Multi-scale brain networks

Combining radiomics and connectomics in MRI studies of the human brain: A systematic literature review

Advances in MRI techniques continue to open new avenues to investigate the structure and function of the human brain. Radiomics, involving the extraction of quantitative image features, and connectomics, involving the estimation of structural and functional neural connections, from large amounts and different types of MRI data sets, represent two key research areas for advancing neuroimaging while exploiting progress in computational and theoretical modelling applied to MRI. This systematic literature review aimed at exploring the combination of radiomics and connectomics in human brain MRI studies, highlighting how the combination of these approaches can provide novel or additional insights into the human brain under normal and pathological conditions. The review was conducted according to the Preferred Reported Item for Systematic Reviews and Meta-Analyses (PRISMA) statement, seeking documents from Scopus and PubMed archives. Eleven studies (out of the initial 675 records) have met the established criteria and reported combined approaches from radiomics and connectomics. Three subgroups of approaches were identified, based on the MRI modalities used to obtain radiomic and connectomic features. The first group of 3 studies combined radiomics and connectomics applied to structural MRI (sMRI) data sets; the second group of 5 studies combined radiomics applied to sMRI data and connectomics applied to diffusion (dMRI) and/or functional MRI (fMRI) data sets; the third group of 3 studies combined radiomics and connectomics applied to fMRI. This review highlighted the recent growing interest in combining MRI-based radiomics and connectomics to explore the human brain for neurological, psychiatric, and oncological conditions. Current methodologies and challenges were discussed, pointing out future research directions to improve or standardize these approaches and the gaps to be filled to advance the field.

Multi-Metric Approach for the Comparison of Denoising Techniques for Resting-State fMRI

Despite the increasing use of resting-state functional magnetic resonance imaging (rs-fMRI) data for studying the spontaneous functional interactions within the brain, the achievement of robust results is often hampered by insufficient data quality and by poor knowledge of the most effective denoising methods. The present study aims to define an appropriate denoising strategy for rs-fMRI data by proposing a robust framework for the quantitative and comprehensive comparison of the performance of multiple pipelines made available by the newly proposed HALFpipe software. This will ultimately contribute to standardizing rs-fMRI preprocessing and denoising steps. Fifty-three participants took part in the study by undergoing a rs-fMRI session. Synthetic rs-fMRI data from one subject were also generated. Nine different denoising pipelines were applied in parallel to the minimally preprocessed fMRI data. The comparison was conducted by computing previously proposed and novel metrics that quantify the degree of artifact removal, signal enhancement, and resting-state network identifiability. A summary performance index, accounting for both noise removal and information preservation, was proposed. The results confirm the performance heterogeneity of different denoising pipelines across the different quality metrics. In both real and synthetic data, the summary performance index favored the denoising strategy including the regression of mean signals from white matter and cerebrospinal fluid brain areas and global signal. This pipeline resulted in the best compromise between artifact removal and preservation of the information on resting-state networks. Our study provided useful methodological tools and key information on the effectiveness of multiple denoising strategies for rs-fMRI data. Besides providing a robust comparison approach that could be adapted to other fMRI studies, a suitable denoising pipeline for rs-fMRI data was identified, which could be used to improve the reproducibility of rs-fMRI findings.

The changes in neural complexity and connectivity in thalamocortical and cortico-cortical systems after propofol-induced unconsciousness in different temporal scales

Existing studies have indicated neural activity across diverse temporal and spatial scales. However, the alterations in complexity, functional connectivity, and directional connectivity within the thalamocortical and corticocortical systems across various scales during propofol-induced unconsciousness remain uncertain. We analyzed the stereo-electroencephalography (SEEG) from wakefulness to unconsciousness among the brain regions of the prefrontal cortex, temporal lobe, and anterior nucleus of the thalamus. The complexity (examined by permutation entropy (PE)), functional connectivity (permutation mutual information (PMI)), and directional connectivity (symbolic conditional mutual information (SCMI) and directionality index (DI)) were calculated across various scales. In the lower-band frequency (0.1-45 Hz) SEEG, after the loss of consciousness, PE significantly decreased (p < 0.001) in all regions and scales, except for the thalamus, which remained relatively unchanged at large scales (τ=32 ms). Following the loss of consciousness, inter-regional PMI either significantly increased or remained stable across different scales (τ=4 ms to 32 ms). During the unconscious state, SCMI between brain regions exhibited inconsistent changes across scales. In the late unconscious stage, the inter-regional DI across all scales indicated a shift from a balanced state of information flow between brain regions to a pattern where the prefrontal cortex and thalamus drive the temporal lobe. Our findings demonstrate that propofol-induced unconsciousness is associated with reduced cortical complexity, diverse functional connectivity, and a disrupted balance of information integration among thalamocortical and cortico-cortical systems. This study enhances the theoretical understanding of anesthetic-induced loss of consciousness by elucidating the scale- and region-specific effects of propofol on thalamocortical and cortico-cortical systems.

Multimodal gradients unify local and global cortical organization

Functional specialization of brain areas and subregions, as well as their integration into large-scale networks, are key principles in neuroscience. Consolidating both local and global perspectives on cortical organization, however, remains challenging. Here, we present an approach to integrate inter- and intra-areal similarities of microstructure, structural connectivity, and functional interactions. Using high-field in-vivo 7 tesla (7 T) Magnetic Resonance Imaging (MRI) data and a probabilistic post-mortem atlas of cortical cytoarchitecture, we derive multimodal gradients that capture cortex-wide organization. Inter-areal similarities follow a canonical sensory-fugal gradient, linking cortical integration with functional diversity across tasks. However, intra-areal heterogeneity does not follow this pattern, with greater variability in association cortices. Findings are replicated in an independent 7 T dataset and a 100-subject 3 tesla (3 T) cohort. These results highlight a robust coupling between local arealization and global cortical motifs, advancing our understanding of how specialization and integration shape human brain function.

Stimulation mapping and whole-brain modeling reveal gradients of excitability and recurrence in cortical networks

The human brain exhibits a modular and hierarchical structure, spanning low-order sensorimotor to high-order cognitive/affective systems. What is the mechanistic significance of this organization for brain dynamics and information processing properties? We investigated this question using rare simultaneous multimodal electrophysiology (stereotactic and scalp electroencephalography - EEG) recordings in 36 patients with drug-resistant focal epilepsy during presurgical intracerebral electrical stimulation (iES) (323 stimulation sessions). Our analyses revealed an anatomical gradient of excitability across the cortex, with stronger iES-evoked EEG responses in high-order compared to low-order regions. Mathematical modeling further showed that this variation in excitability levels results from a differential dependence on recurrent feedback from non-stimulated regions across the anatomical hierarchy, and could be extinguished by suppressing those connections in-silico. High-order brain regions/networks thus show an activity pattern characterized by more inter-network functional integration than low-order ones, which manifests as a spatial gradient of excitability that is emergent from, and causally dependent on, the underlying hierarchical network structure. These findings offer new insights into how hierarchical brain organization influences cognitive functions and could inform strategies for targeted neuromodulation therapies.

Brain overlapping system-level architecture influenced by external magnetic stimulation and internal gene expression in AD-spectrum patients

The brain overlapping system-level architecture is associated with functional information integration in the multiple roles of the same region, and it has been developed as an underlying novel biomarker of brain disease and may characterise the indicators for the treatment of Alzheimer's disease (AD). However, it remains uncertain whether these changes are influenced by external magnetic stimulation and internal gene expression. A total of 73 AD-spectrum patients (52 with true stimulation and 21 with sham stimulation) were underwent four-week neuronavigated transcranial magnetic stimulation (rTMS). Shannon-entropy diversity coefficient analysis was used to explore the brain overlapping system of the neuroimaging data in these pre- and posttreatment patients. Transcription-neuroimaging association analysis was further performed via gene expression data from the Allen Human Brain Atlas. Compared with the rTMS_sham stimulation group, the rTMS_true stimulation group achieved the goal of cognitive improvement through the reconstruction of functional information integration in the multiple roles of 27 regions associated with the brain overlapping system, involving the attentional network, sensorimotor network, default mode network and limbic network. Furthermore, these overlapping regions were closely linked to gene expression on cellular homeostasis and immune inflammation, and support vector regression analysis revealed that the baseline diversity coefficients of the attentional and sensorimotor networks can effectively predict memory improvement after rTMS treatment. These findings highlight the brain overlapping system associated with cognitive improvement, and provide the first evidence that external magnetic stimulation and internal gene expression could influence these overlapping regions in AD-spectrum patients.

Heterogeneous nucleation due to adaptation disparity and phase lag in a finite-size adaptive dynamical network

We investigate the influence of adaptation disparity and phase lag on the heterogeneous nucleation leading to multi-step and single-step phase transitions in a finite-size adaptive network due to frequency disorders. We elucidate that the adaptation disparity predominates the effect of frequency disorder in seeding the heterogeneous nucleation. Further, a large phase lag facilitates almost a continuous spectrum of partially and fully synchronized frequency clusters, and multistability among them. We also find that the underlying mechanisms of heterogeneous nucleation due to the adaptation disparity and phase lag parameters are distinctly different from that observed only in the presence of disorders. Furthermore, we also analytically deduce the macroscopic evolution equations for the cluster dynamics using the collective coordinates framework and show that resulting reduced dynamics mimic the observed heterogeneous phase transitions of the adaptive network under adaptation disparity and phase lag. Further, we deduce the upper bound for the coupling strength for the existence of two intra-clusters explicitly in terms of the adaptation disparity and phase lag parameters for the onset of the abrupt single-step transition.

Modeling the interplay between regional heterogeneity and critical dynamics underlying brain functional networks

The human brain exhibits heterogeneity across regions and network connectivity patterns; However, how these heterogeneities contribute to whole-brain network functions and cognitive capacities remains unclear. In this study, we focus on the regional heterogeneity reflected in local dynamics and study how it contributes to the emergence of functional connectivity patterns, network ignition dynamics of the empirical brains. We find that the level of synchrony among voxelwise neural activities measured from the fMRI data is significantly correlated with the transcriptional variations in excitatory and inhibitory receptor gene expression. Consequently, we construct heterogeneous whole-brain network models with nodal excitability calibrated by the synchronization measure of regional dynamics. We demonstrate that as the extent of heterogeneity increases, the models operating around the critical point between order and disorder generate simulated functional connectivity networks increasingly similar to empirical resting-state or working memory task-evoked function connectivity networks. Furthermore, the heterogeneous models can predict individual differences in resting-state and task-evoked reconfiguration of the functional connectivity, as well as the comparative causal effect of empirical brain networks-that is, how the dynamics of one brain region affect whole-brain synchronization. Overall, this work demonstrates the viability of using regional heterogeneous functional signals to improve the performance of the whole-brain models, and illustrates how regional heterogeneity in human brains interplays with structural connections and critical dynamics to contribute to the emergence of functional connectivity networks.

From Dyadic to Higher-Order Interactions: Enhanced Representation of Homotopic Functional Connectivity Through Control of Intervening Variables

Background: The brain's complex functionality emerges from network interactions that go beyond dyadic connections, with higher-order interactions significantly contributing to this complexity. Homotopic functional connectivity (HoFC) is a key neurophysiological characteristic of the human brain, reflecting synchronized activity between corresponding regions in the brain's hemispheres. Materials and Methods: Using resting-state functional magnetic resonance imaging data from the Human Connectome Project, we evaluate dyadic and higher-order interactions of three functional connectivity (FC) parameterizations-bivariate correlation, partial correlation, and tangent space embedding-in their effectiveness at capturing HoFC through the inter-hemispheric analogy test. Results: Higher-order feature vectors are generated through node2vec, a random walk-based node embedding technique applied to FC networks. Our results show that higher-order feature vectors derived from partial correlation most effectively represent HoFC, while tangent space embedding performs best for dyadic interactions. Discussion: These findings validate HoFC and underscore the importance of the FC construction method in capturing intrinsic characteristics of the human brain.

The multiscale self-similarity of the weighted human brain connectome

Anatomical connectivity between different brain regions can be mapped to a network representation, the connectome, where the intensities of the links, the weights, influence resilience and functional processes. Yet, many features associated with these weights are not fully understood, particularly their multiscale organization. In this paper, we elucidate the architecture of weights, including weak ties, in multiscale human brain connectomes reconstructed from empirical data. Our findings reveal multiscale self-similarity, including the ordering of weak ties, in every individual connectome and group representative. This phenomenon is captured by a renormalization technique based on a geometric network model that replicates the observed structure of connectomes across all length scales, using the same connectivity law and weighting function for both weak and strong ties. The observed symmetry represents a signature of criticality in the weighted connectivity of the human brain and raises important questions for future research, such as the existence of symmetry breaking at some scale or whether it is preserved in cases of neurodegeneration or psychiatric disorder.

Further N-Frame networking dynamics of conscious observer-self agents via a functional contextual interface: predictive coding, double-slit quantum mechanical experiment, and decision-making fallacy modeling as applied to the measurement problem in humans and AI

Artificial intelligence (AI) has made some remarkable advances in recent years, particularly within the area of large language models (LLMs) that produce human-like conversational abilities via utilizing transformer-based architecture. These advancements have sparked growing calls to develop tests not only for intelligence but also for consciousness. However, existing benchmarks assess reasoning abilities across various domains but fail to directly address consciousness. To bridge this gap, this paper introduces the functional contextual N-Frame model, a novel framework integrating predictive coding, quantum Bayesian (QBism), and evolutionary dynamics. This comprehensive model explicates how conscious observers, whether human or artificial, should update beliefs and interact within a quantum cognitive system. It provides a dynamic account of belief evolution through the interplay of internal observer states and external stimuli. By modeling decision-making fallacies such as the conjunction fallacy and conscious intent collapse experiments within this quantum probabilistic framework, the N-Frame model establishes structural and functional equivalence between cognitive processes identified within these experiments and traditional quantum mechanics (QM). It is hypothesized that consciousness serves as an active participant in wavefunction collapse (or actualization of the physical definite states we see), bridging quantum potentiality and classical outcomes via internal observer states and contextual interactions via a self-referential loop. This framework formalizes decision-making processes within a Hilbert space, mapping cognitive states to quantum operators and contextual dependencies, and demonstrates structural and functional equivalence between cognitive and quantum systems in order to address the measurement problem. Furthermore, the model extends to testable predictions about AI consciousness by specifying informational boundaries, contextual parameters, and a conscious-time dimension derived from Anti-de Sitter/Conformal Field Theory correspondence (AdS/CFT). This paper theorizes that human cognitive biases reflect adaptive, evolutionarily stable strategies that optimize predictive accuracy (i.e., evolved quantum heuristic strategies rather than errors relative to classical rationality) under uncertainty within a quantum framework, challenging the classical interpretation of irrationality. The N-Frame model offers a unified account of consciousness, decision-making, behavior, and quantum mechanics, incorporating the idea of finding truth without proof (thus overcoming Gödelian uncertainty), insights from quantum probability theory (such as the Linda cognitive bias findings), and the possibility that consciousness can cause waveform collapse (or perturbation) accounting for the measurement problem. It proposes a process for conscious time and branching worldlines to explain subjective experiences of time flow and conscious free will. These theoretical advancements provide a foundation for interdisciplinary exploration into consciousness, cognition, and quantum systems, offering a path toward developing tests for AI consciousness and addressing the limitations of classical computation in representing conscious agency.

Neural correlates of pain acceptance and the role of the cerebellum: Functional connectivity and anatomical differences in individuals with headaches versus matched controls

BACKGROUND

Despite functional connectivity network dysfunction among individuals with headaches, no studies have examined functional connectivity neural correlates and anatomical differences in coping with headaches.

METHODS

This study investigated inter-individual variability in whole-brain functional connectivity and anatomical differences among 37 individuals with primary headaches and 24 age- and gender-matched controls, and neural correlates of psychological flexibility (PF) that was previously found to contribute to headache adjustment. Participants (84% women; M headache severity = 4/10; M age = 43 years) underwent functional magnetic resonance imaging scans and completed questionnaires to examine global and subnetwork brain areas, and their relations with PF components, controlling for age, gender, education, and head-motion.

RESULTS

Seed and voxel-based contrast analyses between groups showed atypical functional connectivity of regions involved in pain matrix and core resting-state networks. Pain acceptance was the sole PF component that correlated with the cerebellum (x, y, z: 28, -72, -34, p-false discovery rate <0.001), where individuals with headaches showed higher grey matter density compared to controls.

CONCLUSIONS

The cerebellum, recently implicated in modulating emotional and cognitive processes, was indicated to process information resembling what individuals do when practicing pain acceptance. Our findings establish for the first time this connection of the cerebellum and its role in pain acceptance. We propose that pain acceptance might be a behavioural biomarker target that could modulate problematic headache perceptions and brain networks abnormalities.

SIGNIFICANCE

This study highlights the potential use of emerging behavioural biomarkers in headache management, such as pain acceptance, and their role in modifying the headache experience. Notably, grey matter reorganization in the cerebellum and other known brain pain networks, could indicate brain networks that can be modified from targeted behavioural interventions to help decode the nociplastic mechanisms that predominates in headaches.

Understanding cognitive processes across spatial scales of the brain

Cognition arises from neural operations at multiple spatial scales, from individual neurons to large-scale networks. Despite extensive research on coding principles and emergent cognitive processes across brain areas, investigation across scales has been limited. Here, we propose ways to test the idea that different cognitive processes emerge from distinct information coding principles at various scales, which collectively give rise to complex behavior. This approach involves comparing brain-behavior associations and the underlying neural geometry across scales, alongside an investigation of global and local scale interactions. Bridging findings across species and techniques through open science and collaborations is essential to comprehensively understand the multiscale brain and its functions.

When neuromodulation met control theory

The brain is a highly complex physical system made of assemblies of neurons that work together to accomplish elaborate tasks such as motor control, memory and perception. How these parts work together has been studied for decades by neuroscientists using neuroimaging, psychological manipulations, and neurostimulation. Neurostimulation has gained particular interest, given the possibility to perturb the brain and elicit a specific response. This response depends on different parameters such as the intensity, the location and the timing of the stimulation. However, most of the studies performed so far used previously established protocols without considering the ongoing brain activity and, thus, without adaptively targeting the stimulation. In control theory, this approach is called open-loop control, and it is always paired with a different form of control called closed-loop, in which the current activity of the brain is used to establish the next stimulation. Recently, neuroscientists are beginning to shift from classical fixed neuromodulation studies to closed-loop experiments. This new approach allows the control of brain activity based on responses to stimulation and thus to personalize individual treatment in clinical conditions. Here, we review this new approach by introducing control theory and focusing on how these aspects are applied in brain studies. We also present the different stimulation techniques and the control approaches used to steer the brain. Finally, we explore how the closed-loop framework will revolutionize the way the human brain can be studied, including a discussion on open questions and an outlook on future advances.

Bias in data-driven replicability analysis of univariate brain-wide association studies

Recent studies have used big neuroimaging datasets to answer an important question: how many subjects are required for reproducible brain-wide association studies? These data-driven approaches could be considered a framework for testing the reproducibility of several neuroimaging models and measures. Here we test part of this framework, namely estimates of statistical errors of univariate brain-behaviour associations obtained from resampling large datasets with replacement. We demonstrate that reported estimates of statistical errors are largely a consequence of bias introduced by random effects when sampling with replacement close to the full sample size. We show that future meta-analyses can largely avoid these biases by only resampling up to 10% of the full sample size. We discuss implications that reproducing mass-univariate association studies requires tens-of-thousands of participants, urging researchers to adopt other methodological approaches.

Coarse-graining network flow through statistical physics and machine learning

Information dynamics plays a crucial role in complex systems, from cells to societies. Recent advances in statistical physics have made it possible to capture key network properties, such as flow diversity and signal speed, using entropy and free energy. However, large system sizes pose computational challenges. We use graph neural networks to identify suitable groups of components for coarse-graining a network and achieve a low computational complexity, suitable for practical application. Our approach preserves information flow even under significant compression, as shown through theoretical analysis and experiments on synthetic and empirical networks. We find that the model merges nodes with similar structural properties, suggesting they perform redundant roles in information transmission. This method enables low-complexity compression for extremely large networks, offering a multiscale perspective that preserves information flow in biological, social, and technological networks better than existing methods mostly focused on network structure.

Mapping and modeling age-related changes in intrinsic neural timescales

Intrinsic timescales of brain regions exhibit heterogeneity, escalating with hierarchical levels, and are crucial for the temporal integration of external stimuli. Aging, often associated with cognitive decline, involves progressive neuronal and synaptic loss, reshaping brain structure and dynamics. However, the impact of these structural changes on temporal coding in the aging brain remains unclear. We mapped intrinsic timescales and gray matter volume (GMV) using magnetic resonance imaging (MRI) in young and elderly adults. We found shorter intrinsic timescales across multiple large-scale functional networks in the elderly cohort, and a significant positive association between intrinsic timescales and GMV. Additionally, age-related decline in performance on visual discrimination tasks was linked to a reduction in intrinsic timescales in the cuneus. To explain these age-related shifts, we developed an age-dependent spiking neuron network model. In younger subjects, brain regions were near a critical branching regime, while regions in elderly subjects had fewer neurons and synapses, pushing the dynamics toward a subcritical regime. The model accurately reproduced the empirical results, showing longer intrinsic timescales in young adults due to critical slowing down. Our findings reveal how age-related structural brain changes may drive alterations in brain dynamics, offering testable predictions and informing possible interventions targeting cognitive decline.

Geometric influences on the regional organization of the mammalian brain

The mammalian brain is comprised of anatomically and functionally distinct regions. Substantial work over the past century has pursued the generation of ever-more accurate maps of regional boundaries, using either expert judgement or data-driven clustering of functional, connectional, and/or architectonic properties. However, these approaches are often purely descriptive, have limited generalizability, and do not elucidate the underlying generative mechanisms that shape the regional organization of the brain. Here, we develop a novel approach that leverages a simple, hierarchical principle for generating a multiscale parcellation of any brain structure in any mammalian species using only its geometry. We show that this approach yields regions at any resolution scale that are more homogeneous than those defined in nearly all existing benchmark brain parcellations in use today across hundreds of anatomical, functional, cellular, and molecular brain properties measured in humans, macaques, marmosets, and mice. We additionally show how our method can be generalized to previously unstudied mammalian species for which no parcellations exist. Finally, we demonstrate how our approach captures the essence of a simple, hierarchical reaction-diffusion mechanism, in which the geometry of a brain structure shapes the spatial expression of putative patterning molecules linked to the formation of distinct regions through development. Our findings point to a highly conserved and universal influence of geometry on the regional organization of the mammalian brain.

Multilayer network instability underlying persistent auditory verbal hallucinations in schizophrenia

BACKGROUND

Auditory verbal hallucinations (AVHs) in schizophrenia (SCZ) are linked to brain network abnormalities. Resting-state fMRI studies often assume stable networks during scans, yet dynamic changes related to AVHs are not well understood.

METHODS

We analyzed resting-state fMRI data from 60 SCZ patients with persistent AVHs (p-AVHs), 39 SCZ patients without AVHs (n-AVHs), and 59 healthy controls (HCs), matched for demographics. Using graph theory, we constructed a time-varying modular structure of brain networks, focusing on multilayer modularity. Network switching rates at global, subnetwork, and nodal levels were compared across groups and related to AVH severity.

RESULTS

SCZ groups had higher switching rates in the subcortical network compared to HCs. Increased switching was found in two thalamic nodes for both patient groups. The p-AVH group showed lower switching rates in the default mode network (DMN) and two superior frontal gyrus nodes compared to HC and n-AVH groups. DMN switching rates negatively correlated with AVH severity in the p-AVH group.

CONCLUSIONS

Dynamic changes in brain networks, especially lower DMN and frontal region switching rates, may contribute to the development and persistence of AVHs in SCZ.

Network Segregation and Integration Changes in Healthy Aging: Evidence From EEG Subbands During the Visual Short-Term Memory Binding Task

Working memory, which tends to be the most vulnerable cognitive domain to aging, is thought to depend on a functional brain network for efficient communication. The dynamic communication within this network is represented by segregation and integration. This study aimed to investigate healthy aging by examining age effect on outcomes of graph theory analysis during the visual short-term memory binding (VSTMB) task. VSTMB tasks rely on the integration of visual features and are less sensitive to semantic and verbal strategies. Effects of age on neuropsychological test scores, along with the EEG graph-theoretical integration, segregation and global organization metrics in frequencies from delta to gamma band were investigated. Neuropsychological assessment showed low sensitivity as a measure of age-related changes. EEG results indicated that network architecture changed more effectively during middle age, while this effectiveness appears to vanish or show compensatory mechanisms in the elderly. These differences were further found to be related to cognitive domain scores. This study is the first to demonstrate differences in working memory network architecture across a broad age range.

Multimodal neurophenomenology of advanced concentration absorption meditation: An intensively sampled case study of Jhana

Using a combination of fMRI, EEG, and phenomenology ratings, we examined the neurophenomenology of advanced concentrative absorption meditation, namely jhanas (ACAM-J), in a practitioner with over 23,000 h of meditation practice. Our study shows that ACAM-J states induce reliable changes in conscious experience and that these experiences are related to neural activity. Using resting-state fMRI functional connectivity, we found that ACAM-J is associated with decreased within-network modularity, increased global functional connectivity (GFC), and desegregation of the default mode and visual networks. Compared to control tasks, the ACAM-J were also related to widespread decreases in broadband EEG oscillatory power and increases in Lempel-Ziv complexity (LZ, a measure of brain entropy). Some fMRI findings varied by the control task used, while EEG results remained consistent, emphasizing both shared and unique neural features of ACAM-J. These differences in fMRI and EEG-measured neurophysiological properties correlated with specific changes in phenomenology - and especially with ACAM-J-induced states of bliss - enriching our understanding of these advanced meditative states. Our results show that advanced meditation practices markedly dysregulate high-level brain systems via practices of enhanced attention to sensations, corroborating recent neurocognitive theories of meditation as the deconstruction of the brain's cortical hierarchy. Overall, our results suggest that ACAM-J is associated with the modulation of large-scale brain networks in both fMRI and EEG, with potential implications for understanding the mechanisms of deep concentration practices and their effects on subjective experience.

Multi-Scale Spatial-Temporal Attention Networks for Functional Connectome Classification

Many neuropsychiatric disorders are considered to be associated with abnormalities in the functional connectivity networks of the brain. The research on the classification of functional connectivity can therefore provide new perspectives for understanding the pathology of disorders and contribute to early diagnosis and treatment. Functional connectivity exhibits a nature of dynamically changing over time, however, the majority of existing methods are unable to collectively reveal the spatial topology and time-varying characteristics. Furthermore, despite the efforts of limited spatial-temporal studies to capture rich information across different spatial scales, they have not delved into the temporal characteristics among different scales. To address above issues, we propose a novel Multi-Scale Spatial-Temporal Attention Networks (MSSTAN) to exploit the multi-scale spatial-temporal information provided by functional connectome for classification. To fully extract spatial features of brain regions, we propose a Topology Enhanced Graph Transformer module to guide the attention calculations in the learning of spatial features by incorporating topology priors. A Multi-Scale Pooling Strategy is introduced to obtain representations of brain connectome at various scales. Considering the temporal dynamic characteristics between dynamic functional connectome, we employ Locality Sensitive Hashing attention to further capture long-term dependencies in time dynamics across multiple scales and reduce the computational complexity of the original attention mechanism. Experiments on three brain fMRI datasets of MDD and ASD demonstrate the superiority of our proposed approach. In addition, benefiting from the attention mechanism in Transformer, our results are interpretable, which can contribute to the discovery of biomarkers. The code is available at https://github.com/LIST-KONG/MSSTAN.

Perspective on equal and cross-frequency neural coupling: Integration and segregation of the function of brain networks

We introduce a perspective that has not appeared before in the field of equal and multifrequency coupling derived from considering neuronal synchrony as a possible equivalence relation. The experimental results agree with the theoretical prediction that cross-frequency coupling results in a partition of the brain synchrony state space. We place these results in the framework of the integration and segregation of information in the processing of sensorimotor transformations by the brain cell circuits and propose that equal-frequency (1:1) connectivity favors integration of information in the brain whereas cross-frequency coupling (n:m) favors segregation. These observations may provide an outlook about how to reconcile the need for stability in the brain's operations with the requirement for diversity of activity in order to process many sensorimotor transformations simultaneously.

Investigating the predictive models of efficacy of accelerated neuronavigation-guided rTMS for suicidal depression based on multimodal large-scale brain networks

Background

Accelerated neuronavigation-guided high-dose repetitive transcranial magnetic stimulation (NH-rTMS) can rapidly reduce suicidal ideation and alleviate depressive symptoms in one week. Exploring accelerated NH-rTMS-related biomarkers will enhance the precision of treatment decisions for patients with major depressive disorder (MDD). This study aimed to establish predictive models of treatment response to accelerated NH-rTMS in MDD based on multimodal large-scale brain networks.

Method

In this study, morphological, structural, and functional brain networks were constructed for untreated MDD patients with suicidal ideation before accelerated NH-rTMS treatment. Linear support vector regression methods were utilized to examine the ability of multimodal brain networks in predicting antidepressant and anti-suicidal effects of accelerated NH-rTMS.

Results

We found that both the morphological and structural networks predicted the percentage changes of total Beck Scale of Suicidal Ideation and 24-item Hamilton Depression Rating Scale (HAMD-24) scores. Additionally, the functional networks predicted the percentage changes of total HAMD-24 scores. Further analyses revealed that the structural networks outperformed the morphological and functional networks and the somatomotor module outperformed other subnetworks in the prediction.

Conclusions

In summary, our study provides brain connectome-based predictive models of treatment response to accelerated NH-rTMS in MDD patients with suicidal ideation.

Regression and alignment for functional data and network topology

In the brain, functional connections form a network whose topological organization can be described by graph-theoretic network diagnostics. These include characterizations of the community structure, such as modularity and participation coefficient, which have been shown to change over the course of childhood and adolescence. To investigate if such changes in the functional network are associated with changes in cognitive performance during development, network studies often rely on an arbitrary choice of preprocessing parameters, in particular the proportional threshold of network edges. Because the choice of parameter can impact the value of the network diagnostic, and therefore downstream conclusions, we propose to circumvent that choice by conceptualizing the network diagnostic as a function of the parameter. As opposed to a single value, a network diagnostic curve describes the connectome topology at multiple scales-from the sparsest group of the strongest edges to the entire edge set. To relate these curves to executive function and other covariates, we use scalar-on-function regression, which is more flexible than previous functional data-based models used in network neuroscience. We then consider how systematic differences between networks can manifest in misalignment of diagnostic curves, and consequently propose a supervised curve alignment method that incorporates auxiliary information from other variables. Our algorithm performs both functional regression and alignment via an iterative, penalized, and nonlinear likelihood optimization. The illustrated method has the potential to improve the interpretability and generalizability of neuroscience studies where the goal is to study heterogeneity among a mixture of function- and scalar-valued measures.

Reorganization of Dynamic Network in Stroke Patients and Its Potential for Predicting Motor Recovery

Objective: The investigation of brain functional network dynamics offers a promising approach to understanding network reorganization poststroke. This study aims to explore the dynamic network configurations associated with motor recovery in stroke patients and assess their predictive potential using multilayer network analysis. Methods: Resting-state functional magnetic resonance imaging data were collected from patients with subacute stroke within 2 weeks of onset and from matched healthy controls (HCs). Group-independent component analysis and a sliding window approach were utilized to construct dynamic functional networks. A multilayer network model was applied to quantify the switching rates of individual nodes, subnetworks, and the global network across the dynamic network. Correlation analyses assessed the relationship between switching rates and motor function recovery, while linear regression models evaluated the predictive potential of global network switching rate on motor recovery outcomes. Results: Stroke patients exhibited a significant increase in the switching rates of specific brain regions, including the medial frontal gyrus, precentral gyrus, inferior parietal lobule, anterior cingulate, superior frontal gyrus, and postcentral gyrus, compared to HCs. Additionally, elevated switching rates were observed in the frontoparietal network, default mode network, cerebellar network, and in the global network. These increased switching rates were positively correlated with baseline Fugl-Meyer assessment (FMA) scores and changes in FMA scores at 90 days poststroke. Importantly, the global network's switching rate emerged as a significant predictor of motor recovery in stroke patients. Conclusions: The reorganization of dynamic network configurations in stroke patients reveals crucial insights into the mechanisms of motor recovery. These findings suggest that metrics of dynamic network reorganization, particularly global network switching rate, may offer a robust predictor of motor recovery.

Diverging network architecture of the C. elegans connectome and signaling network

The connectome describes the complete set of synaptic contacts through which neurons communicate. While the architecture of the C. elegans connectome has been extensively characterized, much less is known about the organization of causal signaling networks arising from functional interactions between neurons. Understanding how effective communication pathways relate to or diverge from the underlying structure is a central question in neuroscience. Here, we analyze the modular architecture of the C. elegans signal propagation network, measured via calcium imaging and optogenetics, and compare it to the underlying anatomical wiring measured by electron microscopy. Compared to the connectome, we find that signaling modules are not aligned with the modular boundaries of the anatomical network, highlighting an instance where function deviates from structure. An exception to this is the pharynx which is delineated into a separate community in both anatomy and signaling. We analyze the cellular compositions of the signaling architecture and find that its modules are enriched for specific cell types and functions, suggesting that the network modules are neurobiologically relevant. Lastly, we identify a "rich club" of hub neurons in the signaling network. The membership of the signaling rich club differs from the rich club detected in the anatomical network, challenging the view that structural hubs occupy positions of influence in functional (signaling) networks. Our results provide new insight into the interplay between brain structure, in the form of a complete synaptic-level connectome, and brain function, in the form of a system-wide causal signal propagation atlas.

Multilayer Network Analysis across Cortical Depths in Resting-State 7T fMRI

In graph theory, "multilayer networks" represent systems involving several interconnected topological levels. One example in neuroscience is the stratification of connections between different cortical depths or "laminae", which is becoming non-invasively accessible in humans using ultra-high-resolution functional MRI (fMRI). Here, we applied multilayer graph theory to examine functional connectivity across different cortical depths in humans, using 7T fMRI (1-mm3 voxels; 30 participants). Blood oxygenation level dependent (BOLD) signals were derived from five depths between the white matter and pial surface. We compared networks where the inter-regional connections were limited to a single cortical depth only ("layer-by-layer matrices") to those considering all possible connections between areas and cortical depths ("multilayer matrix"). We utilized global and local graph theory features that quantitatively characterize network attributes including network composition, nodal centrality, path-based measures, and hub segregation. Detecting functional differences between cortical depths was improved using multilayer connectomics compared to the layer-by-layer versions. Superficial depths of the cortex dominated information transfer and deeper depths drove clustering. These differences were largest in frontotemporal and limbic regions. fMRI functional connectivity across different cortical depths may contain neurophysiologically relevant information; thus, multilayer connectomics could provide a methodological framework for studies on how information flows across this stratification.

CoCoNest: A continuous structural connectivity-based nested family of parcellations of the human cerebral cortex

Despite the widespread exploration and availability of parcellations for the functional connectome, parcellations designed for the structural connectome are comparatively limited. Current research suggests that there may be no single "correct" parcellation and that the human brain is intrinsically a multiresolution entity. In this work, we propose the Continuous Structural Connectivitity-based, Nested (CoCoNest) family of parcellations-a fully data-driven, multiresolution family of parcellations derived from structural connectome data. The CoCoNest family is created using agglomerative (bottom-up) clustering and error-complexity pruning, which strikes a balance between the complexity of each parcellation and how well it preserves patterns in vertex-level, high-resolution connectivity data. We draw on a comprehensive battery of internal and external evaluation metrics to show that the CoCoNest family is competitive with or outperforms widely used parcellations in the literature. Additionally, we show how the CoCoNest family can serve as an exploratory tool for researchers to investigate the multiresolution organization of the structural connectome.

Decoding cortical chronotopy-Comparing the influence of different cortical organizational schemes

The brain's diverse intrinsic timescales enable us to perceive stimuli with varying temporal persistency. This study aimed to uncover the cortical organizational schemes underlying these variations, revealing the neural architecture for processing a wide range of sensory experiences. We collected resting-state fMRI, task-fMRI, and diffusion-weighted imaging data from 47 individuals. Based on this data, we extracted six organizational schemes: (1) the structural Rich Club (RC) architecture, shown to synchronize the connectome; (2) the structural Diverse Club architecture, as an alternative to the RC based on the network's module structure; (3) the functional uni-to-multimodal gradient, reflected in a wide range of structural and functional features; and (4) the spatial posterior/lateral-to-anterior/medial gradient, established for hierarchical levels of cognitive control. Also, we explored the effects of (5) structural graph theoretical measures of centrality and (6) cytoarchitectural differences. Using Bayesian model comparison, we contrasted the impact of these organizational schemes on (1) intrinsic resting-state timescales and (2) inter-subject correlation (ISC) from a task involving hierarchically nested digit sequences. As expected, resting-state timescales were slower in structural network hubs, hierarchically higher areas defined by the functional and spatial gradients, and thicker cortical regions. ISC analysis demonstrated hints for the engagement of higher cortical areas with more temporally persistent stimuli. Finally, the model comparison identified the uni-to-multimodal gradient as the best organizational scheme for explaining the chronotopy in both task and rest. Future research should explore the microarchitectural features that shape this gradient, elucidating how our brain adapts and evolves across different modes of processing.

A network control theory pipeline for studying the dynamics of the structural connectome

Network control theory (NCT) is a simple and powerful tool for studying how network topology informs and constrains the dynamics of a system. Compared to other structure-function coupling approaches, the strength of NCT lies in its capacity to predict the patterns of external control signals that may alter the dynamics of a system in a desired way. An interesting development for NCT in the neuroscience field is its application to study behavior and mental health symptoms. To date, NCT has been validated to study different aspects of the human structural connectome. NCT outputs can be monitored throughout developmental stages to study the effects of connectome topology on neural dynamics and, separately, to test the coherence of empirical datasets with brain function and stimulation. Here, we provide a comprehensive pipeline for applying NCT to structural connectomes by following two procedures. The main procedure focuses on computing the control energy associated with the transitions between specific neural activity states. The second procedure focuses on computing average controllability, which indexes nodes' general capacity to control the dynamics of the system. We provide recommendations for comparing NCT outputs against null network models, and we further support this approach with a Python-based software package called 'network control theory for python'. The procedures in this protocol are appropriate for users with a background in network neuroscience and experience in dynamical systems theory.

Ventral frontostriatal circuitry mediates the computation of reinforcement from symbolic gains and losses

Reinforcement learning (RL), particularly in primates, is often driven by symbolic outcomes. However, it is usually studied with primary reinforcers. To examine the neural mechanisms underlying learning from symbolic outcomes, we trained monkeys on a task in which they learned to choose options that led to gains of tokens and avoid choosing options that led to losses of tokens. We then recorded simultaneously from the orbitofrontal cortex (OFC), ventral striatum (VS), amygdala (AMY), and mediodorsal thalamus (MDt). We found that the OFC played a dominant role in coding token outcomes and token prediction errors. The other areas contributed complementary functions, with the VS coding appetitive outcomes and the AMY coding the salience of outcomes. The MDt coded actions and relayed information about tokens between the OFC and VS. Thus, the OFC leads the processing of symbolic RL in the ventral frontostriatal circuitry.

MMF-NNs: Multi-modal Multi-granularity Fusion Neural Networks for brain networks and its application to epilepsy identification

Structural and functional brain networks are generated from two scan sequences of magnetic resonance imaging data, which can provide different perspectives for describing pathological changes caused by brain diseases. Recent studies found that fusing these two types of brain networks improves performance in brain disease identification. However, traditional fusion models combine these brain networks at a single granularity, ignoring the natural multi-granularity structure of brain networks that can be divided into the edge, node, and graph levels. To this end, this paper proposes a Multi-modal Multi-granularity Fusion Neural Networks (MMF-NNs) framework for brain networks, which integrates the features of the multi-modal brain network from global (i.e., graph-level) and local (i.e., edge-level and node-level) granularities to take full advantage of the topological information. Specifically, we design an interactive feature learning module at the local granularity to learn feature maps of structural and functional brain networks at the edge-level and the node-level, respectively. In that way, these two types of brain networks are fused during the feature learning process. At the global granularity, a multi-modal decomposition bilinear pooling module is designed to learn the graph-level joint representation of these brain networks. Experiments on real epilepsy datasets demonstrate that MMF-NNs are superior to several state-of-the-art methods in epilepsy identification.

Hierarchical Graph Convolutional Network Built by Multiscale Atlases for Brain Disorder Diagnosis Using Functional Connectivity

Functional connectivity network (FCN) data from functional magnetic resonance imaging (fMRI) is increasingly used for the diagnosis of brain disorders. However, state-of-the-art studies used to build the FCN using a single brain parcellation atlas at a certain spatial scale, which largely neglected functional interactions across different spatial scales in hierarchical manners. In this study, we propose a novel framework to perform multiscale FCN analysis for brain disorder diagnosis. We first use a set of well-defined multiscale atlases to compute multiscale FCNs. Then, we utilize biologically meaningful brain hierarchical relationships among the regions in multiscale atlases to perform nodal pooling across multiple spatial scales, namely "Atlas-guided Pooling (AP)." Accordingly, we propose a multiscale-atlases-based hierarchical graph convolutional network (MAHGCN), built on the stacked layers of graph convolution and the AP, for a comprehensive extraction of diagnostic information from multiscale FCNs. Experiments on neuroimaging data from 1792 subjects demonstrate the effectiveness of our proposed method in the diagnoses of Alzheimer's disease (AD), the prodromal stage of AD [i.e., mild cognitive impairment (MCI)], as well as autism spectrum disorder (ASD), with the accuracy of 88.9%, 78.6%, and 72.7%, respectively. All results show significant advantages of our proposed method over other competing methods. This study not only demonstrates the feasibility of brain disorder diagnosis using resting-state fMRI empowered by deep learning but also highlights that the functional interactions in the multiscale brain hierarchy are worth being explored and integrated into deep learning network architectures for a better understanding of the neuropathology of brain disorders. The codes for MAHGCN are publicly available at "https://github.com/MianxinLiu/MAHGCN-code."

Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics

Modeling the network topology of the human brain within the mesoscale has become an increasing focus within the neuroscientific community due to its variation across diverse cognitive processes, in the presence of neuropsychiatric disease or injury, and over the lifespan. Much research has been done on the creation of algorithms to detect these mesoscopic structures, called communities or modules, but less has been done to conduct inference on these structures. The literature on analysis of these community detection algorithms has focused on comparing them within the same subject. These approaches, however, either do not accomodate a more general association between community structure and an outcome or cannot accommodate additional covariates that may confound the association of interest. We propose a semiparametric kernel machine regression model for either a continuous or binary outcome, where covariate effects are modeled parametrically and brain connectivity measures are measured nonparametrically. By incorporating notions of similarity between network community structures into a kernel distance function, the high-dimensional feature space of brain networks, defined on input pairs, can be generalized to non-linear spaces, allowing for a wider class of distance-based algorithms. We evaluate our proposed methodology on both simulated and real datasets.

Probing heterogeneity to identify individualized treatment approaches in autism: Specific clusters of executive function challenges link to distinct co-occurring mental health problems

LAY ABSTRACT

Many autistic people struggle with mental health problems like anxiety, depression, inattention, and aggression, which can be challenging to treat. Executive function challenges, which impact many autistic individuals, may serve as a risk factor for mental health problems or make treating mental health conditions more difficult. While some people respond well to medication or therapy, others do not. This study tried to understand if there are different subgroups of autistic young people who may have similar patterns of executive function strengths and challenges-like flexibility, planning, self-monitoring, and emotion regulation. Then, we investigated whether executive function subgroups were related to mental health problems in autistic youth. We found three different types of executive function subgroups in autistic youth, each with different patterns of mental health problems. This helps us identify specific profiles of executive function strengths and challenges that may be helpful with identifying personalized supports, services, and treatment strategies for mental health conditions.

Adaptive rewiring: a general principle for neural network development

The nervous system, especially the human brain, is characterized by its highly complex network topology. The neurodevelopment of some of its features has been described in terms of dynamic optimization rules. We discuss the principle of adaptive rewiring, i.e., the dynamic reorganization of a network according to the intensity of internal signal communication as measured by synchronization or diffusion, and its recent generalization for applications in directed networks. These have extended the principle of adaptive rewiring from highly oversimplified networks to more neurally plausible ones. Adaptive rewiring captures all the key features of the complex brain topology: it transforms initially random or regular networks into networks with a modular small-world structure and a rich-club core. This effect is specific in the sense that it can be tailored to computational needs, robust in the sense that it does not depend on a critical regime, and flexible in the sense that parametric variation generates a range of variant network configurations. Extreme variant networks can be associated at macroscopic level with disorders such as schizophrenia, autism, and dyslexia, and suggest a relationship between dyslexia and creativity. Adaptive rewiring cooperates with network growth and interacts constructively with spatial organization principles in the formation of topographically distinct modules and structures such as ganglia and chains. At the mesoscopic level, adaptive rewiring enables the development of functional architectures, such as convergent-divergent units, and sheds light on the early development of divergence and convergence in, for example, the visual system. Finally, we discuss future prospects for the principle of adaptive rewiring.

Sex Differences in Hierarchical and Modular Organization of Functional Brain Networks: Insights from Hierarchical Entropy and Modularity Analysis

Existing studies have demonstrated significant sex differences in the neural mechanisms of daily life and neuropsychiatric disorders. The hierarchical organization of the functional brain network is a critical feature for assessing these neural mechanisms. But the sex differences in hierarchical organization have not been fully investigated. Here, we explore whether the hierarchical structure of the brain network differs between females and males using resting-state fMRI data. We measure the hierarchical entropy and the maximum modularity of each individual, and identify a significant negative correlation between the complexity of hierarchy and modularity in brain networks. At the mean level, females show higher modularity, whereas males exhibit a more complex hierarchy. At the consensus level, we use a co-classification matrix to perform a detailed investigation of the differences in the hierarchical organization between sexes and observe that the female group and the male group exhibit different interaction patterns of brain regions in the dorsal attention network (DAN) and visual network (VIN). Our findings suggest that the brains of females and males employ different network topologies to carry out brain functions. In addition, the negative correlation between hierarchy and modularity implies a need to balance the complexity in the hierarchical organization of the brain network, which sheds light on future studies of brain functions.

Effects of oral contraceptive pills on brain networks: A replication and extension

Neuroimaging research has identified significant effects of oral contraceptive pills (OCPs) on brain networks. A wide variety of approaches have been employed, largely in observational samples, with few converging results. This study therefore was designed to test for replication and extend this previous work using a randomized, double-blind, placebo-controlled crossover trial of the effects of OCPs on brain networks. Using functional MRI, we focused on brain regions identified in prior studies. Our analyses did not strictly replicate previously reported effects of OCPs on functional connectivity. Exploratory analyses suggested that traditional seed-based approaches may miss broader, network-level effects of OCPs on brain circuits. We applied data-driven, multivariate techniques to assess these network-level changes, A deeper understanding of neural effects of OCPs can be important in helping patients make informed decisions regarding contraception, mitigating unwanted side effects. Such information can also identify potentially confounding effects of OCPs in other neuroimaging investigations.

Cognitive modelling of concepts in the mental lexicon with multilayer networks: Insights, advancements, and future challenges

The mental lexicon is a complex cognitive system representing information about the words/concepts that one knows. Over decades psychological experiments have shown that conceptual associations across multiple, interactive cognitive levels can greatly influence word acquisition, storage, and processing. How can semantic, phonological, syntactic, and other types of conceptual associations be mapped within a coherent mathematical framework to study how the mental lexicon works? Here we review cognitive multilayer networks as a promising quantitative and interpretative framework for investigating the mental lexicon. Cognitive multilayer networks can map multiple types of information at once, thus capturing how different layers of associations might co-exist within the mental lexicon and influence cognitive processing. This review starts with a gentle introduction to the structure and formalism of multilayer networks. We then discuss quantitative mechanisms of psychological phenomena that could not be observed in single-layer networks and were only unveiled by combining multiple layers of the lexicon: (i) multiplex viability highlights language kernels and facilitative effects of knowledge processing in healthy and clinical populations; (ii) multilayer community detection enables contextual meaning reconstruction depending on psycholinguistic features; (iii) layer analysis can mediate latent interactions of mediation, suppression, and facilitation for lexical access. By outlining novel quantitative perspectives where multilayer networks can shed light on cognitive knowledge representations, including in next-generation brain/mind models, we discuss key limitations and promising directions for cutting-edge future research.

Artificial intelligence role in advancement of human brain connectome studies

Neurons are interactive cells that connect via ions to develop electromagnetic fields in the brain. This structure functions directly in the brain. Connectome is the data obtained from neuronal connections. Since neural circuits change in the brain in various diseases, studying connectome sheds light on the clinical changes in special diseases. The ability to explore this data and its relation to the disorders leads us to find new therapeutic methods. Artificial intelligence (AI) is a collection of powerful algorithms used for finding the relationship between input data and the outcome. AI is used for extraction of valuable features from connectome data and in turn uses them for development of prognostic and diagnostic models in neurological diseases. Studying the changes of brain circuits in neurodegenerative diseases and behavioral disorders makes it possible to provide early diagnosis and development of efficient treatment strategies. Considering the difficulties in studying brain diseases, the use of connectome data is one of the beneficial methods for improvement of knowledge of this organ. In the present study, we provide a systematic review on the studies published using connectome data and AI for studying various diseases and we focus on the strength and weaknesses of studies aiming to provide a viewpoint for the future studies. Throughout, AI is very useful for development of diagnostic and prognostic tools using neuroimaging data, while bias in data collection and decay in addition to using small datasets restricts applications of AI-based tools using connectome data which should be covered in the future studies.

Hierarchical communities in the larval Drosophila connectome: Links to cellular annotations and network topology

One of the longstanding aims of network neuroscience is to link a connectome's topological properties-i.e., features defined from connectivity alone-with an organism's neurobiology. One approach for doing so is to compare connectome properties with annotational maps. This type of analysis is popular at the meso-/macroscale, but is less common at the nano-scale, owing to a paucity of neuron-level connectome data. However, recent methodological advances have made possible the reconstruction of whole-brain connectomes at single-neuron resolution for a select set of organisms. These include the fruit fly, Drosophila melanogaster, and its developing larvae. In addition to fine-scale descriptions of connectivity, these datasets are accompanied by rich annotations. Here, we use a variant of the stochastic blockmodel to detect multilevel communities in the larval Drosophila connectome. We find that communities partition neurons based on function and cell type and that most interact assortatively, reflecting the principle of functional segregation. However, a small number of communities interact nonassortatively, forming form a "rich-club" of interneurons that receive sensory/ascending inputs and deliver outputs along descending pathways. Next, we investigate the role of community structure in shaping communication patterns. We find that polysynaptic signaling follows specific trajectories across modular hierarchies, with interneurons playing a key role in mediating communication routes between modules and hierarchical scales. Our work suggests a relationship between system-level architecture and the biological function and classification of individual neurons. We envision our study as an important step toward bridging the gap between complex systems and neurobiological lines of investigation in brain sciences.

Brain markers of subtraction and multiplication skills in childhood: task-based functional connectivity and individualized structural similarity

Arithmetic, a high-order cognitive ability, show marked individual difference over development. Despite recent advancements in neuroimaging techniques have enabled the identification of brain markers for individual differences in high-order cognitive abilities, it remains largely unknown about the brain markers for arithmetic. This study used a data-driven connectome-based prediction model to identify brain markers of arithmetic skills from arithmetic-state functional connectivity and individualized structural similarity in 132 children aged 8 to 15 years. We found that both subtraction-state functional connectivity and individualized SS successfully predicted subtraction and multiplication skills but multiplication-state functional connectivity failed to predict either skill. Among the four successful prediction models, most predictive connections were located in frontal-parietal, default-mode, and secondary visual networks. Further computational lesion analyses revealed the essential structural role of frontal-parietal network in predicting subtraction and the essential functional roles of secondary visual, language, and ventral multimodal networks in predicting multiplication. Finally, a few shared nodes but largely nonoverlapping functional and structural connections were found to predict subtraction and multiplication skills. Altogether, our findings provide new insights into the brain markers of arithmetic skills in children and highlight the importance of studying different connectivity modalities and different arithmetic domains to advance our understanding of children's arithmetic skills.

Functional network modules overlap and are linked to interindividual connectome differences during human brain development

The modular structure of functional connectomes in the human brain undergoes substantial reorganization during development. However, previous studies have implicitly assumed that each region participates in one single module, ignoring the potential spatial overlap between modules. How the overlapping functional modules develop and whether this development is related to gray and white matter features remain unknown. Using longitudinal multimodal structural, functional, and diffusion MRI data from 305 children (aged 6 to 14 years), we investigated the maturation of overlapping modules of functional networks and further revealed their structural associations. An edge-centric network model was used to identify the overlapping modules, and the nodal overlap in module affiliations was quantified using the entropy measure. We showed a regionally heterogeneous spatial topography of the overlapping extent of brain nodes in module affiliations in children, with higher entropy (i.e., more module involvement) in the ventral attention, somatomotor, and subcortical regions and lower entropy (i.e., less module involvement) in the visual and default-mode regions. The overlapping modules developed in a linear, spatially dissociable manner, with decreased entropy (i.e., decreased module involvement) in the dorsomedial prefrontal cortex, ventral prefrontal cortex, and putamen and increased entropy (i.e., increased module involvement) in the parietal lobules and lateral prefrontal cortex. The overlapping modular patterns captured individual brain maturity as characterized by chronological age and were predicted by integrating gray matter morphology and white matter microstructural properties. Our findings highlight the maturation of overlapping functional modules and their structural substrates, thereby advancing our understanding of the principles of connectome development.

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.

Sleep-like cortical dynamics during wakefulness and their network effects following brain injury

By connecting old and recent notions, different spatial scales, and research domains, we introduce a novel framework on the consequences of brain injury focusing on a key role of slow waves. We argue that the long-standing finding of EEG slow waves after brain injury reflects the intrusion of sleep-like cortical dynamics during wakefulness; we illustrate how these dynamics are generated and how they can lead to functional network disruption and behavioral impairment. Finally, we outline a scenario whereby post-injury slow waves can be modulated to reawaken parts of the brain that have fallen asleep to optimize rehabilitation strategies and promote recovery.

Integrative role of attention networks in frequency-dependent modular organization of human brain

Despite converging evidence of hierarchical organization in the cerebral cortex, with sensory-motor and association regions at opposite ends, the mechanism of such hierarchical interactions remains elusive. This organization was primarily investigated regarding the spatiotemporal dynamics of intrinsic connectivity networks (ICNs). However, more effort is needed to investigate network dynamics in the frequency domain. We aimed to examine the integrative role of brain regions in the frequency domain with graph metrics. Phase-based connectivity estimation was performed in three frequency bands (0.011-0.038, 0.043-0.071, and 0.076-0.103 Hz) in the BOLD signal during rest. We applied modularity analysis to connectivity matrices and investigated those areas, which we called integrative regions, that showed frequency-domain flexibility. Integrative regions, mostly belonging to attention networks, were densely connected to higher-order cognitive ICNs in lower frequency bands but to sensory-motor ICNs in higher frequency bands. We compared the normalized participation coefficient (Pnorm) values of integrative and core regions with respect to their relation to higher-order cognition using a permutation-based t-test for multiple linear regression. Regression parameters of integrative regions in relation to three cognitive scores in executive functions, and working memory were significantly larger than those of core regions (Pfdr < 0.05) for salience ventral attention network. Parameters of integrative regions in relation to intelligence scores were significantly larger than those with core regions (Pfdr < 0.05) in dorsal attention network. Larger parameters of neuropsychological test scores in relation to these flexible parcels further indicate their essential role at an intermediate level in behavior. Results emphasize the importance of frequency-band analysis of brain networks.

Brain Network Interconnectivity Dynamics Explain Metacognitive Differences in Listening Behavior

Complex auditory scenes pose a challenge to attentive listening, rendering listeners slower and more uncertain in their perceptual decisions. How can we explain such behaviors from the dynamics of cortical networks that pertain to the control of listening behavior? We here follow up on the hypothesis that human adaptive perception in challenging listening situations is supported by modular reconfiguration of auditory-control networks in a sample of N = 40 participants (13 males) who underwent resting-state and task functional magnetic resonance imaging (fMRI). Individual titration of a spatial selective auditory attention task maintained an average accuracy of ∼70% but yielded considerable interindividual differences in listeners' response speed and reported confidence in their own perceptual decisions. Whole-brain network modularity increased from rest to task by reconfiguring auditory, cinguloopercular, and dorsal attention networks. Specifically, interconnectivity between the auditory network and cinguloopercular network decreased during the task relative to the resting state. Additionally, interconnectivity between the dorsal attention network and cinguloopercular network increased. These interconnectivity dynamics were predictive of individual differences in response confidence, the degree of which was more pronounced after incorrect judgments. Our findings uncover the behavioral relevance of functional cross talk between auditory and attentional-control networks during metacognitive assessment of one's own perception in challenging listening situations and suggest two functionally dissociable cortical networked systems that shape the considerable metacognitive differences between individuals in adaptive listening behavior.

Distinct rich and diverse clubs regulate coarse and fine binocular disparity processing: Evidence from stereoscopic task-based fMRI

While cortical regions involved in processing binocular disparities have been studied extensively, little is known on how the human visual system adapts to changing disparity magnitudes. In this paper, we investigate causal mechanisms of coarse and fine binocular disparity processing using fMRI with a clinically validated, custom anaglyph-based stimulus. We make use of Granger causality and graph measures to reveal the existence of distinct rich and diverse clubs across different disparity magnitudes. We demonstrate that Middle Temporal area (MT) plays a specialized role with overlapping rich and diverse characteristics. Next, we show that subtle interhemispheric differences exist across various brain regions, despite an overall right hemisphere dominance. Finally, we pass the graph measures through the decision tree and found that the diverse clubs outperform rich clubs in decoding disparity magnitudes. Our study sets the stage for conducting further investigations on binocular disparity processing, particularly in the context of neuro-ophthalmic disorders with binocular impairments.

Fast connectivity gradient approximation: maintaining spatially fine-grained connectivity gradients while reducing computational costs

Brain connectome analysis suffers from the high dimensionality of connectivity data, often forcing a reduced representation of the brain at a lower spatial resolution or parcellation. This is particularly true for graph-based representations, which are increasingly used to characterize connectivity gradients, capturing patterns of systematic spatial variation in the functional connectivity structure. However, maintaining a high spatial resolution is crucial for enabling fine-grained topographical analysis and preserving subtle individual differences that might otherwise be lost. Here we introduce a computationally efficient approach to establish spatially fine-grained connectivity gradients. At its core, it leverages a set of landmarks to approximate the underlying connectivity structure at the full spatial resolution without requiring a full-scale vertex-by-vertex connectivity matrix. We show that this approach reduces computational time and memory usage while preserving informative individual features and demonstrate its application in improving brain-behavior predictions. Overall, its efficiency can remove computational barriers and enable the widespread application of connectivity gradients to capture spatial signatures of the connectome. Importantly, maintaining a spatially fine-grained resolution facilitates to characterize the spatial transitions inherent in the core concept of gradients of brain organization.