Tensorial extensions of independent component analysis for multisubject FMRI analysis

Characterizing the distribution of neural and non-neural components in multi-echo EPI data across echo times based on tensor-ICA

Multi-echo echo-planar imaging (ME-EPI) acquires images at multiple echo times (TEs), enabling the differentiation of BOLD and non-BOLD fluctuations through TE-dependent analysis of transverse relaxation time and initial intensity. Decomposing ME-EPI in tensor space is a promising approach to characterize the distribution of changes across TEs (TE patterns) directly and aid the classification of components by providing information from an additional domain. In this study, the tensorial extension of independent component analysis (tensor-ICA) is used to characterize the TE patterns of neural and non-neural components in ME-EPI data. With the constraints of independent spatial maps, an ME-EPI dataset was decomposed into spatial, temporal, and TE domains to understand the TE patterns of noise or signal-related independent components. Our analysis revealed three distinct groups of components based on their TE patterns. Motion-related and other non-BOLD origin components followed decreased TE patterns. While the long-TE-peak components showed a large overlay on grey matter and signal patterns, the components that peaked at short TEs reflected noise that may be related to the vascular system, respiration, or cardiac pulsation, amongst others. Accordingly, removing short-TE peak components as part of a denoising strategy significantly improved quality control metrics and revealed clearer, more interpretable activation patterns compared to non-denoised data. To our knowledge, this work is the first application of decomposing ME-EPI in a tensor way. Our findings demonstrate that tensor-ICA is efficient in decomposing ME-EPI and characterizing the neural and non-neural TE patterns aiding in classifying components which is important for denoising fMRI data.

Deep linear matrix approximate reconstruction with integrated BOLD signal denoising reveals reproducible hierarchical brain connectivity networks from multiband multi-echo fMRI

The hierarchical modular functional structure in the human brain has not been adequately depicted by conventional functional magnetic resonance imaging (fMRI) acquisition techniques and traditional functional connectivity reconstruction methods. Fortunately, rapid advancements in fMRI scanning techniques and deep learning methods open a novel frontier to map the spatial hierarchy within Brain Connectivity Networks (BCNs). The novel multiband multi-echo (MBME) fMRI technique has increased spatiotemporal resolution and peak functional sensitivity, while the advanced deep linear model (multilayer-stacked) named DEep Linear Matrix Approximate Reconstruction (DELMAR) enables the identification of hierarchical features without extensive hyperparameter tuning. We incorporate a multi-echo blood oxygenation level-dependent (BOLD) signal and DELMAR for denoising in its first layer, thereby eliminating the need for a separate multi-echo independent component analysis (ME-ICA) denoising step. Our results demonstrate that the DELMAR/Denoising/Mapping strategy produces more accurate and reproducible hierarchical BCNs than traditional ME-ICA denoising followed by DELMAR. Additionally, we showcase that MBME fMRI outperforms multiband (MB) fMRI in terms of hierarchical BCN mapping accuracy and precision. These reproducible spatial hierarchies in BCNs have significant potential for developing improved fMRI diagnostic and prognostic biomarkers of functional connectivity across a wide range of neurological and psychiatric disorders.

The Use of fMRI Regional Analysis to Automatically Detect ADHD Through a 3D CNN-Based Approach

Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder characterized by a reduced attention span, hyperactivity, and impulsive behaviors, which typically manifest during childhood. This study employs functional magnetic resonance imaging (fMRI) to use spontaneous brain activity for classifying individuals with ADHD, focusing on a 3D convolutional neural network (CNN) architecture to facilitate the design of decision support systems. We developed a novel deep learning model based on 3D CNNs using the ADHD-200 database, which comprises datasets from NeuroImage (NI), New York University (NYU), and Peking University (PU). We used fractional amplitude of low-frequency fluctuations (fALFF) and regional homogeneity (ReHo) data in three dimensions and performed a fivefold cross-validation to address the dataset imbalance. We aimed to verify the efficacy of our proposed 3D CNN by contrasting it with a fully connected neural network (FCNN) architecture. The 3D CNN achieved accuracy rates of 76.19% (NI), 69.92% (NYU), and 70.77% (PU) for fALFF data. The FCNN model yielded lower accuracy rates across all datasets. For generalizability, we trained on NI and NYU datasets and tested on PU. The 3D CNN achieved 69.48% accuracy on fALFF outperforming the FCNN. Our results demonstrate that using 3D CNNs for classifying fALFF data is an effective approach for diagnosing ADHD. Also, FCNN confirmed the efficiency of the designed model.

Sensitivity of Functional Arterial Spin Labelling in Detecting Cerebral Blood Flow Changes

Aims/Background Arterial spin labelling (ASL) is a non-invasive magnetic resonance imaging (MRI) method. ASL techniques can quantitatively measure cerebral perfusion by fitting a kinetic model to the difference between labelled images (tag images) and ones which are acquired without labelling (control images). ASL functional MRI (fMRI) provides quantitative perfusion maps by using arterial water as an endogenous tracer instead of depending on vascular blood oxygenation level.This study aimed to assess the number of pulsed ASL blocks that were needed to provide accurate and reliable regional estimates of cerebral blood flow (CBF) changes when participants engaged in visually guided saccade and fixation task; evaluate the localization to cortical control saccade versus fixation; investigate the relationship between the sensitivity of ASL fMRI and the number of blocks; and compare the sensitivity of blood oxygen level-dependent (BOLD) fMRI and ASL fMRI. Methods The experiment was a block-design paradigm consisting of two conditions: fixation and saccade. No response other than the eye movements of the participants was recorded during the scans. ASL and BOLD fMRI scans were conducted on all participants during the same session. The fMRI study consisted of two functional experiments: a CBF contrast was provided using the ASL sequence, and an optimized BOLD contrast was provided using the BOLD sequence. Results From group analysis in all divided blocks of ASL sessions (4, 6, 8...... 14, 16, 18......26, 28, 30), ASL yielded significant activation clusters in the visual cortex of the bilateral hemisphere from block 4. There was no false activation from block 4. No activation cluster was found by reversing analysis of block 2. Robust and consistent activation in the visual cortex was observed in each of the 14 divided blocks group analysis, and no activation was found in the eye field of the brain. The sensitivity of 4-block was found to be better than that of 8-block. More significant activation clusters of the visual cortex were found in BOLD than in ASL. No activation cluster of parietal eye field (PEF), frontal eye field (FEF) and supplementary eye field (SEF) was detected in ASL. The voxel size of the activation cluster increased with the increasing number of blocks, and the percent signal change in the activation cluster decreased with the escalating block number. The voxel size was positively correlated with the number of blocks (correlation coefficient = 0.98, p < 0.0001), and the percent signal change negatively correlated with the number of blocks (correlation coefficient = -0.90, p < 0.0001). Conclusion The 4-block pulsed functional ASL (fASL) presents accurate and reliable activation, with minimal time-on-task effect and little adverse impact of time, in participants engaging in visually guided saccade and fixation tasks. Despite having lower sensitivity than BOLD fMRI, ASL can determine accurate activation location. Although the time-on-task effects affect the observation for the sensitivity of ASL over task time, it is suggested that ASL fMRI may provide a powerful method for pinpointing the time-on-task effect over a long period of time.

Group Integrative Dynamic Factor Models With Application to Multiple Subject Brain Connectivity

This work introduces a novel framework for dynamic factor model-based group-level analysis of multiple subjects time-series data, called GRoup Integrative DYnamic factor (GRIDY) models. The framework identifies and characterizes intersubject similarities and differences between two predetermined groups by considering a combination of group spatial information and individual temporal dynamics. Furthermore, it enables the identification of intrasubject similarities and differences over time by employing different model configurations for each subject. Methodologically, the framework combines a novel principal angle-based rank selection algorithm and a noniterative integrative analysis framework. Inspired by simultaneous component analysis, this approach also reconstructs identifiable latent factor series with flexible covariance structures. The performance of the GRIDY models is evaluated through simulations conducted under various scenarios. An application is also presented to compare resting-state functional MRI data collected from multiple subjects in autism spectrum disorder and control groups.

Constrained Independent Vector Analysis With Reference for Multi-Subject fMRI Analysis

OBJECTIVE

Independent component analysis (ICA) is now a widely used solution for the analysis of multi-subject functional magnetic resonance imaging (fMRI) data. Independent vector analysis (IVA) generalizes ICA to multiple datasets (multi-subject data). Along with higher-order statistical information in ICA, it leverages the statistical dependence across the datasets as an additional type of statistical diversity. As such, IVA preserves variability in the estimation of single-subject maps but its performance might suffer when the number of datasets increases. Constrained IVA is an effective way to bypass computational issues and improve the quality of separation by incorporating available prior information. Existing constrained IVA approaches often rely on user-defined threshold values to define the constraints. However, an improperly selected threshold can have a negative impact on the final results. This paper proposes two novel methods for constrained IVA: one using an adaptive-reverse scheme to select variable thresholds for the constraints and a second one based on a threshold-free formulation by leveraging the unique structure of IVA. Notably, the proposed algorithms do not require all components to be constrained, utilizing free components to model interferences and components that might not be in the reference set. We demonstrate that our solutions provide an attractive solution to multi-subject fMRI analysis both by simulations and through analysis of resting state fMRI data collected from 98 subjects - the highest number of subjects ever used by IVA algorithms. Our results show that both proposed approaches obtain significantly better separation quality and model match while providing computationally efficient and highly reproducible solutions.

Comparing mouse and human cingulate cortex organization using functional connectivity

The subdivisions of the extended cingulate cortex of the human brain are implicated in a number of high-level behaviors and affected by a range of neuropsychiatric disorders. Its anatomy, function, and response to therapeutics are often studied using non-human animals, including the mouse. However, the similarity of human and mouse frontal cortex, including cingulate areas, is still not fully understood. Some accounts emphasize resemblances between mouse cingulate cortex and human cingulate cortex while others emphasize similarities with human granular prefrontal cortex. We use comparative neuroimaging to study the connectivity of the cingulate cortex in the mouse and human, allowing comparisons between mouse 'gold standard' tracer and imaging data, and, in addition, comparison between the mouse and the human using comparable imaging data. We find overall similarities in organization of the cingulate between species, including anterior and midcingulate areas and a retrosplenial area. However, human cingulate contains subareas with a more fine-grained organization than is apparent in the mouse and it has connections to prefrontal areas not present in the mouse. Results such as these help formally address between-species brain organization and aim to improve the translation from preclinical to human results.

The effects of cannabis abstinence on cognition and resting state network activity in people with multiple sclerosis: A preliminary study

We previously reported that people with multiple sclerosis (pwMS) who have been using cannabis frequently over many years can have significant cognitive improvements accompanied by concomitant task-specific changes in brain activation following 28 days of cannabis abstinence. We now hypothesize that the default Mode Network (DMN), known to modulate cognition, would also show an improved pattern of activation align with cognitive improvement following 28 days of drug abstinence. Thirty three cognitively impaired pwMS who were frequent cannabis users underwent a neuropsychological assessment and fMRI at baseline. Individuals were then assigned to a cannabis continuation (CC, n = 15) or withdrawal (CW, n = 18) group and the cognitive and imaging assessments were repeated after 28 days. Compliance with cannabis withdrawal was checked with regular urine monitoring. Following acquisition of resting state fMRI (rs-fMRI), data were processed using independent component analysis (ICA) to identify the DMN spatial map. Between and within group analyses were carried out using dual regression for voxel-wise comparisons of the DMN. Clusters of voxels were considered statistically significant if they survived threshold-free cluster enhancement (TFCE) correction at p < 0.05. The two groups were well matched demographically and neurologically at baseline. The dual regression analysis revealed no between group differences at baseline in the DMN. By day 28, the CW group in comparison to the CC group had increased activation in the left posterior cingulate, and right, angular gyrus (p < 0.05 for both, TFCE). A within group analysis for the CC group revealed no changes in resting state (RS) networks. Within group analysis of the CW group revealed increased activation at day 28 versus baseline in the left posterior cingulate, right angular gyrus, left hippocampus (BA 36), and the right medial prefrontal cortex (p < 0.05). The CW group showed significant improvements in multiple cognitive domains. In summary, our study revealed that abstaining from cannabis for 28 days reverses activation of DMN activity in pwMS in association with improved cognition across several domains.

Nonconvex Robust High-Order Tensor Completion Using Randomized Low-Rank Approximation

Within the tensor singular value decomposition (T-SVD) framework, existing robust low-rank tensor completion approaches have made great achievements in various areas of science and engineering. Nevertheless, these methods involve the T-SVD based low-rank approximation, which suffers from high computational costs when dealing with large-scale tensor data. Moreover, most of them are only applicable to third-order tensors. Against these issues, in this article, two efficient low-rank tensor approximation approaches fusing random projection techniques are first devised under the order-d ( d ≥ 3 ) T-SVD framework. Theoretical results on error bounds for the proposed randomized algorithms are provided. On this basis, we then further investigate the robust high-order tensor completion problem, in which a double nonconvex model along with its corresponding fast optimization algorithms with convergence guarantees are developed. Experimental results on large-scale synthetic and real tensor data illustrate that the proposed method outperforms other state-of-the-art approaches in terms of both computational efficiency and estimated precision.

Hierarchical Principal Components for Data-Driven Multiresolution fMRI Analyses

Understanding the organization of neural processing is a fundamental goal of neuroscience. Recent work suggests that these systems are organized as a multiscale hierarchy, with increasingly specialized subsystems nested inside general processing systems. Current neuroimaging methods, such as independent component analysis (ICA), cannot fully capture this hierarchy since they are limited to a single spatial scale. In this manuscript, we introduce multiresolution hierarchical principal components analysis (hPCA) and compare it to ICA using simulated fMRI datasets. Furthermore, we describe a parametric statistical filtering method developed to focus analyses on biologically relevant features. Lastly, we apply hPCA to the Human Connectome Project (HCP) to demonstrate its ability to estimate a hierarchy from real fMRI data. hPCA accurately estimated spatial maps and time series from networks with diverse hierarchical structures. Simulated hierarchies varied in the degree of branching, such as two-way or three-way subdivisions, and the total number of levels, with varying equal or unequal subdivision sizes at each branch. In each case, as well as in the HCP, hPCA was able to reconstruct a known hierarchy of networks. Our results suggest that hPCA can facilitate more detailed and comprehensive analyses of the brain's network of networks and the multiscale regional specializations underlying neural processing and cognition.

Explainable artificial intelligence (xAI) in neuromarketing/consumer neuroscience: an fMRI study on brand perception

Introduction

The research in consumer neuroscience has identified computational methods, particularly artificial intelligence (AI) and machine learning, as a significant frontier for advancement. Previously, we utilized functional magnetic resonance imaging (fMRI) and artificial neural networks (ANNs) to model brain processes related to brand preferences in a paradigm exempted from motor actions. In the current study, we revisit this data, introducing recent advancements in explainable artificial intelligence (xAI) to gain insights into this domain. By integrating fMRI data analysis, machine learning, and xAI, our study aims to search for functional brain networks that support brand perception and, ultimately, search for brain networks that disentangle between preferred and indifferent brands, focusing on the early processing stages.

Methods

We applied independent component analysis (ICA) to overcome the expected fMRI data's high dimensionality, which raises hurdles in AI applications. We extracted pertinent features from the returned ICs. An ANN is then trained on this data, followed by pruning and retraining processes. We then apply explanation techniques, based on path-weights and Shapley values, to make the network more transparent, explainable, and interpretable, and to obtain insights into the underlying brain processes.

Results

The fully connected ANN model obtained an accuracy of 54.6%, which dropped to 50.4% after pruning. However, the retraining process allowed it to surpass the fully connected network, achieving an accuracy of 55.9%. The path-weights and Shapley-based analysis concludes that, regarding brand perception, the expected initial participation of the primary visual system is followed. Other brain areas participate in early processing and discriminate between preferred and indifferent brands, such as the cuneal and the lateral occipital cortices.

Discussion

The most important finding is that a split between processing brands|preferred from brands|indifferent may occur during early processing stages, still in the visual system. However, we found no evidence of a "decision pipeline" that would yield if a brand is preferred or indifferent. The results suggest the existence of a "tagging"-like process in parallel flows in the extrastriate. Network training dynamics aggregate specific processes within the hidden nodes by analyzing the model's hidden layer. This yielded that some nodes contribute to both global brand appraisal and specific brand category classification, shedding light on the neural substrates of decision-making in response to brand stimuli.

EiDA: A lossless approach for dynamic functional connectivity; application to fMRI data of a model of ageing

Dynamic Functional Connectivity (dFC) is the study of the dynamic patterns of interaction that characterise brain function. Numerous numerical methods are available to compute and analyse dFC from high-dimensional data. In fMRI, a number of them rely on the computation of the instantaneous Phase Alignment (iPA) matrix (also known as instantaneous Phase Locking). Their limitations are the high computational cost and the concomitant need to introduce approximations with ensuing information loss. Here, we introduce the analytical decomposition of the iPA. This has two advantages. Firstly, we achieve an up to 1000-fold reduction in computing time without information loss. Secondly, we can formally introduce two alternative approaches to the analysis of the resulting time-varying instantaneous connectivity patterns, Discrete and Continuous EiDA (Eigenvector Dynamic Analysis), and a related set of metrics to quantify the total amount of instantaneous connectivity, drawn from dynamical systems and information theory. We applied EiDA to a dataset from 48 rats that underwent functional magnetic resonance imaging (fMRI) at four stages during a longitudinal study of ageing. Using EiDA, we found that the metrics we introduce provided robust markers of ageing with decreases in total connectivity and metastability, and an increase in informational complexity over the life span. This suggests that ageing reduces the available functional repertoire that is postulated to support cognitive functions and overt behaviours, slows down the exploration of this reduced repertoire, and decreases the coherence of its structure. In summary, EiDA is a method to extract lossless connectivity information that requires significantly less computational time, and provides robust and analytically principled metrics for brain dynamics. These metrics are interpretable and promising for studies on neurodevelopmental and neurodegenerative disorders.

Age-Related Differences in Affective Behaviors in Mice: Possible Role of Prefrontal Cortical-Hippocampal Functional Connectivity and Metabolomic Profiles

The differential expression of emotional reactivity from early to late adulthood may involve maturation of prefrontal cortical responses to negative valence stimuli. In mice, age-related changes in affective behaviors have been reported, but the functional neural circuitry warrants further investigation. We assessed age variations in affective behaviors and functional connectivity in male and female C57BL6/J mice. Mice aged 10, 30 and 60 weeks (wo) were tested over 8 weeks for open field activity, sucrose preference, social interactions, fear conditioning, and functional neuroimaging. Prefrontal cortical and hippocampal tissues were excised for metabolomics. Our results indicate that young and old mice differ significantly in affective behavioral, functional connectome and prefrontal cortical-hippocampal metabolome. Young mice show a greater responsivity to novel environmental and social stimuli compared to older mice. Conversely, late middle-aged mice (60wo group) display variable patterns of fear conditioning and with re-testing with a modified context. Functional connectivity between a temporal cortical/auditory cortex network and subregions of the anterior cingulate cortex and ventral hippocampus, and a greater network modularity and assortative mixing of nodes was stronger in young versus older adult mice. Metabolome analyses identified differences in several essential amino acids between 10wo mice and the other age groups. The results support differential expression of 'emotionality' across distinct stages of the mouse lifespan involving greater prefrontal-hippocampal connectivity and neurochemistry.

Functional neuroimaging biomarkers of anhedonia response to escitalopram plus adjunct aripiprazole treatment for major depressive disorder

BACKGROUND

Identifying neuroimaging biomarkers of antidepressant response may help guide treatment decisions and advance precision medicine.

AIMS

To examine the relationship between anhedonia and functional neurocircuitry in key reward processing brain regions in people with major depressive disorder receiving aripiprazole adjunct therapy with escitalopram.

METHOD

Data were collected as part of the CAN-BIND-1 study. Participants experiencing a current major depressive episode received escitalopram for 8 weeks; escitalopram non-responders received adjunct aripiprazole for an additional 8 weeks. Functional magnetic resonance imaging (on weeks 0 and 8) and clinical assessment of anhedonia (on weeks 0, 8 and 16) were completed. Seed-based correlational analysis was employed to examine the relationship between baseline resting-state functional connectivity (rsFC), using the nucleus accumbens (NAc) and anterior cingulate cortex (ACC) as key regions of interest, and change in anhedonia severity after adjunct aripiprazole.

RESULTS

Anhedonia severity significantly improved after treatment with adjunct aripiprazole.There was a positive correlation between anhedonia improvement and rsFC between the ACC and posterior cingulate cortex, ACC and posterior praecuneus, and NAc and posterior praecuneus. There was a negative correlation between anhedonia improvement and rsFC between the ACC and anterior praecuneus and NAc and anterior praecuneus.

CONCLUSIONS

Eight weeks of aripiprazole, adjunct to escitalopram, was associated with improved anhedonia symptoms. Changes in functional connectivity between key reward regions were associated with anhedonia improvement, suggesting aripiprazole may be an effective treatment for individuals experiencing reward-related deficits. Future studies are required to replicate our findings and explore their generalisability, using other agents with partial dopamine (D2) agonism and/or serotonin (5-HT2A) antagonism.

Delineating a Pathway for the Discovery of Functional Connectome Biomarkers of Autism

The promise of individually tailored care for autism has driven efforts to establish biomarkers. This chapter appraises the state of precision-medicine research focused on biomarkers based on the functional brain connectome. This work is grounded on abundant evidence supporting the brain dysconnection model of autism and the advantages of resting-state functional MRI (R-fMRI) for studying the brain in vivo. After considering biomarker requirements of consistency and clinical relevance, we provide a scoping review of R-fMRI studies of individual prediction in autism. In the past 10 years, responding to the availability of open data through the Autism Brain Imaging Data Exchange, machine learning studies have surged. Nearly all have focused on diagnostic label classification. These efforts have shown that autism prediction is feasible using functional connectome markers, with accuracy reported well above chance. In parallel, emerging approaches more directly addressing autism heterogeneity are paving the way for much-needed biomarkers of longitudinal outcome and treatment response. We conclude with key challenges to be addressed by the next generation of studies.

Functional connectivity patterns in parosmia

OBJECTIVE

Parosmia is a qualitative olfactory dysfunction presenting as "distorted odor perception" in presence of an odor source. Aim of this study was to use resting state functional connectivity to gain more information on the alteration of olfactory processing at the level of the central nervous system level.

METHODS

A cross sectional study was performed in 145 patients with parosmia (age range 20-76 years; 90 women). Presence and degree of parosmia was diagnosed on the basis of standardized questionnaires. Participants also received olfactory testing using the "Sniffin' Sticks". Then they underwent resting state scans using a 3 T magnetic resonance imaging scanner while fixating on a cross.

RESULTS

Whole brain analyses revealed reduced functional connectivity in salience as well as executive control networks. Region of interest-based analyses also supported reduced functional connectivity measures between primary and secondary olfactory eloquent areas (temporal pole, supramarginal gyrus and right orbitofrontal cortex; dorso-lateral pre-frontal cortex and the right piriform cortex).

CONCLUSIONS

Participants with parosmia exhibited a reduced information flow between memory, decision making centers, and primary and secondary olfactory areas.

Denoising brain networks using a fixed mathematical phase change in independent component analysis of magnitude-only fMRI data

Brain networks extracted by independent component analysis (ICA) from magnitude-only fMRI data are usually denoised using various amplitude-based thresholds. By contrast, spatial source phase (SSP) or the phase information of ICA brain networks extracted from complex-valued fMRI data, has provided a simple yet effective way to perform the denoising using a fixed phase change. In this work, we extend the approach to magnitude-only fMRI data to avoid testing various amplitude thresholds for denoising magnitude maps extracted by ICA, as most studies do not save the complex-valued data. The main idea is to generate a mathematical SSP map for a magnitude map using a mapping framework, and the mapping framework is built using complex-valued fMRI data with a known SSP map. Here we leverage the fact that the phase map derived from phase fMRI data has similar phase information to the SSP map. After verifying the use of the magnitude data of complex-valued fMRI, this framework is generalized to work with magnitude-only data, allowing use of our approach even without the availability of the corresponding phase fMRI datasets. We test the proposed method using both simulated and experimental fMRI data including complex-valued data from University of New Mexico and magnitude-only data from Human Connectome Project. The results provide evidence that the mathematical SSP denoising with a fixed phase change is effective for denoising spatial maps from magnitude-only fMRI data in terms of retaining more BOLD-related activity and fewer unwanted voxels, compared with amplitude-based thresholding. The proposed method provides a unified and efficient SSP approach to denoise ICA brain networks in fMRI data.

Sparse Bayesian modeling of hierarchical independent component analysis: Reliable estimation of individual differences in brain networks

Independent component analysis (ICA) is one of the leading approaches for studying brain functional networks. There is increasing interest in neuroscience studies to investigate individual differences in brain networks and their association with demographic characteristics and clinical outcomes. In this work, we develop a sparse Bayesian group hierarchical ICA model that offers significant improvements over existing ICA techniques for identifying covariate effects on the brain network. Specifically, we model the population-level ICA source signals for brain networks using a Dirichlet process mixture. To reliably capture individual differences on brain networks, we propose sparse estimation of the covariate effects in the hierarchical ICA model via a horseshoe prior. Through extensive simulation studies, we show that our approach performs considerably better in detecting covariate effects in comparison with the leading group ICA methods. We then perform an ICA decomposition of a between-subject meditation study. Our method is able to identify significant effects related to meditative practice in brain regions that are consistent with previous research into the default mode network, whereas other group ICA approaches find few to no effects.

Data-driven multimodal fusion: approaches and applications in psychiatric research

In the era of big data, where vast amounts of information are being generated and collected at an unprecedented rate, there is a pressing demand for innovative data-driven multi-modal fusion methods. These methods aim to integrate diverse neuroimaging perspectives to extract meaningful insights and attain a more comprehensive understanding of complex psychiatric disorders. However, analyzing each modality separately may only reveal partial insights or miss out on important correlations between different types of data. This is where data-driven multi-modal fusion techniques come into play. By combining information from multiple modalities in a synergistic manner, these methods enable us to uncover hidden patterns and relationships that would otherwise remain unnoticed. In this paper, we present an extensive overview of data-driven multimodal fusion approaches with or without prior information, with specific emphasis on canonical correlation analysis and independent component analysis. The applications of such fusion methods are wide-ranging and allow us to incorporate multiple factors such as genetics, environment, cognition, and treatment outcomes across various brain disorders. After summarizing the diverse neuropsychiatric magnetic resonance imaging fusion applications, we further discuss the emerging neuroimaging analyzing trends in big data, such as N-way multimodal fusion, deep learning approaches, and clinical translation. Overall, multimodal fusion emerges as an imperative approach providing valuable insights into the underlying neural basis of mental disorders, which can uncover subtle abnormalities or potential biomarkers that may benefit targeted treatments and personalized medical interventions.

Neuromodulation of striatal D1 cells shapes BOLD fluctuations in anatomically connected thalamic and cortical regions

Understanding how the brain's macroscale dynamics are shaped by underlying microscale mechanisms is a key problem in neuroscience. In animal models, we can now investigate this relationship in unprecedented detail by directly manipulating cellular-level properties while measuring the whole-brain response using resting-state fMRI. Here, we focused on understanding how blood-oxygen-level-dependent (BOLD) dynamics, measured within a structurally well-defined striato-thalamo-cortical circuit in mice, are shaped by chemogenetically exciting or inhibiting D1 medium spiny neurons (MSNs) of the right dorsomedial caudate putamen (CPdm). We characterize changes in both the BOLD dynamics of individual cortical and subcortical brain areas, and patterns of inter-regional coupling (functional connectivity) between pairs of areas. Using a classification approach based on a large and diverse set of time-series properties, we found that CPdm neuromodulation alters BOLD dynamics within thalamic subregions that project back to dorsomedial striatum. In the cortex, changes in local dynamics were strongest in unimodal regions (which process information from a single sensory modality) and weakened along a hierarchical gradient towards transmodal regions. In contrast, a decrease in functional connectivity was observed only for cortico-striatal connections after D1 excitation. Our results show that targeted cellular-level manipulations affect local BOLD dynamics at the macroscale, such as by making BOLD dynamics more predictable over time by increasing its self-correlation structure. This contributes to ongoing attempts to understand the influence of structure-function relationships in shaping inter-regional communication at subcortical and cortical levels.

Age-related brain deviations and aggression

BACKGROUND

Disruptive behavior disorders (DBD) are heterogeneous at the clinical and the biological level. Therefore, the aims were to dissect the heterogeneous neurodevelopmental deviations of the affective brain circuitry and provide an integration of these differences across modalities.

METHODS

We combined two novel approaches. First, normative modeling to map deviations from the typical age-related pattern at the level of the individual of (i) activity during emotion matching and (ii) of anatomical images derived from DBD cases (n = 77) and controls (n = 52) aged 8-18 years from the EU-funded Aggressotype and MATRICS consortia. Second, linked independent component analysis to integrate subject-specific deviations from both modalities.

RESULTS

While cases exhibited on average a higher activity than would be expected for their age during face processing in regions such as the amygdala when compared to controls these positive deviations were widespread at the individual level. A multimodal integration of all functional and anatomical deviations explained 23% of the variance in the clinical DBD phenotype. Most notably, the top marker, encompassing the default mode network (DMN) and subcortical regions such as the amygdala and the striatum, was related to aggression across the whole sample.

CONCLUSIONS

Overall increased age-related deviations in the amygdala in DBD suggest a maturational delay, which has to be further validated in future studies. Further, the integration of individual deviation patterns from multiple imaging modalities allowed to dissect some of the heterogeneity of DBD and identified the DMN, the striatum and the amygdala as neural signatures that were associated with aggression.

A topography-based predictive framework for naturalistic viewing fMRI

Functional magnetic resonance imaging (fMRI) during naturalistic viewing (NV) provides exciting opportunities for studying brain functions in more ecologically valid settings. Understanding individual differences in brain functions during NV and their behavioural relevance has recently become an important goal. However, methods specifically designed for this purpose remain limited. Here, we propose a topography-based predictive framework (TOPF) to fill this methodological gap. TOPF identifies individual-specific evoked activity topographies in a data-driven manner and examines their behavioural relevance using a machine learning-based predictive framework. We validate TOPF on both NV and task-based fMRI data from multiple conditions. Our results show that TOPF effectively and stably captures individual differences in evoked brain activity and successfully predicts phenotypes across cognition, emotion and personality on unseen subjects from their activity topographies. Moreover, TOPF compares favourably with functional connectivity-based approaches in prediction performance, with the identified predictive brain regions being neurobiologically interpretable. Crucially, we highlight the importance of examining individual evoked brain activity topographies in advancing our understanding of the brain-behaviour relationship. We believe that the TOPF approach provides a simple but powerful tool for understanding brain-behaviour relationships on an individual level with a strong potential for clinical applications.

LOCUS: A REGULARIZED BLIND SOURCE SEPARATION METHOD WITH LOW-RANK STRUCTURE FOR INVESTIGATING BRAIN CONNECTIVITY

Network-oriented research has been increasingly popular in many scientific areas. In neuroscience research, imaging-based network connectivity measures have become the key for understanding brain organizations, potentially serving as individual neural fingerprints. There are major challenges in analyzing connectivity matrices, including the high dimensionality of brain networks, unknown latent sources underlying the observed connectivity, and the large number of brain connections leading to spurious findings. In this paper we propose a novel blind source separation method with low-rank structure and uniform sparsity (LOCUS) as a fully data-driven decomposition method for network measures. Compared with the existing method that vectorizes connectivity matrices ignoring brain network topology, LOCUS achieves more efficient and accurate source separation for connectivity matrices using low-rank structure. We propose a novel angle-based uniform sparsity regularization that demonstrates better performance than the existing sparsity controls for low-rank tensor methods. We propose a highly efficient iterative node-rotation algorithm that exploits the block multiconvexity of the objective function to solve the nonconvex optimization problem for learning LOCUS. We illustrate the advantage of LOCUS through extensive simulation studies. Application of LOCUS to Philadelphia Neurodevelopmental Cohort neuroimaging study reveals biologically insightful connectivity traits which are not found using the existing method.

Edge-centric functional network predicts risk propensity in economic decision-making: evidence from a resting-state fMRI study

Despite node-centric studies revealing an association between resting-state functional connectivity and individual risk propensity, the prediction of future risk decisions remains undetermined. Herein, we applied a recently emerging edge-centric method, the edge community similarity network (ECSN), to alternatively describe the community structure of resting-state brain activity and to probe its contribution to predicting risk propensity during gambling. Results demonstrated that inter-individual variability of risk decisions correlates with the inter-subnetwork couplings spanning the visual network (VN) and default mode network (DMN), cingulo-opercular task control network, and sensory/somatomotor hand network (SSHN). Particularly, participants who have higher community similarity of these subnetworks during the resting state tend to choose riskier and higher yielding bets. And in contrast to low-risk propensity participants, those who behave high-risky show stronger couplings spanning the VN and SSHN/DMN. Eventually, based on the resting-state ECSN properties, the risk rate during the gambling task is effectively predicted by the multivariable linear regression model at the individual level. These findings provide new insights into the neural substrates of the inter-individual variability in risk propensity and new neuroimaging metrics to predict individual risk decisions in advance.

Tensorial independent component analysis reveals social and reward networks associated with major depressive disorder

Major depressive disorder (MDD) has been associated with changes in functional brain connectivity. Yet, typical analyses of functional connectivity, such as spatial independent components analysis (ICA) for resting-state data, often ignore sources of between-subject variability, which may be crucial for identifying functional connectivity patterns associated with MDD. Typically, methods like spatial ICA will identify a single component to represent a network like the default mode network (DMN), even if groups within the data show differential DMN coactivation. To address this gap, this project applies a tensorial extension of ICA (tensorial ICA)-which explicitly incorporates between-subject variability-to identify functionally connected networks using functional MRI data from the Human Connectome Project (HCP). Data from the HCP included individuals with a diagnosis of MDD, a family history of MDD, and healthy controls performing a gambling and social cognition task. Based on evidence associating MDD with blunted neural activation to rewards and social stimuli, we predicted that tensorial ICA would identify networks associated with reduced spatiotemporal coherence and blunted social and reward-based network activity in MDD. Across both tasks, tensorial ICA identified three networks showing decreased coherence in MDD. All three networks included ventromedial prefrontal cortex, striatum, and cerebellum and showed different activation across the conditions of their respective tasks. However, MDD was only associated with differences in task-based activation in one network from the social task. Additionally, these results suggest that tensorial ICA could be a valuable tool for understanding clinical differences in relation to network activation and connectivity.

A cross-sectional and longitudinal study of human brain development: The integration of cortical thickness, surface area, gyrification index, and cortical curvature into a unified analytical framework

Brain maturation studies typically examine relationships linking a single morphometric feature with cognition, behavior, age, or other demographic characteristics. However, the coordinated spatiotemporal arrangement of morphological features across development and their associations with behavior are unclear. Here, we examine covariation across multiple cortical features (cortical thickness [CT], surface area [SA], local gyrification index [GI], and mean curvature [MC]) using magnetic resonance images from the NIMH developmental cohort (ages 5-25). Neuroanatomical covariance was examined using non-negative matrix factorization (NMF), which decomposes covariance resulting in a parts-based representation. Cross-sectionally, we identified six components of covariation which demonstrate differential contributions of CT, GI, and SA in hetero- vs. unimodal areas. Using this technique to examine covariance in rates of change to identify longitudinal sources of covariance highlighted preserved SA in unimodal areas and changes in CT and GI in heteromodal areas. Using behavioral partial least squares (PLS), we identified a single latent variable (LV) that recapitulated patterns of reduced CT, GI, and SA related to older age, with limited contributions of IQ and SES. Longitudinally, PLS revealed three LVs that demonstrated a nuanced developmental pattern that highlighted a higher rate of maturational change in SA and CT in higher IQ and SES females. Finally, we situated the components in the changing architecture of cortical gradients. This novel characterization of brain maturation provides an important understanding of the interdependencies between morphological measures, their coordinated development, and their relationship to biological sex, cognitive ability, and the resources of the local environment.

Functional magnetic resonance imaging of headache: Issues, best-practices, and new directions, a narrative review

OBJECTIVE

To ensure readers are informed consumers of functional magnetic resonance imaging (fMRI) research in headache, to outline ongoing challenges in this area of research, and to describe potential considerations when asked to collaborate on fMRI research in headache, as well as to suggest future directions for improvement in the field.

BACKGROUND

Functional MRI has played a key role in understanding headache pathophysiology, and mapping networks involved with headache-related brain activity have the potential to identify intervention targets. Some investigators have also begun to explore its use for diagnosis.

METHODS/RESULTS

The manuscript is a narrative review of the current best practices in fMRI in headache research, including guidelines on transparency and reproducibility. It also contains an outline of the fundamentals of MRI theory, task-related study design, resting-state functional connectivity, relevant statistics and power analysis, image preprocessing, and other considerations essential to the field.

CONCLUSION

Best practices to increase reproducibility include methods transparency, eliminating error, using a priori hypotheses and power calculations, using standardized instruments and diagnostic criteria, and developing large-scale, publicly available datasets.

The effects of repetitive transcranial magnetic stimulation and aerobic exercise on cognition, balance and functional brain networks in patients with Alzheimer's disease

The purpose of this study was to investigate the effects of high-frequency repetitive Transcranial Magnetic Stimulation (rTMS) and aerobic exercises (AE) in addition to the pharmacological therapy (PT) in Alzheimer's Disease (AD). Twenty-seven patients with AD aged ≥ 60 years were included in the study and divided into 3 groups (rTMS, AE and control). All groups received PT. rTMS group (n = 10) received 20 Hz rTMS over dorsolateral prefrontal cortex (dlPFC) bilaterally and AE group (n = 9) received the structured moderate-intensity AE for 5 consecutive days/week over 2 weeks. Control group (n = 8) only received PT. Cognition, balance, mobility, quality of life (QoL), and resting state functional brain activity were evaluated one week before and one week after the interventions. (ClinicalTrials.gov ID:NCT05102045). Significant improvements were found in executive functions, behavior, and QoL in the rTMS group, in balance and mobility in the AE group, and in the visual memory and behavior in the control group (p < 0.05). Significant differences were found in the behavior in favor of the rTMS group, and balance in favor of the AE group (p < 0.05). There was a significant increase in activation on middle temporal gyrus, intra calcarine, central opercular cortex, superior parietal lobule, and paracingulate cortex in Default Mode Network (DMN) in the rTMS group (p < 0.05). High-frequency rTMS over bilateral dlPFC may improve executive functions and behavior and lead to increased activation in DMN, structured moderate-intensity AE may improve balance and mobility, and PT may improve memory and behaviour compared to pretreatment in AD.

Protocol for an observational cohort study investigating biomarkers predicting seizure recurrence following a first unprovoked seizure in adults

INTRODUCTION

A first unprovoked seizure is a common presentation, reliably identifying those that will have recurrent seizures is a challenge. This study will be the first to explore the combined utility of serum biomarkers, quantitative electroencephalogram (EEG) and quantitative MRI to predict seizure recurrence. This will inform patient stratification for counselling and the inclusion of high-risk patients in clinical trials of disease-modifying agents in early epilepsy.

METHODS AND ANALYSIS

100 patients with first unprovoked seizure will be recruited from a tertiary neuroscience centre and baseline assessments will include structural MRI, EEG and a blood sample. As part of a nested pilot study, a subset of 40 patients will have advanced MRI sequences performed that are usually reserved for patients with refractory chronic epilepsy. The remaining 60 patients will have standard clinical MRI sequences. Patients will be followed up every 6 months for a 24-month period to assess seizure recurrence. Connectivity and network-based analyses of EEG and MRI data will be carried out and examined in relation to seizure recurrence. Patient outcomes will also be investigated with respect to analysis of high-mobility group box-1 from blood serum samples.

ETHICS AND DISSEMINATION

This study was approved by North East-Tyne & Wear South Research Ethics Committee (20/NE/0078) and funded by an Association of British Neurologists and Guarantors of Brain clinical research training fellowship. Findings will be presented at national and international meetings published in peer-reviewed journals.

TRIAL REGISTRATION NUMBER

NIHR Clinical Research Network's (CRN) Central Portfolio Management System (CPMS)-44976.

Clusterwise Independent Component Analysis (C-ICA): Using fMRI resting state networks to cluster subjects and find neurofunctional subtypes

BACKGROUND

FMRI resting state networks (RSNs) are used to characterize brain disorders. They also show extensive heterogeneity across patients. Identifying systematic differences between RSNs in patients, i.e. discovering neurofunctional subtypes, may further increase our understanding of disease heterogeneity. Currently, no methodology is available to estimate neurofunctional subtypes and their associated RSNs simultaneously.

NEW METHOD

We present an unsupervised learning method for fMRI data, called Clusterwise Independent Component Analysis (C-ICA). This enables the clustering of patients into neurofunctional subtypes based on differences in shared ICA-derived RSNs. The parameters are estimated simultaneously, which leads to an improved estimation of subtypes and their associated RSNs.

RESULTS

In five simulation studies, the C-ICA model is successfully validated using both artificially and realistically simulated data (N = 30-40). The successful performance of the C-ICA model is also illustrated on an empirical data set consisting of Alzheimer's disease patients and elderly control subjects (N = 250). C-ICA is able to uncover a meaningful clustering that partially matches (balanced accuracy = .72) the diagnostic labels and identifies differences in RSNs between the Alzheimer and control cluster.

COMPARISON WITH OTHER METHODS

Both in the simulation study and the empirical application, C-ICA yields better results compared to competing clustering methods (i.e., a two step clustering procedure based on single subject ICA's and a Group ICA plus dual regression variant thereof) that do not simultaneously estimate a clustering and associated RSNs. Indeed, the overall mean adjusted Rand Index, a measure for cluster recovery, equals 0.65 for C-ICA and ranges from 0.27 to 0.46 for competing methods.

CONCLUSIONS

The successful performance of C-ICA indicates that it is a promising method to extract neurofunctional subtypes from multi-subject resting state-fMRI data. This method can be applied on fMRI scans of patient groups to study (neurofunctional) subtypes, which may eventually further increase understanding of disease heterogeneity.

Bayesian Spatial Blind Source Separation via the Thresholded Gaussian Process

Blind source separation (BSS) aims to separate latent source signals from their mixtures. For spatially dependent signals in high dimensional and large-scale data, such as neuroimaging, most existing BSS methods do not take into account the spatial dependence and the sparsity of the latent source signals. To address these major limitations, we propose a Bayesian spatial blind source separation (BSP-BSS) approach for neuroimaging data analysis. We assume the expectation of the observed images as a linear mixture of multiple sparse and piece-wise smooth latent source signals, for which we construct a new class of Bayesian nonparametric prior models by thresholding Gaussian processes. We assign the vMF priors to mixing coefficients in the model. Under some regularity conditions, we show that the proposed method has several desirable theoretical properties including the large support for the priors, the consistency of joint posterior distribution of the latent source intensity functions and the mixing coefficients, and the selection consistency on the number of latent sources. We use extensive simulation studies and an analysis of the resting-state fMRI data in the Autism Brain Imaging Data Exchange (ABIDE) study to demonstrate that BSP-BSS outperforms the existing method for separating latent brain networks and detecting activated brain activation in the latent sources.

Constrained CPD of Complex-Valued Multi-Subject fMRI Data via Alternating Rank-R and Rank-1 Least Squares

Complex-valued shift-invariant canonical polyadic decomposition (CPD) under a spatial phase sparsity constraint (pcsCPD) shows excellent separation performance when applied to band-pass filtered complex-valued multi-subject fMRI data. However, some useful information may also be eliminated when using a band-pass filter to suppress unwanted noise. As such, we propose an alternating rank- R and rank-1 least squares optimization to relax the CPD model. Based upon this optimization method, we present a novel constrained CPD algorithm with temporal shift-invariance and spatial sparsity and orthonormality constraints. More specifically, four steps are conducted until convergence for each iteration of the proposed algorithm: 1) use rank- R least-squares fit under spatial phase sparsity constraint to update shared spatial maps after phase de-ambiguity; 2) use orthonormality constraint to minimize the cross-talk between shared spatial maps; 3) update the aggregating mixing matrix using rank- R least-squares fit; 4) utilize shift-invariant rank-1 least-squares on a series of rank-1 matrices reconstructed by each column of the aggregating mixing matrix to update shared time courses, and subject-specific time delays and intensities. The experimental results of simulated and actual complex-valued fMRI data show that the proposed algorithm improves the estimates for task-related sensorimotor and auditory networks, compared to pcsCPD and tensorial spatial ICA. The proposed alternating rank- R and rank-1 least squares optimization is also flexible to improve CPD-related algorithm using alternating least squares.

Extracting electrophysiological correlates of functional magnetic resonance imaging data using the canonical polyadic decomposition

The relation between electrophysiology and BOLD-fMRI requires further elucidation. One approach for studying this relation is to find time-frequency features from electrophysiology that explain the variance of BOLD time-series. Convolution of these features with a canonical hemodynamic response function (HRF) is often required to model neurovascular coupling mechanisms and thus account for time shifts between electrophysiological and BOLD-fMRI data. We propose a framework for extracting the spatial distribution of these time-frequency features while also estimating more flexible, region-specific HRFs. The core component of this method is the decomposition of a tensor containing impulse response functions using the Canonical Polyadic Decomposition. The outputs of this decomposition provide insight into the relation between electrophysiology and BOLD-fMRI and can be used to construct estimates of BOLD time-series. We demonstrated the performance of this method on simulated data while also examining the effects of simulated measurement noise and physiological confounds. Afterwards, we validated our method on publicly available task-based and resting-state EEG-fMRI data. We adjusted our method to accommodate the multisubject nature of these datasets, enabling the investigation of inter-subject variability with regards to EEG-to-BOLD neurovascular coupling mechanisms. We thus also demonstrate how EEG features for modelling the BOLD signal differ across subjects.

Modulation of cortical resting state functional connectivity during a visuospatial attention task in Parkinson's disease

Visual dysfunction is a recognized early symptom of Parkinson's disease (PD) that partly scales motor symptoms, yet its background is heterogeneous. With additional deficits in visuospatial attention, the two systems are hard to disentangle and it is not known whether impaired functional connectivity in the visual cortex is translative in nature or disrupted attentional modulation also contributes. In this study, we investigate functional connectivity modulation during a visuospatial attention task in patients with PD. In total, 15 PD and 16 age-matched healthy controls performed a visuospatial attention task while undergoing fMRI, in addition to a resting-state fMRI scan. Tensorial independent component analysis was used to investigate task-related network activity patterns. Independently, an atlas-based connectivity modulation analysis was performed using the task potency method. Spearman's rank correlation was calculated between task-related network expression, connectivity modulation, and clinical characteristics. Task-related networks including mostly visual, parietal, and prefrontal cortices were expressed to a significantly lesser degree in patients with PD (p < 0.027). Resting-state functional connectivity did not differ between the healthy and diseased cohorts. Connectivity between the precuneus and ventromedial prefrontal cortex was modulated to a higher degree in patients with PD (p < 0.004), while connections between the posterior parietal cortex and primary visual cortex, and also the superior frontal gyrus and opercular cortex were modulated to a lesser degree (p < 0.001 and p < 0.011). Task-related network expression and superior frontal gyrus–opercular cortex connectivity modulation were significantly associated with UPDRSIII motor scores and the Hoehn–Yahr stages (R = −0.72, p < 0.006 and R = −0.90, p < 0.001; R = −0.68, p < 0.01 and R = −0.71, p < 0.007). Task-related networks function differently in patients with PD in association with motor symptoms, whereas impaired modulation of visual and default-mode network connectivity was not correlated with motor function.

Discovering hidden brain network responses to naturalistic stimuli via tensor component analysis of multi-subject fMRI data

The study of brain network interactions during naturalistic stimuli facilitates a deeper understanding of human brain function. To estimate large-scale brain networks evoked with naturalistic stimuli, a tensor component analysis (TCA) based framework was used to characterize shared spatio-temporal patterns across subjects in a purely data-driven manner. In this framework, a third-order tensor is constructed from the timeseries extracted from all brain regions from a given parcellation, for all participants, with modes of the tensor corresponding to spatial distribution, time series and participants. TCA then reveals spatially and temporally shared components, i.e., evoked networks with the naturalistic stimuli, their time courses of activity and subject loadings of each component. To enhance the reproducibility of the estimation with the adaptive TCA algorithm, a novel spectral clustering method, tensor spectral clustering, was proposed and applied to evaluate the stability of the TCA algorithm. We demonstrated the effectiveness of the proposed framework via simulations and real fMRI data collected during a motor task with a traditional fMRI study design. We also applied the proposed framework to fMRI data collected during passive movie watching to illustrate how reproducible brain networks are evoked by naturalistic movie viewing.

Functional alterations in large-scale resting-state networks of amyotrophic lateral sclerosis: A multi-site study across Canada and the United States

Amyotrophic lateral sclerosis (ALS) is a multisystem neurodegenerative disorder characterized by progressive degeneration of upper motor neurons and lower motor neurons, and frontotemporal regions resulting in impaired bulbar, limb, and cognitive function. Magnetic resonance imaging studies have reported cortical and subcortical brain involvement in the pathophysiology of ALS. The present study investigates the functional integrity of resting-state networks (RSNs) and their importance in ALS. Intra- and inter-network resting-state functional connectivity (Rs-FC) was examined using an independent component analysis approach in a large multi-center cohort. A total of 235 subjects (120 ALS patients; 115 healthy controls (HC) were recruited across North America through the Canadian ALS Neuroimaging Consortium (CALSNIC). Intra-network and inter-network Rs-FC was evaluated by the FSL-MELODIC and FSLNets software packages. As compared to HC, ALS patients displayed higher intra-network Rs-FC in the sensorimotor, default mode, right and left fronto-parietal, and orbitofrontal RSNs, and in previously undescribed networks including auditory, dorsal attention, basal ganglia, medial temporal, ventral streams, and cerebellum which negatively correlated with disease severity. Furthermore, ALS patients displayed higher inter-network Rs-FC between the orbitofrontal and basal ganglia RSNs which negatively correlated with cognitive impairment. In summary, in ALS there is an increase in intra- and inter-network functional connectivity of RSNs underpinning both motor and cognitive impairment. Moreover, the large multi-center CALSNIC dataset permitted the exploration of RSNs in unprecedented detail, revealing previously undescribed network involvement in ALS.

Multisubject Task-Related fMRI Data Processing via a Two-Stage Generalized Canonical Correlation Analysis

Functional magnetic resonance imaging (fMRI) is one of the most popular methods for studying the human brain. Task-related fMRI data processing aims to determine which brain areas are activated when a specific task is performed and is usually based on the Blood Oxygen Level Dependent (BOLD) signal. The background BOLD signal also reflects systematic fluctuations in regional brain activity which are attributed to the existence of resting-state brain networks. We propose a new fMRI data generating model which takes into consideration the existence of common task-related and resting-state components. We first estimate the common task-related temporal component, via two successive stages of generalized canonical correlation analysis and, then, we estimate the common task-related spatial component, leading to a task-related activation map. The experimental tests of our method with synthetic data reveal that we are able to obtain very accurate temporal and spatial estimates even at very low Signal to Noise Ratio (SNR), which is usually the case in fMRI data processing. The tests with real-world fMRI data show significant advantages over standard procedures based on General Linear Models (GLMs).

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.

Default mode network connectivity and treatment response in geriatric depression

OBJECTIVES

Default mode network (DMN) connectivity is altered in depression. We evaluated the relationship between changes in within-network DMN connectivity and improvement in depression in a subsample of our parent clinical trial comparing escitalopram/memantine (ESC/MEM) to escitalopram/placebo (ESC/PBO) in older depressed adults (NCT01902004).

METHODS

Twenty-six participants with major depression (age > 60 years) and subjective memory complaints underwent treatment with ESC/MEM (n = 13) or ESC/PBO (n = 13), and completed baseline and 3-month follow-up resting state magnetic resonance imaging scans. Multi-block partial least squares correlation analysis was used to evaluate the impact of treatment on within-network DMN connectivity changes and their relationship with symptom improvement at 3 months (controlling for age and sex).

RESULTS

A significant latent variable was identified, reflecting within-network DMN connectivity changes correlated with symptom improvement (p = .01). Specifically, although overall group differences in within-network DMN connectivity changes failed to reach significance, increased within-network connectivity of posterior/lateral DMN regions (precuneus, angular gyrus, superior/middle temporal cortex) was more strongly and positively correlated with symptom improvement in the ESC/MEM group (r = 0.97, 95% confidence interval: 0.86-0.98) than in the ESC/PBO group (r = 0.36, 95% confidence interval: 0.13-0.72).

CONCLUSIONS

Increased within-network connectivity of core DMN nodes was more strongly correlated with depressive symptom improvement with ESC/MEM than with ESC/PBO, supporting an improved engagement of brain circuitry implicated in the amelioration of depressive symptoms with combined ESC/MEM treatment in older adults with depression and subjective memory complaints.

Functional Connectivity Methods and Their Applications in fMRI Data

The availability of powerful non-invasive neuroimaging techniques has given rise to various studies that aim to map the human brain. These studies focus on not only finding brain activation signatures but also on understanding the overall organization of functional communication in the brain network. Based on the principle that distinct brain regions are functionally connected and continuously share information with each other, various approaches to finding these functional networks have been proposed in the literature. In this paper, we present an overview of the most common methods to estimate and characterize functional connectivity in fMRI data. We illustrate these methodologies with resting-state functional MRI data from the Human Connectome Project, providing details of their implementation and insights on the interpretations of the results. We aim to guide researchers that are new to the field of neuroimaging by providing the necessary tools to estimate and characterize brain circuitry.

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

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

Increased resting state connectivity in the anterior default mode network of idiopathic epileptic dogs

Epilepsy is one of the most common chronic, neurological diseases in humans and dogs and considered to be a network disease. In human epilepsy altered functional connectivity in different large-scale networks have been identified with functional resting state magnetic resonance imaging. Since large-scale resting state networks have been consistently identified in anesthetised dogs’ application of this technique became promising in canine epilepsy research. The aim of the present study was to investigate differences in large-scale resting state networks in epileptic dogs compared to healthy controls. Our hypothesis was, that large-scale networks differ between epileptic dogs and healthy control dogs. A group of 17 dogs (Border Collies and Greater Swiss Mountain Dogs) with idiopathic epilepsy was compared to 20 healthy control dogs under a standardized sevoflurane anaesthesia protocol. Group level independent component analysis with dimensionality of 20 components, dual regression and two-sample t test were performed and revealed significantly increased functional connectivity in the anterior default mode network of idiopathic epileptic dogs compared to healthy control dogs (p = 0.00060). This group level differences between epileptic dogs and healthy control dogs identified using a rather simple data driven approach could serve as a starting point for more advanced resting state network analysis in epileptic dogs.

Progressive modulation of resting-state brain activity during neurofeedback of positive-social emotion regulation networks

Neurofeedback allows for the self-regulation of brain circuits implicated in specific maladaptive behaviors, leading to persistent changes in brain activity and connectivity. Positive-social emotion regulation neurofeedback enhances emotion regulation capabilities, which is critical for reducing the severity of various psychiatric disorders. Training dorsomedial prefrontal cortex (dmPFC) to exert a top-down influence on bilateral amygdala during positive-social emotion regulation progressively (linearly) modulates connectivity within the trained network and induces positive mood. However, the processes during rest that interleave the neurofeedback training remain poorly understood. We hypothesized that short resting periods at the end of training sessions of positive-social emotion regulation neurofeedback would show alterations within emotion regulation and neurofeedback learning networks. We used complementary model-based and data-driven approaches to assess how resting-state connectivity relates to neurofeedback changes at the end of training sessions. In the experimental group, we found lower progressive dmPFC self-inhibition and an increase of connectivity in networks engaged in emotion regulation, neurofeedback learning, visuospatial processing, and memory. Our findings highlight a large-scale synergy between neurofeedback and resting-state brain activity and connectivity changes within the target network and beyond. This work contributes to our understanding of concomitant learning mechanisms post training and facilitates development of efficient neurofeedback training.

Stationary EEG pattern relates to large-scale resting state networks - An EEG-fMRI study connecting brain networks across time-scales

Relating brain dynamics acting on time scales that differ by at least an order of magnitude is a fundamental issue in brain research. The same is true for the observation of stable dynamical structures in otherwise highly non-stationary signals. The present study addresses both problems by the analysis of simultaneous resting state EEG-fMRI recordings of 53 patients with epilepsy. Confirming previous findings, we observe a generic and temporally stable average correlation pattern in EEG recordings. We design a predictor for the General Linear Model describing fluctuations around the stationary EEG correlation pattern and detect resting state networks in fMRI data. The acquired statistical maps are contrasted to several surrogate tests and compared with maps derived by spatial Independent Component Analysis of the fMRI data. By means of the proposed EEG-predictor we observe core nodes of known fMRI resting state networks with high specificity in the default mode, the executive control and the salience network. Our results suggest that both, the stationary EEG pattern as well as resting state fMRI networks are different expressions of the same brain activity. This activity is interpreted as the dynamics on (or close to) a stable attractor in phase space that is necessary to maintain the brain in an efficient operational mode. We discuss that this interpretation is congruent with the theoretical framework of complex systems as well as with the brain's energy balance.

Early soft and flexible fusion of electroencephalography and functional magnetic resonance imaging via double coupled matrix tensor factorization for multisubject group analysis

Data fusion refers to the joint analysis of multiple datasets that provide different (e.g., complementary) views of the same task. In general, it can extract more information than separate analyses can. Jointly analyzing electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) measurements has been proved to be highly beneficial to the study of the brain function, mainly because these neuroimaging modalities have complementary spatiotemporal resolution: EEG offers good temporal resolution while fMRI is better in its spatial resolution. The EEG–fMRI fusion methods that have been reported so far ignore the underlying multiway nature of the data in at least one of the modalities and/or rely on very strong assumptions concerning the relation of the respective datasets. For example, in multisubject analysis, it is commonly assumed that the hemodynamic response function is a priori known for all subjects and/or the coupling across corresponding modes is assumed to be exact (hard). In this article, these two limitations are overcome by adopting tensor models for both modalities and by following soft and flexible coupling approaches to implement the multimodal fusion. The obtained results are compared against those of parallel independent component analysis and hard coupling alternatives, with both synthetic and real data (epilepsy and visual oddball paradigm). Our results demonstrate the clear advantage of using soft and flexible coupled tensor decompositions in scenarios that do not conform with the hard coupling assumption.

Functional network dynamics and decreased conscientiousness in multiple sclerosis

BACKGROUND

Conscientiousness is a personality trait that declines in people with multiple sclerosis (PwMS) and its decline predicts worse clinical outcomes. This study aims to investigate the neural underpinnings of lower Conscientiousness in PwMS by examining MRI anomalies in functional network dynamics.

METHODS

70 PwMS and 50 healthy controls underwent personality assessment and resting-state MRI. Associations with dynamic functional network properties (i.e., eigenvector centrality) were evaluated, using a dynamic sliding-window approach.

RESULTS

In PwMS, lower Conscientiousness was associated with increased variability of centrality in the left insula (t_max = 4.21) and right inferior parietal lobule (t_max = 3.79); a relationship also observed in regressions accounting for handedness, disease duration, disability, and tract disruption in relevant structural networks (ΔR² = 0.071, p = 0.003; ΔR² = 0.094, p = 0.004). Centrality dynamics of the observed regions were not associated with Neuroticism (R² < 0.001, p = 0.956; R² < 0.001, p = 0.945). As well, higher Conscientiousness was associated with greater variability in connectivity for the left insula with the default-mode network (F = 3.92, p = 0.023) and limbic network (F = 5.66, p = 0.005).

CONCLUSION

Lower Conscientiousness in PwMS was associated with increased variability in network centrality, most prominently for the left insula and right inferior parietal cortex. This effect, specific to Conscientiousness and significant after accounting for disability and structural network damage, could indicate that overall stable network centrality is lost in patients with low Conscientiousness, especially for the insula and right parietal cortex. The positive relationship between Conscientiousness and variability of connectivity between left insula and default-mode network potentially affirms that dynamics between the salience and default-mode networks is related to the regulation of behavior.

Differential effects of long-term aerobic versus cognitively-engaging physical activity on children's visuospatial working memory related brain activation: A cluster RCT

Different types of physical activity are thought to differentially affect children's brain activation, via physiological mechanisms, or by activating similar brain areas during physical and cognitive tasks. Despite many behavioral studies relying on these mechanisms, they have been rarely studied. This study looks at both mechanisms simultaneously, by examining effects of two physical activity interventions (aerobic vs. cognitively-engaging) on children's brain activation. Functional Magnetic Resonance Imaging (fMRI) data of 62 children (48.4% boys, mean age 9.2 years) was analyzed. Children's visuospatial working memory related brain activity patterns were tested using a Spatial Span Task before and after the 14-week interventions consisting of four physical education lessons per week. The control group followed their regular program of two lessons per week. Analyses of activation patterns in SPM 12.0 revealed no activation changes between pretest and posttest (p > .05), and no differences between the three conditions in pretest-posttest changes in brain activation (p > .05). Large inter-individual differences were found, suggesting that not every child benefited from the interventions in the same way. To get more insight into the assumed mechanisms, further research is needed to understand whether, when, for whom, and how physical activity results in changed brain activation patterns.