NeuroMark: An automated and adaptive ICA based pipeline to identify reproducible fMRI markers of brain disorders

Association of Normative and Non-Normative Brain Networks With Cognitive Function in Patients With Temporal Lobe Epilepsy

BACKGROUND AND OBJECTIVES

Despite their temporal lobe pathology, a significant subgroup of patients with temporal lobe epilepsy (TLE) is able to maintain normative cognitive functioning. In this study, we identify patients with TLE with intact vs impaired neurocognitive profiles and interrogate for the presence of both normative and highly individual intrinsic connectivity networks (ICNs)-all toward understanding the transition from impaired to intact neurocognitive status.

METHODS

This retrospective cross-sectional study included patients with TLE and matched healthy controls (HCs) from the Thomas Jefferson Comprehensive Epilepsy Center. Functional MRI data were decomposed using independent component analysis to obtain individualized ICNs. In this article, we calculated the degree of match between individualized ICNs and canonical ICNs (e.g., 17 resting-state networks by Yeo et al.) and divided each participant's ICNs into normative or non-normative status based on the degree of match.

RESULTS

100 patients with TLE (mean age 42.0 [SD: 13.7] years, 47 women) and 92 HCs were included in this study. We found that the individualized networks matched to the canonical networks less well in the cognitively impaired (n = 24) compared with the cognitively intact (n = 63) patients with TLE by 2-way mixed-measures analysis of variance (impaired vs intact mean difference [MD] -0.165 [-0.317, -0.013], p = 0.028). The cognitively impaired patients showed significant abnormalities in the profiles of both normative (impaired vs intact MD -0.537 [-0.998, -0.076], p = 0.017, intact vs HC MD -0.221 [-0.536, 0.924], p = 0.220, and impaired vs HC MD -0.759 [-1.200, -0.319], p < 0.001) and non-normative networks (impaired vs intact MD 0.484 [0.030, 0.937], p = 0.033, intact vs HC MD 0.369 [0.059, 0.678], p = 0.014, and impaired vs HC MD 0.853 [0.419, 1.286], p < 0.001) while the intact patients showed abnormalities only in non-normative networks. At the same time, we found that normative networks held a strong, positive association with the neuropsychological measures, with this association negative in non-normative networks.

DISCUSSION

Our data demonstrated that significant cognitive deficits are associated with the status of both canonical and highly individual ICNs, making clear that the transition from intact to impaired cognitive status is not simply the result of disruption to normative brain networks.

Common and unique brain aging patterns between females and males quantified by large-scale deep learning

There has been extensive evidence that aging affects human brain function. However, there is no complete picture of what brain functional changes are mostly related to normal aging and how aging affects brain function similarly and differently between males and females. Based on resting-state brain functional connectivity (FC) of 25,582 healthy participants (13,373 females) aged 49-76 years from the UK Biobank project, we employ deep learning with explainable AI to discover primary FCs related to progressive aging and reveal similarity and difference between females and males in brain aging. Using a nested cross-validation scheme, we conduct 4200 deep learning models to classify all paired age groups on the main data for females and males separately and then extract gender-common and gender-specific aging-related FCs. Next, we validate those FCs using additional 21,000 classifiers on the independent data. Our results support that aging results in reduced brain functional interactions for both females and males, primarily relating to the positive connectivity within the same functional domain and the negative connectivity between different functional domains. Regions linked to cognitive control show the most significant age-related changes in both genders. Unique aging effects in males and females mainly involve the interaction between cognitive control and the default mode, vision, auditory, and frontoparietal domains. Results also indicate females exhibit faster brain functional changes than males. Overall, our study provides new evidence about common and unique patterns of brain aging in females and males.

Static and Dynamic Dysconnectivity in Early Psychosis: Relationship With Symptom Dimensions

BACKGROUND AND HYPOTHESIS

Altered functional connectivity (FC) has been frequently reported in psychosis. Studying FC and its time-varying patterns in early-stage psychosis allows the investigation of the neural mechanisms of this disorder without the confounding effects of drug treatment or illness-related factors.

STUDY DESIGN

We employed resting-state functional magnetic resonance imaging (rs-fMRI) to explore FC in individuals with early psychosis (EP), who also underwent clinical and neuropsychological assessments. 96 EP and 56 demographically matched healthy controls (HC) from the Human Connectome Project for Early Psychosis database were included. Multivariate analyses using spatial group independent component analysis were used to compute static FC and dynamic functional network connectivity (dFNC). Partial correlations between FC measures and clinical and cognitive variables were performed to test brain-behavior associations.

STUDY RESULTS

Compared to HC, EP showed higher static FC in the striatum and temporal, frontal, and parietal cortex, as well as lower FC in the frontal, parietal, and occipital gyrus. We found a negative correlation in EP between cognitive function and FC in the right striatum FC (pFWE = 0.009). All dFNC parameters, including dynamism and fluidity measures, were altered in EP, and positive symptoms were negatively correlated with the meta-state changes and the total distance (pFWE = 0.040 and pFWE = 0.049).

CONCLUSIONS

Our findings support the view that psychosis is characterized from the early stages by complex alterations in intrinsic static and dynamic FC, that may ultimately result in positive symptoms and cognitive deficits.

Effects of connectivity hyperalignment (CHA) on estimated brain network properties: from coarse-scale to fine-scale

Recent gains in functional magnetic resonance imaging (fMRI) studies have been driven by increasingly sophisticated statistical and computational techniques and the ability to capture brain data at finer spatial and temporal resolution. These advances allow researchers to develop population-level models of the functional brain representations underlying behavior, performance, clinical status, and prognosis. However, even following conventional preprocessing pipelines, considerable inter-individual disparities in functional localization persist, posing a hurdle to performing compelling population-level inference. Persistent misalignment in functional topography after registration and spatial normalization will reduce power in developing predictive models and biomarkers, reduce the specificity of estimated brain responses and patterns, and provide misleading results on local neural representations and individual differences. This study aims to determine how connectivity hyperalignment (CHA)-an analytic approach for handling functional misalignment-can change estimated functional brain network topologies at various spatial scales from the coarsest set of parcels down to the vertex-level scale. The findings highlight the role of CHA in improving inter-subject similarities, while retaining individual-specific information and idiosyncrasies at finer spatial granularities. This highlights the potential for fine-grained connectivity analysis using this approach to reveal previously unexplored facets of brain structure and function.

Unraveling the Neural Landscape of Mental Disorders using Double Functional Independent Primitives (dFIPs)

Mental illnesses extract a high personal and societal cost, and thus explorations of the links between mental illness and functional connectivity in the brain are critical. Investigating major mental illnesses, believed to arise from disruptions in sophisticated neural connections, allows us to comprehend how these neural network disruptions may be linked to altered cognition, emotional regulation, and social interactions. Although neuroimaging has opened new avenues to explore neural alterations linked to mental illnesses, the field still requires precise and sensitive methodologies to inspect these neural substrates of various psychological disorders. In this study, we employ a hierarchical methodology to derive double functionally independent primitives (dFIPs) from resting state functional magnetic resonance neuroimaging data (rs-fMRI). These dFIPs encapsulate canonical overlapping patterns of functional network connectivity (FNC) within the brain. Our investigation focuses on the examination of how combinations of these dFIPs relate to different mental disorder diagnoses. The central aim is to unravel the complex patterns of FNC that correspond to the diverse manifestations of mental illnesses. To achieve this objective, we used a large brain imaging dataset from multiple sites, comprising 5805 total individuals diagnosed with schizophrenia (SCZ), autism spectrum disorder (ASD), bipolar disorder (BPD), major depressive disorder (MDD), and controls. The key revelations of our study unveil distinct patterns associated with each mental disorder through the combination of dFIPs. Notably, certain individual dFIPs exhibit disorder-specific characteristics, while others demonstrate commonalities across disorders. This approach offers a novel, data-driven synthesis of intricate neuroimaging data, thereby illuminating the functional changes intertwined with various mental illnesses. Our results show distinct signatures associated with psychiatric disorders, revealing unique connectivity patterns such as heightened cerebellar connectivity in SCZ and sensory domain hyperconnectivity in ASD, both contrasted with reduced cerebellar-subcortical connectivity. Utilizing the dFIP concept, we pinpoint specific functional connections that differentiate healthy controls from individuals with mental illness, underscoring its utility in identifying neurobiological markers. In summary, our findings delineate how dFIPs serve as unique fingerprints for different mental disorders.

Association between the oral microbiome and brain resting state connectivity in schizophrenia

Recent microbiome-brain axis findings have shown evidence of the modulation of microbiome community as an environmental mediator in brain function and psychiatric illness. This work is focused on the role of the microbiome in understanding a rarely investigated environmental involvement in schizophrenia (SZ), especially in relation to brain circuit dysfunction. We leveraged high throughput microbial 16s rRNA sequencing and functional neuroimaging techniques to enable the delineation of microbiome-brain network links in SZ. N = 213 SZ and healthy control subjects were assessed for the oral microbiome. Among them, 139 subjects were scanned by resting-state functional magnetic resonance imaging (rsfMRI) to derive brain functional connectivity. We found a significant microbiome compositional shift in SZ beta diversity (weighted UniFrac distance, p = 6 × 10-3; Bray-Curtis distance p = 0.021). Fourteen microbial species involving pro-inflammatory and neurotransmitter signaling and H2S production, showed significant abundance alterations in SZ. Multivariate analysis revealed one pair of microbial and functional connectivity components showing a significant correlation of 0.46. Thirty five percent of microbial species and 87.8 % of brain functional network connectivity from each component also showed significant differences between SZ and healthy controls with strong performance in classifying SZ from healthy controls, with an area under curve (AUC) = 0.84 and 0.87, respectively. The results suggest a potential link between oral microbiome dysbiosis and brain functional connectivity alteration in relation to SZ, possibly through immunological and neurotransmitter signaling pathways and the hypothalamic-pituitary-adrenal axis, supporting for future work in characterizing the role of oral microbiome in mediating effects on SZ brain functional activity.

A survey of brain functional network extraction methods using fMRI data

Functional network (FN) analyses play a pivotal role in uncovering insights into brain function and understanding the pathophysiology of various brain disorders. This paper focuses on classical and advanced methods for deriving brain FNs from functional magnetic resonance imaging (fMRI) data. We systematically review their foundational principles, advantages, shortcomings, and interrelations, encompassing both static and dynamic FN extraction approaches. In the context of static FN extraction, we present hypothesis-driven methods such as region of interest (ROI)-based approaches as well as data-driven methods including matrix decomposition, clustering, and deep learning. For dynamic FN extraction, both window-based and windowless methods are surveyed with respect to the estimation of time-varying FN and the subsequent computation of FN states. We also discuss the scope of application of the various methods and avenues for future improvements.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

Cognitive and psychiatric relevance of dynamic functional connectivity states in a large (N > 10,000) children population

Children's brains dynamically adapt to the stimuli from the internal state and the external environment, allowing for changes in cognitive and mental behavior. In this work, we performed a large-scale analysis of dynamic functional connectivity (DFC) in children aged 9~11 years, investigating how brain dynamics relate to cognitive performance and mental health at an early age. A hybrid independent component analysis framework was applied to the Adolescent Brain Cognitive Development (ABCD) data containing 10,988 children. We combined a sliding-window approach with k-means clustering to identify five brain states with distinct DFC patterns. Interestingly, the occurrence of a strongly connected state with the most within-network synchrony and the anticorrelations between networks, especially between the sensory networks and between the cerebellum and other networks, was negatively correlated with cognitive performance and positively correlated with dimensional psychopathology in children. Meanwhile, opposite relationships were observed for a DFC state showing integration of sensory networks and antagonism between default-mode and sensorimotor networks but weak segregation of the cerebellum. The mediation analysis further showed that attention problems mediated the effect of DFC states on cognitive performance. This investigation unveils the neurological underpinnings of DFC states, which suggests that tracking the transient dynamic connectivity may help to characterize cognitive and mental problems in children and guide people to provide early intervention to buffer adverse influences.

Neuroimage Analysis Methods and Artificial Intelligence Techniques for Reliable Biomarkers and Accurate Diagnosis of Schizophrenia: Achievements Made by Chinese Scholars Around the Past Decade

BACKGROUND AND HYPOTHESIS

Schizophrenia (SZ) is characterized by significant cognitive and behavioral disruptions. Neuroimaging techniques, particularly magnetic resonance imaging (MRI), have been widely utilized to investigate biomarkers of SZ, distinguish SZ from healthy conditions or other mental disorders, and explore biotypes within SZ or across SZ and other mental disorders, which aim to promote the accurate diagnosis of SZ. In China, research on SZ using MRI has grown considerably in recent years.

STUDY DESIGN

The article reviews advanced neuroimaging and artificial intelligence (AI) methods using single-modal or multimodal MRI to reveal the mechanism of SZ and promote accurate diagnosis of SZ, with a particular emphasis on the achievements made by Chinese scholars around the past decade.

STUDY RESULTS

Our article focuses on the methods for capturing subtle brain functional and structural properties from the high-dimensional MRI data, the multimodal fusion and feature selection methods for obtaining important and sparse neuroimaging features, the supervised statistical analysis and classification for distinguishing disorders, and the unsupervised clustering and semi-supervised learning methods for identifying neuroimage-based biotypes. Crucially, our article highlights the characteristics of each method and underscores the interconnections among various approaches regarding biomarker extraction and neuroimage-based diagnosis, which is beneficial not only for comprehending SZ but also for exploring other mental disorders.

CONCLUSIONS

We offer a valuable review of advanced neuroimage analysis and AI methods primarily focused on SZ research by Chinese scholars, aiming to promote the diagnosis, treatment, and prevention of SZ, as well as other mental disorders, both within China and internationally.

Time-varying phase synchronization of resting-state functional magnetic resonance imaging reveals a shift toward self-referential processes during sustained pain

ABSTRACT

Growing evidence has suggested that time-varying functional connectivity between different brain regions might underlie the dynamic experience of pain. This study used a novel, data-driven framework to characterize the dynamic interactions of large-scale brain networks during sustained pain by estimating recurrent patterns of phase-synchronization. Resting-state functional magnetic resonance imaging signals were collected from 50 healthy participants before (once) and after (twice) the onset of sustained pain that was induced by topical application of capsaicin cream. We first decoded the instantaneous phase of neural activity and then applied leading eigenvector dynamic analysis on the time-varying phase-synchronization. We identified 3 recurrent brain states that show distinctive phase-synchronization. The presence of state 1, characterized by phase-synchronization between the default mode network and auditory, visual, and sensorimotor networks, together with transitions towards this brain state, increased during sustained pain. These changes can account for the perceived pain intensity and reported unpleasantness induced by capsaicin application. In contrast, state 3, characterized by phase-synchronization between the cognitive control network and sensory networks, decreased after the onset of sustained pain. These results are indicative of a shift toward internally directed self-referential processes (state 1) and away from externally directed cognitive control processes (state 3) during sustained pain.

Characteristics of pain empathic networks in healthy and primary dysmenorrhea women: an fMRI study

Pain empathy enables us to understand and share how others feel pain. Few studies have investigated pain empathy-related functional interactions at the whole-brain level across all networks. Additionally, women with primary dysmenorrhea (PDM) have abnormal pain empathy, and the association among the whole-brain functional network, pain, and pain empathy remain unclear. Using resting-state functional magnetic resonance imaging (fMRI) and machine learning analysis, we identified the brain functional network connectivity (FNC)-based features that are associated with pain empathy in two studies. Specifically, Study 1 examined 41 healthy controls (HCs), while Study 2 investigated 45 women with PDM. Additionally, in Study 3, a classification analysis was performed to examine the differences in FNC between HCs and women with PDM. Pain empathy was evaluated using a visual stimuli experiment, and trait and state of menstrual pain were recorded. In Study 1, the results showed that pain empathy in HCs relied on dynamic interactions across whole-brain networks and was not concentrated in a single or two brain networks, suggesting the dynamic cooperation of networks for pain empathy in HCs. In Study 2, PDM exhibited a distinctive network for pain empathy. The features associated with pain empathy were concentrated in the sensorimotor network (SMN). In Study 3, the SMN-related dynamic FNC could accurately distinguish women with PDM from HCs and exhibited a significant association with trait menstrual pain. This study may deepen our understanding of the neural mechanisms underpinning pain empathy and suggest that menstrual pain may affect pain empathy through maladaptive dynamic interaction between brain networks.

SMART (Splitting-Merging Assisted Reliable) Independent Component Analysis for Extracting Accurate Brain Functional Networks

Functional networks (FNs) hold significant promise in understanding brain function. Independent component analysis (ICA) has been applied in estimating FNs from functional magnetic resonance imaging (fMRI). However, determining an optimal model order for ICA remains challenging, leading to criticism about the reliability of FN estimation. Here, we propose a SMART (splitting-merging assisted reliable) ICA method that automatically extracts reliable FNs by clustering independent components (ICs) obtained from multi-model-order ICA using a simplified graph while providing linkages among FNs deduced from different-model orders. We extend SMART ICA to multi-subject fMRI analysis, validating its effectiveness using simulated and real fMRI data. Based on simulated data, the method accurately estimates both group-common and group-unique components and demonstrates robustness to parameters. Using two age-matched cohorts of resting fMRI data comprising 1,950 healthy subjects, the resulting reliable group-level FNs are greatly similar between the two cohorts, and interestingly the subject-specific FNs show progressive changes while age increases. Furthermore, both small-scale and large-scale brain FN templates are provided as benchmarks for future studies. Taken together, SMART ICA can automatically obtain reliable FNs in analyzing multi-subject fMRI data, while also providing linkages between different FNs.

The overlap across psychotic disorders: A functional network connectivity analysis

Functional network connectivity (FNC) has previously been shown to distinguish patient groups from healthy controls (HC). However, the overlap across psychiatric disorders such as schizophrenia (SZ), bipolar (BP), and schizoaffective disorder (SAD) is not evident yet. This study focuses on studying the overlap across these three psychotic disorders in both dynamic and static FNC (dFNC/sFNC). We used resting-state fMRI, demographics, and clinical information from the Bipolar-Schizophrenia Network on Intermediate Phenotypes cohort (BSNIP). The data includes three groups of patients with schizophrenia (SZ, N = 181), bipolar (BP, N = 163), and schizoaffective (SAD, N = 130) and HC (N = 238) groups. After estimating each individual's dFNC, we group them into three distinct states. We evaluated two dFNC features, including occupancy rate (OCR) and distance travelled over time. Finally, the extracted features, including both sFNC and dFNC, are tested statistically across patients and HC groups. In addition, we explored the link between the clinical scores and the extracted features. We evaluated the connectivity patterns and their overlap among SZ, BP, and SAD disorders (false discovery rate or FDR corrected p < 0.05). Results showed dFNC captured unique information about overlap across disorders where all disorder groups showed similar pattern of activity in state 2. Moreover, the results showed similar patterns between SZ and SAD in state 1 which was different than BP. Finally, the distance travelled feature of SZ (average R = 0.245, p < 0.01) and combined distance travelled from all disorders was predictive of the PANSS symptoms scores (average R = 0.147, p < 0.01).

Providing context: Extracting non-linear and dynamic temporal motifs from brain activity

Approaches studying the dynamics of resting-state functional magnetic resonance imaging (rs-fMRI) activity often focus on time-resolved functional connectivity (tr-FC). While many approaches have been proposed, these typically focus on linear approaches like computing the linear correlation at a timestep or within a window. In this work, we propose to use a generative non-linear deep learning model, a disentangled variational autoencoder (DSVAE), that factorizes out window-specific (context) information from timestep-specific (local) information. This has the advantage of allowing our model to capture differences at multiple temporal scales. For the timestep-specific scale, which has higher temporal precision, we find significant differences between schizophrenia patients and control subjects in their temporal step distance through our model's latent space. We also find that window-specific embeddings, or as we refer to them, context embeddings, more accurately separate windows from schizophrenia patients and control subjects than the standard tr-FC approach. Moreover, we find that for individuals with schizophrenia, our model's context embedding space is significantly correlated with both age and symptom severity. Interestingly, patients appear to spend more time in three clusters, one closer to controls which shows increased visual-sensorimotor, cerebellar-subcortical, and reduced cerebellar-sensorimotor functional network connectivity (FNC), an intermediate station showing increased subcortical-sensorimotor FNC, and one that shows decreased visual-sensorimotor, decreased subcortical-sensorimotor, and increased visual-subcortical domains. We verify that our model captures features that are complementary to - but not the same as - standard tr-FC features. Our model can thus help broaden the neuroimaging toolset in analyzing fMRI dynamics and shows potential as an approach for finding psychiatric links that are more sensitive to individual and group characteristics.

A Dynamic Entropy Approach Reveals Reduced Functional Network Connectivity Trajectory Complexity in Schizophrenia

Over the past decade and a half, dynamic functional imaging has revealed low-dimensional brain connectivity measures, identified potential common human spatial connectivity states, tracked the transition patterns of these states, and demonstrated meaningful transition alterations in disorders and over the course of development. Recently, researchers have begun to analyze these data from the perspective of dynamic systems and information theory in the hopes of understanding how these dynamics support less easily quantified processes, such as information processing, cortical hierarchy, and consciousness. Little attention has been paid to the effects of psychiatric disease on these measures, however. We begin to rectify this by examining the complexity of subject trajectories in state space through the lens of information theory. Specifically, we identify a basis for the dynamic functional connectivity state space and track subject trajectories through this space over the course of the scan. The dynamic complexity of these trajectories is assessed along each dimension of the proposed basis space. Using these estimates, we demonstrate that schizophrenia patients display substantially simpler trajectories than demographically matched healthy controls and that this drop in complexity concentrates along specific dimensions. We also demonstrate that entropy generation in at least one of these dimensions is linked to cognitive performance. Overall, the results suggest great value in applying dynamic systems theory to problems of neuroimaging and reveal a substantial drop in the complexity of schizophrenia patients' brain function.

An interpretable generative multimodal neuroimaging-genomics framework for decoding Alzheimer's disease

Alzheimer's disease (AD) is the most prevalent form of dementia, affecting millions worldwide with a progressive decline in cognitive abilities. The AD continuum encompasses a prodormal stage known as Mild Cognitive Impairment (MCI), where patients may either progress to AD (MCIc) or remain stable (MCInc). Understanding the underlying mechanisms of AD requires complementary analysis derived from different data sources, leading to the development of multimodal deep learning models. In this study, we leveraged structural and functional Magnetic Resonance Imaging (sMRI/fMRI) to investigate the disease-induced grey matter and functional network connectivity changes. Moreover, considering AD's strong genetic component, we introduce Single Nucleotide Polymorphisms (SNPs) as a third channel. Given such diverse inputs, missing one or more modalities is a typical concern of multimodal methods. We hence propose a novel deep learning based classification framework where generative module employing Cycle Generative Adversarial Networks (cGAN) was adopted to impute missing data within the latent space. Additionally, we adopted an Explainable Artificial Intelligence (XAI) method, Integrated Gradients (IG), to extract input features relevance, enhancing our understanding of the learned representations. Two critical tasks were addressed: AD detection and MCI conversion prediction. Experimental results showed that our framework was able to reach the state-of-the-art in the classification of CN vs AD reaching an average test accuracy of 0.926 ± 0.02. For the MCInc vs MCIc task, we achieved an average prediction accuracy of 0.711 ± 0.01 using the pre-trained model for CN and AD. The interpretability analysis revealed that the classification performance was led by significant grey matter modulations in cortical and subcortical brain areas well known for their association with AD. Moreover, impairments in sensory-motor and visual resting state network connectivity along the disease continuum, as well as mutations in SNPs defining biological processes linked to amyloid-beta and cholesterol formation clearance and regulation, were identified as contributors to the achieved performance. Overall, our integrative deep learning approach shows promise for AD detection and MCI prediction, while shading light on important biological insights.

A method for estimating dynamic functional network connectivity gradients (dFNG) from ICA captures smooth inter-network modulation

Dynamic functional network connectivity (dFNC) analysis is a widely used approach for studying brain function and offering insight into how brain networks evolve over time. Typically, dFNC studies utilized fixed spatial maps and evaluate transient changes in coupling among time courses estimated from independent component analysis (ICA). This manuscript presents a complementary approach that relaxes this assumption by spatially reordering the components dynamically at each timepoint to optimize for a smooth gradient in the FNC (i.e., a smooth gradient among ICA connectivity values). Several methods are presented to summarize dynamic FNC gradients (dFNGs) over time, starting with static FNC gradients (sFNGs), then exploring the reordering properties as well as the dynamics of the gradients themselves. We then apply this approach to a dataset of schizophrenia (SZ) patients and healthy controls (HC). Functional dysconnectivity between different brain regions has been reported in schizophrenia, yet the neural mechanisms behind it remain elusive. Using resting state fMRI and ICA on a dataset consisting of 151 schizophrenia patients and 160 age and gender-matched healthy controls, we extracted 53 intrinsic connectivity networks (ICNs) for each subject using a fully automated spatially constrained ICA approach. We develop several summaries of our functional network connectivity gradient analysis, both in a static sense, computed as the Pearson correlation coefficient between full time series, and a dynamic sense, computed using a sliding window approach followed by reordering based on the computed gradient, and evaluate group differences. Static connectivity analysis revealed significantly stronger connectivity between subcortical (SC), auditory (AUD) and visual (VIS) networks in patients, as well as hypoconnectivity in sensorimotor (SM) network relative to controls. sFNG analysis highlighted distinctive clustering patterns in patients and HCs along cognitive control (CC)/ default mode network (DMN), as well as SC/ AUD/ SM/ cerebellar (CB), and VIS gradients. Furthermore, we observed significant differences in the sFNGs between groups in SC and CB domains. dFNG analysis suggested that SZ patients spend significantly more time in a SC/ CB state based on the first gradient, while HCs favor the SM/DMN state. For the second gradient, however, patients exhibited significantly higher activity in CB domains, contrasting with HCs' DMN engagement. The gradient synchrony analysis conveyed more shifts between SM/ SC networks and transmodal CC/ DMN networks in patients. In addition, the dFNG coupling revealed distinct connectivity patterns between SC, SM and CB domains in SZ patients compared to HCs. To recap, our results advance our understanding of brain network modulation by examining smooth connectivity trajectories. This provides a more complete spatiotemporal summary of the data, contributing to the growing body of current literature regarding the functional dysconnectivity in schizophrenia patients. By employing dFNG, we highlight a new perspective to capture large scale fluctuations across the brain while maintaining the convenience of brain networks and low dimensional summary measures.

Static and Dynamic Cross-Network Functional Connectivity Shows Elevated Entropy in Schizophrenia Patients

Schizophrenia (SZ) patients exhibit abnormal static and dynamic functional connectivity across various brain domains. We present a novel approach based on static and dynamic inter-network connectivity entropy (ICE), which represents the entropy of a given network's connectivity to all the other brain networks. This novel approach enables the investigation of how connectivity strength is heterogeneously distributed across available targets in both SZ patients and healthy controls. We analyzed fMRI data from 151 schizophrenia patients and demographically matched 160 healthy controls. Our assessment encompassed both static and dynamic ICE, revealing significant differences in the heterogeneity of connectivity levels across available brain networks between SZ patients and healthy controls (HC). These networks are associated with subcortical (SC), auditory (AUD), sensorimotor (SM), visual (VIS), cognitive control (CC), default mode network (DMN) and cerebellar (CB) functional brain domains. Elevated ICE observed in individuals with SZ suggests that patients exhibit significantly higher randomness in the distribution of time-varying connectivity strength across functional regions from each source network, compared to healthy control group. C-means fuzzy clustering analysis of functional ICE correlation matrices revealed that SZ patients exhibit significantly higher occupancy weights in clusters with weak, low-scale functional entropy correlation, while the control group shows greater occupancy weights in clusters with strong, large-scale functional entropy correlation. k-means clustering analysis on time-indexed ICE vectors revealed that cluster with highest ICE have higher occupancy rates in SZ patients whereas clusters characterized by lowest ICE have larger occupancy rates for control group. Furthermore, our dynamic ICE approach revealed that it appears healthy for a brain to primarily circulate through complex, less structured connectivity patterns, with occasional transitions into more focused patterns. However, individuals with SZ seem to struggle with transiently attaining these more focused and structured connectivity patterns. Proposed ICE measure presents a novel framework for gaining deeper insights into understanding mechanisms of healthy and disease brain states and a substantial step forward in the developing advanced methods of diagnostics of mental health conditions.

Studying time-resolved functional connectivity via communication theory: on the complementary nature of phase synchronization and sliding window Pearson correlation

Time-resolved functional connectivity (trFC) assesses the time-resolved coupling between brain regions using functional magnetic resonance imaging (fMRI) data. This study aims to compare two techniques used to estimate trFC, to investigate their similarities and differences when applied to fMRI data. These techniques are the sliding window Pearson correlation (SWPC), an amplitude-based approach, and phase synchronization (PS), a phase-based technique. To accomplish our objective, we used resting-state fMRI data from the Human Connectome Project (HCP) with 827 subjects (repetition time: 0.7s) and the Function Biomedical Informatics Research Network (fBIRN) with 311 subjects (repetition time: 2s), which included 151 schizophrenia patients and 160 controls. Our simulations reveal distinct strengths in two connectivity methods: SWPC captures high-magnitude, low-frequency connectivity, while PS detects low-magnitude, high-frequency connectivity. Stronger correlations between SWPC and PS align with pronounced fMRI oscillations. For fMRI data, higher correlations between SWPC and PS occur with matched frequencies and smaller SWPC window sizes (~30s), but larger windows (~88s) sacrifice clinically relevant information. Both methods identify a schizophrenia-associated brain network state but show different patterns: SWPC highlights low anti-correlations between visual, subcortical, auditory, and sensory-motor networks, while PS shows reduced positive synchronization among these networks. In sum, our findings underscore the complementary nature of SWPC and PS, elucidating their respective strengths and limitations without implying the superiority of one over the other.

Parallel Multilink Group Joint ICA: Fusion of 3D Structural and 4D Functional Data Across Multiple Resting fMRI Networks

Multimodal neuroimaging research plays a pivotal role in understanding the complexities of the human brain and its disorders. Independent component analysis (ICA) has emerged as a widely used and powerful tool for disentangling mixed independent sources, particularly in the analysis of functional magnetic resonance imaging (fMRI) data. This paper extends the use of ICA as a unifying framework for multimodal fusion, introducing a novel approach termed parallel multilink group joint ICA (pmg-jICA). The method allows for the fusion of gray matter maps from structural MRI (sMRI) data to multiple fMRI intrinsic networks, addressing the limitations of previous models. The effectiveness of pmg-jICA is demonstrated through its application to an Alzheimer's dataset, yielding linked structure-function outputs for 53 brain networks. Our approach leverages the complementary information from various imaging modalities, providing a unique perspective on brain alterations in Alzheimer's disease. The pmg-jICA identifies several components with significant differences between HC and AD groups including thalamus, caudate, putamen with in the subcortical (SC) domain, insula, parahippocampal gyrus within the cognitive control (CC) domain, and the lingual gyrus within the visual (VS) domain, providing localized insights into the links between AD and specific brain regions. In addition, because we link across multiple brain networks, we can also compute functional network connectivity (FNC) from spatial maps and subject loadings, providing a detailed exploration of the relationships between different brain regions and allowing us to visualize spatial patterns and loading parameters in sMRI along with intrinsic networks and FNC from the fMRI data. In essence, developed approach combines concepts from joint ICA and group ICA to provide a rich set of output characterizing data-driven links between covarying gray matter networks, and a (potentially large number of) resting fMRI networks allowing further study in the context of structure/function links. We demonstrate the utility of the approach by highlighting key structure/function disruptions in Alzheimer's individuals.

SpaDE: Semantic Locality Preserving Biclustering for Neuroimaging Data

The most discriminative and revealing patterns in the neuroimaging population are often confined to smaller subdivisions of the samples and features. Especially in neuropsychiatric conditions, symptoms are expressed within micro subgroups of individuals and may only underly a subset of neurological mechanisms. As such, running a whole-population analysis yields suboptimal outcomes leading to reduced specificity and interpretability. Biclustering is a potential solution since subject heterogeneity makes one-dimensional clustering less effective in this realm. Yet, high dimensional sparse input space and semantically incoherent grouping of attributes make post hoc analysis challenging. Therefore, we propose a deep neural network called semantic locality preserving auto decoder (SpaDE), for unsupervised feature learning and biclustering. SpaDE produces coherent subgroups of subjects and neural features preserving semantic locality and enhancing neurobiological interpretability. Also, it regularizes for sparsity to improve representation learning. We employ SpaDE on human brain connectome collected from schizophrenia (SZ) and healthy control (HC) subjects. The model outperforms several state-of-the-art biclustering methods. Our method extracts modular neural communities showing significant (HC/SZ) group differences in distinct brain networks including visual, sensorimotor, and subcortical. Moreover, these bi-clustered connectivity substructures exhibit substantial relations with various cognitive measures such as attention, working memory, and visual learning.

Cognitive impairment in schizophrenia is associated with prefrontal-striatal functional hypoconnectivity and striatal dopaminergic abnormalities

BACKGROUND

A better understanding of the mechanisms underlying cognitive impairment in schizophrenia is imperative, as it causes poor functional outcomes and a lack of effective treatments.

AIMS

This study aimed to investigate the relationships of two proposed main pathophysiology of schizophrenia, altered prefrontal-striatal connectivity and the dopamine system, with cognitive impairment and their interactions.

METHODS

Thirty-three patients with schizophrenia and 27 healthy controls (HCs) who are right-handed and matched for age and sex were recruited. We evaluated their cognition, functional connectivity (FC) between the dorsolateral prefrontal cortex (DLPFC)/middle frontal gyrus (MiFG) and striatum, and the availability of striatal dopamine transporter (DAT) using a cognitive battery investigating attention, memory, and executive function, resting-state functional magnetic resonance imaging with group independent component analysis and single-photon emission computed tomography with 99mTc-TRODAT.

RESULTS

Patients with schizophrenia exhibited poorer cognitive performance, reduced FC between DLPFC/MiFG and the caudate nucleus (CN) or putamen, decreased DAT availability in the left CN, and decreased right-left DAT asymmetry in the CN compared to HCs. In patients with schizophrenia, altered imaging markers are associated with cognitive impairments, especially the relationship between DLPFC/MiFG-putamen FC and attention and between DAT asymmetry in the CN and executive function.

CONCLUSIONS

This study is the first to demonstrate how prefrontal-striatal hypoconnectivity and altered striatal DAT markers are associated with different domains of cognitive impairment in schizophrenia. More research is needed to evaluate their complex relationships and potential therapeutic implications.

A spatially constrained independent component analysis jointly informed by structural and functional network connectivity

There are a growing number of neuroimaging studies motivating joint structural and functional brain connectivity. Brain connectivity of different modalities provides insight into brain functional organization by leveraging complementary information, especially for brain disorders such as schizophrenia. In this paper, we propose a multi-modal independent component analysis (ICA) model that utilizes information from both structural and functional brain connectivity guided by spatial maps to estimate intrinsic connectivity networks (ICNs). Structural connectivity is estimated through whole-brain tractography on diffusion-weighted MRI (dMRI), while functional connectivity is derived from resting-state functional MRI (rs-fMRI). The proposed structural-functional connectivity and spatially constrained ICA (sfCICA) model estimates ICNs at the subject level using a multi-objective optimization framework. We evaluated our model using synthetic and real datasets (including dMRI and rs-fMRI from 149 schizophrenia patients and 162 controls). Multi-modal ICNs revealed enhanced functional coupling between ICNs with higher structural connectivity, improved modularity, and network distinction, particularly in schizophrenia. Statistical analysis of group differences showed more significant differences in the proposed model compared to the unimodal model. In summary, the sfCICA model showed benefits from being jointly informed by structural and functional connectivity. These findings suggest advantages in simultaneously learning effectively and enhancing connectivity estimates using structural connectivity.

Assistive tools for classifying neurological disorders using fMRI and deep learning: A guide and example

BACKGROUND

Deep-learning (DL) methods are rapidly changing the way researchers classify neurological disorders. For example, combining functional magnetic resonance imaging (fMRI) and DL has helped researchers identify functional biomarkers of neurological disorders (e.g., brain activation and connectivity) and pilot innovative diagnostic models. However, the knowledge required to perform DL analyses is often domain-specific and is not widely taught in the brain sciences (e.g., psychology, neuroscience, and cognitive science). Conversely, neurological diagnoses and neuroimaging training (e.g., fMRI) are largely restricted to the brain and medical sciences. In turn, these disciplinary knowledge barriers and distinct specializations can act as hurdles that prevent the combination of fMRI and DL pipelines. The complexity of fMRI and DL methods also hinders their clinical adoption and generalization to real-world diagnoses. For example, most current models are not designed for clinical settings or use by nonspecialized populations such as students, clinicians, and healthcare workers. Accordingly, there is a growing area of assistive tools (e.g., software and programming packages) that aim to streamline and increase the accessibility of fMRI and DL pipelines for the diagnoses of neurological disorders.

OBJECTIVES AND METHODS

In this study, we present an introductory guide to some popular DL and fMRI assistive tools. We also create an example autism spectrum disorder (ASD) classification model using assistive tools (e.g., Optuna, GIFT, and the ABIDE preprocessed repository), fMRI, and a convolutional neural network.

RESULTS

In turn, we provide researchers with a guide to assistive tools and give an example of a streamlined fMRI and DL pipeline.

CONCLUSIONS

We are confident that this study can help more researchers enter the field and create accessible fMRI and deep-learning diagnostic models for neurological disorders.

A deep learning approach for mental health quality prediction using functional network connectivity and assessment data

While one can characterize mental health using questionnaires, such tools do not provide direct insight into the underlying biology. By linking approaches that visualize brain activity to questionnaires in the context of individualized prediction, we can gain new insights into the biology and behavioral aspects of brain health. Resting-state fMRI (rs-fMRI) can be used to identify biomarkers of these conditions and study patterns of abnormal connectivity. In this work, we estimate mental health quality for individual participants using static functional network connectivity (sFNC) data from rs-fMRI. The deep learning model uses the sFNC data as input to predict four categories of mental health quality and visualize the neural patterns indicative of each group. We used guided gradient class activation maps (guided Grad-CAM) to identify the most discriminative sFNC patterns. The effectiveness of this model was validated using the UK Biobank dataset, in which we showed that our approach outperformed four alternative models by 4-18% accuracy. The proposed model's performance evaluation yielded a classification accuracy of 76%, 78%, 88%, and 98% for the excellent, good, fair, and poor mental health categories, with poor mental health accuracy being the highest. The findings show distinct sFNC patterns across each group. The patterns associated with excellent mental health consist of the cerebellar-subcortical regions, whereas the most prominent areas in the poor mental health category are in the sensorimotor and visual domains. Thus the combination of rs-fMRI and deep learning opens a promising path for developing a comprehensive framework to evaluate and measure mental health. Moreover, this approach had the potential to guide the development of personalized interventions and enable the monitoring of treatment response. Overall this highlights the crucial role of advanced imaging modalities and deep learning algorithms in advancing our understanding and management of mental health.

Multimodal Predictive Modeling: Scalable Imaging Informed Approaches to Predict Future Brain Health

Background

Predicting future brain health is a complex endeavor that often requires integrating diverse data sources. The neural patterns and interactions identified through neuroimaging serve as the fundamental basis and early indicators that precede the manifestation of observable behaviors or psychological states.

New Method

In this work, we introduce a multimodal predictive modeling approach that leverages an imaging-informed methodology to gain insights into future behavioral outcomes. We employed three methodologies for evaluation: an assessment-only approach using support vector regression (SVR), a neuroimaging-only approach using random forest (RF), and an image-assisted method integrating the static functional network connectivity (sFNC) matrix from resting-state functional magnetic resonance imaging (rs-fMRI) alongside assessments. The image-assisted approach utilized a partially conditional variational autoencoder (PCVAE) to predict brain health constructs in future visits from the behavioral data alone.

Results

Our performance evaluation indicates that the image-assisted method excels in handling conditional information to predict brain health constructs in subsequent visits and their longitudinal changes. These results suggest that during the training stage, the PCVAE model effectively captures relevant information from neuroimaging data, thereby potentially improving accuracy in making future predictions using only assessment data.

Comparison with Existing Methods

The proposed image-assisted method outperforms traditional assessment-only and neuroimaging-only approaches by effectively integrating neuroimaging data with assessment factors.

Conclusion

This study underscores the potential of neuroimaging-informed predictive modeling to advance our comprehension of the complex relationships between cognitive performance and neural connectivity.

A confounder controlled machine learning approach: Group analysis and classification of schizophrenia and Alzheimer's disease using resting-state functional network connectivity

Resting-state functional magnetic resonance imaging (rs-fMRI) has increasingly been used to study both Alzheimer's disease (AD) and schizophrenia (SZ). While most rs-fMRI studies being conducted in AD and SZ compare patients to healthy controls, it is also of interest to directly compare AD and SZ patients with each other to identify potential biomarkers shared between the disorders. However, comparing patient groups collected in different studies can be challenging due to potential confounds, such as differences in the patient's age, scan protocols, etc. In this study, we compared and contrasted resting-state functional network connectivity (rs-FNC) of 162 patients with AD and late mild cognitive impairment (LMCI), 181 schizophrenia patients, and 315 cognitively normal (CN) subjects. We used confounder-controlled rs-FNC and applied machine learning algorithms (including support vector machine, logistic regression, random forest, and k-nearest neighbor) and deep learning models (i.e., fully-connected neural networks) to classify subjects in binary and three-class categories according to their diagnosis labels (e.g., AD, SZ, and CN). Our statistical analysis revealed that FNC between the following network pairs is stronger in AD compared to SZ: subcortical-cerebellum, subcortical-cognitive control, cognitive control-cerebellum, and visual-sensory motor networks. On the other hand, FNC is stronger in SZ than AD for the following network pairs: subcortical-visual, subcortical-auditory, subcortical-sensory motor, cerebellum-visual, sensory motor-cognitive control, and within the cerebellum networks. Furthermore, we observed that while AD and SZ disorders each have unique FNC abnormalities, they also share some common functional abnormalities that can be due to similar neurobiological mechanisms or genetic factors contributing to these disorders' development. Moreover, we achieved an accuracy of 85% in classifying subjects into AD and SZ where default mode, visual, and subcortical networks contributed the most to the classification and accuracy of 68% in classifying subjects into AD, SZ, and CN with the subcortical domain appearing as the most contributing features to the three-way classification. Finally, our findings indicated that for all classification tasks, except AD vs. SZ, males are more predictable than females.

Exploring Schizophrenia Classification Through Multimodal MRI and Deep Graph Neural Networks: Unveiling Brain Region-Specific Weight Discrepancies and Their Association With Cell-Type Specific Transcriptomic Features

BACKGROUND AND HYPOTHESIS

Schizophrenia (SZ) is a prevalent mental disorder that imposes significant health burdens. Diagnostic accuracy remains challenging due to clinical subjectivity. To address this issue, we explore magnetic resonance imaging (MRI) as a tool to enhance SZ diagnosis and provide objective references and biomarkers. Using deep learning with graph convolution, we represent MRI data as graphs, aligning with brain structure, and improving feature extraction, and classification. Integration of multiple modalities is expected to enhance classification.

STUDY DESIGN

Our study enrolled 683 SZ patients and 606 healthy controls from 7 hospitals, collecting structural MRI and functional MRI data. Both data types were represented as graphs, processed by 2 graph attention networks, and fused for classification. Grad-CAM with graph convolution ensured interpretability, and partial least squares analyzed gene expression in brain regions.

STUDY RESULTS

Our method excelled in the classification task, achieving 83.32% accuracy, 83.41% sensitivity, and 83.20% specificity in 10-fold cross-validation, surpassing traditional methods. And our multimodal approach outperformed unimodal methods. Grad-CAM identified potential brain biomarkers consistent with gene analysis and prior research.

CONCLUSIONS

Our study demonstrates the effectiveness of deep learning with graph attention networks, surpassing previous SZ diagnostic methods. Multimodal MRI's superiority over unimodal MRI confirms our initial hypothesis. Identifying potential brain biomarkers alongside gene biomarkers holds promise for advancing objective SZ diagnosis and research in SZ.

Neurobiology-based Cognitive Biotypes Using Multi-scale Intrinsic Connectivity Networks in Psychotic Disorders

Objective

Understanding the neurobiology of cognitive dysfunction in psychotic disorders remains elusive, as does developing effective interventions. Limited knowledge about the biological heterogeneity of cognitive dysfunction hinders progress. This study aimed to identify subgroups of patients with psychosis with distinct patterns of functional brain alterations related to cognition (cognitive biotypes).

Methods

B-SNIP consortium data (2,270 participants including participants with psychotic disorders, relatives, and controls) was analyzed. Researchers used reference-informed independent component analysis and the NeuroMark 100k multi-scale intrinsic connectivity networks (ICN) template to obtain subject-specific ICNs and whole-brain functional network connectivity (FNC). FNC features associated with cognitive performance were identified through multivariate joint analysis. K-means clustering identified subgroups of patients based on these features in a discovery set. Subgroups were further evaluated in a replication set and in relatives.

Results

Two biotypes with different functional brain alteration patterns were identified. Biotype 1 exhibited brain-wide alterations, involving hypoconnectivity in cerebellar-subcortical and somatomotor-visual networks and worse cognitive performance. Biotype 2 exhibited hyperconnectivity in somatomotor-subcortical networks and hypoconnectivity in somatomotor-high cognitive processing networks, and better preserved cognitive performance. Demographic, clinical, cognitive, and FNC characteristics of biotypes were consistent in discovery and replication sets, and in relatives. 70.12% of relatives belonged to the same biotype as their affected family members.

Conclusions

These findings suggest two distinctive psychosis-related cognitive biotypes with differing functional brain patterns shared with their relatives. Patient stratification based on these biotypes instead of traditional diagnosis may help to optimize future research and clinical trials addressing cognitive dysfunction in psychotic disorders.

The risk of cannabis use disorder is mediated by altered brain connectivity: A chronnectome study

The brain mechanisms underlying the risk of cannabis use disorder (CUD) are poorly understood. Several studies have reported changes in functional connectivity (FC) in CUD, although none have focused on the study of time-varying patterns of FC. To fill this important gap of knowledge, 39 individuals at risk for CUD and 55 controls, stratified by their score on a self-screening questionnaire for cannabis-related problems (CUDIT-R), underwent resting-state functional magnetic resonance imaging. Dynamic functional connectivity (dFNC) was estimated using independent component analysis, sliding-time window correlations, cluster states and meta-state indices of global dynamics and were compared among groups. At-risk individuals stayed longer in a cluster state with higher within and reduced between network dFNC for the subcortical, sensory-motor, visual, cognitive-control and default-mode networks, relative to controls. More globally, at-risk individuals had a greater number of meta-states and transitions between them and a longer state span and total distance between meta-states in the state space. Our findings suggest that the risk of CUD is associated with an increased dynamic fluidity and dynamic range of FC. This may result in altered stability and engagement of the brain networks, which can ultimately translate into altered cortical and subcortical function conveying CUD risk. Identifying these changes in brain function can pave the way for early pharmacological and neurostimulation treatment of CUD, as much as they could facilitate the stratification of high-risk individuals.

Uncovering Effects of Schizophrenia upon a Maximally Significant, Minimally Complex Subset of Default Mode Network Connectivity Features

A common analysis approach for resting state functional magnetic resonance imaging (rs-fMRI) dynamic functional network connectivity (dFNC) data involves clustering windowed correlation time-series and assigning time windows to clusters (i.e., states) that can be quantified to summarize aspects of the dFNC dynamics. However, those methods can be dominated by a select few features and obscure key dynamics related to less dominant features. This study presents an iterative feature learning approach to identify a maximally significant and minimally complex subset of dFNC features within the default mode network (DMN) in schizophrenia (SZ). Utilizing dFNC data from individuals with SZ and healthy controls (HC), our approach uncovers a subset of features that has a greater number of dFNC states with disorder-related dynamics than is found when all features are present in the clustering. We find that anterior cingulate cortex/posterior cingulate cortex (ACC/PCC) interactions are consistently related to SZ across the most significant iterations of the feature learning analysis and that individuals with SZ tend to spend more time in states with greater intra-ACC anticorrelation and almost no time in a state of high intra-ACC correlation that HCs periodically enter. Our findings highlight the need for nuanced analyses to reveal disorder-related dynamics and advance our understanding of neuropsychiatric disorders.

Searching Reproducible Brain Features using NeuroMark: Templates for Different Age Populations and Imaging Modalities

A primary challenge to the data-driven analysis is the balance between poor generalizability of population-based research and characterizing more subject-, study- and population-specific variability. We previously introduced a fully automated spatially constrained independent component analysis (ICA) framework called NeuroMark and its functional MRI (fMRI) template. NeuroMark has been successfully applied in numerous studies, identifying brain markers reproducible across datasets and disorders. The first NeuroMark template was constructed based on young adult cohorts. We recently expanded on this initiative by creating a standardized normative multi-spatial-scale functional template using over 100,000 subjects, aiming to improve generalizability and comparability across studies involving diverse cohorts. While a unified template across the lifespan is desirable, a comprehensive investigation of the similarities and differences between components from different age populations might help systematically transform our understanding of the human brain by revealing the most well-replicated and variable network features throughout the lifespan. In this work, we introduced two significant expansions of NeuroMark templates first by generating replicable fMRI templates for infants, adolescents, and aging cohorts, and second by incorporating structural MRI (sMRI) and diffusion MRI (dMRI) modalities. Specifically, we built spatiotemporal fMRI templates based on 6,000 resting-state scans from four datasets. This is the first attempt to create robust ICA templates covering dynamic brain development across the lifespan. For the sMRI and dMRI data, we used two large publicly available datasets including more than 30,000 scans to build reliable templates. We employed a spatial similarity analysis to identify replicable templates and investigate the degree to which unique and similar patterns are reflective in different age populations. Our results suggest remarkably high similarity of the resulting adapted components, even across extreme age differences. With the new templates, the NeuroMark framework allows us to perform age-specific adaptations and to capture features adaptable to each modality, therefore facilitating biomarker identification across brain disorders. In sum, the present work demonstrates the generalizability of NeuroMark templates and suggests the potential of new templates to boost accuracy in mental health research and advance our understanding of lifespan and cross-modal alterations.

Analysis of Longitudinal Change Patterns in Developing Brain Using Functional and Structural Magnetic Resonance Imaging via Multimodal Fusion

Functional and structural magnetic resonance imaging (fMRI and sMRI) are complementary approaches that can be used to study longitudinal brain changes in adolescents. Each individual modality offers distinct insights into the brain. Each individual modality may overlook crucial aspects of brain analysis. By combining them, we can uncover hidden brain connections and gain a more comprehensive understanding. In previous work, we identified multivariate patterns of change in whole-brain function during adolescence. In this work, we focus on linking functional change patterns (FCPs) to brain structure. We introduce two approaches and applied them to data from the Adolescent Brain and Cognitive Development (ABCD) dataset. First, we evaluate voxelwise sMRI-FCP coupling to identify structural patterns linked to our previously identified FCPs. Our approach revealed multiple interesting patterns in functional network connectivity (FNC) and gray matter volume (GMV) data that were linked to subject level variation. FCP components 2 and 4 exhibit extensive associations between their loadings and voxel-wise GMV data. Secondly, we leveraged a symmetric multimodal fusion technique called multiset canonical correlation analysis (mCCA) + joint independent component analysis (jICA). Using this approach, we identify structured FCPs such as one showing increased connectivity between visual and sensorimotor domains and decreased connectivity between sensorimotor and cognitive control domains, linked to structural change patterns (SCPs) including alterations in the bilateral sensorimotor cortex. Interestingly, females exhibit stronger coupling between brain functional and structural changes than males, highlighting sex-related differences. The combined results from both asymmetric and symmetric multimodal fusion methods underscore the intricate sex-specific nuances in neural dynamics. By utilizing two complementary multimodal approaches, our study enhances our understanding of the dynamic nature of brain connectivity and structure during the adolescent period, shedding light on the nuanced processes underlying adolescent brain development.

Brain Networks and Intelligence: A Graph Neural Network Based Approach to Resting State fMRI Data

Resting-state functional magnetic resonance imaging (rsfMRI) is a powerful tool for investigating the relationship between brain function and cognitive processes as it allows for the functional organization of the brain to be captured without relying on a specific task or stimuli. In this paper, we present a novel modeling architecture called BrainRGIN for predicting intelligence (fluid, crystallized and total intelligence) using graph neural networks on rsfMRI derived static functional network connectivity matrices. Extending from the existing graph convolution networks, our approach incorporates a clustering-based embedding and graph isomorphism network in the graph convolutional layer to reflect the nature of the brain sub-network organization and efficient network expression, in combination with TopK pooling and attention-based readout functions. We evaluated our proposed architecture on a large dataset, specifically the Adolescent Brain Cognitive Development Dataset, and demonstrated its effectiveness in predicting individual differences in intelligence. Our model achieved lower mean squared errors, and higher correlation scores than existing relevant graph architectures and other traditional machine learning models for all of the intelligence prediction tasks. The middle frontal gyrus exhibited a significant contribution to both fluid and crystallized intelligence, suggesting their pivotal role in these cognitive processes. Total composite scores identified a diverse set of brain regions to be relevant which underscores the complex nature of total intelligence.

More reliable biomarkers and more accurate prediction for mental disorders using a label-noise filtering-based dimensional prediction method

The integration of neuroimaging with artificial intelligence is crucial for advancing the diagnosis of mental disorders. However, challenges arise from incomplete matching between diagnostic labels and neuroimaging. Here, we propose a label-noise filtering-based dimensional prediction (LAMP) method to identify reliable biomarkers and achieve accurate prediction for mental disorders. Our method proposes to utilize a label-noise filtering model to automatically filter out unclear cases from a neuroimaging perspective, and then the typical subjects whose diagnostic labels align with neuroimaging measures are used to construct a dimensional prediction model to score independent subjects. Using fMRI data of schizophrenia patients and healthy controls (n = 1,245), our method yields consistent scores to independent subjects, leading to more distinguishable relabeled groups with an enhanced classification accuracy of 31.89%. Additionally, it enables the exploration of stable abnormalities in schizophrenia. In summary, our LAMP method facilitates the identification of reliable biomarkers and accurate diagnosis of mental disorders using neuroimages.

Towards a multimodal neuroimaging-based risk score for mild cognitive impairment by combining clinical studies with a large (N>37000) population-based study

Alzheimer's disease (AD) is the most common form of age-related dementia, leading to a decline in memory, reasoning, and social skills. While numerous studies have investigated the genetic risk factors associated with AD, less attention has been given to identifying a brain imaging-based measure of AD risk. This study introduces a novel approach to assess mild cognitive impairment MCI, as a stage before AD, risk using neuroimaging data, referred to as a brain-wide risk score (BRS), which incorporates multimodal brain imaging. To begin, we first categorized participants from the Open Access Series of Imaging Studies (OASIS)-3 cohort into two groups: controls (CN) and individuals with MCI. Next, we computed structure and functional imaging features from all the OASIS data as well as all the UK Biobank data. For resting functional magnetic resonance imaging (fMRI) data, we computed functional network connectivity (FNC) matrices using fully automated spatially constrained independent component analysis. For structural MRI data we computed gray matter (GM) segmentation maps. We then evaluated the similarity between each participant's neuroimaging features from the UK Biobank and the difference in the average of those features between CN individuals and those with MCI, which we refer to as the brain-wide risk score (BRS). Both GM and FNC features were utilized in determining the BRS. We first evaluated the differences in the distribution of the BRS for CN vs MCI within the OASIS-3 (using OASIS-3 as the reference group). Next, we evaluated the BRS in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort (using OASIS-3 as the reference group), showing that the BRS can differentiate MCI from CN in an independent data set. Subsequently, using the sMRI BRS, we identified 10 distinct subgroups and similarly, we identified another set of 10 subgroups using the FNC BRS. For sMRI and FNC we observed results that mutually validate each other, with certain aspects being complementary. For the unimodal analysis, sMRI provides greater differentiation between MCI and CN individuals than the fMRI data, consistent with prior work. Additionally, by utilizing a multimodal BRS approach, which combines both GM and FNC assessments, we identified two groups of subjects using the multimodal BRS scores. One group exhibits high MCI risk with both negative GM and FNC BRS, while the other shows low MCI risk with both positive GM and FNC BRS. Moreover, in the UKBB we have 46 participants diagnosed with AD showed FNC and GM patterns similar to those in high-risk groups, defined in both unimodal and multimodal BRS. Finally, to ensure the reproducibility of our findings, we conducted a validation analysis using the ADNI as an additional reference dataset and repeated the above analysis. The results were consistently replicated across different reference groups, highlighting the potential of FNC and sMRI-based BRS in early Alzheimer's detection.

Brain dynamics reflecting an intra-network brain state is associated with increased posttraumatic stress symptoms in the early aftermath of trauma

This study examines the association between brain dynamic functional network connectivity (dFNC) and current/future posttraumatic stress (PTS) symptom severity, and the impact of sex on this relationship. By analyzing 275 participants' dFNC data obtained ~2 weeks after trauma exposure, we noted that brain dynamics of an inter-network brain state link negatively with current (r=-0.179, pcorrected= 0.021) and future (r=-0.166, pcorrected= 0.029) PTS symptom severity. Also, dynamics of an intra-network brain state correlated with future symptom intensity (r = 0.192, pcorrected = 0.021). We additionally observed that the association between the network dynamics of the inter-network brain state with symptom severity is more pronounced in females (r=-0.244, pcorrected = 0.014). Our findings highlight a potential link between brain network dynamics in the aftermath of trauma with current and future PTSD outcomes, with a stronger protective effect of inter-network brain states against symptom severity in females, underscoring the importance of sex differences.

Multimodal Mental Health Digital Biomarker Analysis From Remote Interviews Using Facial, Vocal, Linguistic, and Cardiovascular Patterns

OBJECTIVE

Psychiatric evaluation suffers from subjectivity and bias, and is hard to scale due to intensive professional training requirements. In this work, we investigated whether behavioral and physiological signals, extracted from tele-video interviews, differ in individuals with psychiatric disorders.

METHODS

Temporal variations in facial expression, vocal expression, linguistic expression, and cardiovascular modulation were extracted from simultaneously recorded audio and video of remote interviews. Averages, standard deviations, and Markovian process-derived statistics of these features were computed from 73 subjects. Four binary classification tasks were defined: detecting 1) any clinically-diagnosed psychiatric disorder, 2) major depressive disorder, 3) self-rated depression, and 4) self-rated anxiety. Each modality was evaluated individually and in combination.

RESULTS

Statistically significant feature differences were found between psychiatric and control subjects. Correlations were found between features and self-rated depression and anxiety scores. Heart rate dynamics provided the best unimodal performance with areas under the receiver-operator curve (AUROCs) of 0.68-0.75 (depending on the classification task). Combining multiple modalities provided AUROCs of 0.72-0.82.

CONCLUSION

Multimodal features extracted from remote interviews revealed informative characteristics of clinically diagnosed and self-rated mental health status.

SIGNIFICANCE

The proposed multimodal approach has the potential to facilitate scalable, remote, and low-cost assessment for low-burden automated mental health services.

Explainable fuzzy clustering framework reveals divergent default mode network connectivity dynamics in schizophrenia

Introduction

Dynamic functional network connectivity (dFNC) analysis of resting state functional magnetic resonance imaging data has yielded insights into many neurological and neuropsychiatric disorders. A common dFNC analysis approach uses hard clustering methods like k-means clustering to assign samples to states that summarize network dynamics. However, hard clustering methods obscure network dynamics by assuming (1) that all samples within a cluster are equally like their assigned centroids and (2) that samples closer to one another in the data space than to their centroids are well-represented by their centroids. In addition, it can be hard to compare subjects, as in some cases an individual may not manifest a state strongly enough to enter a hard cluster. Approaches that allow a dimensional approach to connectivity patterns (e.g., fuzzy clustering) can mitigate these issues. In this study, we present an explainable fuzzy clustering framework by combining fuzzy c-means clustering with several explainability metrics and novel summary features.

Methods

We apply our framework for schizophrenia (SZ) default mode network analysis. Namely, we extract dFNC from individuals with SZ and controls, identify 5 dFNC states, and characterize the dFNC features most crucial to those states with a new perturbation-based clustering explainability approach. We then extract several features typically used in hard clustering and further present a variety of unique features specially designed for use with fuzzy clustering to quantify state dynamics. We examine differences in those features between individuals with SZ and controls and further search for relationships between those features and SZ symptom severity.

Results

Importantly, we find that individuals with SZ spend more time in states of moderate anticorrelation between the anterior and posterior cingulate cortices and strong anticorrelation between the precuneus and anterior cingulate cortex. We further find that individuals with SZ tend to transition more rapidly than controls between low-magnitude and high-magnitude dFNC states.

Conclusion

We present a novel dFNC analysis framework and use it to identify effects of SZ upon network dynamics. Given the ease of implementing our framework and its enhanced insight into network dynamics, it has great potential for use in future dFNC studies.

Intra-Atlas Node Size Effects on Graph Metrics in fMRI Data: Implications for Alzheimer's Disease and Cognitive Impairment

Network neuroscience, a multidisciplinary field merging insights from neuroscience and network theory, offers a profound understanding of neural network intricacies. However, the impact of varying node sizes on computed graph metrics in neuroimaging data remains underexplored. This study addresses this gap by adopting a data-driven methodology to delineate functional nodes and assess their influence on graph metrics. Using the Neuromark framework, automated independent component analysis is applied to resting state fMRI data, capturing functional network connectivity (FNC) matrices. Global and local graph metrics reveal intricate connectivity patterns, emphasizing the need for nuanced analysis. Notably, node sizes, computed based on voxel counts, contribute to a novel metric termed 'node-metric coupling' (NMC). Correlations between graph metrics and node dimensions are consistently observed. The study extends its analysis to a dataset comprising Alzheimer's disease, mild cognitive impairment, and control subjects, showcasing the potential of NMC as a biomarker for brain disorders. The two key outcomes underscore the interplay between node sizes and resultant graph metrics within a given atlas, shedding light on an often-overlooked source of variability. Additionally, the study highlights the utility of NMC as a valuable biomarker, emphasizing the necessity of accounting for node sizes in future neuroimaging investigations. This work contributes to refining comparative studies employing diverse atlases and advocates for thoughtful consideration of intra-atlas node size in shaping graph metrics, paving the way for more robust neuroimaging research.

Neuromark PET: A multivariate method for Estimating and comparing whole brain functional networks and connectomes from fMRI and PET data

Positron emission tomography (PET) and magnetic resonance imaging (MRI) are both widely used neuroimaging techniques to study brain function. Although whole brain resting functional MRI (fMRI) connectomes are widely used, the integration or association of whole brain functional connectomes with PET data are rarely done. This likely stems from the fact that PET data is typically analyzed by using a regions of interest approach, while whole brain spatial networks and their connectivity (covariation) receive much less attention. As a result, to date, there have been no direct comparisons between whole brain PET and fMRI connectomes. In this study, we present a method that uses spatially constrained independent component analysis (scICA) to estimate corresponding PET and fMRI connectomes and examine the relationship between them using mild cognitive impairment (MCI) datasets. Our results demonstrate highly modularized PET connectome patterns that complement those identified from resting fMRI. In particular, fMRI showed strong intra-domain connectivity with interdomain anticorrelation in sensorimotor and visual domains as well as default mode network. PET amyloid data showed similar strong intra-domain effects, but showed much higher correlations within cognitive control and default mode domains, as well as anticorrelation between cerebellum and other domains. The estimated PET networks have similar, but not identical, network spatial patterns to the resting fMRI networks, with the PET networks being slightly smoother and, in some cases, showing variations in subnodes. We also analyzed the differences between individuals with MCI receiving medication versus a placebo. Results show both common and modality specific treatment effects on fMRI and PET connectomes. From our fMRI analysis, we observed higher activation differences in various regions, such as the connection between the thalamus and middle occipital gyrus, as well as the insula and right middle occipital gyrus. Meanwhile, the PET analysis revealed increased activation between the anterior cingulate cortex and the left inferior parietal lobe, along with other regions, in individuals who received medication versus placebo. In sum, our novel approach identifies corresponding whole-brain PET and fMRI networks and connectomes. While we observed common patterns of network connectivity, our analysis of the MCI treatment and placebo groups revealed that each modality identifies a unique set of networks, highlighting differences between the two groups.

Dynamic fusion of genomics and functional network connectivity in UK biobank reveals static and time-varying SNP manifolds

Many psychiatric and neurological disorders show significant heritability, indicating strong genetic influence. In parallel, dynamic functional network connectivity (dFNC) measures functional temporal coupling between brain networks in a time-varying manner and has proven to identify disease-related changes in the brain. However, it remains largely unclear how genetic risk contributes to brain dysconnectivity that further manifests into clinical symptoms. The current work aimed to address this gap by proposing a novel joint ICA (jICA)-based "dynamic fusion" framework to identify dynamically tuned SNP manifolds by linking static SNPs to dynamic functional information of the brain. The sliding window approach was utilized to estimate four dFNC states and compute subject-level state-specific dFNC features. Each state of dFNC features were then combined with 12946 SZ risk SNPs for jICA decomposition, resulting in four parallel fusions in 32861 European ancestry individuals within the UK Biobank cohort. The identified joint SNP-dFNC components were further validated for SZ relevance in an aggregated SZ cohort, and compared for across-state similarity to indicate level of dynamism. The results supported that dynamic fusion yielded "static" and "dynamic" components (i.e., high and low across-state similarity, respectively) for SNP and dFNC modalities. As expected, the SNP components presented a mixture of static and dynamic manifolds, with the latter largely driven by fusion with dFNC. We also showed that some of the dynamic SNP manifolds uniquely elicited by fusion with state-specific dFNC features complemented each other in terms of biological interpretation. This dynamic fusion framework thus allows expanding the SNP modality to manifolds in the time dimension, which provides a unique lens to elicit unique SNP correlates of dFNC otherwise unseen, promising additional insights on how genetic risk links to disease-related dysconnectivity.

Longitudinal resting-state network connectivity changes in electroconvulsive therapy patients compared to healthy controls

OBJECTIVE

Electroconvulsive therapy (ECT) is effective for major depressive episodes. Understanding of underlying mechanisms has been increased by examining changes of brain connectivity but studies often do not correct for test-retest variability in healthy controls (HC). In this study, we investigated changes in resting-state networks after ECT in a multicenter study.

METHODS

Functional resting-state magnetic resonance imaging data, acquired before start and within one week after ECT, from 90 depressed patients were analyzed, as well as longitudinal data of 24 HC. Group-information guided independent component analysis (GIG-ICA) was used to spatially restrict decomposition to twelve canonical resting-state networks. Selected networks of interest were the default mode network (DMN), salience network (SN), and left and right frontoparietal network (LFPN, and RFPN). Whole-brain voxel-wise analyses were used to assess group differences at baseline, group by time interactions, and correlations with treatment effectiveness. In addition, between-network connectivity and within-network strengths were computed.

RESULTS

Within-network strength of the DMN was lower at baseline in ECT patients which increased after ECT compared to HC, after which no differences were detected. At baseline, ECT patients showed lower whole-brain voxel-wise DMN connectivity in the precuneus. Increase of within-network strength of the LFPN was correlated with treatment effectiveness. We did not find whole-brain voxel-wise or between-network changes.

CONCLUSION

DMN within-network connectivity normalized after ECT. Within-network increase of the LFPN in ECT patients was correlated with higher treatment effectiveness. In contrast to earlier studies, we found no whole-brain voxel-wise changes, which highlights the necessity to account for test-retest effects.

Association between the oral microbiome and brain resting state connectivity in schizophrenia

Recent microbiome-brain axis findings have shown evidence of the modulation of microbiome community as an environmental mediator in brain function and psychiatric illness. This work is focused on the role of the microbiome in understanding a rarely investigated environmental involvement in schizophrenia (SZ), especially in relation to brain circuit dysfunction. We leveraged high throughput microbial 16s rRNA sequencing and functional neuroimaging techniques to enable the delineation of microbiome-brain network links in SZ. N=213 SZ and healthy control (HC) subjects were assessed for the oral microbiome. Among them, 139 subjects were scanned by resting-state functional magnetic resonance imaging (rsfMRI) to derive brain functional connectivity. We found a significant microbiome compositional shift in SZ beta diversity (weighted UniFrac distance, p= 6×10 -3 ; Bray-Curtis distance p = 0.021). Fourteen microbial species involving pro-inflammatory and neurotransmitter signaling and H 2 S production, showed significant abundance alterations in SZ. Multivariate analysis revealed one pair of microbial and functional connectivity components showing a significant correlation of 0.46. Thirty five percent of microbial species and 87.8% of brain functional network connectivity from each component also showed significant differences between SZ and HC with strong performance in classifying SZ from HC, with an area under curve (AUC) = 0.84 and 0.87, respectively. The results suggest a potential link between oral microbiome dysbiosis and brain functional connectivity alteration in relation to SZ, possibly through immunological and neurotransmitter signaling pathways and the hypothalamic-pituitary-adrenal axis, supporting for future work in characterizing the role of oral microbiome in mediating effects on SZ brain functional activity.

Dynamic phase-locking states and personality in sub-acute mild traumatic brain injury: An exploratory study

Research has shown that maladaptive personality characteristics, such as Neuroticism, are associated with poor outcome after mild traumatic brain injury (mTBI). The current exploratory study investigated the neural underpinnings of this process using dynamic functional network connectivity (dFNC) analyses of resting-state (rs) fMRI, and diffusion MRI (dMRI). Twenty-seven mTBI patients and 21 healthy controls (HC) were included. After measuring the Big Five personality dimensions, principal component analysis (PCA) was used to obtain a superordinate factor representing emotional instability, consisting of high Neuroticism, moderate Openness, and low Extraversion, Agreeableness, and Conscientiousness. Persistent symptoms were measured using the head injury symptom checklist at six months post-injury; symptom severity (i.e., sum of all items) was used for further analyses. For patients, brain MRI was performed in the sub-acute phase (~1 month) post-injury. Following parcellation of rs-fMRI using independent component analysis, leading eigenvector dynamic analysis (LEiDA) was performed to compute dynamic phase-locking brain states. Main patterns of brain diffusion were computed using tract-based spatial statistics followed by PCA. No differences in phase-locking state measures were found between patients and HC. Regarding dMRI, a trend significant decrease in fractional anisotropy was found in patients relative to HC, particularly in the fornix, genu of the corpus callosum, anterior and posterior corona radiata. Visiting one specific phase-locking state was associated with lower symptom severity after mTBI. This state was characterized by two clearly delineated communities (each community consisting of areas with synchronized phases): one representing an executive/saliency system, with a strong contribution of the insulae and basal ganglia; the other representing the canonical default mode network. In patients who scored high on emotional instability, this relationship was even more pronounced. Dynamic phase-locking states were not related to findings on dMRI. Altogether, our results provide preliminary evidence for the coupling between personality and dFNC in the development of long-term symptoms after mTBI.

Voxel-wise Fusion of Resting fMRI Networks and Gray Matter Volume for Alzheimer's Disease Classification using Deep Multimodal Learning

Alzheimer's disease (AD) is a prevalent neurodegenerative disorder requiring accurate and early diagnosis for effective treatment. Resting-state functional magnetic resonance imaging (rs-fMRI) and gray matter volume analysis from structural MRI have emerged as valuable tools for investigating AD-related brain alterations. However, the potential benefits of integrating these modalities using deep learning techniques remain unexplored. In this study, we propose a novel framework that fuses composite images of multiple rs-fMRI networks (called voxelwise intensity projection) and gray matter segmentation images through a deep learning approach for improved AD classification. We demonstrate the superiority of fMRI networks over commonly used metrics such as amplitude of low-frequency fluctuations (ALFF) and fractional ALFF in capturing spatial maps critical for AD classification. We use a multi-channel convolutional neural network incorporating the AlexNet dropout architecture to effectively model spatial and temporal dependencies in the integrated data. Extensive experiments on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset of AD patients and cognitively normal (CN) validate the efficacy of our approach, showcasing improved classification performance of 94.12% test accuracy and an area under the curve (AUC) score of 97.79 compared to existing methods. Our results show that the fusion results generally outperformed the unimodal results. The saliency visualizations also show significant differences in the hippocampus, amygdala, putamen, caudate nucleus, and regions of basal ganglia which are in line with the previous neurobiological literature. Our research offers a novel method to enhance our grasp of AD pathology. By integrating data from various functional networks with structural MRI insights, we significantly improve diagnostic accuracy. This accuracy is further boosted by the effective visualization of this combined information. This lays the groundwork for further studies focused on providing a more accurate and personalized approach to AD diagnosis. The proposed framework and insights gained from fMRI networks provide a promising avenue for future research in deep multimodal fusion and neuroimaging analysis.

Identifying canonical and replicable multi-scale intrinsic connectivity networks in 100k+ resting-state fMRI datasets

Despite the known benefits of data-driven approaches, the lack of approaches for identifying functional neuroimaging patterns that capture both individual variations and inter-subject correspondence limits the clinical utility of rsfMRI and its application to single-subject analyses. Here, using rsfMRI data from over 100k individuals across private and public datasets, we identify replicable multi-spatial-scale canonical intrinsic connectivity network (ICN) templates via the use of multi-model-order independent component analysis (ICA). We also study the feasibility of estimating subject-specific ICNs via spatially constrained ICA. The results show that the subject-level ICN estimations vary as a function of the ICN itself, the data length, and the spatial resolution. In general, large-scale ICNs require less data to achieve specific levels of (within- and between-subject) spatial similarity with their templates. Importantly, increasing data length can reduce an ICN's subject-level specificity, suggesting longer scans may not always be desirable. We also find a positive linear relationship between data length and spatial smoothness (possibly due to averaging over intrinsic dynamics), suggesting studies examining optimized data length should consider spatial smoothness. Finally, consistency in spatial similarity between ICNs estimated using the full data and subsets across different data lengths suggests lower within-subject spatial similarity in shorter data is not wholly defined by lower reliability in ICN estimates, but may be an indication of meaningful brain dynamics which average out as data length increases.

dcSBM: A federated constrained source-based morphometry approach for multivariate brain structure mapping

The examination of multivariate brain morphometry patterns has gained attention in recent years, especially for their powerful exploratory capabilities in the study of differences between patients and controls. Among the many existing methods and tools for the analysis of brain anatomy based on structural magnetic resonance imaging data, data-driven source-based morphometry (SBM) focuses on the exploratory detection of such patterns. Here, we implement a semi-blind extension of SBM, called constrained source-based morphometry (constrained SBM), which enables the extraction of maximally independent reference-alike sources using the constrained independent component analysis (ICA) approach. To do this, we combine SBM with a set of reference components covering the full brain, derived from a large independent data set (UKBiobank), to provide a fully automated SBM framework. This also allows us to implement a federated version of constrained SBM (cSBM) to allow analysis of data that is not locally accessible. In our proposed decentralized constrained source-based morphometry (dcSBM), the original data never leaves the local site. Each site operates constrained ICA on its private local data using a common distributed computation platform. Next, an aggregator/master node aggregates the results estimated from each local site and applies statistical analysis to estimate the significance of the sources. Finally, we utilize two additional multisite patient data sets to validate our model by comparing the resulting group difference estimates from both cSBM and dcSBM.

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

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