Challenges and future directions for representations of functional brain organization

Dynamic and low-dimensional modeling of brain functional connectivity on Riemannian manifolds

Modeling brain functional connectivity (FC) is key in investigating brain functions and dysfunctions. FC is typically quantified by symmetric positive definite (SPD) matrices that are located on a Riemannian manifold rather than the regular Euclidean space, whose modeling faces three challenges. First, FC can be time-varying and the temporal dynamics of FC matrix time-series need to be modeled within the constraint of the SPD Riemannian manifold geometry, which remains elusive. Second, the FC matrix time-series exhibits considerable stochasticity, whose probability distribution is difficult to model on the Riemannian manifold. Third, FC matrices are high-dimensional and dimensionality reduction methods for SPD matrix time-series are still lacking. Here, we develop a Riemannian state-space modeling framework to simultaneously address the challenges. First, we construct a new Riemannian state-space model (RSSM) to define a hidden SPD matrix state to achieve dynamic, stochastic, and low-dimensional modeling of FC matrix time-series on the SPD Riemannian manifold. Second, we develop a new Riemannian Particle Filter (RPF) algorithm to estimate the hidden low-dimensional SPD matrix state and predict the FC matrix time-series. Third, we develop a new Riemannian Expectation Maximization (REM) algorithm to fit the RSSM parameters. We evaluate the proposed RSSM, RPF, and REM using simulation and real-world EEG datasets, demonstrating that the RSSM enables accurate prediction of the EEG FC time-series and classification of emotional states, outperforming traditional Euclidean methods. Our results have implications for modeling brain FC on the SPD Riemannian manifold to study various brain functions and dysfunctions.

High-Order Graphical Topology Analysis of Brain Functional Connectivity Networks Using fMRI

The brain connectivity network can be represented as a graph to reveal its intrinsic topological properties. While classical graph theory provides a powerful framework for examining brain connectivity patterns, it often focuses on low-order graphical indicators and pays less attention to high-order topological metrics, which are crucial to the comprehensive understanding of brain topology. In this paper, we capture high-order topological features via a graphical topology analysis framework for brain connectivity networks derived from functional Magnetic Resonance Imaging (fMRI). Several high-order metrics are examined across varying sparsity levels of binary graphs to trace the evolution of brain networks. Topological phase transitions are primarily investigated that reflect brain criticality, and a novel indicator called "redundant energy" is proposed to measure the chaos level of the brain. Extensive experiments on diverse datasets from healthy controls validate the reproducibility and generalizability of our framework. The results demonstrate that around critical points, classical graph theoretical indicators change sharply, driven by crucial brain regions that have high node curvatures. Further investigations on fMRI of subjects with and without Parkinson's disease uncover significant alterations in high-order topological features which are further associated with the severity of the disease. This study provides a fresh perspective on studying topological architectures of the brain, with the potential to expand our comprehension on brain function in both healthy and diseased states.

The generalizability of cortical area parcellations across early childhood

The cerebral cortex consists of distinct areas that develop through intrinsic embryonic patterning and postnatal experiences. Accurate parcellation of these areas in neuroimaging studies improves statistical power and cross-study comparability. Given significant brain changes in volume, microstructure, and connectivity during early life, we hypothesized that cortical areas in 1- to 3-year-olds would differ markedly from neonates and increasingly resemble adult patterns as development progresses. Here, we parcellated the cerebral cortex into putative areas using local functional connectivity (FC) gradients in 92 toddlers at 2 years old. We demonstrate high reproducibility of these cortical areas across 1- to 3-year-olds in two independent datasets. The area boundaries in 1- to 3-year-olds were more similar to those in adults than those in neonates. While the age-specific group area parcellation better fits the underlying FC in individuals during the first 3 years, adult area parcellations still have utility in developmental studies, especially in children older than 6 years. Additionally, we provide connectivity-based community assignments of the area parcels, showing fragmented anterior and posterior components based on the strongest connectivity, yet alignment with adult systems when weaker connectivity was included.

Social Cognition and Functional Connectivity in Early and Chronic Schizophrenia

BACKGROUND

Individuals with schizophrenia (SZ) experience impairments in social cognition that contribute to poor functional outcomes. However, mechanisms of social cognitive dysfunction in SZ remain poorly understood, which impedes the design of novel interventions to improve outcomes. In this preregistered project, we examined the representation of social cognition in the brain's functional architecture in early and chronic SZ.

METHODS

The study contains 2 parts: a confirmatory and an exploratory portion. In the confirmatory portion, we identified resting-state connectivity disruptions evident in early and chronic SZ. We performed a connectivity analysis using regions associated with social cognitive dysfunction in early and chronic SZ to test whether aberrant connectivity observed in chronic SZ (n = 47 chronic SZ and n = 52 healthy control participants) was also present in early SZ (n = 71 early SZ and n = 47 healthy control participants). In the exploratory portion, we assessed the out-of-sample generalizability and precision of predictive models of social cognition. We used machine learning to predict social cognition and established generalizability with out-of-sample testing and confound control.

RESULTS

Results revealed decreases between the left inferior frontal gyrus and the intraparietal sulcus in early and chronic SZ, which were significantly associated with social and general cognition and global functioning in chronic SZ and with general cognition and global functioning in early SZ. Predictive modeling revealed the importance of out-of-sample evaluation and confound control.

CONCLUSIONS

This work provides insights into the functional architecture in early and chronic SZ and suggests that inferior frontal gyrus-intraparietal sulcus connectivity could be a prognostic biomarker of social impairments and a target for future interventions (e.g., neuromodulation) focused on improved social functioning.

Replicability of a resting-state functional connectivity study in profound early blindness

It has been shown that the choice of preprocessing pipelines to remove contamination from functional magnetic resonance images can significantly impact the results, particularly in resting-state functional connectivity (rsFC) studies. This underscores the critical importance of replication studies with different preprocessing methodologies. In this study, we attempted to reproduce the rsFC results presented in an original study by Bauer et al. in 2017 on a group of sighted control (SC) and early blind (EB) subjects. By using the original dataset, we utilized another widely used software package to investigate how applying different implementations of the original pipeline (RMin model) or a more rigorous and extensive preprocessing stream (RExt model) can alter the whole-brain rsFC results. Our replication study was not able to fully reproduce the findings of the original paper. Overall, RExt shifted the distribution of rsFC values and reduced functional network density more drastically compared with RMin and the original pipeline. Remarkably, the largest rsFC effects appeared to primarily belong to certain connection pairs, irrespective of the pipeline used, likely demonstrating immunity of the larger effects and the true results against suboptimal processing. This may highlight the significance of results verification across different computational streams in pursuit of the true findings.

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.

Neurobiology-based cognitive biotypes using multi-scale intrinsic connectivity networks in psychotic disorders

Understanding neurobiology and developing effective interventions for cognitive dysfunction in psychotic disorders remain elusive. Insufficient knowledge about the biological heterogeneity of cognitive dysfunction hinders progress. We aimed to identify subgroups of patients with psychosis and distinct patterns of functional brain alterations related to cognition (cognitive biotypes). We analyzed B-SNIP consortium data (2 270 participants including participants with psychotic disorders, relatives, and controls, 55% females). We used reference-informed independent component analysis with the standardized and fully automated framework NeuroMark and the 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 using multivariate joint analysis. K-means clustering identified patient subgroups based on these features. Two biotypes with different functional brain alteration patterns were identified. Relative to controls, biotype 1 exhibited hypoconnectivity in cerebellar-subcortical and somatomotor-visual networks and worse cognitive performance. Biotype 2 exhibited hyperconnectivity in somatomotor-subcortical networks, 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. 76.56% of relatives were assigned to a psychosis biotype, of those, 70.12% were to the same biotype as their affected family members. These findings suggest two distinctive psychosis-related cognitive biotypes with differing functional brain patterns shared with their relatives. Instead of traditional diagnosis, patient stratification based on these biotypes may help optimize future research and identify biological targets for the treatment of cognitive dysfunction in psychosis.

Contractions in human cerebellar-cortical manifold structure underlie motor reinforcement learning

How the brain learns new motor commands through reinforcement involves distributed neural circuits beyond known frontal-striatal pathways, yet a comprehensive understanding of this broader neural architecture remains elusive. Here, using human functional MRI (N = 46, 27 females) and manifold learning techniques, we identified a low-dimensional neural space that captured the dynamic changes in whole-brain functional organization during a reward-based trajectory learning task. By quantifying participants' learning rates through an Actor-Critic model, we discovered that periods of accelerated learning were characterized by significant manifold contractions across multiple brain regions, including areas of limbic and hippocampal cortex, as well as the cerebellum. This contraction reflected enhanced network integration, with notably stronger connectivity between several of these regions and the sensorimotor cerebellum correlating with higher learning rates. These findings challenge the traditional view of the cerebellum as solely involved in error-based learning, supporting the emerging view that it coordinates with other brain regions during reinforcement learning.Significance Statement This study reveals how distributed brain systems, including the cerebellum and hippocampus, alter their functional connectivity to support motor learning through reinforcement. Using advanced manifold learning techniques on functional MRI data, we examined changes in regional connectivity during reward-based learning and their relationship to learning rate. For several brain regions, we found that periods of heightened learning were associated with increased cerebellar connectivity, suggesting a key role for the cerebellum in reward-based motor learning. These findings challenge the traditional view of the cerebellum as solely involved in supervised (error-based) learning and add to a growing rodent literature supporting a role for cerebellar circuits in reward-driven learning.

Imaging Biomarker Studies of Antipsychotic-Naïve First-Episode Schizophrenia in China: Progress and Future Directions

BACKGROUND AND HYPOTHESIS

Identifying biomarkers at onset and specifying the progression over the early course of schizophrenia is critical for better understanding of illness pathophysiology and providing novel information relevant to illness prognosis and treatment selection. Studies of antipsychotic-naïve first-episode schizophrenia in China are making contributions to this goal.

STUDY DESIGN

A review was conducted for how antipsychotic-naïve first-episode patients were identified and studied, the investigated biological measures, with a focus on neuroimaging, and how they extend the understanding of schizophrenia regarding the illness-related brain abnormality, treatment effect characterization and outcome prediction, and subtype discovery and patient stratification, in comparison to findings from western populations. Finally, how biomarker studies should be conducted in the future was also discussed.

STUDY RESULTS

Gray matter reduction has been most robust within temporo-frontal regions and cerebellum, whereas altered brain function has been most pronounced in cerebello-cortical connections and default mode network, each might be related to long-standing illness alterations and acute physiological alterations at measurement. By studying untreated patients, the progressive alterations in temporal and frontal regions and enlargements in bilateral putamen were found more likely effects of illness, not just treatment. Some of these changes were found with potential to predict clinical outcomes and differentiate biologically patient subgroups.

CONCLUSIONS

Mostly with data-driven approaches, the studies from China are helping identify candidate imaging biomarkers in schizophrenia that are related to early-stage illness, treatment effects, and biological subgroup differentiation. Future work is needed to translate these biomarkers for clinical application.

The Generalizability of Cortical Area Parcellations Across Early Childhood

The cerebral cortex consists of distinct areas that develop through intrinsic embryonic patterning and postnatal experiences. Accurate parcellation of these areas in neuroimaging studies improves statistical power and cross-study comparability. Given significant brain changes in volume, microstructure, and connectivity during early life, we hypothesized that cortical areas in 1- to 3-year-olds would differ markedly from neonates and increasingly resemble adult patterns as development progresses. Here, we parcellated the cerebral cortex into putative areas using local functional connectivity gradients in 92 toddlers at 2 years old. We demonstrate high reproducibility of these cortical regions across 1- to 3-year-olds in two independent datasets. The area boundaries in 1- to 3-year-olds were more similar to those in adults than those in neonates. While the age-specific group area parcellation better fit the underlying functional connectivity in individuals during the first 3 years, adult area parcellations might still have some utility in developmental studies, especially in children older than 6 years. Additionally, we provide connectivity-based community assignments of the parcels, showing fragmented anterior and posterior components based on the strongest connectivity, yet alignment with adult systems when weaker connectivity was included.

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.

Global brain asymmetry

Lateralization is a defining characteristic of the human brain, often studied through localized approaches that focus on interhemispheric differences between homologous pairs of regions. It is also important to emphasize an integrative perspective of global brain asymmetry, in which hemispheric differences are understood through global patterns across the entire brain.

Using precision approaches to improve brain-behavior prediction

Predicting individual behavioral traits from brain idiosyncrasies has broad practical implications, yet predictions vary widely. This constraint may be driven by a combination of signal and noise in both brain and behavioral variables. Here, we expand on this idea, highlighting the potential of extended sampling 'precision' studies. First, we discuss their relevance to improving the reliability of individualized estimates by minimizing measurement noise. Second, we review how targeted within-subject experiments, when combined with individualized analysis or modeling frameworks, can maximize signal. These improvements in signal-to-noise facilitated by precision designs can help boost prediction studies. We close by discussing the integration of precision approaches with large-sample consortia studies to leverage the advantages of both.

Opaque ontology: neuroimaging classification of ICD-10 diagnostic groups in the UK Biobank

BACKGROUND

The use of machine learning to classify diagnostic cases versus controls defined based on diagnostic ontologies such as the International Classification of Diseases, Tenth Revision (ICD-10) from neuroimaging features is now commonplace across a wide range of diagnostic fields. However, transdiagnostic comparisons of such classifications are lacking. Such transdiagnostic comparisons are important to establish the specificity of classification models, set benchmarks, and assess the value of diagnostic ontologies.

RESULTS

We investigated case-control classification accuracy in 17 different ICD-10 diagnostic groups from Chapter V (mental and behavioral disorders) and Chapter VI (diseases of the nervous system) using data from the UK Biobank. Classification models were trained using either neuroimaging (structural or functional brain magnetic resonance imaging feature sets) or sociodemographic features. Random forest classification models were adopted using rigorous shuffle-splits to estimate stability as well as accuracy of case-control classifications. Diagnostic classification accuracies were benchmarked against age classification (oldest vs. youngest) from the same feature sets and against additional classifier types (k-nearest neighbors and linear support vector machine). In contrast to age classification accuracy, which was high for all feature sets, few ICD-10 diagnostic groups were classified significantly above chance (namely, demyelinating diseases based on structural neuroimaging features and depression based on sociodemographic and functional neuroimaging features).

CONCLUSION

These findings highlight challenges with the current disease classification system, leading us to recommend caution with the use of ICD-10 diagnostic groups as target labels in brain-based disease prediction studies.

Reconfiguration of brain network dynamics in bipolar disorder: a hidden Markov model approach

Bipolar disorder (BD) is a neuropsychiatric disorder characterized by severe disturbance and fluctuation in mood. Dynamic functional connectivity (dFC) has the potential to more accurately capture the evolving processes of emotion and cognition in BD. Nevertheless, prior investigations of dFC typically centered on larger time scales, limiting the sensitivity to transient changes. This study employed hidden Markov model (HMM) analysis to delve deeper into the moment-to-moment temporal patterns of brain activity in BD. We utilized resting-state functional magnetic resonance imaging (rs-fMRI) data from 43 BD patients and 51 controls to evaluate the altered dynamic spatiotemporal architecture of the whole-brain network and identify unique activation patterns in BD. Additionally, we investigated the relationship between altered brain dynamics and structural disruption through the ridge regression (RR) algorithm. The results demonstrated that BD spent less time in a hyperconnected state with higher network efficiency and lower segregation. Conversely, BD spent more time in anticorrelated states featuring overall negative correlations, particularly among pairs of default mode network (DMN) and sensorimotor network (SMN), DMN and insular-opercular ventral attention networks (ION), subcortical network (SCN) and SMN, as well as SCN and ION. Interestingly, the hypoactivation of the cognitive control network in BD may be associated with the structural disruption primarily situated in the frontal and parietal lobes. This study investigated the dynamic mechanisms of brain network dysfunction in BD and offered fresh perspectives for exploring the physiological foundation of altered brain dynamics.

A quantitative comparison of atlas parcellations on the human superior temporal sulcus

The superior temporal sulcus (STS) has a functional topography that has been difficult to characterize through traditional approaches. Automated atlas parcellations may be one solution while also being beneficial for both dimensional reduction and standardizing regions of interest, but they yield very different boundary definitions along the STS. Here we evaluate how well machine learning classifiers can correctly identify six social cognitive tasks from STS activation patterns dimensionally reduced using four popular atlases (Glasser et al., 2016; Gordon et al., 2016; Power et al., 2011 as projected onto the surface by Arslan et al., 2018; Schaefer et al., 2018). Functional data was summarized within each STS parcel in one of four ways, then subjected to leave-one-subject-out cross-validation SVM classification. We found that the classifiers could readily label conditions when data was parcellated using any of the four atlases, evidence that dimensional reduction to parcels did not compromise functional fingerprints. Mean activation for the social conditions was the most effective metric for classification in the right STS, whereas all the metrics classified equally well in the left STS. Interestingly, even atlases constructed from random parcellation schemes (null atlases) classified the conditions with high accuracy. We therefore conclude that the complex activation maps on the STS are readily differentiated at a coarse granular level, despite a strict topography having not yet been identified. Further work is required to identify what features have greatest potential to improve the utility of atlases in replacing functional localizers.

Imaging genetics of language network functional connectivity reveals links with language-related abilities, dyslexia and handedness

Language is supported by a distributed network of brain regions with a particular contribution from the left hemisphere. A multi-level understanding of this network requires studying its genetic architecture. We used resting-state imaging data from 29,681 participants (UK Biobank) to measure connectivity between 18 left-hemisphere regions involved in multimodal sentence-level processing, as well as their right-hemisphere homotopes, and interhemispheric connections. Multivariate genome-wide association analysis of this total network, based on genetic variants with population frequencies  >1%, identified 14 genomic loci, of which three were also associated with asymmetry of intrahemispheric connectivity. Polygenic dispositions to lower language-related abilities, dyslexia and left-handedness were associated with generally reduced leftward asymmetry of functional connectivity. Exome-wide association analysis based on rare, protein-altering variants (frequencies <1%) suggested 7 additional genes. These findings shed new light on genetic contributions to language network organization and related behavioural traits.

A hierarchical atlas of the human cerebellum for functional precision mapping

The human cerebellum is activated by a wide variety of cognitive and motor tasks. Previous functional atlases have relied on single task-based or resting-state fMRI datasets. Here, we present a functional atlas that integrates information from seven large-scale datasets, outperforming existing group atlases. The atlas has three further advantages. First, the atlas allows for precision mapping in individuals: the integration of the probabilistic group atlas with an individual localizer scan results in a marked improvement in prediction of individual boundaries. Second, we provide both asymmetric and symmetric versions of the atlas. The symmetric version, which is obtained by constraining the boundaries to be the same across hemispheres, is especially useful in studying functional lateralization. Finally, the regions are hierarchically organized across three levels, allowing analyses at the appropriate level of granularity. Overall, the present atlas is an important resource for the study of the interdigitated functional organization of the human cerebellum in health and disease.

Deep multimodal saliency parcellation of cerebellar pathways: Linking microstructure and individual function through explainable multitask learning

Parcellation of human cerebellar pathways is essential for advancing our understanding of the human brain. Existing diffusion magnetic resonance imaging tractography parcellation methods have been successful in defining major cerebellar fibre tracts, while relying solely on fibre tract structure. However, each fibre tract may relay information related to multiple cognitive and motor functions of the cerebellum. Hence, it may be beneficial for parcellation to consider the potential importance of the fibre tracts for individual motor and cognitive functional performance measures. In this work, we propose a multimodal data-driven method for cerebellar pathway parcellation, which incorporates both measures of microstructure and connectivity, and measures of individual functional performance. Our method involves first training a multitask deep network to predict various cognitive and motor measures from a set of fibre tract structural features. The importance of each structural feature for predicting each functional measure is then computed, resulting in a set of structure-function saliency values that are clustered to parcellate cerebellar pathways. We refer to our method as Deep Multimodal Saliency Parcellation (DeepMSP), as it computes the saliency of structural measures for predicting cognitive and motor functional performance, with these saliencies being applied to the task of parcellation. Applying DeepMSP to a large-scale dataset from the Human Connectome Project Young Adult study (n = 1065), we found that it was feasible to identify multiple cerebellar pathway parcels with unique structure-function saliency patterns that were stable across training folds. We thoroughly experimented with all stages of the DeepMSP pipeline, including network selection, structure-function saliency representation, clustering algorithm, and cluster count. We found that a 1D convolutional neural network architecture and a transformer network architecture both performed comparably for the multitask prediction of endurance, strength, reading decoding, and vocabulary comprehension, with both architectures outperforming a fully connected network architecture. Quantitative experiments demonstrated that a proposed low-dimensional saliency representation with an explicit measure of motor versus cognitive category bias achieved the best parcellation results, while a parcel count of four was most successful according to standard cluster quality metrics. Our results suggested that motor and cognitive saliencies are distributed across the cerebellar white matter pathways. Inspection of the final k = 4 parcellation revealed that the highest-saliency parcel was most salient for the prediction of both motor and cognitive performance scores and included parts of the middle and superior cerebellar peduncles. Our proposed saliency-based parcellation framework, DeepMSP, enables multimodal, data-driven tractography parcellation. Through utilising both structural features and functional performance measures, this parcellation strategy may have the potential to enhance the study of structure-function relationships of the cerebellar pathways.

fMRI-based spatio-temporal parcellations of the human brain

PURPOSE OF REVIEW

Human brain parcellation based on functional magnetic resonance imaging (fMRI) plays an essential role in neuroscience research. By segmenting vast and intricate fMRI data into functionally similar units, researchers can better decipher the brain's structure in both healthy and diseased states. This article reviews current methodologies and ideas in this field, while also outlining the obstacles and directions for future research.

RECENT FINDINGS

Traditional brain parcellation techniques, which often rely on cytoarchitectonic criteria, overlook the functional and temporal information accessible through fMRI. The adoption of machine learning techniques, notably deep learning, offers the potential to harness both spatial and temporal information for more nuanced brain segmentation. However, the search for a one-size-fits-all solution to brain segmentation is impractical, with the choice between group-level or individual-level models and the intended downstream analysis influencing the optimal parcellation strategy. Additionally, evaluating these models is complicated by our incomplete understanding of brain function and the absence of a definitive "ground truth".

SUMMARY

While recent methodological advancements have significantly enhanced our grasp of the brain's spatial and temporal dynamics, challenges persist in advancing fMRI-based spatio-temporal representations. Future efforts will likely focus on refining model evaluation and selection as well as developing methods that offer clear interpretability for clinical usage, thereby facilitating further breakthroughs in our comprehension of the brain.

How sex and gender shape functional brain networks

Sex and gender differences exist in the prevalence and clinical manifestation of common brain disorders. Identifying their neural correlates may help improve clinical care.

Brain network functional connectivity changes in long illness duration chronic schizophrenia

Introduction

Chronic schizophrenia has a course of 5 years or more and has a widespread abnormalities in brain functional connectivity. This study aimed to find characteristic functional and structural changes in a long illness duration chronic schizophrenia (10 years or more).

Methods

Thirty-six patients with a long illness duration chronic schizophrenia and 38 healthy controls were analyzed by independent component analysis of brain network functional connectivity. Correlation analysis with clinical duration was performed on six resting state networks: auditory network, default mode network, dorsal attention network, fronto-parietal network, somatomotor network, and visual network.

Results

The differences in the resting state network between the two groups revealed that patients exhibited enhanced inter-network connections between default mode network and multiple brain networks, while the inter-network connections between somatomotor network, default mode network and visual network were reduced. In patients, functional connectivity of Cuneus_L was negatively correlated with illness duration. Furthermore, receiver operating characteristic curve of functional connectivity showed that changes in Thalamus_L, Rectus_L, Frontal_Mid_R, and Cerebelum_9_L may indicate a longer illness duration chronic schizophrenia.

Discussion

In our study, we also confirmed that the course of disease is significantly associated with specific brain regions, and the changes in specific brain regions may indicate that chronic schizophrenia has a course of 10 years or more.

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.

Systematic evaluation of fMRI data-processing pipelines for consistent functional connectomics

Functional interactions between brain regions can be viewed as a network, enabling neuroscientists to investigate brain function through network science. Here, we systematically evaluate 768 data-processing pipelines for network reconstruction from resting-state functional MRI, evaluating the effect of brain parcellation, connectivity definition, and global signal regression. Our criteria seek pipelines that minimise motion confounds and spurious test-retest discrepancies of network topology, while being sensitive to both inter-subject differences and experimental effects of interest. We reveal vast and systematic variability across pipelines' suitability for functional connectomics. Inappropriate choice of data-processing pipeline can produce results that are not only misleading, but systematically so, with the majority of pipelines failing at least one criterion. However, a set of optimal pipelines consistently satisfy all criteria across different datasets, spanning minutes, weeks, and months. We provide a full breakdown of each pipeline's performance across criteria and datasets, to inform future best practices in functional connectomics.

Never-Ending Learning for Explainable Brain Computing

Exploring the nature of human intelligence and behavior is a longstanding pursuit in cognitive neuroscience, driven by the accumulation of knowledge, information, and data across various studies. However, achieving a unified and transparent interpretation of findings presents formidable challenges. In response, an explainable brain computing framework is proposed that employs the never-ending learning paradigm, integrating evidence combination and fusion computing within a Knowledge-Information-Data (KID) architecture. The framework supports continuous brain cognition investigation, utilizing joint knowledge-driven forward inference and data-driven reverse inference, bolstered by the pre-trained language modeling techniques and the human-in-the-loop mechanisms. In particular, it incorporates internal evidence learning through multi-task functional neuroimaging analyses and external evidence learning via topic modeling of published neuroimaging studies, all of which involve human interactions at different stages. Based on two case studies, the intricate uncertainty surrounding brain localization in human reasoning is revealed. The present study also highlights the potential of systematization to advance explainable brain computing, offering a finer-grained understanding of brain activity patterns related to human intelligence.

A hierarchical atlas of the human cerebellum for functional precision mapping

The human cerebellum is activated by a wide variety of cognitive and motor tasks. Previous functional atlases have relied on single task-based or resting-state fMRI datasets. Here, we present a functional atlas that integrates information from 7 large-scale datasets, outperforming existing group atlasses. The new atlas has three further advantages: First, the atlas allows for precision mapping in individuals: The integration of the probabilistic group atlas with an individual localizer scan results in a marked improvement in prediction of individual boundaries. Second, we provide both asymmetric and symmetric versions of the atlas. The symmetric version, which is obtained by constraining the boundaries to be the same across hemispheres, is especially useful in studying functional lateralization. Finally, the regions are hierarchically organized across 3 levels, allowing analyses at the appropriate level of granularity. Overall, the new atlas is an important resource for the study of the interdigitated functional organization of the human cerebellum in health and disease.

A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution

To fully understand how the human brain works, knowledge of its structure at high resolution is needed. Presented here is a computationally intensive reconstruction of the ultrastructure of a cubic millimeter of human temporal cortex that was surgically removed to gain access to an underlying epileptic focus. It contains about 57,000 cells, about 230 millimeters of blood vessels, and about 150 million synapses and comprises 1.4 petabytes. Our analysis showed that glia outnumber neurons 2:1, oligodendrocytes were the most common cell, deep layer excitatory neurons could be classified on the basis of dendritic orientation, and among thousands of weak connections to each neuron, there exist rare powerful axonal inputs of up to 50 synapses. Further studies using this resource may bring valuable insights into the mysteries of the human brain.

Atypical connectome topography and signal flow in temporal lobe epilepsy

Temporal lobe epilepsy (TLE) is the most common pharmaco-resistant epilepsy in adults. While primarily associated with mesiotemporal pathology, recent evidence suggests that brain alterations in TLE extend beyond the paralimbic epicenter and impact macroscale function and cognitive functions, particularly memory. Using connectome-wide manifold learning and generative models of effective connectivity, we examined functional topography and directional signal flow patterns between large-scale neural circuits in TLE at rest. Studying a multisite cohort of 95 patients with TLE and 95 healthy controls, we observed atypical functional topographies in the former group, characterized by reduced differentiation between sensory and transmodal association cortices, with most marked effects in bilateral temporo-limbic and ventromedial prefrontal cortices. These findings were consistent across all study sites, present in left and right lateralized patients, and validated in a subgroup of patients with histopathological validation of mesiotemporal sclerosis and post-surgical seizure freedom. Moreover, they were replicated in an independent cohort of 30 TLE patients and 40 healthy controls. Further analyses demonstrated that reduced differentiation related to decreased functional signal flow into and out of temporolimbic cortical systems and other brain networks. Parallel analyses of structural and diffusion-weighted MRI data revealed that topographic alterations were independent of TLE-related cortical thinning but partially mediated by white matter microstructural changes that radiated away from paralimbic circuits. Finally, we found a strong association between the degree of functional alterations and behavioral markers of memory dysfunction. Our work illustrates the complex landscape of macroscale functional imbalances in TLE, which can serve as intermediate markers bridging microstructural changes and cognitive impairment.

Co-representation of Functional Brain Networks Is Shaped by Cortical Myeloarchitecture and Reveals Individual Behavioral Ability

Large-scale functional networks are spatially distributed in the human brain. Despite recent progress in differentiating their functional roles, how the brain navigates the spatial coordination among them and the biological relevance of this coordination is still not fully understood. Capitalizing on canonical individualized networks derived from functional MRI data, we proposed a new concept, that is, co-representation of functional brain networks, to delineate the spatial coordination among them. To further quantify the co-representation pattern, we defined two indexes, that is, the co-representation specificity (CoRS) and intensity (CoRI), for separately measuring the extent of specific and average expression of functional networks at each brain location by using the data from both sexes. We found that the identified pattern of co-representation was anchored by cortical regions with three types of cytoarchitectural classes along a sensory-fugal axis, including, at the first end, primary (idiotypic) regions showing high CoRS, at the second end, heteromodal regions showing low CoRS and high CoRI, at the third end, paralimbic regions showing low CoRI. Importantly, we demonstrated the critical role of myeloarchitecture in sculpting the spatial distribution of co-representation by assessing the association with the myelin-related neuroanatomical and transcriptomic profiles. Furthermore, the significance of manifesting the co-representation was revealed in its prediction of individual behavioral ability. Our findings indicated that the spatial coordination among functional networks was built upon an anatomically configured blueprint to facilitate neural information processing, while advancing our understanding of the topographical organization of the brain by emphasizing the assembly of functional networks.

Individualized brain mapping for navigated neuromodulation

ABSTRACT

The brain is a complex organ that requires precise mapping to understand its structure and function. Brain atlases provide a powerful tool for studying brain circuits, discovering biological markers for early diagnosis, and developing personalized treatments for neuropsychiatric disorders. Neuromodulation techniques, such as transcranial magnetic stimulation and deep brain stimulation, have revolutionized clinical therapies for neuropsychiatric disorders. However, the lack of fine-scale brain atlases limits the precision and effectiveness of these techniques. Advances in neuroimaging and machine learning techniques have led to the emergence of stereotactic-assisted neurosurgery and navigation systems. Still, the individual variability among patients and the diversity of brain diseases make it necessary to develop personalized solutions. The article provides an overview of recent advances in individualized brain mapping and navigated neuromodulation and discusses the methodological profiles, advantages, disadvantages, and future trends of these techniques. The article concludes by posing open questions about the future development of individualized brain mapping and navigated neuromodulation.

Efficient Estimation of Directed Connectivity in Nonlinear and Nonstationary Spiking Neuron Networks

OBJECTIVE

Studying directed connectivity within spiking neuron networks can help understand neural mechanisms. Existing methods assume linear time-invariant neural dynamics with a fixed time lag in information transmission, while spiking networks usually involve complex dynamics that are nonlinear and nonstationary, and have varying time lags.

METHODS

We develop a Gated Recurrent Unit (GRU)-Point Process (PP) method to estimate directed connectivity within spiking networks. We use a GRU to describe the dependency of the target neuron's current firing rate on the source neurons' past spiking events and a PP to relate the target neuron's firing rate to its current 0-1 spiking event. The GRU model uses recurrent states and gate/activation functions to deal with varying time lags, nonlinearity, and nonstationarity in a parameter-efficient manner. We estimate the model using maximum likelihood and compute directed information as our measure of directed connectivity.

RESULTS

We conduct simulations using artificial spiking networks and a biophysical model of Parkinson's disease to show that GRU-PP systematically addresses varying time lags, nonlinearity, and nonstationarity, and estimates directed connectivity with high accuracy and data efficiency. We also use a non-human-primate dataset to show that GRU-PP correctly identifies the biophysically-plausible stronger PMd-to-M1 connectivity than M1-to-PMd connectivity during reaching. In all experiments, the GRU-PP consistently outperforms state-of-the-art methods.

CONCLUSION

The GRU-PP method efficiently estimates directed connectivity in varying time lag, nonlinear, and nonstationary spiking neuron networks.

SIGNIFICANCE

The proposed method can serve as a directed connectivity analysis tool for investigating complex spiking neuron network dynamics.

Libet's legacy: A primer to the neuroscience of volition

The neuroscience of volition is an emerging subfield of the brain sciences, with hundreds of papers on the role of consciousness in action formation published each year. This makes the state-of-the-art in the discipline poorly accessible to newcomers and difficult to follow even for experts in the field. Here we provide a comprehensive summary of research in this field since its inception that will be useful to both groups. We also discuss important ideas that have received little coverage in the literature so far. We systematically reviewed a set of 2220 publications, with detailed consideration of almost 500 of the most relevant papers. We provide a thorough introduction to the seminal work of Benjamin Libet from the 1960s to 1980s. We also discuss common criticisms of Libet's method, including temporal introspection, the interpretation of the assumed physiological correlates of volition, and various conceptual issues. We conclude with recent advances and potential future directions in the field, highlighting modern methodological approaches to volition, as well as important recent findings.

Chronic Mild Sleep Restriction Does Not Lead to Marked Neuronal Alterations Compared With Maintained Adequate Sleep in Adults

BACKGROUND

Sleep restriction (SR) has been shown to upregulate neuronal reward networks in response to food stimuli, but prior studies were short-term and employed severe SR paradigms.

OBJECTIVE

Our goal was to determine whether mild SR, achieved by delaying bedtimes by 1.5 h, influences neuronal networks responsive to food stimuli compared with maintained adequate sleep (AS) >7 h/night.

METHODS

A randomized controlled crossover study with 2 6-wk phases, AS (≥7 h sleep/night) and SR (-1.5 h/night relative to screening), was conducted. Adults with AS duration, measured using wrist actigraphy over a 2-wk screening period, and self-reported good sleep quality were enrolled. Resting-state and food-stimulated functional neuroimaging (fMRI) was performed at the endpoint of each phase. Resting-state fMRI data analyses included a priori region-of-interest seed-based functional connectivity, whole-brain voxel-wise analyses, and network analyses. Food task-fMRI analyses compared brain activity patterns in response to food cues between conditions. Paired-sample t tests tested differences between conditions.

RESULTS

Twenty-six participants (16 males; age 29.6 ± 5.3 y, body mass index 26.9 ± 4.0 kg/m2) contributed complete data. Total sleep time was 7 h 30 ± 28 min/night during AS compared with 6 h 12 ± 26 min/night during SR. We employed different statistical approaches to replicate prior studies in the field and to apply more robust approaches that are currently advocated in the field. Using uncorrected P value of <0.01, cluster ≥10-voxel thresholds, we replicated prior findings of increased activation in response to foods in reward networks after SR compared with AS (right insula, right inferior frontal gyrus, and right supramarginal gyrus). These findings did not survive more rigorous analytical approaches (Gaussian Random Field theory correction at 2-tailed voxel P < 0.001, cluster P < 0.05).

CONCLUSIONS

The results suggest that mild SR leads to increased reward responsivity to foods but with low confidence given the failure to meet significance from rigorous statistical analyses. Further research is necessary to inform the mechanisms underlying the role of sleep on food intake regulation. This trial was registered at clinicaltrials.gov as NCT02960776.

The time-evolving epileptic brain network: concepts, definitions, accomplishments, perspectives

Epilepsy is now considered a network disease that affects the brain across multiple levels of spatial and temporal scales. The paradigm shift from an epileptic focus-a discrete cortical area from which seizures originate-to a widespread epileptic network-spanning lobes and hemispheres-considerably advanced our understanding of epilepsy and continues to influence both research and clinical treatment of this multi-faceted high-impact neurological disorder. The epileptic network, however, is not static but evolves in time which requires novel approaches for an in-depth characterization. In this review, we discuss conceptual basics of network theory and critically examine state-of-the-art recording techniques and analysis tools used to assess and characterize a time-evolving human epileptic brain network. We give an account on current shortcomings and highlight potential developments towards an improved clinical management of epilepsy.

Multifractal long-range dependence pattern of functional magnetic resonance imaging in the human brain at rest

Long-range dependence is a prevalent phenomenon in various biological systems that characterizes the long-memory effect of temporal fluctuations. While recent research suggests that functional magnetic resonance imaging signal has fractal property, it remains unknown about the multifractal long-range dependence pattern of resting-state functional magnetic resonance imaging signals. The current study adopted the multifractal detrended fluctuation analysis on highly sampled resting-state functional magnetic resonance imaging scans to investigate long-range dependence profile associated with the whole-brain voxels as specific functional networks. Our findings revealed the long-range dependence's multifractal properties. Moreover, long-term persistent fluctuations are found for all stations with stronger persistency in whole-brain regions. Subsets with large fluctuations contribute more to the multifractal spectrum in the whole brain. Additionally, we found that the preprocessing with band-pass filtering provided significantly higher reliability for estimating long-range dependence. Our validation analysis confirmed that the optimal pipeline of long-range dependence analysis should include band-pass filtering and removal of daily temporal dependence. Furthermore, multifractal long-range dependence characteristics in healthy control and schizophrenia are different significantly. This work has provided an analytical pipeline for the multifractal long-range dependence in the resting-state functional magnetic resonance imaging signal. The findings suggest differential long-memory effects in the intrinsic functional networks, which may offer a neural marker finding for understanding brain function and pathology.

Inside the mindful moment: The effects of brief mindfulness practice on large-scale network organization and intimate partner aggression

Mindfulness can produce neuroplastic changes that support adaptive cognitive and emotional functioning. Recently interest in single-exercise mindfulness instruction has grown considerably because of the advent of mobile health technology. Accordingly, the current study sought to extend neural models of mindfulness by investigating transient states of mindfulness during single-dose exposure to focused attention meditation. Specifically, we examined the ability of a brief mindfulness induction to attenuate intimate partner aggression via adaptive changes to intrinsic functional brain networks. We employed a dual-regression approach to examine a large-scale functional network organization in 50 intimate partner dyads (total n = 100) while they received either mindfulness (n = 50) or relaxation (n = 50) instruction. Mindfulness instruction reduced coherence within the Default Mode Network and increased functional connectivity within the Frontoparietal Control and Salience Networks. Additionally, mindfulness decoupled primary visual and attention-linked networks. Yet, this induction was unable to elicit changes in subsequent intimate partner aggression, and such aggression was broadly unassociated with any of our network indices. These findings suggest that minimal doses of focused attention-based mindfulness can promote transient changes in large-scale brain networks that have uncertain implications for aggressive behavior.

The abilities of movie-watching functional connectivity in individual identifications and individualized predictions

Quite a few studies have been performed based on movie-watching functional connectivity (FC). As compared to its resting-state counterpart, however, there is still much to know about its abilities in individual identifications and individualized predictions. To pave the way for appropriate usage of movie-watching FC, we systemically evaluated the minimum number of time points, as well as the exact functional networks, supporting individual identifications and individualized predictions of apparent traits based on it. We performed the study based on the 7T movie-watching fMRI data included in the HCP S1200 Release, and took IQ as the test case for the prediction analyses. The results indicate that movie-watching FC based on only 15 time points can support successful individual identifications (99.47%), and the connectivity contributed more to identifications were much associated with higher-order cognitive processes (the secondary visual network, the frontoparietal network and the posterior multimodal network). For individualized predictions of IQ, it was found that successful predictions necessitated 60 time points (predicted vs. actual IQ correlation significant at P < 0.05, based on 5,000 permutations), and the prediction accuracy increased logarithmically with the number of time points used for connectivity calculation. Furthermore, the connectivity that contributed more to individual identifications exhibited the strongest prediction ability. Collectively, our findings demonstrate that movie-watching FC can capture rich information about human brain function, and its ability in individualized predictions depends heavily on the length of fMRI scans.

The individualized neural tuning model: Precise and generalizable cartography of functional architecture in individual brains

Quantifying how brain functional architecture differs from person to person is a key challenge in human neuroscience. Current individualized models of brain functional organization are based on brain regions and networks, limiting their use in studying fine-grained vertex-level differences. In this work, we present the individualized neural tuning (INT) model, a fine-grained individualized model of brain functional organization. The INT model is designed to have vertex-level granularity, to capture both representational and topographic differences, and to model stimulus-general neural tuning. Through a series of analyses, we demonstrate that (a) our INT model provides a reliable individualized measure of fine-grained brain functional organization, (b) it accurately predicts individualized brain response patterns to new stimuli, and (c) for many benchmarks, it requires only 10-20 minutes of data for good performance. The high reliability, specificity, precision, and generalizability of our INT model affords new opportunities for building brain-based biomarkers based on naturalistic neuroimaging paradigms.

A personalized cortical atlas for functional regions of interest

Advances in functional MRI (fMRI) allow mapping an individual's brain function in vivo. Task fMRI can localize domain-specific regions of cognitive processing or functional regions of interest (fROIs) within an individual. Moreover, data from resting state (no task) fMRI can be used to define an individual's connectome, which can characterize that individual's functional organization via connectivity-based parcellations. However, can connectivity-based parcellations alone predict an individual's fROIs? Here, we describe an approach to compute individualized rs-fROIs (i.e., regions that correspond to given fROI constructed using only resting state data) for motor control, working memory, high-level vision, and language comprehension. The rs-fROIs were computed and validated using a large sample of young adults (n = 1,018) with resting state and task fMRI from the Human Connectome Project. First, resting state parcellations were defined across a sequence of resolutions from broadscale to fine-grained networks in a training group of 500 individuals. Second, 21 rs-fROIs were defined from the training group by identifying the rs network that most closely matched task-defined fROIs across all individuals. Third, the selectivity of rs-fROIs was investigated in a training set of the remaining 518 individuals. All computed rs-fROIs were indeed selective for their preferred category. Critically, the rs-fROIs had higher selectivity than probabilistic atlas parcels for nearly all fROIs. In conclusion, we present a potential approach to define selective fROIs on an individual-level circumventing the need for multiple task-based localizers.NEW & NOTEWORTHY We compute individualized resting state parcels that identify an individual's own functional regions of interest (fROIs) for high-level vision, language comprehension, motor control, and working memory, using only their functional connectome. This approach demonstrates a rapid and powerful alternative for finding a large set of fROIs in an individual, using only their unique connectivity pattern, which does not require the costly acquisition of multiple fMRI localizer tasks.

Controversies and progress on standardization of large-scale brain network nomenclature

Progress in scientific disciplines is accompanied by standardization of terminology. Network neuroscience, at the level of macroscale organization of the brain, is beginning to confront the challenges associated with developing a taxonomy of its fundamental explanatory constructs. The Workgroup for HArmonized Taxonomy of NETworks (WHATNET) was formed in 2020 as an Organization for Human Brain Mapping (OHBM)-endorsed best practices committee to provide recommendations on points of consensus, identify open questions, and highlight areas of ongoing debate in the service of moving the field toward standardized reporting of network neuroscience results. The committee conducted a survey to catalog current practices in large-scale brain network nomenclature. A few well-known network names (e.g., default mode network) dominated responses to the survey, and a number of illuminating points of disagreement emerged. We summarize survey results and provide initial considerations and recommendations from the workgroup. This perspective piece includes a selective review of challenges to this enterprise, including (1) network scale, resolution, and hierarchies; (2) interindividual variability of networks; (3) dynamics and nonstationarity of networks; (4) consideration of network affiliations of subcortical structures; and (5) consideration of multimodal information. We close with minimal reporting guidelines for the cognitive and network neuroscience communities to adopt.

Evaluating functional brain organization in individuals and identifying contributions to network overlap

Individual differences in the spatial organization of resting state networks have received increased attention in recent years. Measures of individual-specific spatial organization of brain networks and overlapping network organization have been linked to important behavioral and clinical traits and are therefore potential biomarker targets for personalized psychiatry approaches. To better understand individual-specific spatial brain organization, this paper addressed three key goals. First, we determined whether it is possible to reliably estimate weighted (non-binarized) resting state network maps using data from only a single individual, while also maintaining maximum spatial correspondence across individuals. Second, we determined the degree of spatial overlap between distinct networks, using test-retest and twin data. Third, we systematically tested multiple hypotheses (spatial mixing, temporal switching, and coupling) as candidate explanations for why networks overlap spatially. To estimate weighted network organization, we adopt the Probabilistic Functional Modes (PROFUMO) algorithm, which implements a Bayesian framework with hemodynamic and connectivity priors to supplement optimization for spatial sparsity/independence. Our findings showed that replicable individual-specific estimates of weighted resting state networks can be derived using high quality fMRI data within individual subjects. Network organization estimates using only data from each individual subject closely resembled group-informed network estimates (which was not explicitly modeled in our individual-specific analyses), suggesting that cross-subject correspondence was largely maintained. Furthermore, our results confirmed the presence of spatial overlap in network organization, which was replicable across sessions within individuals and in monozygotic twin pairs. Intriguingly, our findings provide evidence that network overlap is indicative of linear additive coupling. These results suggest that regions of network overlap concurrently process information from all contributing networks, potentially pointing to the role of overlapping network organization in the integration of information across multiple brain systems.

Investigating the heterogeneity within the somatosensory-motor network and its relationship with the attention and default systems

The somatosensory-motor network (SMN) not only plays an important role in primary somatosensory and motor processing but is also central to many disorders. However, the SMN heterogeneity related to higher-order systems still remains unclear. Here, we investigated SMN heterogeneity from multiple perspectives. To characterize the SMN substructures in more detail, we used ultra-high-field functional MRI to delineate a finer-grained cortical parcellation containing 430 parcels that is more homogenous than the state-of-the-art parcellation. We personalized the new parcellation to account for individual differences and identified multiscale individual-specific brain structures. We found that the SMN subnetworks showed distinct resting-state functional connectivity (RSFC) patterns. The Hand subnetwork was central within the SMN and exhibited stronger RSFC with the attention systems than the other subnetworks, whereas the Tongue subnetwork exhibited stronger RSFC with the default systems. This two-fold differentiation was observed in the temporal ordering patterns within the SMN. Furthermore, we characterized how the distinct attention and default streams were carried forward into the functions of the SMN using dynamic causal modeling and identified two behavioral domains associated with this SMN fractionation using meta-analytic tools. Overall, our findings provided important insights into the heterogeneous SMN organization at the system level and suggested that the Hand subnetwork may be preferentially involved in exogenous processes, whereas the Tongue subnetwork may be more important in endogenous processes.

Functional connectomics in depression: insights into therapies

Depression is a common mental disorder characterized by heterogeneous cognitive and behavioral symptoms. The emerging research paradigm of functional connectomics has provided a quantitative theoretical framework and analytic tools for parsing variations in the organization and function of brain networks in depression. In this review, we first discuss recent progress in depression-associated functional connectome variations. We then discuss treatment-specific brain network outcomes in depression and propose a hypothetical model highlighting the advantages and uniqueness of each treatment in relation to the modulation of specific brain network connectivity and symptoms of depression. Finally, we look to the future promise of combining multiple treatment types in clinical practice, using multisite datasets and multimodal neuroimaging approaches, and identifying biological depression subtypes.

Model connectivity: leveraging the power of encoding models to overcome the limitations of functional connectivity

Functional connectivity (FC) is the most popular method for recovering functional networks of brain areas with fMRI. However, because FC is defined as temporal correlations in brain activity, FC networks are confounded by noise and lack a precise functional role. To overcome these limitations, we developed model connectivity (MC). MC is defined as similarities in encoding model weights, which quantify reliable functional activity in terms of interpretable stimulus- or task-related features. To compare FC and MC, both methods were applied to a naturalistic story listening dataset. FC recovered spatially broad networks that are confounded by noise, and that lack a clear role during natural language comprehension. By contrast, MC recovered spatially localized networks that are robust to noise, and that represent distinct categories of semantic concepts. Thus, MC is a powerful data-driven approach for recovering and interpreting the functional networks that support complex cognitive processes.

Image harmonization: A review of statistical and deep learning methods for removing batch effects and evaluation metrics for effective harmonization

Magnetic resonance imaging and computed tomography from multiple batches (e.g. sites, scanners, datasets, etc.) are increasingly used alongside complex downstream analyses to obtain new insights into the human brain. However, significant confounding due to batch-related technical variation, called batch effects, is present in this data; direct application of downstream analyses to the data may lead to biased results. Image harmonization methods seek to remove these batch effects and enable increased generalizability and reproducibility of downstream results. In this review, we describe and categorize current approaches in statistical and deep learning harmonization methods. We also describe current evaluation metrics used to assess harmonization methods and provide a standardized framework to evaluate newly-proposed methods for effective harmonization and preservation of biological information. Finally, we provide recommendations to end-users to advocate for more effective use of current methods and to methodologists to direct future efforts and accelerate development of the field.

Cortex-wide neural dynamics predict behavioral states and provide a neural basis for resting-state dynamic functional connectivity

Although resting-state functional magnetic resonance imaging (fMRI) studies have observed dynamically changing brain-wide networks of correlated activity, fMRI's dependence on hemodynamic signals makes results challenging to interpret. Meanwhile, emerging techniques for real-time recording of large populations of neurons have revealed compelling fluctuations in neuronal activity across the brain that are obscured by traditional trial averaging. To reconcile these observations, we use wide-field optical mapping to simultaneously record pan-cortical neuronal and hemodynamic activity in awake, spontaneously behaving mice. Some components of observed neuronal activity clearly represent sensory and motor function. However, particularly during quiet rest, strongly fluctuating patterns of activity across diverse brain regions contribute greatly to interregional correlations. Dynamic changes in these correlations coincide with changes in arousal state. Simultaneously acquired hemodynamics depict similar brain-state-dependent correlation shifts. These results support a neural basis for dynamic resting-state fMRI, while highlighting the importance of brain-wide neuronal fluctuations in the study of brain state.

Atypical connectome topography and signal flow in temporal lobe epilepsy

Temporal lobe epilepsy (TLE) is one of the most common pharmaco-resistant epilepsies in adults. While hippocampal pathology is the hallmark of this condition, emerging evidence indicates that brain alterations extend beyond the mesiotemporal epicenter and affect macroscale brain function and cognition. We studied macroscale functional reorganization in TLE, explored structural substrates, and examined cognitive associations. We investigated a multisite cohort of 95 patients with pharmaco-resistant TLE and 95 healthy controls using state-of-the-art multimodal 3T magnetic resonance imaging (MRI). We quantified macroscale functional topographic organization using connectome dimensionality reduction techniques and estimated directional functional flow using generative models of effective connectivity. We observed atypical functional topographies in patients with TLE relative to controls, manifesting as reduced functional differentiation between sensory/motor networks and transmodal systems such as the default mode network, with peak alterations in bilateral temporal and ventromedial prefrontal cortices. TLE-related topographic changes were consistent in all three included sites and reflected reductions in hierarchical flow patterns between cortical systems. Integration of parallel multimodal MRI data indicated that these findings were independent of TLE-related cortical grey matter atrophy, but mediated by microstructural alterations in the superficial white matter immediately beneath the cortex. The magnitude of functional perturbations was robustly associated with behavioral markers of memory function. Overall, this work provides converging evidence for macroscale functional imbalances, contributing microstructural alterations, and their associations with cognitive dysfunction in TLE.

Assortative mixing in micro-architecturally annotated brain connectomes

The wiring of the brain connects micro-architecturally diverse neuronal populations, but the conventional graph model, which encodes macroscale brain connectivity as a network of nodes and edges, abstracts away the rich biological detail of each regional node. Here, we annotate connectomes with multiple biological attributes and formally study assortative mixing in annotated connectomes. Namely, we quantify the tendency for regions to be connected based on the similarity of their micro-architectural attributes. We perform all experiments using four cortico-cortical connectome datasets from three different species, and consider a range of molecular, cellular, and laminar annotations. We show that mixing between micro-architecturally diverse neuronal populations is supported by long-distance connections and find that the arrangement of connections with respect to biological annotations is associated to patterns of regional functional specialization. By bridging scales of cortical organization, from microscale attributes to macroscale connectivity, this work lays the foundation for next-generation annotated connectomics.

Influence of vigilance-related arousal on brain dynamics: Potentials of new approaches

Growing research has focused on how mesoscopic activity in the brain develops over time and space. Recent influential studies using functional imaging have characterized brain dynamics in terms of the spread of activation across the brain following a unimodal to transmodal axis. In parallel, a number of studies have assessed changes of brain connectivity in terms of vigilance-linked arousal. Here I offer a view on how these two lines of research can lead to a deeper understanding of how arousal shapes the brain's dynamic behavior. This knowledge could have great impact on the investigation of mental disease.

Noninvasive modulation of human corticostriatal activity

Corticostriatal activity is an appealing target for nonpharmacological treatments of brain disorders. In humans, corticostriatal activity may be modulated with noninvasive brain stimulation (NIBS). However, a NIBS protocol with a sound neuroimaging measure demonstrating a change in corticostriatal activity is currently lacking. Here, we combine transcranial static magnetic field stimulation (tSMS) with resting-state functional MRI (fMRI). We first present and validate the ISAAC analysis, a well-principled framework that disambiguates functional connectivity between regions from local activity within regions. All measures of the framework suggested that the region along the medial cortex displaying greater functional connectivity with the striatum is the supplementary motor area (SMA), where we applied tSMS. We then use a data-driven version of the framework to show that tSMS of the SMA modulates the local activity in the SMA proper, in the adjacent sensorimotor cortex, and in the motor striatum. We finally use a model-driven version of the framework to clarify that the tSMS-induced modulation of striatal activity can be primarily explained by a change in the shared activity between the modulated motor cortical areas and the motor striatum. These results suggest that corticostriatal activity can be targeted, monitored, and modulated noninvasively in humans.