A review of group ICA for fMRI data and ICA for joint inference of imaging, genetic, and ERP data

A hybrid high-resolution anatomical MRI atlas with sub-parcellation of cortical gyri using resting fMRI

We present a new high-quality, single-subject atlas with sub-millimeter voxel resolution, high SNR, and excellent gray-white tissue contrast to resolve fine anatomical details. The atlas is labeled into two parcellation schemes: 1) the anatomical BCI-DNI atlas, which is manually labeled based on known morphological and anatomical features, and 2) the hybrid USCBrain atlas, which incorporates functional information to guide the sub-parcellation of cerebral cortex. In both cases, we provide consistent volumetric and cortical surface-based parcellation and labeling. The intended use of the atlas is as a reference template for structural coregistration and labeling of individual brains. A single-subject T1-weighted image was acquired five times at a resolution of 0.547 mm × 0.547 mm × 0.800 mm and averaged. Images were processed by an expert neuroanatomist using semi-automated methods in BrainSuite to extract the brain, classify tissue-types, and render anatomical surfaces. Sixty-six cortical and 29 noncortical regions were manually labeled to generate the BCI-DNI atlas. The cortical regions were further sub-parcellated into 130 cortical regions based on multi-subject connectivity analysis using resting fMRI (rfMRI) data from the Human Connectome Project (HCP) database to produce the USCBrain atlas. In addition, we provide a delineation between sulcal valleys and gyral crowns, which offer an additional set of 26 sulcal subregions per hemisphere. Lastly, a probabilistic map is provided to give users a quantitative measure of reliability for each gyral subdivision. Utility of the atlas was assessed by computing Adjusted Rand Indices (ARIs) between individual sub-parcellations obtained through structural-only coregistration to the USCBrain atlas and sub-parcellations obtained directly from each subject's resting fMRI data. Both atlas parcellations can be used with the BrainSuite, FreeSurfer, and FSL software packages.

Regularized Functional Connectivity in Schizophrenia

Regularization may be used as an alternative to dimensionality reduction when the number of variables in a model is much larger than the number of available observations. In a recent study from our group regularized regression was employed to quantify brain functional connectivity in a sample of healthy controls using a brain parcellation and resting state fMRI images. Here regularization is applied to evaluate resting state connectivity abnormalities at the voxel level in a sample of patients with schizophrenia. Specifically, ridge regression is implemented with different degrees of regularization. Results are compared to those delivered by the weighted global brain connectivity method (GBC), which is based on averaged bivariate correlations and from the non-redundant connectivity method (NRC), a dimensionality reduction approach that applies supervised principal component regressions. Ridge regression is able to detect a larger set of abnormally connected regions than both GBC and NRC methods, including schizophrenia related connectivity reductions in fronto-medial, somatosensory and occipital structures. Due to its multivariate nature, the proposed method is much more sensitive to group abnormalities than the GBC, but it also outperforms the NRC, which is multivariate too. Voxel based regularized regression is a simple and sensitive alternative for quantifying brain functional connectivity.

Combination of Group Singular Value Decomposition and eLORETA Identifies Human EEG Networks and Responses to Transcranial Photobiomodulation

Transcranial Photobiomodulation (tPBM) has demonstrated its ability to alter electrophysiological activity in the human brain. However, it is unclear how tPBM modulates brain electroencephalogram (EEG) networks and is related to human cognition. In this study, we recorded 64-channel EEG from 44 healthy humans before, during, and after 8-min, right-forehead, 1,064-nm tPBM or sham stimulation with an irradiance of 257 mW/cm². In data processing, a novel methodology by combining group singular value decomposition (gSVD) with the exact low-resolution brain electromagnetic tomography (eLORETA) was implemented and performed on the 64-channel noise-free EEG time series. The gSVD+eLORETA algorithm produced 11 gSVD-derived principal components (PCs) projected in the 2D sensor and 3D source domain/space. These 11 PCs took more than 70% weight of the entire EEG signals and were justified as 11 EEG brain networks. Finally, baseline-normalized power changes of each EEG brain network in each EEG frequency band (delta, theta, alpha, beta and gamma) were quantified during the first 4-min, second 4-min, and post tPBM/sham periods, followed by comparisons of frequency-specific power changes between tPBM and sham conditions. Our results showed that tPBM-induced increases in alpha powers occurred at default mode network, executive control network, frontal parietal network and lateral visual network. Moreover, the ability to decompose EEG signals into individual, independent brain networks facilitated to better visualize significant decreases in gamma power by tPBM. Many similarities were found between the cortical locations of SVD-revealed EEG networks and fMRI-identified resting-state networks. This consistency may shed light on mechanistic associations between tPBM-modulated brain networks and improved cognition outcomes.

Dynamics of hidden brain states when people solve verbal puzzles

When people try to solve a problem, they go through distinct steps (encoding, ideation, evaluation, etc.) recurrently and spontaneously. To disentangle different cognitive processes that unfold throughout a trial, we applied an unsupervised machine learning method to electroencephalogram (EEG) data continuously recorded while 39 participants attempted 153 Compound Remote Associates problems (CRA). CRA problems are verbal puzzles that can be solved in either insight-leaning or analysis-leaning manner. We fitted a Hidden Markov Model to the time-frequency transformed EEG signals and decoded each trial as a time-resolved state sequence. The model characterizes hidden brain states with spectrally resolved power topography. Seven states were identified with distinct activation patterns in the theta (4-7 Hz), alpha (8-9 Hz and 10-13 Hz), and gamma (25-50 Hz) bands. Notably, a state featuring widespread activation only in alpha-band frequency emerged, from this data-driven approach, which exhibited dynamic characteristics associated with specific temporal stages and outcomes (whether solved with insight or analysis) of the trials. The state dynamics derived from the model overlap and extend previous literature on the cognitive function of alpha oscillation: the "alpha-state" probability peaks before stimulus onset and decreases before response. In trials solved with insight, relative to solved with analysis, the alpha-state is more likely to be visited and maintained during preparation and solving periods, and its probability declines more sharply immediately preceding a response. This novel paradigm provides a way to extract dynamic features that characterize problem-solving stages and potentially provide a novel window into the nature of the underlying cognitive processes.

Morphological Component Analysis of functional MRI Brain Networks

OBJECTIVE

Sparse representations have been utilized to identify functional connectivity (FC) of networks, while ICA employs the assumption of independence among the network sources to demonstrate FC. Here, we investigate a sparse decomposition method based on Morphological Component Analysis and K-SVD dictionary learning-MCA-KSVD-and contrast the effect of the sparsity constraint vs. the independency constraint on FC and denoising.

METHODS

Using a K-SVD algorithm, fMRI signals are decomposed into morphological components which have sparse spatial overlap. We present simulations when the independency assumption of ICA fails and MCA-KSVD recovers more accurate spatial-temporal structures. Denoising performance of both methods is investigated at various noise levels. A comprehensive experimental study was conducted on resting-state and task fMRI.

RESULTS

Validations show that ICA is advantageous when network components are well-separated and sparse. In such cases, the MCA-KSVD method has modest value over ICA in terms of network delineation but is significantly more effective in reducing spatial and temporal noise. Results demonstrate that the sparsity constraint yields sparser networks with higher spatial resolution while suppressing weak signals. Temporally, this localization effect yields higher contrast-to-noise ratios (CNRs) of time series.

CONCLUSION

While marginally improving the spatial decomposition, MCA-KSVD denoises fMRI data much more effectively than ICA, preserving network structures and improving CNR, especially for weak networks.

SIGNIFICANCE

A sparsity-based decomposition approach may be useful for investigating functional connectivity in noisy cases. It may serve as an efficient decomposition method for reduced acquisition time and may prove useful for detecting weak network activations.

Simultaneous EEG-fMRI: What Have We Learned and What Does the Future Hold?

Simultaneous EEG-fMRI has developed into a mature measurement technique in the past 25 years. During this time considerable technical and analytical advances have been made, enabling valuable scientific contributions to a range of research fields. This review will begin with an introduction to the measurement principles involved in EEG and fMRI and the advantages of combining these methods. The challenges faced when combining the two techniques will then be considered. An overview of the leading application fields where EEG-fMRI has made a significant contribution to the scientific literature and emerging applications in EEG-fMRI research trends is then presented.

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.

Intranasal Oxytocin Modulates the Salience Network in Aging

Growing evidence supports a role of the neuropeptide oxytocin in promoting social cognition and prosocial behavior, possibly via modulation of the salience of social information. The effect of intranasal oxytocin administration on the salience network, however, is not well understood, including in the aging brain. To address this research gap, 42 young (22.52 ± 3.02 years; 24 in the oxytocin group) and 43 older (71.12 ± 5.25 years; 21 in the oxytocin group) participants were randomized to either self-administer intranasal oxytocin or placebo prior to resting-state functional imaging. The salience network was identified using independent component analysis (ICA). Independent t-tests showed that individuals in the oxytocin compared to the placebo group had lower within-network resting-state functional connectivity, both for left amygdala (MNI coordinates: x = −18, y = 0, z = −15; corrected p < 0.05) within a more ventral salience network and for right insula (MNI coordinates: x = 39, y = 6, z = −6; corrected p < 0.05) within a more dorsal salience network. Age moderation analysis furthermore demonstrated that the oxytocin-reduced functional connectivity between the ventral salience network and the left amygdala was only present in older participants. These findings suggest a modulatory role of exogenous oxytocin on resting-state functional connectivity within the salience network and support age-differential effects of acute intranasal oxytocin administration on this network.

Integrated Positron Emission Tomography/Magnetic Resonance Imaging for Resting-State Functional and Metabolic Imaging in Human Brain: What Is Correlated and What Is Impacted

Integrated positron emission tomography (PET)/magnetic resonance imaging (MRI) could simultaneously obtain both functional MRI (fMRI) and ¹⁸F-fluorodeoxyglucose (FDG) PET and thus provide multiparametric information for the analysis of brain metabolism. In this study, we aimed to, for the first time, investigate the interplay of simultaneous fMRI and FDG PET scan using a randomized self-control protocol. In total, 24 healthy volunteers underwent PET/MRI scan for 30–40 min after the injection of FDG. A 22-min brain scan was separated into MRI-off mode (without fMRI pulsing) and MRI-on mode (with fMRI pulsing), with each one lasting for 11 min. We calculated the voxel-wise fMRI metrics (regional homogeneity, amplitude of low-frequency fluctuations, fractional amplitude of low-frequency fluctuations, and degree centrality), resting networks, relative standardized uptake value ratios (SUVr), SUVr slope, and regional cerebral metabolic rate of glucose (rCMRGlu) maps. Paired two-sample t-tests were applied to assess the statistical differences between SUVr, SUVr slope, correlation coefficients of fMRI metrics, and rCMRGlu between MRI-off and MRI-on modes, respectively. The voxel-wise whole-brain SUVr revealed no statistical difference (P > 0.05), while the SUVr slope was significantly elevated in sensorimotor, dorsal attention, ventral attention, control, default, and auditory networks (P < 0.05) during fMRI scan. The task-based group independent-component analysis revealed that the most active network components derived from the combined MRI-off and MRI-on static PET images were frontal pole, superior frontal gyrus, middle temporal gyrus, and occipital pole. High correlation coefficients were found among fMRI metrics with rCMRGlu in both MRI-off and MRI-on mode (P < 0.05). Our results systematically evaluated the impact of simultaneous fMRI scan on the quantification of human brain metabolism from an integrated PET/MRI system.

Structural Features Related to Affective Instability Correctly Classify Patients With Borderline Personality Disorder. A Supervised Machine Learning Approach

Previous morphometric studies of Borderline Personality Disorder (BPD) reported inconsistent alterations in cortical and subcortical areas. However, these studies have investigated the brain at the voxel level using mass univariate methods or region of interest approaches, which are subject to several artifacts and do not enable detection of more complex patterns of structural alterations that may separate BPD from other clinical populations and healthy controls (HC). Multiple Kernel Learning (MKL) is a whole-brain multivariate supervised machine learning method able to classify individuals and predict an objective diagnosis based on structural features. As such, this method can help identifying objective biomarkers related to BPD pathophysiology and predict new cases. To this aim, we applied MKL to structural images of patients with BPD and matched HCs. Moreover, to ensure that results are specific for BPD and not for general psychological disorders, we also applied MKL to BPD against a group of patients with bipolar disorder, for their similarities in affective instability. Results showed that a circuit, including basal ganglia, amygdala, and portions of the temporal lobes and of the orbitofrontal cortex, correctly classified BPD against HC (80%). Notably, this circuit positively correlates with the affective sector of the Zanarini questionnaire, thus indicating an involvement of this circuit with affective disturbances. Moreover, by contrasting BPD with BD, the spurious regions were excluded, and a specific circuit for BPD was outlined. These results support that BPD is characterized by anomalies in a cortico-subcortical circuit related to affective instability and that this circuit discriminates BPD from controls and from other clinical populations.

Moral wounds run deep: exaggerated midbrain functional network connectivity across the default mode network in posttraumatic stress disorder

BACKGROUND

A moral injury occurs when a deeply held moral code has been violated, and it can lead to the development of symptoms of posttraumatic stress disorder (PTSD). However, the neural correlates that differentiate moral injury and PTSD remain largely unknown. Intrinsic connectivity networks such as the default mode network (DMN) appear to be altered in people with PTSD who have experienced moral injury. However, brainstem, midbrain and cerebellar systems are rarely integrated into the intrinsic connectivity networks; this is a critical oversight, because these systems display marked differences in people with PTSD and are thought to underlie strong moral emotions such as shame, guilt and betrayal.

METHODS

We conducted an independent component analysis on data generated during script-driven memory recall of moral injury in participants with military- or law enforcement-related PTSD (n = 28), participants with civilian-related PTSD (n = 28) and healthy controls exposed to a potentially morally injurious event (n = 18). We conducted group-wise comparisons of functional network connectivity differences across a DMN-correlated independent component, with a particular focus on brainstem, midbrain and cerebellar systems.

RESULTS

We found stronger functional network connectivity in the midbrain periaqueductal grey (t ₇₁ = 4.95, p _FDR = 0.028, k = 39) and cerebellar lobule IX (t ₇₁ = 4.44, p _FDR = 0.046, k = 49) in participants with civilian-related PTSD as compared to healthy controls. We also found a trend toward stronger functional network connectivity in the midbrain periaqueductal grey (t ₇₁ = 4.22, p _FDR = 0.076, k = 60) in participants with military- or law enforcement-related PTSD as compared to healthy controls.

LIMITATIONS

The significant clusters were large, but resolution is generally lower for subcortical structures.

CONCLUSION

In PTSD, the DMN appears to be biased toward lower-level, midbrain systems, which may drive toxic shame and related moral emotions that are common in PTSD, highlighting the depth at which moral injuries are represented neurobiologically.

Functional brain connectomes reflect acute and chronic cannabis use

Resting state fMRI has been employed to identify alterations in functional connectivity within or between brain regions following acute and chronic exposure to Δ9-tetrahydrocannabinol (THC), the psychoactive component in cannabis. Most studies focused a priori on a limited number of local brain areas or circuits, without considering the impact of cannabis on whole-brain network organization. The present study attempted to identify changes in the whole-brain human functional connectome as assessed with ultra-high field (7T) resting state scans of cannabis users (N = 26) during placebo and following vaporization of cannabis. Two distinct data-driven methodologies, i.e. network-based statistics (NBS) and connICA, were used to identify changes in functional connectomes associated with acute cannabis intoxication and history of cannabis use. Both methodologies revealed a broad state of hyperconnectivity within the entire range of major brain networks in chronic cannabis users compared to occasional cannabis users, which might be reflective of an adaptive network reorganization following prolonged cannabis exposure. The connICA methodology also extracted a distinct spatial connectivity pattern of hypoconnectivity involving the dorsal attention, limbic, subcortical and cerebellum networks and of hyperconnectivity between the default mode and ventral attention network, that was associated with the feeling of subjective high during THC intoxication. Whole-brain network approaches identified spatial patterns in functional brain connectomes that distinguished acute from chronic cannabis use, and offer an important utility for probing the interplay between short and long-term alterations in functional brain dynamics when progressing from occasional to chronic use of cannabis.

A methodological scoping review of the integration of fMRI to guide dMRI tractography. What has been done and what can be improved: A 20-year perspective

Combining MRI modalities is a growing trend in neurosciences. It provides opportunities to investigate the brain architecture supporting cognitive functions. Integrating fMRI activation to guide dMRI tractography offers potential advantages over standard tractography methods. A quick glimpse of the literature on this topic reveals that this technique is challenging, and no consensus or "best practices" currently exist, at least not within a single document. We present the first attempt to systematically analyze and summarize the literature of 80 studies that integrated task-based fMRI results to guide tractography, over the last two decades. We report 19 findings that cover challenges related to sample size, microstructure modelling, seeding methods, multimodal space registration, false negatives/positives, specificity/validity, gray/white matter interface and more. These findings will help the scientific community (1) understand the strengths and limitations of the approaches, (2) design studies using this integrative framework, and (3) motivate researchers to fill the gaps identified. We provide references toward best practices, in order to improve the overall result's replicability, sensitivity, specificity, and validity.

Joint structural-functional magnetic resonance imaging features are associated with diagnosis and real-world functioning in patients with schizophrenia

OBJECTIVE

Earlier evidence suggested that structural-functional covariation in schizophrenia patients (SCZ) is associated with cognition, a predictor of functioning. Moreover, studies suggested that functional brain abnormalities of schizophrenia may be related with structural network features. However, only few studies have investigated the relationship between structural-functional covariation and both diagnosis and functioning in SCZ. We hypothesized that structural-functional covariation networks associated with diagnosis are related to real-world functioning in SCZ.

METHODS

We performed joint Independent Component Analysis on T1 images and resting-state fMRI-based Degree Centrality (DC) maps from 89 SCZ and 285 controls. Structural-functional covariation networks in which we found a main effect of diagnosis underwent correlation analysis to investigate their relationship with functioning. Covariation networks showing a significant association with both diagnosis and functioning underwent univariate analysis to better characterize group-level differences at the spatial level.

RESULTS

A structural-functional covariation network characterized by frontal, temporal, parietal and thalamic structural estimates significantly covaried with temporo-parietal resting-state DC. Compared with controls, SCZ had reduced structural-functional covariation within this network (p_FDR = 0.005). The same measure correlated positively with both social and occupational functioning (both p_FDR = 0.042). Univariate analyses revealed grey matter deviations in SCZ compared with controls within this structural-functional network in hippocampus, cerebellum, thalamus, orbito-frontal cortex, and insula. No group differences were found in DC.

CONCLUSIONS

Findings support the existence of a phenotypical association between group-level differences and inter-individual heterogeneity of functional deficits in SCZ. Given that only the joint structural/functional analysis revealed this association, structural-functional covariation may be a potentially relevant schizophrenia phenotype.

Towards data-driven group inferences of resting-state fMRI data in rodents: Comparison of group ICA, GIG-ICA, and IVA-GL

BACKGROUND

A trend in the development of resting-state fMRI (rsfMRI) data analysis is the drive towards more data-driven methods. Group Independent Component Analysis (GICA) is a well-proven data-driven method for performing fMRI group analysis, though not without issues, especially the back-reconstruction from group-level independent components to individual-level components. Group information-guided ICA (GIG-ICA) and Independent Vector Analysis (IVA) are recent extensions of GICA that were shown to outperform GICA in the identification of unique rsfMRI biomarkers in psychiatric conditions.

NEW METHOD

In this work, GICA, GIG-ICA, and IVA-GL analysis methods were applied to rsfMRI data acquired from 9 mice under different doses of medetomidine (0.1 - 0.3 mg/kg/h) in the before and after forepaw stimulation, and their performance was compared to determine whether GIG-ICA and IVA-GL outperform GICA in identifying robust and reliable resting-state networks in the rodent brain.

RESULTS

Our results showed IVA-GL method had certain desirable performance characteristics over the other two methods under minimal data pre-processing and data-driven assumptions in application to analysis of mouse resting-state functional MRI.

COMPARISON WITH EXISTING METHODS

IVA-GL provides better stability towards detecting group differences at different model order assumptions and performed better at separating data well-defined and functionally reasonable components in mouse resting-state fMRI. At higher model order and more likely functional component assumptions, GIG-ICA and IVA-GL were found to have greater sensitivity at detecting functional connectivity changes due to physiological challenges compared to GICA.

CONCLUSIONS

This study indicates that IVA-GL yields better detection of resting-state networks in the rodent brain compared to other ICA methods and a promising data-driven analysis method for rodent rsfMRI.

Multivariate patterns of brain-behavior associations across the adult lifespan

The nature of brain-behavior covariations with increasing age is poorly understood. In the current study, we used a multivariate approach to investigate the covariation between behavioral-health variables and brain features across adulthood. We recruited healthy adults aged 20–73 years-old (29 younger, mean age = 25.6 years; 30 older, mean age = 62.5 years), and collected structural and functional MRI (s/fMRI) during a resting-state and three tasks. From the sMRI, we extracted cortical thickness and subcortical volumes; from the fMRI, we extracted activation peaks and functional network connectivity (FNC) for each task. We conducted canonical correlation analyses between behavioral-health variables and the sMRI, or the fMRI variables, across all participants. We found significant covariations for both types of neuroimaging phenotypes (ps = 0.0004) across all individuals, with cognitive capacity and age being the largest opposite contributors. We further identified different variables contributing to the models across phenotypes and age groups. Particularly, we found behavior was associated with different neuroimaging patterns between the younger and older groups. Higher cognitive capacity was supported by activation and FNC within the executive networks in the younger adults, while it was supported by the visual networks’ FNC in the older adults. This study highlights how the brain-behavior covariations vary across adulthood and provides further support that cognitive performance relies on regional recruitment that differs between older and younger individuals.

A functional magnetic resonance imaging study of frontal networks in obsessive-compulsive disorder during cognitive reappraisal

Background

Patients with obsessive-compulsive disorder (OCD) present difficulties in the cognitive regulation of emotions, possibly because of inefficient recruitment of distributed patterns of frontal cortex regions. The aim of the present study is to characterize the brain networks, and their dysfunctions, related to emotion regulation alterations observed during cognitive reappraisal in OCD.

Methods

Adult patients with OCD (n = 31) and healthy controls (HC; n = 30) were compared during performance of a functional magnetic resonance imaging cognitive reappraisal protocol. We used a free independent component analysis approach to analyze network-level alterations during emotional experience and regulation. Correlations with behavioral scores were also explored.

Results

Analyses were focused on six networks encompassing the frontal cortex. OCD patients showed decreased activation of the frontotemporal network in comparison with HC (F(1,58) = 7.81, p = 0.007) during cognitive reappraisal. A similar trend was observed in the left frontoparietal network.

Conclusions

The present study demonstrates that patients with OCD show decreased activation of specific networks implicating the frontal cortex during cognitive reappraisal. These outcomes should help to better characterize the psychological processes modulating fear, anxiety, and other core symptoms of patients with OCD, as well as the associated neurobiological alterations, from a system-level perspective.

Improving the Sensitivity of Task-Related Functional Magnetic Resonance Imaging Data Using Generalized Canonical Correlation Analysis

General Linear Modeling (GLM) is the most commonly used method for signal detection in Functional Magnetic Resonance Imaging (fMRI) experiments, despite its main limitation of not taking into consideration common spatial dependencies between voxels. Multivariate analysis methods, such as Generalized Canonical Correlation Analysis (gCCA), have been increasingly employed in fMRI data analysis, due to their ability to overcome this limitation. This study, evaluates the improvement of sensitivity of the GLM, by applying gCCA to fMRI data after standard preprocessing steps. Data from a block-design fMRI experiment was used, where 25 healthy volunteers completed two action observation tasks at 1.5T. Whole brain analysis results indicated that the application of gCCA resulted in significantly higher intensity of activation in several regions in both tasks and helped reveal activation in the primary somatosensory and ventral premotor area, theoretically known to become engaged during action observation. In subject-level ROI analyses, gCCA improved the signal to noise ratio in the averaged timeseries in each preselected ROI, and resulted in increased extent of activation, although peak intensity was considerably higher in just two of them. In conclusion, gCCA is a promising method for improving the sensitivity of conventional statistical modeling in task related fMRI experiments.

Altered resting-state functional connectivity of the dorsal anterior cingulate cortex with intrinsic brain networks in male problematic smartphone users

The excessive use of smartphones is associated with various medical complications and mental health problems. However, existing research findings on neurobiological mechanisms behind problematic smartphone use are limited. In this study, we investigated functional connectivity in problematic smartphone users, focusing on the default mode network (DMN) and attentional networks. We hypothesized that problematic smartphone users would have alterations in functional connectivity between the DMN and attentional networks and that such alterations would correlate with the severity of problematic smartphone use. This study included 30 problematic smartphone users and 35 non-problematic smartphone users. We carried out group independent component analysis (group ICA) to decompose resting-state functional magnetic resonance imaging (fMRI) data into distinct networks. We examined functional connectivity using seed-to-seed analysis and identified the nodes of networks in group ICA, which we used as region of interest. We identified greater functional connectivity of the dorsal anterior cingulate cortex (dACC) with the ventral attention network (VAN) and with the DMN in problematic smartphone users. In seed-to-seed analysis, problematic smartphone users showed atypical dACC-VAN functional connectivity which correlated with the smartphone addiction proneness scale total scores. Our resting-state fMRI study found greater functional connectivity between the dACC and attentional networks in problematic smartphone users. Our findings suggest that increased bottom-up and interoceptive attentional processing might play an important role in problematic smartphone use.

A Triple-Network Dynamic Connection Study in Alzheimer's Disease

Alzheimer's disease (AD) was associated with abnormal organization and function of large-scale brain networks. We applied group independent component analysis (Group ICA) to construct the triple-network consisting of the saliency network (SN), the central executive network (CEN), and the default mode network (DMN) in 25 AD, 60 mild cognitive impairment (MCI) and 60 cognitively normal (CN) subjects. To explore the dynamic functional network connectivity (dFNC), we investigated dynamic time-varying triple-network interactions in subjects using Group ICA analysis based on k-means clustering (GDA-k-means). The mean of brain state-specific network interaction indices (meanNII) in the three groups (AD, MCI, CN) showed significant differences by ANOVA analysis. To verify the robustness of the findings, a support vector machine (SVM) was taken meanNII, gender and age as features to classify. This method obtained accuracy values of 95, 94, and 77% when classifying AD vs. CN, AD vs. MCI, and MCI vs. CN, respectively. In our work, the findings demonstrated that the dynamic characteristics of functional interactions of the triple-networks contributed to studying the underlying pathophysiology of AD. It provided strong evidence for dysregulation of brain dynamics of AD.

Structural covariance pattern abnormalities of insula in major depressive disorder: A CAN-BIND study report

BACKGROUND AND METHODS

Investigation of the insula may inform understanding of the etiopathogenesis of major depressive disorder (MDD). In the present study, we introduced a novel gray matter volume (GMV) based structural covariance technique, and applied it to a multi-centre study of insular subregions of 157 patients with MDD and 93 healthy controls from the Canadian Biomarker Integration Network in Depression (CAN-BIND, https://www.canbind.ca/). Specifically, we divided the unilateral insula into three subregions, and investigated their coupling with whole-brain GMV-based structural brain networks (SBNs). We compared between-group difference of the structural coupling patterns between the insular subregions and SBNs.

RESULTS

The insula was divided into three subregions, including an anterior one, a superior-posterior one and an inferior-posterior one. In the comparison between MDD patients and controls we found that patients' right anterior insula showed increased inter-network coupling with the default mode network, and it showed decreased inter-network coupling with the central executive network; whereas patients' right ventral-posterior insula showed decreased inter-network coupling with the default mode network, and it showed increased inter-network coupling with the central executive network. We also demonstrated that patients' loading parameters of the right ventral-posterior insular structural covariance negatively correlated with their suicidal ideation scores; and controls' loading parameters of the right ventral-posterior insular structural covariance positively correlated with their motor and psychomotor speed scores, whereas these phenomena were not found in patients. Additionally, we did not find significant inter-network coupling between the whole-brain SBNs, including salience network, default mode network, and central executive network.

CONCLUSIONS

Our work proposed a novel technique to investigate the structural covariance coupling between large-scale structural covariance networks, and provided further evidence that MDD is a system-level disorder that shows disrupted structural coupling between brain networks.

Machine learning approaches for parsing comorbidity/heterogeneity in antisociality and substance use disorders: A primer

By some accounts, as many as 93% of individuals diagnosed with antisocial personality disorder (ASPD) or psychopathy also meet criteria for some form of substance use disorder (SUD). This high level of comorbidity, combined with an overlapping biopsychosocial profile, and potentially interacting features, has made it difficult to delineate the shared/unique characteristics of each disorder. Moreover, while rarely acknowledged, both SUD and antisociality exist as highly heterogeneous disorders in need of more targeted parcellation. While emerging data-driven nosology for psychiatric disorders (e.g., Research Domain Criteria (RDoC), Hierarchical Taxonomy of Psychopathology (HiTOP)) offers the opportunity for a more systematic delineation of the externalizing spectrum, the interrogation of large, complex neuroimaging-based datasets may require data-driven approaches that are not yet widely employed in psychiatric neuroscience. With this in mind, the proposed article sets out to provide an introduction into machine learning methods for neuroimaging that can help parse comorbid, heterogeneous externalizing samples. The modest machine learning work conducted to date within the externalizing domain demonstrates the potential utility of the approach but remains highly nascent. Within the paper, we make suggestions for how future work can make use of machine learning methods, in combination with emerging psychiatric nosology systems, to further diagnostic and etiological understandings of the externalizing spectrum. Finally, we briefly consider some challenges that will need to be overcome to encourage further progress in the field.

Shared and Unshared Feature Extraction in Major Depression During Music Listening Using Constrained Tensor Factorization

Ongoing electroencephalography (EEG) signals are recorded as a mixture of stimulus-elicited EEG, spontaneous EEG and noises, which poses a huge challenge to current data analyzing techniques, especially when different groups of participants are expected to have common or highly correlated brain activities and some individual dynamics. In this study, we proposed a data-driven shared and unshared feature extraction framework based on nonnegative and coupled tensor factorization, which aims to conduct group-level analysis for the EEG signals from major depression disorder (MDD) patients and healthy controls (HC) when freely listening to music. Constrained tensor factorization not only preserves the multilinear structure of the data, but also considers the common and individual components between the data. The proposed framework, combined with music information retrieval, correlation analysis, and hierarchical clustering, facilitated the simultaneous extraction of shared and unshared spatio-temporal-spectral feature patterns between/in MDD and HC groups. Finally, we obtained two shared feature patterns between MDD and HC groups, and obtained totally three individual feature patterns from HC and MDD groups. The results showed that the MDD and HC groups triggered similar brain dynamics when listening to music, but at the same time, MDD patients also brought some changes in brain oscillatory network characteristics along with music perception. These changes may provide some basis for the clinical diagnosis and the treatment of MDD patients.

A tutorial on generalized eigendecomposition for denoising, contrast enhancement, and dimension reduction in multichannel electrophysiology

The goal of this paper is to present a theoretical and practical introduction to generalized eigendecomposition (GED), which is a robust and flexible framework used for dimension reduction and source separation in multichannel signal processing. In cognitive electrophysiology, GED is used to create spatial filters that maximize a researcher-specified contrast. For example, one may wish to exploit an assumption that different sources have different frequency content, or that sources vary in magnitude across experimental conditions. GED is fast and easy to compute, performs well in simulated and real data, and is easily adaptable to a variety of specific research goals. This paper introduces GED in a way that ties together myriad individual publications and applications of GED in electrophysiology, and provides sample MATLAB and Python code that can be tested and adapted. Practical considerations and issues that often arise in applications are discussed.

Spatiotemporal trajectories in resting-state FMRI revealed by convolutional variational autoencoder

Recent resting-state fMRI studies have shown that brain activity exhibits temporal variations in functional connectivity by using various approaches including sliding window correlation, co-activation patterns, independent component analysis, quasi-periodic patterns, and hidden Markov models. These methods often model the brain activity as a discretized hopping among several brain states that are defined by the spatial configurations of network activity. However, the discretized states are merely a simplification of what is likely to be a continuous process, where each network evolves over time following its unique path. To model these characteristic spatiotemporal trajectories, we trained a variational autoencoder using rs-fMRI data and evaluated the spatiotemporal features of the latent variables obtained from the trained networks. Our results suggest that there are a relatively small number of approximately orthogonal whole-brain spatiotemporal patterns that capture the most prominent features of rs-fMRI data, which can serve as the building blocks to construct all possible spatiotemporal dynamics in resting state fMRI. These spatiotemporal patterns provide insight into how activity flows across the brain in concordance with known network structures and functional connectivity gradients.

Directed Spectral Measures Improve Latent Network Models Of Neural Populations

Systems neuroscience aims to understand how networks of neurons distributed throughout the brain mediate computational tasks. One popular approach to identify those networks is to first calculate measures of neural activity (e.g. power spectra) from multiple brain regions, and then apply a linear factor model to those measures. Critically, despite the established role of directed communication between brain regions in neural computation, measures of directed communication have been rarely utilized in network estimation because they are incompatible with the implicit assumptions of the linear factor model approach. Here, we develop a novel spectral measure of directed communication called the Directed Spectrum (DS). We prove that it is compatible with the implicit assumptions of linear factor models, and we provide a method to estimate the DS. We demonstrate that latent linear factor models of DS measures better capture underlying brain networks in both simulated and real neural recording data compared to available alternatives. Thus, linear factor models of the Directed Spectrum offer neuroscientists a simple and effective way to explicitly model directed communication in networks of neural populations.

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.

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.

Hierarchical Classification of Event-Related Potentials for the Recognition of Gender Differences in the Attention Task

Research on the functioning of human cognition has been a crucial problem studied for years. Electroencephalography (EEG) classification methods may serve as a precious tool for understanding the temporal dynamics of human brain activity, and the purpose of such an approach is to increase the statistical power of the differences between conditions that are too weak to be detected using standard EEG methods. Following that line of research, in this paper, we focus on recognizing gender differences in the functioning of the human brain in the attention task. For that purpose, we gathered, analyzed, and finally classified event-related potentials (ERPs). We propose a hierarchical approach, in which the electrophysiological signal preprocessing is combined with the classification method, enriched with a segmentation step, which creates a full line of electrophysiological signal classification during an attention task. This approach allowed us to detect differences between men and women in the P3 waveform, an ERP component related to attention, which were not observed using standard ERP analysis. The results provide evidence for the high effectiveness of the proposed method, which outperformed a traditional statistical analysis approach. This is a step towards understanding neuronal differences between men's and women's brains during cognition, aiming to reduce the misdiagnosis and adverse side effects in underrepresented women groups in health and biomedical research.

Deep sr-DDL: Deep structurally regularized dynamic dictionary learning to integrate multimodal and dynamic functional connectomics data for multidimensional clinical characterizations

We propose a novel integrated framework that jointly models complementary information from resting-state functional MRI (rs-fMRI) connectivity and diffusion tensor imaging (DTI) tractography to extract biomarkers of brain connectivity predictive of behavior. Our framework couples a generative model of the connectomics data with a deep network that predicts behavioral scores. The generative component is a structurally-regularized Dynamic Dictionary Learning (sr-DDL) model that decomposes the dynamic rs-fMRI correlation matrices into a collection of shared basis networks and time varying subject-specific loadings. We use the DTI tractography to regularize this matrix factorization and learn anatomically informed functional connectivity profiles. The deep component of our framework is an LSTM-ANN block, which uses the temporal evolution of the subject-specific sr-DDL loadings to predict multidimensional clinical characterizations. Our joint optimization strategy collectively estimates the basis networks, the subject-specific time-varying loadings, and the neural network weights. We validate our framework on a dataset of neurotypical individuals from the Human Connectome Project (HCP) database to map to cognition and on a separate multi-score prediction task on individuals diagnosed with Autism Spectrum Disorder (ASD) in a five-fold cross validation setting. Our hybrid model outperforms several state-of-the-art approaches at clinical outcome prediction and learns interpretable multimodal neural signatures of brain organization.

Multi-modal deep learning of functional and structural neuroimaging and genomic data to predict mental illness

Neuropsychiatric disorders such as schizophrenia are very heterogeneous in nature and typically diagnosed using self-reported symptoms. This makes it difficult to pose a confident prediction on the cases and does not provide insight into the underlying neural and biological mechanisms of these disorders. Combining neuroimaging and genomic data with a multi-modal 'predictome' paves the way for biologically informed markers and may improve prediction reliability. With that, we develop a multi-modal deep learning framework by fusing data from different modalities to capture the interaction between the latent features and evaluate their complementary information in characterizing schizophrenia. Our deep model uses structural MRI, functional MRI, and genome-wide polymorphism data to perform the classification task. It includes a multi-layer feed-forward network, an encoder, and a long short-term memory (LSTM) unit with attention to learn the latent features and adopt a joint training scheme capturing synergies between the modalities. The hybrid network also uses different regularizers for addressing the inherent overfitting and modality-specific bias in the multi-modal setup. Next, we run the network through a saliency model to analyze the learned features. Integrating modalities enhances the performance of the classifier, and our framework acquired 88% (P < 0.0001) accuracy on a dataset of 437 subjects. The trimodal accuracy is comparable to the state-of-the-art performance on a data collection of this size and outperforms the unimodal and bimodal baselines we compared. Model introspection was used to expose the salient neural features and genes/biological pathways associated with schizophrenia. To our best knowledge, this is the first approach that fuses genomic information with structural and functional MRI biomarkers for predicting schizophrenia. We believe this type of modality blending can better explain the disorder's dynamics by adding cross-modal prospects.Clinical Relevance- This study combinedly learns imaging and genomic features for the classification of schizophrenia. The data fusion scheme extracts modality interactions, and the saliency experiments report multiple functional and structural networks closely connected to the disorder.

Default mode network dissociation linking cerebral beta amyloid retention and depression in cognitively normal older adults

Cerebral beta amyloid (Aβ) deposition and late-life depression (LLD) are known to be associated with the trajectory of Alzheimer's disease (AD). However, their neurobiological link is not clear. Previous studies showed aberrant functional connectivity (FC) changes in the default mode network (DMN) in early Aβ deposition and LLD, but its mediating role has not been elucidated. This study was performed to investigate the distinctive association pattern of DMN FC linking LLD and Aβ retention in cognitively normal older adults. A total of 235 cognitively normal older adults with (n = 118) and without depression (n = 117) underwent resting-state functional magnetic resonance imaging and ¹⁸F-flutemetamol positron emission tomography to investigate the associations between Aβ burden, depression, and DMN FC. Independent component analysis showed increased anterior DMN FC and decreased posterior DMN FC in the depression group compared with the no depression group. Global cerebral Aβ retention was positively correlated with anterior and negatively correlated with posterior DMN FC. Anterior DMN FC was positively correlated with severity of depression, whereas posterior DMN FC was negatively correlated with cognitive function. In addition, the effects of global cerebral Aβ retention on severity of depression were mediated by subgenual anterior cingulate FC. Our results of anterior and posterior DMN FC dissociation pattern may be pivotal in linking cerebral Aβ pathology and LLD in the course of AD progression. Further longitudinal studies are needed to confirm the causal relationships between cerebral Aβ retention and LLD.

Role of Deep Learning in Predicting Aging-Related Diseases: A Scoping Review

Aging refers to progressive physiological changes in a cell, an organ, or the whole body of an individual, over time. Aging-related diseases are highly prevalent and could impact an individual’s physical health. Recently, artificial intelligence (AI) methods have been used to predict aging-related diseases and issues, aiding clinical providers in decision-making based on patient’s medical records. Deep learning (DL), as one of the most recent generations of AI technologies, has embraced rapid progress in the early prediction and classification of aging-related issues. In this paper, a scoping review of publications using DL approaches to predict common aging-related diseases (such as age-related macular degeneration, cardiovascular and respiratory diseases, arthritis, Alzheimer’s and lifestyle patterns related to disease progression), was performed. Google Scholar, IEEE and PubMed are used to search DL papers on common aging-related issues published between January 2017 and August 2021. These papers were reviewed, evaluated, and the findings were summarized. Overall, 34 studies met the inclusion criteria. These studies indicate that DL could help clinicians in diagnosing disease at its early stages by mapping diagnostic predictions into observable clinical presentations; and achieving high predictive performance (e.g., more than 90% accurate predictions of diseases in aging).

Distributional independent component analysis for diverse neuroimaging modalities

Recent advances in neuroimaging technologies have provided opportunities to acquire brain images of different modalities for studying human brain organization from both functional and structural perspectives. Analysis of images derived from various modalities involves some common goals such as dimension reduction, denoising, and feature extraction. However, since these modalities have vastly different data characteristics, the current analysis is usually performed using distinct analytical tools that are only suitable for a specific imaging modality. In this paper, we present a Distributional Independent Component Analysis (DICA) that represents a new approach that performs decomposition on the distribution level, providing a unified framework for extracting features across imaging modalities with different scales and representations. When applying DICA to fMRI images, we successfully recover well-established brain functional networks in neuroscience literature, providing empirical validation that DICA delivers neurologically relevant findings. More importantly, we discover several structural network components when applying DICA to DTI images. Through fiber tracking, we find these DICA-derived structural components correspond to several major white fiber bundles. To the best of our knowledge, this is the first time these fiber bundles are successfully identified via blind source separation on single subject DTI images. We also evaluate the performance of DICA as compared with existing ICA methods through extensive simulation studies.

Establishment of Effective Biomarkers for Depression Diagnosis With Fusion of Multiple Resting-State Connectivity Measures

Major depressive disorder (MDD) is a severe mental disorder and is lacking in biomarkers for clinical diagnosis. Previous studies have demonstrated that functional abnormalities of the unifying triple networks are the underlying basis of the neuropathology of depression. However, whether the functional properties of the triple network are effective biomarkers for the diagnosis of depression remains unclear. In our study, we used independent component analysis to define the triple networks, and resting-state functional connectivities (RSFCs), effective connectivities (EC) measured with dynamic causal modeling (DCM), and dynamic functional connectivity (dFC) measured with the sliding window method were applied to map the functional interactions between subcomponents of triple networks. Two-sample t-tests with p < 0.05 with Bonferroni correction were used to identify the significant differences between healthy controls (HCs) and MDD. Compared with HCs, the MDD showed significantly increased intrinsic FC between the left central executive network (CEN) and salience network (SAL), increased EC from the right CEN to left CEN, decreased EC from the right CEN to the default mode network (DMN), and decreased dFC between the right CEN and SAL, DMN. Moreover, by fusion of the changed RSFC, EC, and dFC as features, support vector classification could effectively distinguish the MDD from HCs. Our results demonstrated that fusion of the multiple functional connectivities measures of the triple networks is an effective way to reveal functional disruptions for MDD, which may facilitate establishing the clinical diagnosis biomarkers for depression.

Strategies for multivariate analyses of imaging genetics study in Alzheimer's disease

Alzheimer's disease (AD) is an incurable neurodegenerative disease primarily affecting the elderly population. Early diagnosis of AD is critical for the management of this disease. Imaging genetics examines the influence of genetic variants (i.e., single nucleotide polymorphisms (SNPs)) on brain structure and function and many novel approaches of imaging genetics are proposed for studying AD. We review and synthesize the Alzheimer's Disease Neuroimaging Initiative (ADNI) genetic associations with quantitative disease endophenotypes including structural and functional neuroimaging, diffusion tensor imaging (DTI), positron emission tomography (PET), and fluid biomarker assays. In this review, we survey recent publications using neuroimaging and genetic data of AD, with a focus on methods capturing multivariate effects accommodating the large number variables from both imaging data and genetic data. We review methods focused on bridging the imaging and genetic data by establishing genotype-phenotype association, including sparse canonical correlation analysis, parallel independent component analysis, sparse reduced rank regression, sparse partial least squares, genome-wide association study, and so on. The broad availability and wide scope of ADNI genetic and phenotypic data has advanced our understanding of the genetic basis of AD and has nominated novel targets for future pharmaceutical therapy and biomarker development.

The altered functional modular organization in systemic lupus erythematosus: an independent component analysis study

The aim of this study was to investigate the abnormities in functional connectivity (FC) within each modular network and between modular networks in patients with systemic lupus erythematosus (SLE). Twelve meaningful modular networks were identified via independent component analysis from 41 patients and 40 volunteers. Parametric tests were used to compare the intra- and intermodular FC between the groups. Partial correlation analysis was used to seek the relationships between abnormal FCs and the clinical data. Compared to the controls, SLE patients showed decreased intramodular FC in the anterior default mode network (aDMN), posterior default mode network (pDMN), ventral attention network (VAN), and sensorimotor network (SMN) and increased intramodular FC in the medial visual network (mVN) and left frontoparietal network. In addition, SLE patients showed decreased intermodular FC between the SMN and the lateral visual network (lVN), between the SMN and the VAN, and between the pDMN and the lVN and exhibited increased intermodular FC between the SMN and the salience network (SAN), between the pDMN and the SAN, and between the aDMN and the VAN. Moreover, we found several correlations among the abnormal FCs and the Mini-Mental State Examination in SLE patients. Mild cognitive impairment is compensated by the hyperconnectivity between the aDMN and the VAN, while severe cognitive impairment tends to be compensated by the hyperconnectivity between the SMN and the SAN. The FC value between the SMN and the SAN and between the aDMN and the VAN may serve as neuroimaging markers for monitoring cognitive progression in SLE patients.

Characterizing neural phase-space trajectories via Principal Louvain Clustering

BACKGROUND

With the growing size and richness of neuroscience datasets in terms of dimension, volume, and resolution, identifying spatiotemporal patterns in those datasets is increasingly important. Multivariate dimension-reduction methods are particularly adept at addressing these challenges.

NEW METHOD

In this paper, we propose a novel method, which we refer to as Principal Louvain Clustering (PLC), to identify clusters in a low-dimensional data subspace, based on time-varying trajectories of spectral dynamics across multisite local field potential (LFP) recordings in awake behaving mice. Data were recorded from prefrontal cortex, hippocampus, and parietal cortex in eleven mice while they explored novel and familiar environments.

RESULTS

PLC-identified subspaces and clusters showed high consistency across animals, and were modulated by the animals' ongoing behavior.

CONCLUSIONS

PLC adds to an important growing literature on methods for characterizing dynamics in high-dimensional datasets, using a smaller number of parameters. The method is also applicable to other kinds of datasets, such as EEG or MEG.

Evolutional Neural Architecture Search for Optimization of Spatiotemporal Brain Network Decomposition

Using deep neural networks (DNNs) to explore spatial patterns and temporal dynamics of human brain activities has been an important yet challenging problem because the artificial neural networks are hard to be designed manually. There have been several promising deep learning methods, e.g., deep belief network (DBN), convolutional neural network (CNN), and deep sparse recurrent auto-encoder (DSRAE), that can decompose neuroscientific and meaningful spatiotemporal patterns from 4D functional Magnetic Resonance Imaging (fMRI) data. However, those previous studies still depend on hand-crafted neural network architectures and hyperparameters, which are not optimal in various senses. In this paper, we employ the evolutionary algorithms (EA) to optimize the deep neural architecture of DSRAE by minimizing the expected loss of initialized models, named eNAS-DSRAE (evolutionary Neural Architecture Search on Deep Sparse Recurrent Auto-Encoder). Also, validation experiments are designed and performed on the publicly available human connectome project (HCP) 900 datasets, and the results achieved by the optimized eNAS-DSRAE suggested that our framework can successfully identify the spatiotemporal features and perform better than the hand-crafted neural network models. To our best knowledge, the proposed eNAS-DSRAE is not only among the earliest NAS models that can extract connectome-scale meaningful spatiotemporal brain networks from 4D fMRI data, but also is an effective framework to optimize the RNN-based models.

A single mode of population covariation associates brain networks structure and behavior and predicts individual subjects' age

Multiple human behaviors improve early in life, peaking in young adulthood, and declining thereafter. Several properties of brain structure and function progress similarly across the lifespan. Cognitive and neuroscience research has approached aging primarily using associations between a few behaviors, brain functions, and structures. Because of this, the multivariate, global factors relating brain and behavior across the lifespan are not well understood. We investigated the global patterns of associations between 334 behavioral and clinical measures and 376 brain structural connections in 594 individuals across the lifespan. A single-axis associated changes in multiple behavioral domains and brain structural connections (r = 0.5808). Individual variability within the single association axis well predicted the age of the subject (r = 0.6275). Representational similarity analysis evidenced global patterns of interactions across multiple brain network systems and behavioral domains. Results show that global processes of human aging can be well captured by a multivariate data fusion approach.

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.

Resting-state brain connectivity in healthy young and middle-aged adults at risk of progressive Alzheimer's disease

Functional brain connectivity of the resting-state networks has gained recent attention as a possible biomarker of Alzheimer's Disease (AD). In this paper, we review the literature of functional connectivity differences in young adults and middle-aged cognitively intact individuals with non-modifiable risk factors of AD (n = 17). We focus on three main intrinsic resting-state networks: The Default Mode network, Executive network, and the Salience network. Overall, the evidence from the literature indicated early vulnerability of functional connectivity across different at-risk groups, particularly in the Default Mode Network. While there was little consensus on the interpretation on directionality, the topography of the findings showed frequent overlap across studies, especially in regions that are characteristic of AD (i.e., precuneus, posterior cingulate cortex, and medial prefrontal cortex areas). We conclude that while resting-state functional connectivity markers have great potential to identify at-risk individuals, implementing more data-driven approaches, further longitudinal and cross-validation studies, and the analysis of greater sample sizes are likely to be necessary to fully establish the effectivity and utility of resting-state network-based analyses.

Multivariate semi-blind deconvolution of fMRI time series

Whole brain estimation of the haemodynamic response function (HRF) in functional magnetic resonance imaging (fMRI) is critical to get insight on the global status of the neurovascular coupling of an individual in healthy or pathological condition. Most of existing approaches in the literature works on task-fMRI data and relies on the experimental paradigm as a surrogate of neural activity, hence remaining inoperative on resting-stage fMRI (rs-fMRI) data. To cope with this issue, recent works have performed either a two-step analysis to detect large neural events and then characterize the HRF shape or a joint estimation of both the neural and haemodynamic components in an univariate fashion. In this work, we express the neural activity signals as a combination of piece-wise constant temporal atoms associated with sparse spatial maps and introduce an haemodynamic parcellation of the brain featuring a temporally dilated version of a given HRF model in each parcel with unknown dilation parameters. We formulate the joint estimation of the HRF shapes and spatio-temporal neural representations as a multivariate semi-blind deconvolution problem in a paradigm-free setting and introduce constraints inspired from the dictionary learning literature to ease its identifiability. A fast alternating minimization algorithm, along with its efficient implementation, is proposed and validated on both synthetic and real rs-fMRI data at the subject level. To demonstrate its significance at the population level, we apply this new framework to the UK Biobank data set, first for the discrimination of haemodynamic territories between balanced groups (n=24 individuals in each) patients with an history of stroke and healthy controls and second, for the analysis of normal aging on the neurovascular coupling. Overall, we statistically demonstrate that a pathology like stroke or a condition like normal brain aging induce longer haemodynamic delays in certain brain areas (e.g. Willis polygon, occipital, temporal and frontal cortices) and that this haemodynamic feature may be predictive with an accuracy of 74 % of the individual's age in a supervised classification task performed on n=459 subjects.

NIRS-ICA: A MATLAB Toolbox for Independent Component Analysis Applied in fNIRS Studies

Independent component analysis (ICA) is a multivariate approach that has been widely used in analyzing brain imaging data. In the field of functional near-infrared spectroscopy (fNIRS), its promising effectiveness has been shown in both removing noise and extracting neuronal activity-related sources. The application of ICA remains challenging due to its complexity in usage, and an easy-to-use toolbox dedicated to ICA processing is still lacking in the fNIRS community. In this study, we propose NIRS-ICA, an open-source MATLAB toolbox to ease the difficulty of ICA application for fNIRS studies. NIRS-ICA incorporates commonly used ICA algorithms for source separation, user-friendly GUI, and quantitative evaluation metrics assisting source selection, which facilitate both removing noise and extracting neuronal activity-related sources. The options used in the processing can also be reported easily, which promotes using ICA in a more reproducible way. The proposed toolbox is validated and demonstrated based on both simulative and real fNIRS datasets. We expect the release of the toolbox will extent the application for ICA in the fNIRS community.