functional magnetic resonance imaging (fMRI) data can help explore neurocognitive disorders in adult ADHD. However, there is still a lack of effective methods to extract large-scale brain networks to identify disease-related brain network changes. Hence, this study proposed a spatial constrained non-negative matrix factorization (SCNMF) method based on the fMRI real reference signal. First, non-negative matrix factorization analysis was carried out on each subject to select the brain network components of interest. Subsequently, the available spatial prior information was mined by integrating the interested components of all subjects. This prior constraint was then incorporated into the NMF objective function to improve its efficiency. For the sake of verifying the effectiveness and feasibility of the proposed method, we quantitatively compared the SCNMF method with other classical algorithms and applied it to the dynamic functional connectivity analysis framework. The algorithm successfully extracted ten resting-state brain functional networks from fMRI data of adult ADHD and healthy controls and found large-scale brain network changes in adult ADHD patients, such as enhanced connectivity between executive control network and right frontoparietal network. In addition, we found that older ADHD spent more time in the pattern of relatively weak connectivity. These findings indicate that the method can effectively extract large-scale functional networks and provide new insights into understanding the neurobiological mechanisms of adult ADHD from the perspective of brain networks.

Enhanced design matrix for task-related fMRI data analysis

In this paper, we introduce a novel methodology for the analysis of task-related fMRI data. In particular, we propose an alternative way for constructing the design matrix, based on the newly suggested Information-Assisted Dictionary Learning (IADL) method. This technique offers an enhanced potential, within the conventional GLM framework, (a) to efficiently cope with uncertainties in the modeling of the hemodynamic response function, (b) to accommodate unmodeled brain-induced sources, beyond the task-related ones, as well as potential interfering scanner-induced artifacts, uncorrected head-motion residuals and other unmodeled physiological signals, and (c) to integrate external knowledge regarding the natural sparsity of the brain activity that is associated with both the experimental design and brain atlases. The capabilities of the proposed methodology are evaluated via a realistic synthetic fMRI-like dataset, and demonstrated using a test case of a challenging fMRI study, which verifies that the proposed approach produces substantially more consistent results compared to the standard design matrix method. A toolbox extension for SPM is also provided, to facilitate the use and reproducibility of the proposed methodology.

Internet-like brain hierarchical network model: Alzheimer's disease study as an example

BACKGROUND AND OBJECTIVE

The modular structure and hierarchy are important topological characteristics in real complex networks such as brain networks on temporal scale. However, there are few studies investigating the hierarchical structure at the spatial scale of brain networks, the application of which still remains to be further studied.

METHODS

In this study, a novel model of brain hierarchical network based on the hierarchical characteristic of Internet topology is proposed for the first time, which is called Internet-like brain hierarchical network (IBHN). In this model, the whole brain network is partitioned into multiple levels: brain wide area network (Brain-WAN), brain metropolitan network (Brain-MAN), and brain local area network (Brain-LAN). A Brain-MAN is formed by the interconnection of multiple Brain-LANs, and the interconnection of multiple Brain-MANs forms a Brain-WAN. A multivariate analysis method is employed to measure overall functional connectivity between two brain networks at the same network level rather than detecting the change of each node pair's functional connection. Furthermore, we demonstrate the utility of IBHN model with application to a practical case-control study involving 64 patients with Alzheimer's disease and 75 healthy controls.

RESULTS

The proposed model identified enhanced functional connectivity (P-value<0.05) at Brain-WAN level and reduced functional connectivity (P-value=0.004) at Brain-LAN level of Alzheimer's disease patients, which can be used as a multi-dimension functional reference for AD's diagnosis.

CONCLUSIONS

This study not only provides insight into AD pathophysiology, but also further proves the effectiveness of the proposed IBHN model. In addition, the IBHN model makes it possible to explore the brain's functional organization from multiple dimensions and offers a multi-level perspective for the research of complex brain network.

Brain Connectivity Studies on Structure-Function Relationships: A Short Survey with an Emphasis on Machine Learning

This short survey reviews the recent literature on the relationship between the brain structure and its functional dynamics. Imaging techniques such as diffusion tensor imaging (DTI) make it possible to reconstruct axonal fiber tracks and describe the structural connectivity (SC) between brain regions. By measuring fluctuations in neuronal activity, functional magnetic resonance imaging (fMRI) provides insights into the dynamics within this structural network. One key for a better understanding of brain mechanisms is to investigate how these fast dynamics emerge on a relatively stable structural backbone. So far, computational simulations and methods from graph theory have been mainly used for modeling this relationship. Machine learning techniques have already been established in neuroimaging for identifying functionally independent brain networks and classifying pathological brain states. This survey focuses on methods from machine learning, which contribute to our understanding of functional interactions between brain regions and their relation to the underlying anatomical substrate.

The Brain Alteration of Seafarer Revealed by Activated Functional Connectivity Mode in fMRI Data Analysis

As a special occupational group, the working and living environments faced by seafarers are greatly different from those of land. It is easy to affect the psychological and physiological activities of seafarers, which inevitably lead to changes in the brain functional activities of seafarers. Therefore, it is of great significance to study the neural activity rules of seafarers' brain. In view of this, this paper studied the seafarers' brain alteration at the activated voxel level based on functional magnetic resonance imaging technology by comparing the differences in functional connectivities (FCs) between seafarers and non-seafarers. Firstly, the activated voxels of each group were obtained by independence component analysis, and then the distribution of these voxels in the brain and the common activated voxels between the two groups were statistically analyzed. Next, the FCs between the common activated voxels of the two groups were calculated and obtained the FCs that had significant differences between them through two-sample T-test. Finally, all FCs and FCs with significant differences (DFCs) between the common activated voxels were used as the features for the support vector machine to classify seafarers and non-seafarers. The results showed that DFCs between the activated voxels had better recognition ability for seafarers, especially for Precuneus_L and Precuneus_R, which may play an important role in the classification prediction of seafarers and non-seafarers, so that provided a new perspective for studying the specificity of neurological activities of seafarers.

Extraction and Analysis of Dynamic Functional Connectome Patterns in Migraine Sufferers: A Resting-State fMRI Study

Migraine seriously affects the physical and mental health of patients because of its recurrence and the hypersensitivity to the environment that it causes. However, the pathogenesis and pathophysiology of migraine are not fully understood. We addressed this issue in the present study using an autodynamic functional connectome model (A-DFCM) with twice-clustering to compare dynamic functional connectome patterns (DFCPs) from resting-state functional magnetic resonance imaging data from migraine patients and normal control subjects. We used automatic localization of segment points to improve the efficiency of the model, and intergroup differences and network metrics were analyzed to identify the neural mechanisms of migraine. Using the A-DFCM model, we identified 17 DFCPs-including 1 that was specific and 16 that were general-based on intergroup differences. The specific DFCP was closely associated with neuronal dysfunction in migraine, whereas the general DFCPs showed that the 2 groups had similar functional topology as well as differences in the brain resting state. An analysis of network metrics revealed the critical brain regions in the specific DFCP; these were not only distributed in brain areas related to pain such as Brodmann area 1/2/3, basal ganglia, and thalamus but also located in regions that have been implicated in migraine symptoms such as the occipital lobe. An analysis of the dissimilarities in general DFCPs between the 2 groups identified 6 brain areas belonging to the so-called pain matrix. Our findings provide insight into the neural mechanisms of migraine while also identifying neuroimaging biomarkers that can aid in the diagnosis or monitoring of migraine patients.

Multi-channel hierarchy functional integration analysis between large-scale brain networks for migraine: An fMRI study

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A multi-channel hierarchy functional analysis was performed between MPs and HCs.

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Both static and dynamic FCs between BFNs was studied at group and individual levels.

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A graph metrics based method was used to detect the potential DFC patterns.

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Both global and local topological properties and dynamic volatility were explored.

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The results provided a new perspective for the clinical diagnosis of migraine.

Migraine is a chronic dysfunction characterized by recurrent pain, but its pathogenesis is still unclear. As a result, more and more methods have been focused on the study of migraine in recent years, including functional magnetic resonance imaging (fMRI), which is a mainstream technique for exploring the neural mechanisms of migraine. In this paper, we systematically investigated the fMRI functional connectivities (FCs) between large-scale brain networks in migraine patients from the perspective of multi-channel hierarchy, including static and dynamic FCs of group and individual levels, where the brain networks were obtained using group independent component analysis. Meanwhile, the corresponding topology properties of static and dynamic FCs networks in migraine patients were statistically compared with those in healthy controls. Furthermore, a graph metrics based method was used to detect the potential brain functional connectivity states in dynamic FCs at individual and group levels, and the corresponding topology properties and specificity of these brain functional connectivity states in migraine patients were explored compared with these in healthy controls. The results showed that the dynamic FCs and corresponding global topology properties among nine large-scale brain networks involved in this study have significant differences between migraine patients and healthy controls, while local topological properties and dynamic fluctuations were easily affected by window-widths. Moreover, the implicit dynamic functional connectivity patterns in migraine patients presented specificity and consistency under different window-widths, which suggested that the dynamic changes in FCs and topology structure between them played a key role in the brain functional activity of migraine. Therefore, it may be provided a new perspective for the clinical diagnosis of migraine.

Dynamic visual cortical connectivity analysis based on functional magnetic resonance imaging

BACKGROUND

Studies of brain functional connectivity (FC) and effective connectivity (EC) using the functional magnetic resonance imaging (fMRI) have advanced our understanding of functional organization on visual cortex of human brain. The current studies mainly focus on static or dynamic connectivity, while the relationships between them have not been well characterized especially for static EC (sEC) and dynamic EC (dEC), as well as the consistency characteristics of changing trend of dFCs and dECs, which is of great importance to reveal the neural information processing mechanism in visual cortex region.

METHOD

In this study, we explore these relationships among several subareas of human visual cortex (V1-V5) by calculating the connection intensity and information flow among them over time by sliding window method, which are defined by Pearson correlation coefficient and Granger causality analysis, respectively, in each window.

RESULTS

The results demonstrate that there are extensive connections existing in human visual network, which are time-varying both in resting and task-related states. sFC intensity is negatively correlated with the variance of dFC, while sEC intensity is positively correlated with the variance of dEC. Furthermore, we also find that dFC within visual cortex at rest shows more consistency, while dEC shows less compared with task state in changing trend.

CONCLUSION

Therefore, this study provides novel findings about dynamics of connectivity in human visual cortex from the perspective of functional and effective connectivity.

Kernel Granger Causality Based on Back Propagation Neural Network Fuzzy Inference System on fMRI Data

Granger causality (GC) is one of the most popular measures to investigate causality influence among brain regions and has been achieved significant results for exploring brain networks based on functional magnetic resonance imaging (fMRI). However, the predictors and order selection of conventional GC are based on linear models which result in such restrictions as poorly detection of nonlinearity and so on, in the application. This paper proposes a novel GC model called back propagation (BP) based kernel function Granger causality (BP_KFGC), in which symplectic geometry is used for embedding dimension and fuzzy inference system for predicting time series. The proposed method doesn't depend on the prediction of the vector auto-regression model, so that time series don't need to be wide-sense stationary as linear GC and kernel GC. In addition, it is a multivariate approach which is applicable to both linear and nonlinear systems and eliminates the effects of latent variables. The performance of the new method is evaluated and compared with linear GC, partial GC, neural network GC and kernel GC by simulated data with multiple adjustments to the nonlinearity. The results show that BP_KFGC outperforms the other four methods in detecting both linear and nonlinear causalities. Furthermore, we applied BP_KFGC to construct directed weight network (DWN) of Alzheimer's disease (AD) patients and health controls (HCs), and then nine graph-based features of DWN were used for classification by the classifier of support vector machine with radial basis kernel function. The accuracy of 95.89%, sensitivity of 93.31%, and specificity of 94.97% were achieved which may provide an auxiliary mean for the clinical diagnosis of AD.