Previous research has found that functional connectivity (FC) can accurately predict the identity of a subject performing a task and the type of task being performed. We replicate these results using a large dataset collected at the OSU Center for Cognitive and Behavioral Brain Imaging. We also introduce a novel perspective on task and subject identity prediction: BOLD Variability (BV). Conceptually, BV is a region-specific measure based on the variance within each brain region. BV is simple to compute, interpret, and visualize. We show that both FC and BV are predictive of task and subject, even across scanning sessions separated by multiple years. Subject differences rather than task differences account for the majority of changes in BV and FC. Similar to results in FC, we show that BV is reduced during cognitive tasks relative to rest.
Spontaneous fluctuations of the BOLD (Blood Oxygen Level-Dependent) signal, measured with fMRI (functional Magnetic Resonance Imaging), display a rich and neurobiologically relevant functional connectivity structure. This structure is usually revealed using time averaging methods, which prevent the detection of functional connectivity changes over time. In this work we studied the electrophysiological correlates of dynamical BOLD functional connectivity fluctuations, by means of long (approx. 50 min) joint electroencephalographic (EEG) and fMRI recordings. We identified widespread positive and…
Estimating causal interactions in the brain from functional magnetic resonance imaging (fMRI) data remains a challenging task. Multiple studies have demonstrated that all current approaches to determine direction of connectivity perform poorly even when applied to synthetic fMRI datasets. Recent advances in this field include methods for pairwise inference, which involve creating a sparse connectome in the first step, and then using a classifier in order to determine the directionality of connection between of every pair of nodes in the second step. In this work, we introduce an advance to the…
Resting-state functional magnetic resonance imaging (rs-fMRI), which measures the spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal, is increasingly utilized for the investigation of the brain's physiological and pathological functional activity. Rodents, as a typical animal model in neuroscience, play an important role in the studies that examine the neuronal processes that underpin the spontaneous fluctuations in the BOLD signal and the functional connectivity that results. Translating this knowledge from rodents to humans requires a basic knowledge of the similariti…
This study proposes an approach to estimate the functional localization and connectivity from CBF and BOLD signals simultaneously measured by ASL (arterial spin labeling) MRI, especially using exploratory Structural Equation Modeling analysis. In a visual task experiment, the primary visual cortices were located by analyzing the perfusion data. In the resting state experiment, two structural equation models were estimated at each voxel regarding to the sensory-motor network and default-mode network. The resulting connectivity maps indicate that supplementary motor area has significant connecti…
The most studies on functional connectivity have been done by analyzing the brain's hemodynamic response to a stimulation. On the other hand, the low-frequency spontaneous fluctuations in the blood oxygen level dependent (BOLD) signals of functional MRI have been observed in the resting state. However, the BOLD signals in resting state are significantly corrupted by huge noises arising from cardiac pulsation, respiration, subject motion, scanner, and so forth. Especially, the noise compounds are stronger in the rat brain than in the human brain. To overcome such an artifact, we assumed that fr…
Analysis of brain activity in resting-state is of fundamental importance in identifying functional characteristics of neuronal system. Although resting brain has been extensively investigated for low frequency synchrony between brain regions, namely Functional Connectivity (FC), the other main stream of brain connectivity analysis that seeks causal interactions between brain regions, Effective Connectivity (EC), has been little explored in spontaneous brain oscillations. Inherent complexity of brain activities in resting-state, as is observed in BOLD (Blood Oxygenation-Level Dependant) fluctua…
A great improvement to the insight on brain function that we can get from fMRI data can come from effective connectivity analysis, in which the flow of information between even remote brain regions is inferred by the parameters of a predictive dynamical model. As opposed to biologically inspired models, some techniques as Granger causality (GC) are purely data-driven and rely on statistical prediction and temporal precedence. While powerful and widely applicable, this approach could suffer from two main limitations when applied to BOLD fMRI data: confounding effect of hemodynamic response func…
Investigating neural activity from a global brain perspective in-vivo has been in the domain of functional Magnetic Resonance Imaging (fMRI) over the past few decades. The intricate neurovascular couplings that govern fMRI's blood-oxygenation-level-dependent (BOLD) functional contrast are invaluable in mapping active brain regions, but they also entail significant limitations, such as non-specificity of the signal to active foci. Diffusion-weighted functional MRI (dfMRI) with relatively high diffusion-weighting strives to ameliorate this shortcoming as it offers functional contrasts more intim…
Accurate identification of brain function is necessary to understand the neurobiology of cognitive ageing, and thereby promote well-being across the lifespan. A common tool used to investigate neurocognitive ageing is functional magnetic resonance imaging (fMRI). However, although fMRI data are often interpreted in terms of neuronal activity, the blood-oxygen-level-dependent (BOLD) signal measured by fMRI includes contributions of both vascular and neuronal factors, which change differentially with age. While some studies investigate vascular ageing factors, the results of these studies are no…
Predicting brain maturity using noninvasive magnetic resonance images (MRI) can distinguish different age groups and help to assess neurodevelopmental disorders. However, group-wise differences are often less informative for assessing features of individuals. Here, we propose a simple method to predict the age of an individual subject solely based on structural connectivity data from diffusion tensor imaging (DTI). Our simple predictor computed a weighted sum of the strength of all connections of an individual. The weight consists of the fiber strength, given by the number of streamlines follo…
We investigate the influence of indirect connections, interregional distance and collective effects on the large-scale functional networks of the human cortex. We study topologies of empirically derived resting state networks (RSNs), extracted from fMRI data, and model dynamics on the obtained networks. The RSNs are calculated from mean time-series of blood-oxygen-level-dependent (BOLD) activity of distinct cortical regions via Pearson correlation coefficients. We compare functional-connectivity networks of simulated BOLD activity as a function of coupling strength and correlation threshold. N…
Contemporary neuroscience has embraced network science to study the complex and self-organized structure of the human brain; one of the main outstanding issues is that of inferring from measure data, chiefly functional Magnetic Resonance Imaging (fMRI), the so-called effective connectivity in brain networks, that is the existing interactions among neuronal populations. This inverse problem is complicated by the fact that the BOLD (Blood Oxygenation Level Dependent) signal measured by fMRI represent a dynamic and nonlinear transformation (the hemodynamic response) of neuronal activity. In this …
The study of rapid changes in brain dynamics and functional connectivity (FC) is of increasing interest in neuroimaging. Brain states departing from normal waking consciousness are expected to be accompanied by alterations in the aforementioned dynamics. In particular, the psychedelic experience produced by psilocybin (a substance found in `magic mushrooms`) is characterized by unconstrained cognition and profound alterations in the perception of time, space and selfhood. Considering the spontaneous and subjective manifestation of these effects, we hypothesize that neural correlates of the psy…
In cognitive network neuroscience, the connectivity and community structure of the brain network is related to cognition. Much of this research has focused on two measures of connectivity - modularity and flexibility - which frequently have been examined in isolation. By using resting state fMRI data from 52 young adults, we investigate the relationship between modularity, flexibility and performance on cognitive tasks. We show that flexibility and modularity are highly negatively correlated. However, we also demonstrate that flexibility and modularity make unique contributions to explain task…
Neurofeedback is a non-invasive brain training with long-term medical and non-medical applications. Despite the existence of several emotion regulation studies using neurofeedback, further investigation is needed to understand interactions of the brain regions involved in the process. We implemented EEG neurofeedback with simultaneous fMRI using a modified happiness-inducing task through autobiographical memories to upregulate positive emotion. The results showed increased activity of prefrontal, occipital, parietal, and limbic regions and increased functional connectivity between prefrontal, …
This paper studies the link between resting-state functional connectivity (FC), measured by the correlations of the fMRI BOLD time courses, and structural connectivity (SC), estimated through fiber tractography. Instead of a static analysis based on the correlation between SC and the FC averaged over the entire fMRI time series, we propose a dynamic analysis, based on the time evolution of the correlation between SC and a suitably windowed FC. Assessing the statistical significance of the time series against random phase permutations, our data show a pronounced peak of significance for time wi…
The organization of the connectivity between mammalian cortical areas has become a major subject of study, because of its important role in scaffolding the macroscopic aspects of animal behavior and intelligence. In this study we present a computational reconstruction approach to the problem of network organization, by considering the topological and spatial features of each area in the primate cerebral cortex as subsidy for the reconstruction of the global cortical network connectivity. Starting with all areas being disconnected, pairs of areas with similar sets of features are linked togethe…
Understanding the relationship between the dynamics of neural processes and the anatomical substrate of the brain is a central question in neuroscience. On the one hand, modern neuroimaging technologies, such as diffusion tensor imaging, can be used to construct structural graphs representing the architecture of white matter streamlines linking cortical and subcortical structures. On the other hand, temporal patterns of neural activity can be used to construct functional graphs representing temporal correlations between brain regions. Although some studies provide evidence that whole-brain fun…
Knowing brain connectivity is of great importance both in basic research and for clinical applications. We are proposing a method to infer directed connectivity from zero-lag covariances of neuronal activity recorded at multiple sites. This allows us to identify causal relations that are reflected in neuronal population activity. To derive our strategy, we assume a generic linear model of interacting continuous variables, the components of which represent the activity of local neuronal populations. The suggested method for inferring connectivity from recorded signals exploits the fact that the…
Whole-brain computational modeling based on structural connectivity has shown great promise in successfully simulating fMRI BOLD signals with temporal co-activation patterns that are highly similar to empirical functional connectivity patterns during resting state. Importantly, previous studies have shown that spontaneous fluctuations in co-activation patterns of distributed brain regions have an inherent dynamic nature with regard to the frequency spectrum of intrinsic brain oscillations. In this modeling study, we introduced frequency dynamics into a system of coupled oscillators, where each…
Time-Varying Directed Interactions in Functional Brain Networks: Modeling and Validation
University of Maryland, College Park（马里兰大学帕克分校）；Georgia Institute of Technology and Emory University（佐治亚理工学院和埃默里大学）；Emory University School of Medicine（埃默里大学医学院）；Georgia Institute of Technology（佐治亚理工学院）；Indiana University School of Medicine（印第安纳大学医学院）；Georgia State University and Georgia Institute of Technology and Emory University（佐治亚州立大学和佐治亚理工学院和埃默里大学）
Functional connectivity refers to the temporal statistical relationship between spatially distinct brain regions and is usually inferred from the time series coherence/correlation in brain activity between regions of interest. In human functional brain networks, the network structure is often inferred from functional magnetic resonance imaging (fMRI) blood oxygen level dependent (BOLD) signal. Since the BOLD signal is a proxy for neuronal activity, it is of interest to learn the latent functional network structure. Additionally, despite a core set of observations about functional networks such…
Understanding neurocognitive computations will require not just localizing cognitive information distributed throughout the brain but also determining how that information got there. We review recent advances in linking empirical and simulated brain network organization with cognitive information processing. Building on these advances, we offer a new framework for understanding the role of connectivity in cognition - network coding (encoding/decoding) models. These models utilize connectivity to specify the transfer of information via neural activity flow processes, successfully predicting the…
Learning how to estimate a connectional brain template(CBT) from a population of brain multigraphs, where each graph (e.g., functional) quantifies a particular relationship between pairs of brain regions of interest (ROIs), allows to pin down the unique connectivity patterns shared across individuals. Specifically, a CBT is viewed as an integral representation of a set of highly heterogeneous graphs and ideally meeting the centeredness (i.e., minimum distance to all graphs in the population) and discriminativeness (i.e., distinguishes the healthy from the disordered population) criteria. So fa…
The functional network approach, where fMRI BOLD time series are mapped to networks depicting functional relationships between brain areas, has opened new insights into the function of the human brain. In this approach, the choice of network nodes is of crucial importance. One option is to consider fMRI voxels as nodes. This results in a large number of nodes, making network analysis and interpretation of results challenging. A common alternative is to use pre-defined clusters of anatomically close voxels, Regions of Interest (ROIs). This approach assumes that voxels within ROIs are functional…
Predicting Infant Brain Connectivity with Federated Multi-Trajectory GNNs using Scarce Data
Imperial College London（伦敦帝国理工学院）；University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；ShanghaiTech University（上海科技大学）；Shanghai United Imaging Intelligence Co., Ltd.（上海联影智能医疗科技有限公司）；Shanghai Clinical Research and Trial Center（上海临床研究中心）
Functional connectivity, as estimated using resting state fMRI, has shown potential in bridging the gap between pathophysiology and cognition. However, clinical use of functional connectivity biomarkers is impeded by unreliable estimates of individual functional connectomes and lack of generalizability of models predicting cognitive outcomes from connectivity. To address these issues, we combine the frameworks of connectome predictive modeling and differential identifiability. Using the combined framework, we show that enhancing the individual fingerprint of resting state functional connectome…
Functional connectivity quantifies the statistical dependencies between the activity of brain regions, measured using neuroimaging data such as functional MRI BOLD time series. The network representation of functional connectivity, called a Functional Connectome (FC), has been shown to contain an individual fingerprint allowing participants identification across consecutive testing sessions. Recently, researchers have focused on the extraction of these fingerprints, with potential applications in personalized medicine. Here, we show that a mathematical operation denominated degree-normalizatio…
University of Rajshahi（拉杰沙希大学）；Hajee Mohammad Danesh Science and Technology University（哈吉·穆罕默德·达内什科技大学）；Deakin University（迪肯大学）；COMSATS University Islamabad（伊斯兰堡COMSATS大学）；Charles Sturt University（查尔斯特大学）
In the last two decades, functional magnetic resonance imaging (fMRI) has emerged as one of the most effective technologies in clinical research of the human brain. fMRI allows researchers to study healthy and pathological brains while they perform various neuropsychological functions. Beyond task-related activations, the human brain has some intrinsic activity at a task-negative (resting) state that surprisingly consumes a lot of energy to support communication among neurons. Recent neuroimaging research has also seen an increase in modeling and analyzing brain activity in terms of a graph or…
Psychiatric research has been hampered by an explanatory gap between psychiatric symptoms and their neural underpinnings, which has resulted in poor treatment outcomes. This situation has prompted us to shift from symptom-based diagnosis to data-driven diagnosis, aiming to redefine psychiatric disorders as disorders of neural circuitry. Promising candidates for data-driven diagnosis include resting-state functional connectivity MRI (rs-fcMRI)-based biomarkers. Although biomarkers have been developed with the aim of diagnosing patients and predicting the efficacy of therapy, the focus has shift…
The dynamic characteristics of functional network connectivity have been widely acknowledged and studied. Both shared and unique information has been shown to be present in the connectomes. However, very little has been known about whether and how this common pattern can predict the individual variability of the brain, i.e. "brain fingerprinting", which attempts to reliably identify a particular individual from a pool of subjects. In this paper, we propose to enhance the individual uniqueness based on an autoencoder network. More specifically, we rely on the hypothesis that the common neural a…
Functional connectivity (FC) between brain regions tracks symptom severity in many neuropsychiatric disorders. Transcranial magnetic stimulation (TMS) directly alters regional activity and indirectly alters FC. Predicting how FC will change following TMS is difficult, but would allow novel therapies that target FC to improve symptoms. We address this challenge by proposing a predictive model that explains how TMS-induced activation can change the strength of FC. Here, we focus on the FC of the frontoparietal (FPS) and default mode (DMS) systems given the importance of their FC in executive fun…
Targeted electrical stimulation of the brain perturbs neural networks and modulates their rhythmic activity both at the site of stimulation and at remote brain regions. Understanding, or even predicting, this neuromodulatory effect is crucial for any therapeutic use of brain stimulation. To this end, we analyzed the stimulation responses in 131 stimulation sessions across 66 patients with focal epilepsy recorded through intracranial EEG (iEEG). We considered functional and structural connectivity features as predictors of the response at every iEEG contact. Taking advantage of multiple recordi…
In some cases, the function of a lesioned area can be compensated for by another area. However, it remains unpredictable if and by which other area a lesion can be compensated. We assume that similar incoming and outgoing connections are necessary to encode the same function as the damaged region. The similarity can be measured both locally using the matching index and looking at a more global scale by non-metric multidimensional scaling (NMDS). We tested how well both measures can predict the compensating area for the loss of the visual cortex in kittens. For this case study, the global compa…
In this work we focus on examination and comparison of whole-brain functional connectivity patterns measured with fMRI across experimental conditions. Direct examination and comparison of condition-specific matrices is challenging due to the large number of elements in a connectivity matrix. We present a framework that uses network analysis to describe condition-specific functional connectivity. Treating the brain as a complex system in terms of a network, we extract the most relevant connectivity information by partitioning each network into clusters representing functionally connected brain …
The neuronal circuit that controls obsessive and compulsive behaviors involves a complex network of brain regions (some with known involvement in reward processing). Among these are cortical regions, the striatum and the thalamus (which compose the CSTC pathway), limbic areas such as the amygdala and the hippocampus, and well as dopamine pathways. Abnormal dynamic behavior in this brain network is a hallmark feature of patients with increased anxiety and motor activity, like the ones affected by OCD. There is currently no clear understanding of precisely what mechanisms generates these behavio…
Istanbul Technical University（伊斯坦布尔技术大学）；University of Sousse（苏塞大学）；National School for Computer Science (ENSI)（国家计算机科学学校）；University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；ShanghaiTech University（上海科技大学）；United Imaging Intelligence Co., Ltd.（联影智能有限公司）
Charting the baby connectome evolution trajectory during the first year after birth plays a vital role in understanding dynamic connectivity development of baby brains. Such analysis requires acquisition of longitudinal connectomic datasets. However, both neonatal and postnatal scans are rarely acquired due to various difficulties. A small body of works has focused on predicting baby brain evolution trajectory from a neonatal brain connectome derived from a single modality. Although promising, large training datasets are essential to boost model learning and to generalize to a multi-trajectory…
The goal of the present study is to identify autism using machine learning techniques and resting-state brain imaging data, leveraging the temporal variability of the functional connections (FC) as the only information. We estimated and compared the FC variability across brain regions between typical, healthy subjects and autistic population by analyzing brain imaging data from a world-wide multi-site database known as ABIDE (Autism Brain Imaging Data Exchange). Our analysis revealed that patients diagnosed with autism spectrum disorder (ASD) show increased FC variability in several brain regi…
Cornell University（康奈尔大学）；Weill Cornell Medicine（威尔康奈尔医学院）；Brain and Mind Research Institute, Weill Cornell Medicine（威尔康奈尔医学院脑与心智研究所）；Nancy E. & Peter C. Meinig School of Biomedical Engineering, Cornell University（康奈尔大学南希·E·与彼得·C·梅尼格生物医学工程学院）
Resting-state functional MRI (rsfMRI) yields functional connectomes that can serve as cognitive fingerprints of individuals. Connectomic fingerprints have proven useful in many machine learning tasks, such as predicting subject-specific behavioral traits or task-evoked activity. In this work, we propose a surface-based convolutional neural network (BrainSurfCNN) model to predict individual task contrasts from their resting-state fingerprints. We introduce a reconstructive-contrastive loss that enforces subject-specificity of model outputs while minimizing predictive error. The proposed approac…
A central challenge in training one-shot learning models is the limited representativeness of the available shots of the data space. Particularly in the field of network neuroscience where the brain is represented as a graph, such models may lead to low performance when classifying brain states (e.g., typical vs. autistic). To cope with this, most of the existing works involve a data augmentation step to increase the size of the training set, its diversity and representativeness. Though effective, such augmentation methods are limited to generating samples with the same size as the input shots…
Johns Hopkins University（约翰斯·霍普金斯大学）；Kennedy Krieger Institute（肯尼迪·克里格研究所）；Johns Hopkins School of Medicine（约翰斯·霍普金斯大学医学院）
We propose a novel matrix autoencoder to map functional connectomes from resting state fMRI (rs-fMRI) to structural connectomes from Diffusion Tensor Imaging (DTI), as guided by subject-level phenotypic measures. Our specialized autoencoder infers a low dimensional manifold embedding for the rs-fMRI correlation matrices that mimics a canonical outer-product decomposition. The embedding is simultaneously used to reconstruct DTI tractography matrices via a second manifold alignment decoder and to predict inter-subject phenotypic variability via an artificial neural network. We validate our frame…
The center stage of neuro-imaging is currently occupied by studies of functional correlations between brain regions. These correlations define the brain functional networks, which are the most frequently used framework to represent and interpret a variety of experimental findings. In previous work we first demonstrated that the relatively stronger BOLD activations contain most of the information relevant to understand functional connectivity and subsequent work confirmed that a large compression of the original signals can be obtained without significant loss of information. In this work we re…
McGovern Institute for Brain Research, Massachusetts Institute of Technology（麻省理工学院麦戈文脑研究所）；Complutense University of Madrid（马德里康普顿斯大学）；Harvard Medical School（哈佛医学院）
Characterizing the subtle changes of functional brain networks associated with the pathological cascade of Alzheimer's disease (AD) is important for early diagnosis and prediction of disease progression prior to clinical symptoms. We developed a new deep learning method, termed multiple graph Gaussian embedding model (MG2G), which can learn highly informative network features by mapping high-dimensional resting-state brain networks into a low-dimensional latent space. These latent distribution-based embeddings enable a quantitative characterization of subtle and heterogeneous brain connectivit…
Zuse Institute Berlin（柏林祖斯研究所）；Istanbul Technical University（伊斯坦布尔技术大学）；Ecole Polytechnique de Tunisie（突尼斯理工学院）；University of Dundee（邓迪大学）
Analyzing the relation between intelligence and neural activity is of the utmost importance in understanding the working principles of the human brain in health and disease. In existing literature, functional brain connectomes have been used successfully to predict cognitive measures such as intelligence quotient (IQ) scores in both healthy and disordered cohorts using machine learning models. However, existing methods resort to flattening the brain connectome (i.e., graph) through vectorization which overlooks its topological properties. To address this limitation and inspired from the emergi…
Brain function relies on a precisely coordinated and dynamic balance between the functional integration and segregation of distinct neural systems. Characterizing the way in which neural systems reconfigure their interactions to give rise to distinct but hidden brain states remains an open challenge. In this paper, we propose a Bayesian model-based characterization of latent brain states and showcase a novel method based on posterior predictive discrepancy using the latent block model to detect transitions between latent brain states in blood oxygen level-dependent (BOLD) time series. The set …
