Dynamic changes of spatial functional network connectivity in healthy individuals and schizophrenia patients using independent vector analysis

Altered static and dynamic spontaneous brain activity in patients with dysthyroid optic neuropathy: a resting-state fMRI study

Purpose

To investigate static and dynamic brain functional alterations in dysthyroid optic neuropathy (DON) using resting-state functional MRI (rs-fMRI) with the amplitude of low-frequency fluctuation (ALFF) and regional homogeneity (ReHo).

Materials and methods

Fifty-seven thyroid-associated ophthalmopathy (TAO) patients (23 DON and 34 non-DON) and 27 healthy controls (HCs) underwent rs-fMRI scans. Static and dynamic ALFF (sALFF and dALFF) and ReHo (sReHo and dReHo) values were compared between groups. The support-vector machine (SVM) classification method was used to examine the diagnostic performance of the identified models.

Results

Compared to non-DON patients, DON patients showed decreased sALFF in the bilateral lingual gyrus (LING) and right cuneus (CUN), alongside increased sALFF in the bilateral medial part of the superior frontal gyrus, right dorsolateral part of the superior frontal gyrus (SFGdor), and right precentral gyrus. DON patients also exhibited decreased dALFF in the left LING and right CUN, together with increased dALFF in the right orbital part of the middle frontal gyrus and right SFGdor in comparison to non-DON patients. Meanwhile, DON patients had lower sReHo in the right LING, and higher sReHo and dReHo in the right supramarginal gyrus compared to non-DON patients. When detecting DON, the dALFF model showed optimal diagnostic performance (AUC 0.9987).

Conclusion

Dysthyroid optic neuropathy patients exhibited both static and dynamic brain functional alterations in visual, cognitive, and emotion-related brain regions, deepening our current understanding of the underlying neural mechanisms of this disease. Rs-fMRI-based metrics, especially dALFF, may serve as relevant neuroimaging markers for diagnosing DON.

Resting-state dynamic functional connectivity in major depressive disorder: A systematic review

As a novel measure, dynamic functional connectivity (dFC) provides insight into the dynamic nature of brain networks and their interactions in resting-state, surpassing traditional static functional connectivity in pathological conditions such as depression. Since a comprehensive review is still lacking, we then reviewed forty-five eligible papers to explore pathological mechanisms of major depressive disorder (MDD) from perspectives including abnormal brain regions and functional networks, brain state, topological properties, relevant recognition, along with longitudinal studies. Though inconsistencies could be found, common findings are: (1) From different perspectives based on dFC, default-mode network (DMN) with its subregions exhibited a close relation to the pathological mechanism of MDD. (2) With a corrupted integrity within large-scale functional networks and imbalance between them, longer fraction time in a relatively weakly-connected state may be a possible property of MDD concerning its relation with DMN. Abnormal transition frequencies between states were correlated to the severity of MDD. (3) Including dynamic properties in topological network metrics enhanced recognition effect. In all, this review summarized its use for clinical diagnosis and treatment, elucidating the non-stationary of MDD patients' aberrant brain activity in the absence of stimuli and bringing new views into its underlying neuro mechanism.

Estimation of complete mutual information exploiting nonlinear magnitude-phase dependence: Application to spatial FNC for complex-valued fMRI data

BACKGROUND

Real-valued mutual information (MI) has been used in spatial functional network connectivity (FNC) to measure high-order and nonlinear dependence between spatial maps extracted from magnitude-only functional magnetic resonance imaging (fMRI). However, real-valued MI cannot fully capture the group differences in spatial FNC from complex-valued fMRI data with magnitude and phase dependence.

METHODS

We propose a complete complex-valued MI method according to the chain rule of MI. We fully exploit the dependence among magnitudes and phases of two complex-valued signals using second and fourth-order joint entropies, and propose to use a Gaussian copula transformation with a lower bound property to avoid inaccurate estimation of joint probability density function when computing the joint entropies.

RESULTS

The proposed method achieves more accurate MI estimates than the two histogram-based (normal and symbolic approaches) and kernel density estimation methods for simulated signals, and enhances group differences in spatial functional network connectivity for experimental complex-valued fMRI data.

COMPARISON WITH EXISTING METHODS

Compared with the simplified complex-valued MI and real-valued MI, the proposed method yields higher MI estimation accuracy, leading to 17.4 % and 145.5 % wider MI ranges, and more significant connectivity differences between healthy controls and schizophrenia patients. A unique connection between executive control network (EC) and right frontal parietal areas, and three additional connections mainly related to EC are detected than the simplified complex-valued MI.

CONCLUSIONS

With capability in quantifying MI fully and accurately, the proposed complex-valued MI is promising in providing qualified FNC biomarkers for identifying mental disorders such as schizophrenia.

Sex heterogeneity of dynamic brain activity and functional connectivity in autism spectrum disorder

Sex heterogeneity has been frequently reported in autism spectrum disorders (ASD) and has been linked to static differences in brain function. However, given the complexity of ASD and diagnosis-by-sex interactions, dynamic characteristics of brain activity and functional connectivity may provide important information for distinguishing ASD phenotypes between females and males. The aim of this study was to explore sex heterogeneity of functional networks in the ASD brain from a dynamic perspective. Resting-state functional magnetic resonance imaging data from the Autism Brain Imaging Data Exchange database were analyzed in 128 ASD subjects (64 males/64 females) and 128 typically developing control (TC) subjects (64 males/64 females). A sliding-window approach was adopted for the estimation of dynamic amplitude of low-frequency fluctuation (dALFF) and dynamic functional connectivity (dFC) to characterize time-varying brain activity and functional connectivity respectively. We then examined the sex-related changes in ASD using two-way analysis of variance. Significant diagnosis-by-sex interaction effects were identified in the left anterior cingulate cortex/medial prefrontal cortex (ACC/mPFC) and left precuneus in the dALFF analysis. Furthermore, there were significant diagnosis-by-sex interaction effects of dFC variance between the left ACC/mPFC and right ACC, left postcentral gyrus, left precuneus, right middle temporal gyrus and left inferior frontal gyrus, triangular part. These findings reveal the sex heterogeneity in brain activity and functional connectivity in ASD from a dynamic perspective, and provide new evidence for further exploring sex heterogeneity in ASD.

Spatial Dynamic Subspaces Encode Sex-Specific Schizophrenia Disruptions in Transient Network Overlap and Their Links to Genetic Risk

BACKGROUND

Schizophrenia research reveals sex differences in incidence, symptoms, genetic risk factors, and brain function. However, a knowledge gap remains regarding sex-specific schizophrenia alterations in brain function. Schizophrenia is considered a dysconnectivity syndrome, but the dynamic integration and segregation of brain networks are poorly understood. Recent advances in resting-state functional magnetic resonance imaging allow us to study spatial dynamics, the phenomenon of brain networks spatially evolving over time. Nevertheless, estimating time-resolved networks remains challenging due to low signal-to-noise ratio, limited short-time information, and uncertain network identification.

METHODS

We adapted a reference-informed network estimation technique to capture time-resolved networks and their dynamic spatial integration and segregation for 193 individuals with schizophrenia and 315 control participants. We focused on time-resolved spatial functional network connectivity, an estimate of network spatial coupling, to study sex-specific alterations in schizophrenia and their links to genomic data.

RESULTS

Our findings are consistent with the dysconnectivity and neurodevelopment hypotheses and with the cerebello-thalamo-cortical, triple-network, and frontoparietal dysconnectivity models, helping to unify them. The potential unification offers a new understanding of the underlying mechanisms. Notably, the posterior default mode/salience spatial functional network connectivity exhibits sex-specific schizophrenia alteration during the state with the highest global network integration and is correlated with genetic risk for schizophrenia. This dysfunction is reflected in regions with weak functional connectivity to corresponding networks.

CONCLUSIONS

Our method can effectively capture spatially dynamic networks, detect nuanced schizophrenia effects including sex-specific ones, and reveal the intricate relationship of dynamic information to genomic data. The results also underscore the clinical potential of dynamic spatial dependence and weak connectivity.

Spatial-Temporal Characteristics of Brain Activity in Autism Spectrum Disorder Based on Hidden Markov Model and Dynamic Graph Theory: A Resting-State fMRI Study

Autism spectrum disorder (ASD) is a common neurodevelopmental disorder. Functional magnetic resonance imaging (fMRI) can be used to measure the temporal correlation of blood-oxygen-level-dependent (BOLD) signals in the brain to assess the brain's intrinsic connectivity and capture dynamic changes in the brain. In this study, the hidden Markov model (HMM) and dynamic graph (DG) theory are used to study the spatial-temporal characteristics and dynamics of brain networks based on dynamic functional connectivity (DFC). By using HMM, we identified three typical brain states for ASD and healthy control (HC). Furthermore, we explored the correlation between HMM time-varying properties and clinical autism scale scores. Differences in brain topological characteristics and dynamics between ASD and HC were compared by DG analysis. The experimental results indicate that ASD is more inclined to enter a strongly connected HMM brain state, leading to the isolation of brain networks and alterations in the topological characteristics of brain networks, such as default mode network (DMN), ventral attention network (VAN), and visual network (VN). This work suggests that using different data-driven methods based on DFC to study brain network dynamics would have better information complementarity, which can provide a new direction for the extraction of neuro-biomarkers in the early diagnosis of ASD.

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.

Dynamic functional network connectivity based on spatial source phase maps of complex-valued fMRI data: Application to schizophrenia

BACKGROUND

Dynamic spatial functional network connectivity (dsFNC) has shown advantages in detecting functional alterations impacted by mental disorders using magnitude-only fMRI data. However, complete fMRI data are complex-valued with unique and useful phase information.

METHODS

We propose dsFNC of spatial source phase (SSP) maps, derived from complex-valued fMRI data (named SSP-dsFNC), to capture the dynamics elicited by the phase. We compute mutual information for connectivity quantification, employ statistical analysis and Markov chains to assess dynamics, ultimately classifying schizophrenia patients (SZs) and healthy controls (HCs) based on connectivity variance and Markov chain state transitions across windows.

RESULTS

SSP-dsFNC yielded greater dynamics and more significant HC-SZ differences, due to the use of complete brain information from complex-valued fMRI data.

COMPARISON WITH EXISTING METHODS

Compared with magnitude-dsFNC, SSP-dsFNC detected additional and meaningful connections across windows (e.g., for right frontal parietal) and achieved 14.6% higher accuracy for classifying HCs and SZs.

CONCLUSIONS

This work provides new evidence about how SSP-dsFNC could be impacted by schizophrenia, and this information could be used to identify potential imaging biomarkers for psychotic diagnosis.

Spatial-temporal convolutional attention for discovering and characterizing functional brain networks in task fMRI

Functional brain networks (FBNs) are spatial patterns of brain function that play a critical role in understanding human brain function. There are many proposed methods for mapping the spatial patterns of brain function, however they oversimplify the underlying assumptions of brain function and have various limitations such as linearity and independence. Additionally, current methods fail to account for the dynamic nature of FBNs, which limits their effectiveness in accurately characterizing these networks. To address these limitations, we present a novel deep learning and spatial-wise attention based model called Spatial-Temporal Convolutional Attention (STCA) to accurately model dynamic FBNs. Specifically, we train STCA in a self-supervised manner by utilizing a Convolutional Autoencoder to guide the STCA module in assigning higher attention weights to regions of functional activity. To validate the reliability of the results, we evaluate our approach on the HCP-task motor behavior dataset, the experimental results demonstrate that the STCA derived FBNs have higher spatial similarity with the templates and that the spatial similarity between the templates and the FBNs derived by STCA fluctuates with the task design over time, suggesting that STCA can reflect the dynamic changes of brain function, providing a powerful tool to better understand human brain function. Code is available at https://github.com/SNNUBIAI/STCAE.

Chromatic fusion: Generative multimodal neuroimaging data fusion provides multi-informed insights into schizophrenia

This work proposes a novel generative multimodal approach to jointly analyze multimodal data while linking the multimodal information to colors. We apply our proposed framework, which disentangles multimodal data into private and shared sets of features from pairs of structural (sMRI), functional (sFNC and ICA), and diffusion MRI data (FA maps). With our approach, we find that heterogeneity in schizophrenia is potentially a function of modality pairs. Results show (1) schizophrenia is highly multimodal and includes changes in specific networks, (2) non-linear relationships with schizophrenia are observed when interpolating among shared latent dimensions, and (3) we observe a decrease in the modularity of functional connectivity and decreased visual-sensorimotor connectivity for schizophrenia patients for the FA-sFNC and sMRI-sFNC modality pairs, respectively. Additionally, our results generally indicate decreased fractional corpus callosum anisotropy, and decreased spatial ICA map and voxel-based morphometry strength in the superior frontal lobe as found in the FA-sFNC, sMRI-FA, and sMRI-ICA modality pair clusters. In sum, we introduce a powerful new multimodal neuroimaging framework designed to provide a rich and intuitive understanding of the data which we hope challenges the reader to think differently about how modalities interact.

Altered dynamic brain activity and functional connectivity in thyroid-associated ophthalmopathy

Although previous neuroimaging evidence has confirmed the brain functional disturbances in thyroid-associated ophthalmopathy (TAO), the dynamic characteristics of brain activity and functional connectivity (FC) in TAO were rarely concerned. The present study aims to investigate the alterations of temporal variability of brain activity and FC in TAO using resting-state functional magnetic resonance imaging (rs-fMRI). Forty-seven TAO patients and 30 age-, gender-, education-, and handedness-matched healthy controls (HCs) were enrolled and underwent rs-fMRI scanning. The dynamic amplitude of low-frequency fluctuation (dALFF) was first calculated using a sliding window approach to characterize the temporal variability of brain activity. Based on the dALFF results, seed-based dynamic functional connectivity (dFC) analysis was performed to identify the temporal variability of efficient communication between brain regions in TAO. Additionally, correlations between dALFF and dFC and the clinical indicators were analyzed. Compared with HCs, TAO patients displayed decreased dALFF in the left superior occipital gyrus (SOG) and cuneus (CUN), while showing increased dALFF in the left triangular part of inferior frontal gyrus (IFGtriang), insula (INS), orbital part of inferior frontal gyrus (ORBinf), superior temporal gyrus (STG) and temporal pole of superior temporal gyrus (TPOsup). Furthermore, TAO patients exhibited decreased dFC between the left STG and the right middle occipital gyrus (MOG), as well as decreased dFC between the left TPOsup and the right calcarine fissure and surrounding cortex (CAL) and MOG. Correlation analyses showed that the altered dALFF in the left SOG/CUN was positively related to visual acuity (r = .409, p = .004), as well as the score of QoL for visual functioning (r = .375, p = .009). TAO patients developed abnormal temporal variability of brain activity in areas related to vision, emotion, and cognition, as well as reduced temporal variability of FC associated with vision deficits. These findings provided additional insights into the neurobiological mechanisms of TAO.

Spatial Dynamic Subspaces Encode Sex-Specific Schizophrenia Disruptions in Transient Network Overlap and its Links to Genetic Risk

Background

Recent advances in resting-state fMRI allow us to study spatial dynamics, the phenomenon of brain networks spatially evolving over time. However, most dynamic studies still use subject-specific, spatially-static nodes. As recent studies have demonstrated, incorporating time-resolved spatial properties is crucial for precise functional connectivity estimation and gaining unique insights into brain function. Nevertheless, estimating time-resolved networks poses challenges due to the low signal-to-noise ratio, limited information in short time segments, and uncertain identification of corresponding networks within and between subjects.

Methods

We adapt a reference-informed network estimation technique to capture time-resolved spatial networks and their dynamic spatial integration and segregation. We focus on time-resolved spatial functional network connectivity (spFNC), an estimate of network spatial coupling, to study sex-specific alterations in schizophrenia and their links to multi-factorial genomic data.

Results

Our findings are consistent with the dysconnectivity and neurodevelopment hypotheses and align with the cerebello-thalamo-cortical, triple-network, and frontoparietal dysconnectivity models, helping to unify them. The potential unification offers a new understanding of the underlying mechanisms. Notably, the posterior default mode/salience spFNC exhibits sex-specific schizophrenia alteration during the state with the highest global network integration and correlates with genetic risk for schizophrenia. This dysfunction is also reflected in high-dimensional (voxel-level) space in regions with weak functional connectivity to corresponding networks.

Conclusions

Our method can effectively capture spatially dynamic networks, detect nuanced SZ effects, and reveal the intricate relationship of dynamic information to genomic data. The results also underscore the potential of dynamic spatial dependence and weak connectivity in the clinical landscape.

A Multivariate Method for Estimating and comparing whole brain functional connectomes from fMRI and PET data

Positron emission tomography (PET) and magnetic resonance imaging (MRI) are two commonly used imaging techniques to visualize brain function. The use of inter-network covariation (a functional connectome) is a widely used approach to infer links among different brain networks. While whole brain resting fMRI connectomes are widely used, PET data has mostly been analyzed using a few regions of interest. There has been much less work estimating PET spatial networks and almost no work on their connectivity (covariation) in the context of a whole brain data-driven connectome, nor have there been direct comparisons between whole brain PET and fMRI connectomes. Here we present an approach to leverage spatially constrained ICA to compute an estimate of the PET connectome. Results reveal highly modularized connectome patterns that are complementary to that identified from resting fMRI. Similarly, we were able to identify comparable resting networks from a PiB PET scan that can be directly compared to networks in rest fMRI data and results reveal similar, but not identical, network spatial patterns, with the PET networks being slightly smoother and, in some cases, showing variations in subnodes. The resulting networks, decomposed into spatial maps and subject expressions (loading parameters) linked to resting fMRI provide a new way to evaluate the complementary information in PET and fMRI and open up new possibilities for biomarker development.Clinical Relevance-This study analyzes the whole-brain PET and fMRI connectomes, capturing the complementary information from both imaging modalities, thereby introducing a new scope for biomarker development.

Mapping the time-varying functional brain networks in response to naturalistic movie stimuli

One of human brain's remarkable traits lies in its capacity to dynamically coordinate the activities of multiple brain regions or networks, adapting to an externally changing environment. Studying the dynamic functional brain networks (DFNs) and their role in perception, assessment, and action can significantly advance our comprehension of how the brain responds to patterns of sensory input. Movies provide a valuable tool for studying DFNs, as they offer a naturalistic paradigm that can evoke complex cognitive and emotional experiences through rich multimodal and dynamic stimuli. However, most previous research on DFNs have predominantly concentrated on the resting-state paradigm, investigating the topological structure of temporal dynamic brain networks generated via chosen templates. The dynamic spatial configurations of the functional networks elicited by naturalistic stimuli demand further exploration. In this study, we employed an unsupervised dictionary learning and sparse coding method combing with a sliding window strategy to map and quantify the dynamic spatial patterns of functional brain networks (FBNs) present in naturalistic functional magnetic resonance imaging (NfMRI) data, and further evaluated whether the temporal dynamics of distinct FBNs are aligned to the sensory, cognitive, and affective processes involved in the subjective perception of the movie. The results revealed that movie viewing can evoke complex FBNs, and these FBNs were time-varying with the movie storylines and were correlated with the movie annotations and the subjective ratings of viewing experience. The reliability of DFNs was also validated by assessing the Intra-class coefficient (ICC) among two scanning sessions under the same naturalistic paradigm with a three-month interval. Our findings offer novel insight into comprehending the dynamic properties of FBNs in response to naturalistic stimuli, which could potentially deepen our understanding of the neural mechanisms underlying the brain's dynamic changes during the processing of visual and auditory stimuli.

A Scalable Approach to Independent Vector Analysis by Shared Subspace Separation for Multi-Subject fMRI Analysis

Joint blind source separation (JBSS) has wide applications in modeling latent structures across multiple related datasets. However, JBSS is computationally prohibitive with high-dimensional data, limiting the number of datasets that can be included in a tractable analysis. Furthermore, JBSS may not be effective if the data's true latent dimensionality is not adequately modeled, where severe overparameterization may lead to poor separation and time performance. In this paper, we propose a scalable JBSS method by modeling and separating the "shared" subspace from the data. The shared subspace is defined as the subset of latent sources that exists across all datasets, represented by groups of sources that collectively form a low-rank structure. Our method first provides the efficient initialization of the independent vector analysis (IVA) with a multivariate Gaussian source prior (IVA-G) specifically designed to estimate the shared sources. Estimated sources are then evaluated regarding whether they are shared, upon which further JBSS is applied separately to the shared and non-shared sources. This provides an effective means to reduce the dimensionality of the problem, improving analyses with larger numbers of datasets. We apply our method to resting-state fMRI datasets, demonstrating that our method can achieve an excellent estimation performance with significantly reduced computational costs.

Chromatic fusion: generative multimodal neuroimaging data fusion provides multi-informed insights into schizophrenia

This work proposes a novel generative multimodal approach to jointly analyze multimodal data while linking the multimodal information to colors. By linking colors to private and shared information from modalities, we introduce chromatic fusion, a framework that allows for intuitively interpreting multimodal data. We test our framework on structural, functional, and diffusion modality pairs. In this framework, we use a multimodal variational autoencoder to learn separate latent subspaces; a private space for each modality, and a shared space between both modalities. These subspaces are then used to cluster subjects, and colored based on their distance from the variational prior, to obtain meta-chromatic patterns (MCPs). Each subspace corresponds to a different color, red is the private space of the first modality, green is the shared space, and blue is the private space of the second modality. We further analyze the most schizophrenia-enriched MCPs for each modality pair and find that distinct schizophrenia subgroups are captured by schizophrenia-enriched MCPs for different modality pairs, emphasizing schizophrenia's heterogeneity. For the FA-sFNC, sMRI-ICA, and sMRI-ICA MCPs, we generally find decreased fractional corpus callosum anisotropy and decreased spatial ICA map and voxel-based morphometry strength in the superior frontal lobe for schizophrenia patients. To additionally highlight the importance of the shared space between modalities, we perform a robustness analysis of the latent dimensions in the shared space across folds. These robust latent dimensions are subsequently correlated with schizophrenia to reveal that for each modality pair, multiple shared latent dimensions strongly correlate with schizophrenia. In particular, for FA-sFNC and sMRI-sFNC shared latent dimensions, we respectively observe a reduction in the modularity of the functional connectivity and a decrease in visual-sensorimotor connectivity for schizophrenia patients. The reduction in modularity couples with increased fractional anisotropy in the left part of the cerebellum dorsally. The reduction in the visual-sensorimotor connectivity couples with a reduction in the voxel-based morphometry generally but increased dorsal cerebellum voxel-based morphometry. Since the modalities are trained jointly, we can also use the shared space to try and reconstruct one modality from the other. We show that cross-reconstruction is possible with our network and is generally much better than depending on the variational prior. In sum, we introduce a powerful new multimodal neuroimaging framework designed to provide a rich and intuitive understanding of the data that we hope challenges the reader to think differently about how modalities interact.

Exploring the longitudinal associations of functional network connectivity and psychiatric symptom changes in youth

BACKGROUND

Functional connectivity has been associated with psychiatric problems, both in children and adults, but inconsistencies are present across studies. Prior research has mostly focused on small clinical samples with cross-sectional designs.

METHODS

We adopted a longitudinal design with repeated assessments to investigate associations between functional network connectivity (FNC) and psychiatric problems in youth (9- to 17-year-olds, two time points) from the general population. The largest single-site study of pediatric neurodevelopment was used: Generation R (N = 3,131 with data at either time point). Psychiatric symptoms were measured with the Child Behavioral Checklist as broadband internalizing and externalizing problems, and its eight specific syndrome scales (e.g., anxious-depressed). FNC was assessed with two complementary approaches. First, static FNC (sFNC) was measured with graph theory-based metrics. Second, dynamic FNC (dFNC), where connectivity is allowed to vary over time, was summarized into 5 states that participants spent time in. Cross-lagged panel models were used to investigate the longitudinal bidirectional relationships of sFNC with internalizing and externalizing problems. Similar cross-lagged panel models were run for dFNC.

RESULTS

Small longitudinal relationships between dFNC and certain syndrome scales were observed, especially for baseline syndrome scales (i.e., rule-breaking, somatic complaints, thought problems, and attention problems) predicting connectivity changes. However, no association between any of the psychiatric problems (broadband and syndrome scales) with either measure of FNC survived correction for multiple testing.

CONCLUSION

We found no or very modest evidence for longitudinal associations between psychiatric problems with dynamic and static FNC in this population-based sample. Differences in findings may stem from the population drawn, study design, developmental timing, and sample sizes.

Altered Language-Related Effective Connectivity in Patients with Benign Childhood Epilepsy with Centrotemporal Spikes

Benign childhood epilepsy with centrotemporal spikes (BECTS) is one of the most common childhood epilepsy syndromes and may be associated with language deficits. Resting-state functional magnetic resonance imaging (fMRI) data were collected from a total of 78 children: 52 patients with BECTS (28 drug-naïve and 24 medicated) and 26 healthy controls (HC). Granger causality analysis (GCA) was used to investigate alterations in effective connectivity (EC) between the language network core node (Broca's area) and the whole brain. EC from Broca's area to the left Heschl's gyrus (HG), right putamen, and anterior cingulate cortex (ACC) was significantly increased, while EC from the bilateral putamen and left ACC to Broca's area was significantly decreased in BECTS. Moreover, altered EC of Broca's area to the right putamen was significantly positively correlated with verbal IQ (VIQ), while altered EC of Broca's area to the ACC showed significantly negative correlations with the frequency of seizures. Altered EC from the left putamen to Broca's area was also significantly negatively correlated with performance IQ (PIQ) and full-scale IQ (FSIQ) in the drug-naïve group. In addition, there was a significant positive correlation between the EC of Broca's area to the left HG and the number of seizures, as well as between the EC of Broca's area to the right putamen and the age at onset in the medicated group. These findings suggest abnormal causal effects on the language network related to Broca's area in children with BECTS. Longitudinal investigation of language network development and further follow-up may be needed to illuminate the changes in organization and rebalancing over time.

A deep residual model for characterization of 5D spatiotemporal network dynamics reveals widespread spatiodynamic changes in schizophrenia

Schizophrenia is a severe brain disorder with serious symptoms including delusions, disorganized speech, and hallucinations that can have a long-term detrimental impact on different aspects of a patient's life. It is still unclear what the main cause of schizophrenia is, but a combination of altered brain connectivity and structure may play a role. Neuroimaging data has been useful in characterizing schizophrenia, but there has been very little work focused on voxel-wise changes in multiple brain networks over time, despite evidence that functional networks exhibit complex spatiotemporal changes over time within individual subjects. Recent studies have primarily focused on static (average) features of functional data or on temporal variations between fixed networks; however, such approaches are not able to capture multiple overlapping networks which change at the voxel level. In this work, we employ a deep residual convolutional neural network (CNN) model to extract 53 different spatiotemporal networks each of which captures dynamism within various domains including subcortical, cerebellar, visual, sensori-motor, auditory, cognitive control, and default mode. We apply this approach to study spatiotemporal brain dynamism at the voxel level within multiple functional networks extracted from a large functional magnetic resonance imaging (fMRI) dataset of individuals with schizophrenia (N = 708) and controls (N = 510). Our analysis reveals widespread group level differences across multiple networks and spatiotemporal features including voxel-wise variability, magnitude, and temporal functional network connectivity in widespread regions expected to be impacted by the disorder. We compare with typical average spatial amplitude and show highly structured and neuroanatomically relevant results are missed if one does not consider the voxel-wise spatial dynamics. Importantly, our approach can summarize static, temporal dynamic, spatial dynamic, and spatiotemporal dynamics features, thus proving a powerful approach to unify and compare these various perspectives. In sum, we show the proposed approach highlights the importance of accounting for both temporal and spatial dynamism in whole brain neuroimaging data generally, shows a high-level of sensitivity to schizophrenia highlighting global but spatially unique dynamics showing group differences, and may be especially important in studies focused on the development of brain-based biomarkers.

The influence of high worry on static and dynamic insular functional connectivity

Worry is a form of repetitive negative thought. High worry-proneness is one risk factor leading to anxiety disorder. Several types of research indicated that anxiety disorder was highly associated with disrupted interoception. The insula is consistently considered to play a key role in interoception. However, the relationship between worry and the interoception network is poorly investigated in worry-prone individuals. Thus, it is essential to identify the neural characteristic of high worry-proneness subjects. A total of 32 high worry-proneness (HWP) subjects and 25 low worry-proneness (LWP) subjects were recruited and underwent magnetic resonance imaging scanning. Six subregions of insula were chosen as regions of interest. Then, seed-based static and dynamic functional connectivity were calculated. Increased static functional connectivity was observed between the ventral anterior insula and inferior parietal lobule in HWP compared to LWP. Decreased static functional connectivity was found between the left ventral anterior insula and the pregenual anterior cingulate cortex. Decreased dynamic functional connectivity was also shown between the right posterior insula and the inferior parietal lobule in HWP. Moreover, a post-hoc test exploring the effect of changed function within the insular region confirmed that a significant positive relationship between static functional connectivity (ventral anterior insula-inferior parietal lobule) and dynamic functional connectivity (posterior insula-inferior parietal lobule) in LWP but not in HWP. Our results might suggest that deficient insular function may be an essential factor related to high worry in healthy subjects.

Modern views of machine learning for precision psychiatry

In light of the National Institute of Mental Health (NIMH)'s Research Domain Criteria (RDoC), the advent of functional neuroimaging, novel technologies and methods provide new opportunities to develop precise and personalized prognosis and diagnosis of mental disorders. Machine learning (ML) and artificial intelligence (AI) technologies are playing an increasingly critical role in the new era of precision psychiatry. Combining ML/AI with neuromodulation technologies can potentially provide explainable solutions in clinical practice and effective therapeutic treatment. Advanced wearable and mobile technologies also call for the new role of ML/AI for digital phenotyping in mobile mental health. In this review, we provide a comprehensive review of ML methodologies and applications by combining neuroimaging, neuromodulation, and advanced mobile technologies in psychiatry practice. We further review the role of ML in molecular phenotyping and cross-species biomarker identification in precision psychiatry. We also discuss explainable AI (XAI) and neuromodulation in a closed human-in-the-loop manner and highlight the ML potential in multi-media information extraction and multi-modal data fusion. Finally, we discuss conceptual and practical challenges in precision psychiatry and highlight ML opportunities in future research.

Impaired dynamic functional brain properties and their relationship to symptoms in never treated first-episode patients with schizophrenia

Studies of dynamic functional connectivity (dFC) and topology can provide novel insights into the neurophysiology of brain dysfunction in schizophrenia and its relation to core symptoms of psychosis. Limited investigations of these disturbances have been conducted with never-treated first-episode patients to avoid the confounds of treatment or chronic illness. Therefore, we recruited 95 acutely ill, first-episode, never-treated patients with schizophrenia and examined brain dFC patterns relative to healthy controls using resting-state functional magnetic resonance imaging and a sliding-window approach. We compared the dynamic attributes at the group level and found patients spent more time in a hypoconnected state and correspondingly less time in a hyperconnected state. Patients demonstrated decreased dynamics of nodal efficiency and eigenvector centrality (EC) in the right medial prefrontal cortex, which was associated with psychosis severity reflected in Positive and Negative Syndrome Scale ratings. We also observed increased dynamics of EC in temporal and sensorimotor regions. These findings were supported by validation analysis. To supplement the group comparison analyses, a support vector classifier was used to identify the dynamic attributes that best distinguished patients from controls at the individual level. Selected features for case-control classification were highly coincident with the properties having significant between-group differences. Our findings provide novel neuroimaging evidence about dynamic characteristics of brain physiology in acute schizophrenia. The clinically relevant atypical pattern of dynamic shifting between brain states in schizophrenia may represent a critical aspect of illness pathophysiology underpinning its defining cognitive, behavioral, and affective features.

The expanding horizons of network neuroscience: From description to prediction and control

The field of network neuroscience has emerged as a natural framework for the study of the brain and has been increasingly applied across divergent problems in neuroscience. From a disciplinary perspective, network neuroscience originally emerged as a formal integration of graph theory (from mathematics) and neuroscience (from biology). This early integration afforded marked utility in describing the interconnected nature of neural units, both structurally and functionally, and underscored the relevance of that interconnection for cognition and behavior. But since its inception, the field has not remained static in its methodological composition. Instead, it has grown to use increasingly advanced graph-theoretic tools and to bring in several other disciplinary perspectives-including machine learning and systems engineering-that have proven complementary. In doing so, the problem space amenable to the discipline has expanded markedly. In this review, we discuss three distinct flavors of investigation in state-of-the-art network neuroscience: (i) descriptive network neuroscience, (ii) predictive network neuroscience, and (iii) a perturbative network neuroscience that draws on recent advances in network control theory. In considering each area, we provide a brief summary of the approaches, discuss the nature of the insights obtained, and highlight future directions.

Time-varying dynamic network model for dynamic resting state functional connectivity in fMRI and MEG imaging

Dynamic resting state functional connectivity (RSFC) characterizes fluctuations that occur over time in functional brain networks. Existing methods to extract dynamic RSFCs, such as sliding-window and clustering methods that are inherently non-adaptive, have various limitations such as high-dimensionality, an inability to reconstruct brain signals, insufficiency of data for reliable estimation, insensitivity to rapid changes in dynamics, and a lack of generalizability across multiply functional imaging modalities. To overcome these deficiencies, we develop a novel and unifying time-varying dynamic network (TVDN) framework for examining dynamic resting state functional connectivity. TVDN includes a generative model that describes the relation between a low-dimensional dynamic RSFC and the brain signals, and an inference algorithm that automatically and adaptively learns the low-dimensional manifold of dynamic RSFC and detects dynamic state transitions in data. TVDN is applicable to multiple modalities of functional neuroimaging such as fMRI and MEG/EEG. The estimated low-dimensional dynamic RSFCs manifold directly links to the frequency content of brain signals. Hence we can evaluate TVDN performance by examining whether learnt features can reconstruct observed brain signals. We conduct comprehensive simulations to evaluate TVDN under hypothetical settings. We then demonstrate the application of TVDN with real fMRI and MEG data, and compare the results with existing benchmarks. Results demonstrate that TVDN is able to correctly capture the dynamics of brain activity and more robustly detect brain state switching both in resting state fMRI and MEG data.

May the 4C's be with you: an overview of complexity-inspired frameworks for analysing resting-state neuroimaging data

Competing and complementary models of resting-state brain dynamics contribute to our phenomenological and mechanistic understanding of whole-brain coordination and communication, and provide potential evidence for differential brain functioning associated with normal and pathological behaviour. These neuroscientific theories stem from the perspectives of physics, engineering, mathematics and psychology and create a complicated landscape of domain-specific terminology and meaning, which, when used outside of that domain, may lead to incorrect assumptions and conclusions within the neuroscience community. Here, we review and clarify the key concepts of connectivity, computation, criticality and coherence-the 4C's-and outline a potential role for metastability as a common denominator across these propositions. We analyse and synthesize whole-brain neuroimaging research, examined through functional magnetic imaging, to demonstrate that complexity science offers a principled and integrated approach to describe, and potentially understand, macroscale spontaneous brain functioning.

Multi-spatial-scale dynamic interactions between functional sources reveal sex-specific changes in schizophrenia

We introduce an extension of independent component analysis (ICA), called multiscale ICA, and design an approach to capture dynamic functional source interactions within and between multiple spatial scales. Multiscale ICA estimates functional sources at multiple spatial scales without imposing direct constraints on the size of functional sources, overcomes the limitation of using fixed anatomical locations, and eliminates the need for model-order selection in ICA analysis. We leveraged this approach to study sex-specific and sex-common connectivity patterns in schizophrenia. Results show dynamic reconfiguration and interaction within and between multi-spatial scales. Sex-specific differences occur (a) within the subcortical domain, (b) between the somatomotor and cerebellum domains, and (c) between the temporal domain and several others, including the subcortical, visual, and default mode domains. Most of the sex-specific differences belong to between-spatial-scale functional interactions and are associated with a dynamic state with strong functional interactions between the visual, somatomotor, and temporal domains and their anticorrelation patterns with the rest of the brain. We observed significant correlations between multi-spatial-scale functional interactions and symptom scores, highlighting the importance of multiscale analyses to identify potential biomarkers for schizophrenia. As such, we recommend such analyses as an important option for future functional connectivity studies.

Resting-State Neural-Activity Alterations in Subacute Aphasia after Stroke

Linguistic deficits are frequent symptoms among stroke survivors. The neural mechanism of post-stroke aphasia (PSA) was incompletely understood. Recently, resting-state functional magnetic resonance imaging (rs-fMRI) was widely used among several neuropsychological disorders. However, previous rs-fMRI studies of PSA were limited to very small sample size and the absence of reproducibility with different neuroimaging indexes. The present study performed comparisons with static and dynamic amplitude of low-frequency fluctuations (ALFF) and functional connectivity (FC) based on modest sample size (40 PSA and 37 healthy controls). Compared with controls, PSA showed significantly increased static ALFF predominantly in the bilateral supplementary motor area (SMA) and right hippocampus-parahippocampus (R HIP-ParaHip) and decreased static ALFF in right cerebellum. The increased dynamic ALFF in SMA and decreased dynamic ALFF in right cerebellum were also found in PSA. The static and dynamic ALFF in right cerebellum was positively correlated with spontaneous speech. The FC between the SMA and R HIP-ParaHip was significantly stronger in patients than controls and positively correlated with ALFF in bilateral SMA. In addition, the FC between the R HIP-ParaHip and the right temporal was also enhanced in patients and negatively correlated with repetition, naming, and comprehension score. These findings revealed consistently abnormal intrinsic neural activity in SMA and cerebellum, which may underlie linguistic deficits in PSA.

Tracing Evolving Networks Using Tensor Factorizations vs. ICA-Based Approaches

Analysis of time-evolving data is crucial to understand the functioning of dynamic systems such as the brain. For instance, analysis of functional magnetic resonance imaging (fMRI) data collected during a task may reveal spatial regions of interest, and how they evolve during the task. However, capturing underlying spatial patterns as well as their change in time is challenging. The traditional approach in fMRI data analysis is to assume that underlying spatial regions of interest are static. In this article, using fractional amplitude of low-frequency fluctuations (fALFF) as an effective way to summarize the variability in fMRI data collected during a task, we arrange time-evolving fMRI data as a subjects by voxels by time windows tensor, and analyze the tensor using a tensor factorization-based approach called a PARAFAC2 model to reveal spatial dynamics. The PARAFAC2 model jointly analyzes data from multiple time windows revealing subject-mode patterns, evolving spatial regions (also referred to as networks) and temporal patterns. We compare the PARAFAC2 model with matrix factorization-based approaches relying on independent components, namely, joint independent component analysis (ICA) and independent vector analysis (IVA), commonly used in neuroimaging data analysis. We assess the performance of the methods in terms of capturing evolving networks through extensive numerical experiments demonstrating their modeling assumptions. In particular, we show that (i) PARAFAC2 provides a compact representation in all modes, i.e., subjects, time, and voxels, revealing temporal patterns as well as evolving spatial networks, (ii) joint ICA is as effective as PARAFAC2 in terms of revealing evolving networks but does not reveal temporal patterns, (iii) IVA's performance depends on sample size, data distribution and covariance structure of underlying networks. When these assumptions are satisfied, IVA is as accurate as the other methods, (iv) when subject-mode patterns differ from one time window to another, IVA is the most accurate. Furthermore, we analyze real fMRI data collected during a sensory motor task, and demonstrate that a component indicating statistically significant group difference between patients with schizophrenia and healthy controls is captured, which includes primary and secondary motor regions, cerebellum, and temporal lobe, revealing a meaningful spatial map and its temporal change.

Statelets: Capturing recurrent transient variations in dynamic functional network connectivity

Dynamic functional network connectivity (dFNC) analysis is a widely used approach for capturing brain activation patterns, connectivity states, and network organization. However, a typical sliding window plus clustering (SWC) approach for analyzing dFNC models the system through a fixed sequence of connectivity states. SWC assumes connectivity patterns span throughout the brain, but they are relatively spatially constrained and temporally short‐lived in practice. Thus, SWC is neither designed to capture transient dynamic changes nor heterogeneity across subjects/time. We propose a state‐space time series summarization framework called “statelets” to address these shortcomings. It models functional connectivity dynamics at fine‐grained timescales, adapting time series motifs to changes in connectivity strength, and constructs a concise yet informative representation of the original data that conveys easily comprehensible information about the phenotypes. We leverage the earth mover distance in a nonstandard way to handle scale differences and utilize kernel density estimation to build a probability density profile for local motifs. We apply the framework to study dFNC of patients with schizophrenia (SZ) and healthy control (HC). Results demonstrate SZ subjects exhibit reduced modularity in their brain network organization relative to HC. Statelets in the HC group show an increased recurrence across the dFNC time‐course compared to the SZ. Analyzing the consistency of the connections across time reveals significant differences within visual, sensorimotor, and default mode regions where HC subjects show higher consistency than SZ. The introduced approach also enables handling dynamic information in cross‐modal and multimodal applications to study healthy and disordered brains.

Tri-Clustering Dynamic Functional Network Connectivity Identifies Significant Schizophrenia Effects Across Multiple States in Distinct Subgroups of Individuals

Background: Brain imaging data collected from individuals are highly complex with unique variation; however, such variation is typically ignored in approaches that focus on group averages or even supervised prediction. State-of-the-art methods for analyzing dynamic functional network connectivity (dFNC) subdivide the entire time course into several (possibly overlapping) connectivity states (i.e., sliding window clusters). However, such an approach does not factor in the homogeneity of underlying data and may result in a less meaningful subgrouping of the data set. Methods: Dynamic-N-way tri-clustering (dNTiC) incorporates a homogeneity benchmark to approximate clusters that provide a more "apples-to-apples" comparison between groups within analogous subsets of time-space and subjects. dNTiC sorts the dFNC states by maximizing similarity across individuals and minimizing variance among the pairs of components within a state. Results: Resulting tri-clusters show significant differences between schizophrenia (SZ) and healthy control (HC) in distinct brain regions. Compared with HC subjects, SZ show hypoconnectivity (low positive) among subcortical, default mode, cognitive control, but hyperconnectivity (high positive) between sensory networks in most tri-clusters. In tri-cluster 3, HC subjects show significantly stronger connectivity among sensory networks and anticorrelation between subcortical and sensory networks than SZ. Results also provide a statistically significant difference in SZ and HC subject's reoccurrence time for two distinct dFNC states. Conclusions: Outcomes emphasize the utility of the proposed method for characterizing and leveraging variance within high-dimensional data to enhance the interpretability and sensitivity of measurements in studying a heterogeneous disorder such as SZ and unconstrained experimental conditions as resting functional magnetic resonance imaging. Impact statement The current methods for analyzing dynamic functional network connectivity (dFNC) run k-means on a collection of dFNC windows, and each window includes all the pairs of independent component analysis networks. As such, it depicts a short-time connectivity pattern of the entire brain, and the k-means clusters fixed-length signatures that have an extent throughout the neural system. Consequently, there is a chance of missing connectivity signatures that span across a smaller subset of pairs. Dynamic-N-way tri-clustering further sorts the dFNC states by maximizing similarity across individuals, minimizing variance among the pairs of components within a state, and reporting more complex and transient patterns.

Inside information: Systematic within-node functional connectivity changes observed across tasks or groups

Mapping the human connectome and understanding its relationship to brain function holds tremendous clinical potential. The connectome has two fundamental components: the nodes and the sconnections between them. While much attention has been given to deriving atlases and measuring the connections between nodes, there have been no studies examining the networks within nodes. Here we demonstrate that each node contains significant connectivity information, that varies systematically across task-induced states and subjects, such that measures based on these variations can be used to classify tasks and identify subjects. The results are not specific for any particular atlas but hold across different atlas resolutions. To date, studies examining changes in connectivity have focused on edge changes and assumed there is no useful information within nodes. Our findings illustrate that for typical atlases, within-node changes can be significant and may account for a substantial fraction of the variance currently attributed to edge changes .

Altered Dynamic Functional Connectivity of Cuneus in Schizophrenia Patients: A Resting-State fMRI Study

Objective: Schizophrenia (SZ) is a functional mental condition that has a significant impact on patients’ social lives. As a result, accurate diagnosis of SZ has attracted researchers’ interest. Based on previous research, resting-state functional magnetic resonance imaging (rsfMRI) reported neural alterations in SZ. In this study, we attempted to investigate if dynamic functional connectivity (dFC) could reveal changes in temporal interactions between SZ patients and healthy controls (HC) beyond static functional connectivity (sFC) in the cuneus, using the publicly available COBRE dataset. Methods: Sliding windows were applied to 72 SZ patients’ and 74 healthy controls’ (HC) rsfMRI data to generate temporal correlation maps and, finally, evaluate mean strength (dFC-Str), variability (dFC-SD and ALFF) in each window, and the dwelling time. The difference in functional connectivity (FC) of the cuneus between two groups was compared using a two-sample t-test. Results: Our findings demonstrated decreased mean strength connectivity between the cuneus and calcarine, the cuneus and lingual gyrus, and between the cuneus and middle temporal gyrus (TPOmid) in subjects with SZ. Moreover, no difference was detected in variability (standard deviation and the amplitude of low-frequency fluctuation), the dwelling times of all states, or static functional connectivity (sFC) between the groups. Conclusions: Our verdict suggest that dynamic functional connectivity analyses may play crucial roles in unveiling abnormal patterns that would be obscured in static functional connectivity, providing promising impetus for understanding schizophrenia disease.

Resting state dynamic functional connectivity in children with attention deficit/hyperactivity disorder

Attention deficit/hyperactivity disorder (ADHD) is characterized by inattention, hyperactivity and impulsivity. In this study, we investigated group differences in dynamic functional connectivity (dFC) between 113 children with inattentive (46 ADHD_I) and combined (67 ADHD_C) ADHD and 76 typically developing (TD) children using resting-state functional MRI data. For dynamic connectivity analysis, the data were first decomposed into 100 independent components, among which 88 were classified into eight well-known resting-state networks (RSNs). Three discrete FC states were then identified using k-means clustering and used to estimate transition probabilities between states in both patient and control groups using a hidden Markov model. Our results showed state-dependent alterations in intra and inter-network connectivity in both ADHD subtypes in comparison with TD. Spending less time than healthy controls in state 1, both ADHD_Iand ADHD_Cwere characterized with weaker intra-hemispheric connectivity with functional asymmetries. In this state, ADHD_Ifurther showed weaker inter-hemispheric connectivity. The patients spent more time in state 2, exhibiting characteristic abnormalities in corticosubcortical and corticocerebellar connectivity. In state 3, a less frequently state observed across the ADHD and TD children, ADHD_Cwas differentiated from ADHD_Iby significant alterations in FC between bilateral temporal regions and other brain areas in comparison with TD. Across all three states, several strategic brain regions, mostly bilateral, exhibited significant alterations in both static functional connectivity (sFC) and dFC in the ADHD groups compared to TD, including inferior, middle and superior temporal gyri, middle frontal gyri, insula, anterior cingulum cortex, precuneus, calcarine, fusiform, superior motor area, and cerebellum. Our results show distributed abnormalities in sFC and dFC between different large-scale RSNs including cortical and subcortical regions in both ADHD subtypes compared to TD. Our findings show that the dynamic changes in brain FC can better explain the underlying pathophysiology of ADHD such as deficits in visual cognition, attention, memory and emotion processing, and cognitive and motor control.

Principles and open questions in functional brain network reconstruction

Graph theory is now becoming a standard tool in system-level neuroscience. However, endowing observed brain anatomy and dynamics with a complex network representation involves often covert theoretical assumptions and methodological choices which affect the way networks are reconstructed from experimental data, and ultimately the resulting network properties and their interpretation. Here, we review some fundamental conceptual underpinnings and technical issues associated with brain network reconstruction, and discuss how their mutual influence concurs in clarifying the organization of brain function.

The unbalanced reorganization of weaker functional connections induces the altered brain network topology in schizophrenia

Network neuroscience shed some light on the functional and structural modifications occurring to the brain associated with the phenomenology of schizophrenia. In particular, resting-state functional networks have helped our understanding of the illness by highlighting the global and local alterations within the cerebral organization. We investigated the robustness of the brain functional architecture in 44 medicated schizophrenic patients and 40 healthy comparators through an advanced network analysis of resting-state functional magnetic resonance imaging data. The networks in patients showed more resistance to disconnection than in healthy controls, with an evident discrepancy between the two groups in the node degree distribution computed along a percolation process. Despite a substantial similarity of the basal functional organization between the two groups, the expected hierarchy of healthy brains' modular organization is crumbled in schizophrenia, showing a peculiar arrangement of the functional connections, characterized by several topologically equivalent backbones. Thus, the manifold nature of the functional organization's basal scheme, together with its altered hierarchical modularity, may be crucial in the pathogenesis of schizophrenia. This result fits the disconnection hypothesis that describes schizophrenia as a brain disorder characterized by an abnormal functional integration among brain regions.

Tracking spatial dynamics of functional connectivity during a task

Functional connectivity (FC) measured from functional magnetic resonance imaging (fMRI) provides a powerful tool to explore brain organization. Studies of the temporal dynamics of brain organization have shown a large temporal variability of the functional connectome, which may be associated with mental status transitions and/or adaptive process. Most dynamic studies, e.g. functional connectome and functional network connectivity (FNC), have focused on the macroscopic FC changes, i.e. the changes of temporal coherence across various brain network sources, nodes and/or regions of interest, where it is assumed within the network or node that the FC is static. In this paper, we develop a novel method to examine the spatial dynamics of FC, without the assumption of its intra-network stationarity. We applied our approach to fMRI data during an auditory oddball task (AOD) from twenty-two subjects, in an attempt to capture/validate the approach by evaluating whether spatial connectivity varies with task condition. The results showed that connectivity networks exhibit spatial variability over time, in addition to participating in conventional temporal dynamics, i.e. cross-network variability or dynamic functional network connectivity (dFNC). Furthermore, we studied the relationship of spatial dynamic in FC to cognitive processes, by performing a cluster analysis to evaluate an individual's functional correspondence towards the 'target' (oddball) detection from AOD task, and extracting cognitive task correspondence states as well as their dynamic FC spatial maps segregated by such states. We found a clear trend in different task-guided states, particularly, a prominent reduction of task stimulus synchrony state along with strong anticorrelation between default mode network (DMN) and cognitive attentional networks. We also observed an increasing occurrence of the task desynchrony state which showed an absence of DMN anticorrelation. The results highlight the impact of a well-studied cognitive task on the observed spatial dynamic structure. We also showed that the FC spatial dynamic pattern from our method largely corresponds to macroscopic dFNC patterns, but with more details and specifications over space, meanwhile the connectivity within the source itself provides novel information and varies over time. Overall, we demonstrate clear evidence of the presence of the (usually ignored) spatial dynamics of connectivity, its links to the task and implications of cognition/mental status.

Dynamic Functional Network Connectivity Changes Associated with fMRI Neurofeedback of Right Premotor Cortex

Neurofeedback of real-time functional magnetic resonance imaging (rtfMRI) can enable people to self-regulate motor-related brain regions and lead to alteration of motor performance and functional connectivity (FC) underlying motor execution tasks. Numerous studies suggest that FCs dynamically fluctuate over time. However, little is known about the impact of neurofeedback training of the motor-related region on the dynamic characteristics of FC underlying motor execution tasks. This study aims to investigate the mechanism of self-regulation of the right premotor area (PMA) on the underlying dynamic functional network connectivity (DFNC) of motor execution (ME) tasks and reveal the relationship between DFNC, training effect, and motor performance. The results indicate that the experimental group spent less time on state 2, with overall weak connections, and more time on state 6, having strong positive connections between motor-related networks than the control group after the training. For the experimental group’s state 2, the mean dwell time after the training showed negative correlation with the tapping frequency and the amount of upregulation of PMA. The findings show that rtfMRI neurofeedback can change the temporal properties of DFNC, and the DFNC changes in state with overall weak connections were associated with the training effect and the improvement in motor performance.

Relationship between Dynamic Blood-Oxygen-Level-Dependent Activity and Functional Network Connectivity: Characterization of Schizophrenia Subgroups

Aim: In this work, we propose the novel use of adaptively constrained independent vector analysis (acIVA) to effectively capture the temporal and spatial properties of dynamic blood-oxygen-level-dependent (BOLD) activity (dBA), and we efficiently quantify the spatial property of dBA (sdBA). We also propose to incorporate dBA into the study of brain dynamics to gain insight into activity-connectivity co-evolution patterns. Introduction: Studies of the dynamics of the human brain using functional magnetic resonance imaging (fMRI) have enabled the identification of unique functional network connectivity (FNC) states and provided new insights into mental disorders. There is evidence showing that both BOLD activity, which is captured by fMRI, and FNC are related to mental and cognitive processes. However, a few studies have evaluated the inter-relationships of these two domains of function. Moreover, the identification of subgroups of schizophrenia has gained significant clinical importance due to a need to study the heterogeneity of schizophrenia. Methods: We design a simulation study to verify the effectiveness of acIVA and apply acIVA to the dynamic study of resting-state fMRI data collected from individuals with schizophrenia and healthy controls (HCs) to investigate the relationship between dBA and dynamic FNC (dFNC). Results: The simulation study demonstrates that acIVA accurately captures the spatial variability and provides an efficient quantification of sdBA. The fMRI analysis yields synchronized sdBA-temporal property of dBA (tdBA) patterns and shows that the dBA and dFNC are significantly correlated in the spatial domain. Using these dynamic features, we identify schizophrenia subgroups with significant differences in terms of their clinical symptoms. Conclusion: We find that brain function is abnormally organized in schizophrenia compared with HCs since there are less synchronized sdBA-tdBA patterns in schizophrenia and schizophrenia prefers a component that merges multiple brain regions. Identification of schizophrenia subgroups using dynamic features inspires the use of neuroimaging in studying the heterogeneity of disorders. Impact statement This work introduces the use of joint blind source separation for the study of brain dynamics to enable efficient quantification of the spatial property of dynamic blood-oxygen-level-dependent (BOLD) activity to provide insight into the relationship of dynamic BOLD activity and dynamic functional network connectivity. The identification of subgroups of schizophrenia using dynamic features allows the study of heterogeneity of schizophrenia, emphasizing the importance of functional magnetic resonance imaging analysis in the study of brain activity and functional connectivity to gain a better understanding of the human brain, especially the brain with a mental disorder.

Dynamic Altered Amplitude of Low-Frequency Fluctuations in Patients With Major Depressive Disorder

Background: Major depressive disorder (MDD) has demonstrated abnormalities of static intrinsic brain activity measured by amplitude of low-frequency fluctuation (ALFF). Recent studies regarding the resting-state functional magnetic resonance imaging (rs-fMRI) have found the brain activity is inherently dynamic over time. Little is known, however, regarding the temporal dynamics of local neural activity in MDD. Here, we investigated whether temporal dynamic changes in spontaneous neural activity are influenced by MDD. Methods: We recruited 81 first-episode, drug-naive MDD patients and 64 age-, gender-, and education-matched healthy controls who underwent rs-fMRI. A sliding-window approach was then adopted for the estimation of dynamic ALFF (dALFF), which was used to measure time-varying brain activity and then compared between the two groups. The relationship between altered dALFF variability and clinical variables in MDD patients was also analyzed. Results: MDD patients showed increased temporal variability (dALFF) mainly focused on the bilateral thalamus, the bilateral superior frontal gyrus, the right middle frontal gyrus, the bilateral cerebellum posterior lobe, and the vermis. Furthermore, increased dALFF variability values in the right thalamus and right cerebellum posterior lobe were positively correlated with MDD symptom severity. Conclusions: The overall results suggest that altered temporal variability in corticocerebellar-thalamic-cortical circuit (CCTCC), involved in emotional, executive, and cognitive, is associated with drug-naive, first-episode MDD patients. Moreover, our study highlights the vital role of abnormal dynamic brain activity in the cerebellar hemisphere associated with CCTCC in MDD patients. These findings may provide novel insights into the pathophysiological mechanisms of MDD.

Altered temporal, but intact spatial, features of transient network dynamics in psychosis

Contemporary models of psychosis suggest that a continuum of severity of psychotic symptoms exists, with subthreshold psychotic experiences (PEs) potentially reflecting some genetic and environmental risk factors shared with clinical psychosis. Thus, identifying abnormalities in brain activity that manifest across this continuum can shed new light on the pathophysiology of psychosis. Here, we investigated the moment-to-moment engagement of brain networks ("states") in individuals with schizophrenia (SCZ) and PEs and identified features of these states that are associated with psychosis-spectrum symptoms. Transient brain states were defined by clustering "single snapshots" of blood oxygen level-dependent images, based on spatial similarity of the images. We found that individuals with SCZ (n = 35) demonstrated reduced recruitment of three brain states compared to demographically matched healthy controls (n = 35). Of these three illness-related states, one specific state, involving primarily the visual and salience networks, also occurred at a lower rate in individuals with persistent PEs (n = 22), compared to demographically matched healthy youth (n = 22). Moreover, the occurrence rate of this marker brain state was negatively correlated with the severity of PEs (r = -0.26, p = 0.003, n = 130). In contrast, the spatial map of this state appeared to be unaffected in the SCZ or PE groups. Thus, reduced engagement of a brain state involving the visual and salience networks was demonstrated across the psychosis continuum, suggesting that early disruptions of perceptual and affective function may underlie some of the core symptoms of the illness.

Dynamic functional network reconfiguration underlying the pathophysiology of schizophrenia and autism spectrum disorder

The dynamics of the human brain span multiple spatial scales, from connectivity associated with a specific region/network to the global organization, each representing different brain mechanisms. Yet brain reconfigurations at different spatial scales are seldom explored and whether they are associated with the neural aspects of brain disorders is far from understood. In this study, we introduced a dynamic measure called step-wise functional network reconfiguration (sFNR) to characterize how brain configuration rewires at different spatial scales. We applied sFNR to two independent datasets, one includes 160 healthy controls (HCs) and 151 patients with schizophrenia (SZ) and the other one includes 314 HCs and 255 individuals with autism spectrum disorder (ASD). We found that both SZ and ASD have increased whole-brain sFNR and sFNR between cerebellar and subcortical/sensorimotor domains. At the ICN level, the abnormalities in SZ are mainly located in ICNs within subcortical, sensory, and cerebellar domains, while the abnormalities in ASD are more widespread across domains. Interestingly, the overlap SZ-ASD abnormality in sFNR between cerebellar and sensorimotor domains was correlated with the reasoning-problem-solving performance in SZ (r = -.1652, p = .0058) as well as the Autism Diagnostic Observation Schedule in ASD (r = .1853, p = .0077). Our findings suggest that dynamic reconfiguration deficits may represent a key intersecting point for SZ and ASD. The investigation of brain dynamics at different spatial scales can provide comprehensive insights into the functional reconfiguration, which might advance our knowledge of cognitive decline and other pathophysiology in brain disorders.

Sparse deep dictionary learning identifies differences of time-varying functional connectivity in brain neuro-developmental study

Recently, the focus of functional connectivity analysis of human brain has shifted from merely revealing the inter-regional functional correlation over the entire scan duration to capturing the time-varying information of brain networks and characterizing time-resolved reoccurring patterns of connectivity. Much effort has been invested into developing approaches that can track changes in re-occurring patterns of functional connectivity over time. In this paper, we propose a sparse deep dictionary learning method to characterize the essential differences of reoccurring patterns of time-varying functional connectivity between different age groups. The proposed method combines both the interpretability of sparse dictionary learning and the capability of extracting sparse nonlinear higher-level features in the latent space of sparse deep autoencoder. In other words, it learns a sparse dictionary of the original data by considering the nonlinear representation of the data in the encoder layer based on a sparse deep autoencoder. In this way, the nonlinear structure and higher-level features of the data can be captured by deep dictionary learning. The proposed method is applied to the analysis of the Philadelphia Neurodevelopmental Cohort. It shows that there exist essential differences in the reoccurrence patterns of function connectivity between child and young adult groups. Specially, children have more diffusive functional connectivity patterns while young adults possess more focused functional connectivity patterns, and the brain function transits from undifferentiated systems to specialized neural networks with the growth.

Graph-theoretical analysis identifies transient spatial states of resting-state dynamic functional network connectivity and reveals dysconnectivity in schizophrenia

BACKGROUND

Dynamic functional network connectivity (dFNC) summarizes associations among time-varying brain networks and is widely used for studying dynamics. However, most previous studies compute dFNC using temporal variability while spatial variability started receiving increasing attention. It is hence desirable to investigate spatial variability and the interaction between temporal and spatial variability.

NEW METHOD

We propose to use an adaptive variant of constrained independent vector analysis to simultaneously capture temporal and spatial variability, and introduce a goal-driven scheme for addressing a key challenge in dFNC analysis---determining the number of transient states. We apply our methods to resting-state functional magnetic resonance imaging data of schizophrenia patients (SZs) and healthy controls (HCs).

RESULTS

The results show spatial variability provides more features discriminative between groups than temporal variability. A comprehensive study of graph-theoretical (GT) metrics determines the optimal number of spatial states and suggests centrality as a key metric. Four networks yield significantly different levels of involvement in SZs and HCs. The high involvement of a component that relates to multiple distributed brain regions highlights dysconnectivity in SZ. One frontoparietal component and one frontal component demonstrate higher involvement in HCs, suggesting a more efficient cognitive control system relative to SZs.

COMPARISON WITH EXISTING METHODS

Spatial variability is more informative than temporal variability. The proposed goal-driven scheme determines the optimal number of states in a more interpretable way by making use of discriminative features.

CONCLUSION

GT analysis is promising in dFNC analysis as it identifies distinctive transient spatial states of dFNC and reveals unique biomedical patterns in SZs.

Brain parcellation driven by dynamic functional connectivity better capture intrinsic network dynamics

Until now, dynamic functional connectivity (dFC) based on functional magnetic resonance imaging is typically estimated on a set of predefined regions of interest (ROIs) derived from an anatomical or static functional atlas which follows an implicit assumption of functional homogeneity within ROIs underlying temporal fluctuation of functional coupling, potentially leading to biases or underestimation of brain network dynamics. Here, we presented a novel computational method based on dynamic functional connectivity degree (dFCD) to derive meaningful brain parcellations that can capture functional homogeneous regions in temporal variance of functional connectivity. Several spatially distributed but functionally meaningful areas that are well consistent with known intrinsic connectivity networks were identified through independent component analysis (ICA) of time‐varying dFCD maps. Furthermore, a systematical comparison with commonly used brain atlases, including the Anatomical Automatic Labeling template, static ICA‐driven parcellation and random parcellation, demonstrated that the ROI‐definition strategy based on the proposed dFC‐driven parcellation could better capture the interindividual variability in dFC and predict observed individual cognitive performance (e.g., fluid intelligence, cognitive flexibility, and sustained attention) based on chronnectome. Together, our findings shed new light on the functional organization of resting brains at the timescale of seconds and emphasized the significance of a dFC‐driven and voxel‐wise functional homogeneous parcellation for network dynamics analyses in neuroscience.

Dynamic functional connectivity in temporal lobe epilepsy: a graph theoretical and machine learning approach

PURPOSE

Functional magnetic resonance imaging (fMRI) in resting state can be used to evaluate the functional organization of the human brain in the absence of any task or stimulus. The functional connectivity (FC) has non-stationary nature and consented to be varying over time. By considering the dynamic characteristics of the FC and using graph theoretical analysis and a machine learning approach, we aim to identify the laterality in cases of temporal lobe epilepsy (TLE).

METHODS

Six global graph measures are extracted from static and dynamic functional connectivity matrices using fMRI data of 35 unilateral TLE subjects. Alterations in the time trend of the graph measures are quantified. The random forest (RF) method is used for the determination of feature importance and selection of dynamic graph features including mean, variance, skewness, kurtosis, and Shannon entropy. The selected features are used in the support vector machine (SVM) classifier to identify the left and right epileptogenic sides in patients with TLE.

RESULTS

Our results for the performance of SVM demonstrate that the utility of dynamic features improves the classification outcome in terms of accuracy (88.5% for dynamic features compared with 82% for static features). Selecting the best dynamic features also elevates the accuracy to 91.5%.

CONCLUSION

Accounting for the non-stationary characteristics of functional connectivity, dynamic connectivity analysis of graph measures along with machine learning approach can identify the temporal trend of some specific network features. These network features may be used as potential imaging markers in determining the epileptogenic hemisphere in patients with TLE.

Abnormal static and dynamic functional connectivity of resting-state fMRI in multiple system atrophy

In order to explore the topological alterations in functional brain networks between multiple system atrophy (MSA) patients and healthy controls (HC), a new joint analysis method of static and dynamic functional connectivity (FC) is proposed in this paper. Twenty-four MSA patients and twenty HCs were enrolled in this study. We constructed static and dynamic brain networks from resting-state fMRI data and calculated four graph theory attributes. Statistical comparisons and correlation analysis were carried out for static and dynamic FC separately before combining both cases. We found decreased local efficiency (LE) and weighted degree (WD) in cerebellum from both static and dynamic graph attributes. For static FC alone, we identified increased betweenness centrality (BC) at left dorsolateral prefrontal cortex, left Cerebellum_Crus9 and decreased WD at Vermis_6. For dynamic FC alone, decreased BC, clustering coefficients and LE at several cortical regions and cerebellum were identified. All the features had significant correlation with total UMSARS scores. Receiver operating characteristic analysis showed that dynamic features had the highest area under the curve value. Our work not only added new evidence for the underlying neurobiology and disrupted dynamic disconnection syndrome of MSA, but also proved the possibility of disease diagnosis and progression tracking using rs-fMRI.

Abnormal dynamic resting-state brain network organization in auditory verbal hallucination

Auditory-verbal hallucinations (AVH) are a key symptom of schizophrenia. Recent neuroimaging studies examining dynamic functional connectivity suggest that disrupted dynamic interactions between brain networks characterize complex symptoms in mental illness including schizophrenia. Studying dynamic connectivity may be especially relevant for hallucinations, given their fluctuating phenomenology. Indeed, it remains unknown whether AVH in schizophrenia are directly related to altered dynamic connectivity within and between key brain networks involved in auditory perception and language, emotion processing, and top-down control. In this study, we used dynamic connectivity approaches including sliding window and k-means to examine dynamic interactions among brain networks in schizophrenia patients with and without a recent history of AVH. Dynamic brain network analysis revealed that patients with AVH spent less time in a ‘network-antagonistic’ brain state where the default mode network (DMN) and the language network were anti-correlated, and had lower probability to switch into this brain state. Moreover, patients with AVH showed a lower connectivity within the language network and the auditory network, and lower connectivity was observed between the executive control and the language networks in certain dynamic states. Our study provides the first neuroimaging evidence of altered dynamic brain networks for understanding neural mechanisms of AVH in schizophrenia. The findings may inform and further strengthen cognitive models of AVH that aid the development of new coping strategies for patients.

Separated Channel Attention Convolutional Neural Network (SC-CNN-Attention) to Identify ADHD in Multi-Site Rs-fMRI Dataset

The accurate identification of an attention deficit hyperactivity disorder (ADHD) subject has remained a challenge for both neuroscience research and clinical diagnosis. Unfortunately, the traditional methods concerning the classification model and feature extraction usually depend on the single-channel model and static measurements (i.e., functional connectivity, FC) in the small, homogenous single-site dataset, which is limited and may cause the loss of intrinsic information in functional MRI (fMRI). In this study, we proposed a new two-stage network structure by combing a separated channel convolutional neural network (SC-CNN) with an attention-based network (SC-CNN-attention) to discriminate ADHD and healthy controls on a large-scale multi-site database (5 sites and n = 1019). To utilize both intrinsic temporal feature and the interactions of temporal dependent in whole-brain resting-state fMRI, in the first stage of our proposed network structure, a SC- CNN is used to learn the temporal feature of each brain region, and an attention network in the second stage is adopted to capture temporal dependent features among regions and extract fusion features. Using a “leave-one-site-out” cross-validation framework, our proposed method obtained a mean classification accuracy of 68.6% on five different sites, which is higher than those reported in previous studies. The classification results demonstrate that our proposed network is robust to data variants and is also replicated across sites. The combination of the SC-CNN with the attention network is powerful to capture the intrinsic fMRI information to discriminate ADHD across multi-site resting-state fMRI data.

Tools of the trade: estimating time-varying connectivity patterns from fMRI data

Given the dynamic nature of the brain, there has always been a motivation to move beyond 'static' functional connectivity, which characterizes functional interactions over an extended period of time. Progress in data acquisition and advances in analytical neuroimaging methods now allow us to assess the whole brain's dynamic functional connectivity (dFC) and its network-based analog, dynamic functional network connectivity at the macroscale (mm) using fMRI. This has resulted in the rapid growth of analytical approaches, some of which are very complex, requiring technical expertise that could daunt researchers and neuroscientists. Meanwhile, making real progress toward understanding the association between brain dynamism and brain disorders can only be achieved through research conducted by domain experts, such as neuroscientists and psychiatrists. This article aims to provide a gentle introduction to the application of dFC. We first explain what dFC is and the circumstances under which it can be used. Next, we review two major categories of analytical approaches to capture dFC. We discuss caveats and considerations in dFC analysis. Finally, we walk readers through an openly accessible toolbox to capture dFC properties and briefly review some of the dynamic metrics calculated using this toolbox.

Multifractal and Entropy-Based Analysis of Delta Band Neural Activity Reveals Altered Functional Connectivity Dynamics in Schizophrenia

Dynamic functional connectivity (DFC) was established in the past decade as a potent approach to reveal non-trivial, time-varying properties of neural interactions – such as their multifractality or information content –, that otherwise remain hidden from conventional static methods. Several neuropsychiatric disorders were shown to be associated with altered DFC, with schizophrenia (SZ) being one of the most intensely studied among such conditions. Here we analyzed resting-state electroencephalography recordings of 14 SZ patients and 14 age- and gender-matched healthy controls (HC). We reconstructed dynamic functional networks from delta band (0.5–4 Hz) neural activity and captured their spatiotemporal dynamics in various global network topological measures. The acquired network measure time series were made subject to dynamic analyses including multifractal analysis and entropy estimation. Besides group-level comparisons, we built a classifier to explore the potential of DFC features in classifying individual cases. We found stronger delta-band connectivity, as well as increased variance of DFC in SZ patients. Surrogate data testing verified the true multifractal nature of DFC in SZ, with patients expressing stronger long-range autocorrelation and degree of multifractality when compared to controls. Entropy analysis indicated reduced temporal complexity of DFC in SZ. When using these indices as features, an overall cross-validation accuracy surpassing 89% could be achieved in classifying individual cases. Our results imply that dynamic features of DFC such as its multifractal properties and entropy are potent markers of altered neural dynamics in SZ and carry significant potential not only in better understanding its pathophysiology but also in improving its diagnosis. The proposed framework is readily applicable for neuropsychiatric disorders other than schizophrenia.