Task-induced brain state manipulation improves prediction of individual traits

Intrinsic Connectivity Patterns of Task-Defined Brain Networks Allow Individual Prediction of Cognitive Symptom Dimension of Schizophrenia and Are Linked to Molecular Architecture

BACKGROUND

Despite the marked interindividual variability in the clinical presentation of schizophrenia, the extent to which individual dimensions of psychopathology relate to the functional variability in brain networks among patients remains unclear. Here, we address this question using network-based predictive modeling of individual psychopathology along 4 data-driven symptom dimensions. Follow-up analyses assess the molecular underpinnings of predictive networks by relating them to neurotransmitter-receptor distribution patterns.

METHODS

We investigated resting-state functional magnetic resonance imaging data from 147 patients with schizophrenia recruited at 7 sites. Individual expression along negative, positive, affective, and cognitive symptom dimensions was predicted using a relevance vector machine based on functional connectivity within 17 meta-analytic task networks following repeated 10-fold cross-validation and leave-one-site-out analyses. Results were validated in an independent sample. Networks robustly predicting individual symptom dimensions were spatially correlated with density maps of 9 receptors/transporters from prior molecular imaging in healthy populations.

RESULTS

Tenfold and leave-one-site-out analyses revealed 5 predictive network-symptom associations. Connectivity within theory of mind, cognitive reappraisal, and mirror neuron networks predicted negative, positive, and affective symptom dimensions, respectively. Cognitive dimension was predicted by theory of mind and socioaffective default networks. Importantly, these predictions generalized to the independent sample. Intriguingly, these two networks were positively associated with D₁ receptor and serotonin reuptake transporter densities as well as dopamine synthesis capacity.

CONCLUSIONS

We revealed a robust association between intrinsic functional connectivity within networks for socioaffective processes and the cognitive dimension of psychopathology. By investigating the molecular architecture, this work links dopaminergic and serotonergic systems with the functional topography of brain networks underlying cognitive symptoms in schizophrenia.

A hitchhiker's guide to working with large, open-source neuroimaging datasets

Large datasets that enable researchers to perform investigations with unprecedented rigor are growing increasingly common in neuroimaging. Due to the simultaneous increasing popularity of open science, these state-of-the-art datasets are more accessible than ever to researchers around the world. While analysis of these samples has pushed the field forward, they pose a new set of challenges that might cause difficulties for novice users. Here we offer practical tips for working with large datasets from the end-user's perspective. We cover all aspects of the data lifecycle: from what to consider when downloading and storing the data to tips on how to become acquainted with a dataset one did not collect and what to share when communicating results. This manuscript serves as a practical guide one can use when working with large neuroimaging datasets, thus dissolving barriers to scientific discovery.

Connectome-Based Predictive Modeling of Individual Anxiety

Anxiety-related illnesses are highly prevalent in human society. Being able to identify neurobiological markers signaling high trait anxiety could aid the assessment of individuals with high risk for mental illness. Here, we applied connectome-based predictive modeling (CPM) to whole-brain resting-state functional connectivity (rsFC) data to predict the degree of trait anxiety in 76 healthy participants. Using a computational “lesion” approach in CPM, we then examined the weights of the identified main brain areas as well as their connectivity. Results showed that the CPM successfully predicted individual anxiety based on whole-brain rsFC, especially the rsFC between limbic areas and prefrontal cortex. The prediction power of the model significantly decreased from simulated lesions of limbic areas, lesions of the connectivity within limbic areas, and lesions of the connectivity between limbic areas and prefrontal cortex. Importantly, this neural model generalized to an independent large sample (n = 501). These findings highlight important roles of the limbic system and prefrontal cortex in anxiety prediction. Our work provides evidence for the usefulness of connectome-based modeling in predicting individual personality differences and indicates its potential for identifying personality factors at risk for psychopathology.

Do intrinsic brain functional networks predict working memory from childhood to adulthood?

Working memory (WM) is defined as the ability to maintain a representation online to guide goal‐directed behavior. Its capacity in early childhood predicts academic achievements in late childhood and its deficits are found in various neurodevelopmental disorders. We employed resting‐state fMRI (rs‐fMRI) of 468 participants aged from 4 to 55 years and connectome‐based predictive modeling (CPM) to explore the potential predictive power of intrinsic functional networks to WM in preschoolers, early and late school‐age children, adolescents, and adults. We defined intrinsic functional networks among brain regions identified by activation likelihood estimation (ALE) meta‐analysis on existing WM functional studies (ALE‐based intrinsic functional networks) and intrinsic functional networks generated based on the whole brain (whole‐brain intrinsic functional networks). We employed the CPM on these networks to predict WM in each age group. The CPM using the ALE‐based and whole‐brain intrinsic functional networks predicted WM of individual adults, while the prediction power of the ALE‐based intrinsic functional networks was superior to that of the whole‐brain intrinsic functional networks. Nevertheless, the CPM using the whole‐brain but not the ALE‐based intrinsic functional networks predicted WM in adolescents. And, the CPM using neither the ALE‐based nor whole‐brain networks predicted WM in any of the children groups. Our findings showed the trend of the prediction power of the intrinsic functional networks to cognition in individuals from early childhood to adulthood.

Fear-induced brain activations distinguish anxious and trauma-exposed brains

Translational models of fear conditioning and extinction have elucidated a core neural network involved in the learning, consolidation, and expression of conditioned fear and its extinction. Anxious or trauma-exposed brains are characterized by dysregulated neural activations within regions of this fear network. In this study, we examined how the functional MRI activations of 10 brain regions commonly activated during fear conditioning and extinction might distinguish anxious or trauma-exposed brains from controls. To achieve this, activations during four phases of a fear conditioning and extinction paradigm in 304 participants with or without a psychiatric diagnosis were studied. By training convolutional neural networks (CNNs) using task-specific brain activations, we reliably distinguished the anxious and trauma-exposed brains from controls. The performance of models decreased significantly when we trained our CNN using activations from task-irrelevant brain regions or from a brain network that is irrelevant to fear. Our results suggest that neuroimaging data analytics of task-induced brain activations within the fear network might provide novel prospects for development of brain-based psychiatric diagnosis.

Linking Brain Biology to Intellectual Endowment: A Review on the Associations of Human Intelligence With Neuroimaging Data

Human intelligence has always been a fascinating subject for scientists. Since the inception of Spearman's general intelligence in the early 1900s, there has been significant progress towards characterizing different aspects of intelligence and its relationship with structural and functional features of the brain. In recent years, the invention of sophisticated brain imaging devices using Diffusion-Weighted Imaging (DWI) and functional Magnetic Resonance Imaging (fMRI) has allowed researchers to test hypotheses about neural correlates of intelligence in humans.This review summarizes recent findings on the associations of human intelligence with neuroimaging data. To this end, first, we review the literature that has related brain morphometry to intelligence. Next, we elaborate on the applications of DWI and restingstate fMRI on the investigation of intelligence. Then, we provide a survey of literature that has used multimodal DWI-fMRI to shed light on intelligence. Finally, we discuss the state-of-the-art of individualized prediction of intelligence from neuroimaging data and point out future strategies. Future studies hold promising outcomes for machine learning-based predictive frameworks using neuroimaging features to estimate human intelligence.

Functional Connectivity Predicts Individual Development of Inhibitory Control during Adolescence

Derailment of inhibitory control (IC) underlies numerous psychiatric and behavioral disorders, many of which emerge during adolescence. Identifying reliable predictive biomarkers that place the adolescents at elevated risk for future IC deficits can help guide early interventions, yet the scarcity of longitudinal research has hindered the progress. Here, using a large-scale longitudinal dataset in which the same subjects performed a stop signal task during functional magnetic resonance imaging at ages 14 and 19, we tracked their IC development individually and tried to find the brain features predicting their development by constructing prediction models using 14-year-olds' functional connections within a network or between a pair of networks. The participants had distinct between-subject trajectories in their IC development. Of the candidate connections used for prediction, ventral attention-subcortical network interconnections could predict the individual development of IC and formed a prediction model that generalized to previously unseen individuals. Furthermore, we found that connectivity between these two networks was related to substance abuse problems, an IC-deficit related problematic behavior, within 5 years. Our study reveals individual differences in IC development from mid- to late-adolescence and highlights the importance of ventral attention-subcortical network interconnections in predicting future IC development and substance abuse in adolescents.

Transdiagnostic, Connectome-Based Prediction of Memory Constructs Across Psychiatric Disorders

Memory deficits are observed in a range of psychiatric disorders, but it is unclear whether memory deficits arise from a shared brain correlate across disorders or from various dysfunctions unique to each disorder. Connectome-based predictive modeling is a computational method that captures individual differences in functional connectomes associated with behavioral phenotypes such as memory. We used publicly available task-based functional MRI data from patients with schizophrenia (n = 33), bipolar disorder (n = 34), attention deficit hyper-activity disorder (n = 32), and healthy controls (n = 73) to model the macroscale brain networks associated with working, short- and long-term memory. First, we use 10-fold and leave-group-out analyses to demonstrate that the same macroscale brain networks subserve memory across diagnostic groups and that individual differences in memory performance are related to individual differences within networks distributed throughout the brain, including the subcortex, default mode network, limbic network, and cerebellum. Next, we show that diagnostic groups are associated with significant differences in whole-brain functional connectivity that are distinct from the predictive models of memory. Finally, we show that models trained on the transdiagnostic sample generalize to novel, healthy participants (n = 515) from the Human Connectome Project. These results suggest that despite significant differences in whole-brain patterns of functional connectivity between diagnostic groups, the core macroscale brain networks that subserve memory are shared.

Low-motion fMRI data can be obtained in pediatric participants undergoing a 60-minute scan protocol

Performing functional magnetic resonance imaging (fMRI) scans of children can be a difficult task, as participants tend to move while being scanned. Head motion represents a significant confound in fMRI connectivity analyses. One approach to limit motion has been to use shorter MRI protocols, though this reduces the reliability of results. Hence, there is a need to implement methods to achieve high-quality, low-motion data while not sacrificing data quantity. Here we show that by using a mock scan protocol prior to a scan, in conjunction with other in-scan steps (weighted blanket and incentive system), it is possible to achieve low-motion fMRI data in pediatric participants (age range: 7-17 years old) undergoing a 60 min MRI session. We also observe that motion is low during the MRI protocol in a separate replication group of participants, including some with autism spectrum disorder. Collectively, the results indicate it is possible to conduct long scan protocols in difficult-to-scan populations and still achieve high-quality data, thus potentially allowing more reliable fMRI findings.

Connectome-based models can predict processing speed in older adults

Decrement in processing speed (PS) is a primary cognitive morbidity in clinical populations and could significantly influence other cognitive functions, such as attention and memory. Verifying the usefulness of connectome-based models for predicting neurocognitive abilities has significant translational implications on clinical and aging research. In this study, we verified that resting-state functional connectivity could be used to predict PS in 99 older adults by using connectome-based predictive modeling (CPM). We identified two distinct connectome patterns across the whole brain: the fast-PS and slow-PS networks. Relative to the slow-PS network, the fast-PS network showed more within-network connectivity in the motor and visual networks and less between-network connectivity in the motor-visual, motor-subcortical/cerebellum and motor-frontoparietal networks. We further verified that the connectivity patterns for prediction of PS were also useful for predicting attention and memory in the same sample. To test the generalizability and specificity of the connectome-based predictive models, we applied these two connectome models to an independent sample of three age groups (101 younger adults, 103 middle-aged adults and 91 older adults) and confirmed these models could specifically be generalized to predict PS of the older adults, but not the younger and middle-aged adults. Taking all the findings together, the identified connectome-based predictive models are strong for predicting PS in older adults. The application of CPM to predict neurocognitive abilities can complement conventional neurocognitive assessments, bring significant clinical benefits to patient management and aid the clinical diagnoses, prognoses and management of people undergoing the aging process.

Neuroimaging-based Individualized Prediction of Cognition and Behavior for Mental Disorders and Health: Methods and Promises

The neuroimaging community has witnessed a paradigm shift in biomarker discovery from using traditional univariate brain mapping approaches to multivariate predictive models, allowing the field to move toward a translational neuroscience era. Regression-based multivariate models (hereafter "predictive modeling") provide a powerful and widely used approach to predict human behavior with neuroimaging features. These studies maintain a focus on decoding individual differences in a continuously behavioral phenotype from neuroimaging data, opening up an exciting opportunity to describe the human brain at the single-subject level. In this survey, we provide an overview of recent studies that utilize machine learning approaches to identify neuroimaging predictors over the past decade. We first review regression-based approaches and highlight connectome-based predictive modeling, which has grown in popularity in recent years. Next, we systematically describe recent representative studies using these tools in the context of cognitive function, symptom severity, personality traits, and emotion processing. Finally, we highlight a few challenges related to combining multimodal data, longitudinal prediction, external validations, and the employment of deep learning methods that have emerged from our review of the existing literature, as well as present some promising and challenging future directions.

Intrinsic organization of cortical networks predicts state anxiety: an functional near-infrared spectroscopy (fNIRS) study

Although state anxiety has been characterized by hyper-responsive subcortical activity and its bottom-up connectivity with cortical regions, the role of cortical networks in state anxiety is not yet well understood. To this end, we decoded individual state anxiety by using a machine-learning approach based on resting-state functional connectivity (RSFC) with functional near-infrared spectroscopy (fNIRS). Our results showed that the RSFC among a set of cortical networks were highly predictive of state anxiety, rather than trait anxiety. Specifically, these networks included connectivity between cortical areas in the default mode network (DMN) and dorsal attention network (DAN), and connectivity within the DMN, which were negatively correlated with state anxiety; connectivity between cortical areas in the DMN and frontoparietal network (FPN), FPN and salience network (SN), FPN and DAN, DMN and SN, which were positively correlated with state anxiety. These findings suggest a predictive role of intrinsic cortical organization in the assessment of state anxiety. The work provides new insights into potential neural mechanisms of emotion states and implications for prognosis, diagnosis, and treatment of affective disorders.

Behavioral and brain signatures of substance use vulnerability in childhood

The prevalence of risky behavior such as substance use increases during adolescence; however, the neurobiological precursors to adolescent substance use remain unclear. Predictive modeling may complement previous work observing associations with known risk factors or substance use outcomes by developing generalizable models that predict early susceptibility. The aims of the current study were to identify and characterize behavioral and brain models of vulnerability to future substance use. Principal components analysis (PCA) of behavioral risk factors were used together with connectome-based predictive modeling (CPM) during rest and task-based functional imaging to generate predictive models in a large cohort of nine- and ten-year-olds enrolled in the Adolescent Brain & Cognitive Development (ABCD) study (NDA release 2.0.1). Dimensionality reduction (n = 9,437) of behavioral measures associated with substance use identified two latent dimensions that explained the largest amount of variance: risk-seeking (PC1; e.g., curiosity to try substances) and familial factors (PC2; e.g., family history of substance use disorder). Using cross-validated regularized regression in a subset of data (Year 1 Fast Track data; n>1,500), functional connectivity during rest and task conditions (resting-state; monetary incentive delay task; stop signal task; emotional n-back task) significantly predicted individual differences in risk-seeking (PC1) in held-out participants (partial correlations between predicted and observed scores controlling for motion and number of frames [r_p]: 0.07-0.21). By contrast, functional connectivity was a weak predictor of familial risk factors associated with substance use (PC2) (r_p: 0.03-0.06). These results demonstrate a novel approach to understanding substance use vulnerability, which—together with mechanistic perspectives—may inform strategies aimed at early identification of risk for addiction.

Brain Structure and Functional Connectivity Associated with Individual Differences in the Attentional Blink

The attentional blink (AB) has been central in characterizing the limit of temporal attention and consciousness. The neural mechanism of the AB is still in hot debate. With a large sample size, we combined multiple behavioral tests, multimodal MRI measures, and transcranial magnetic stimulation to investigate the neural basis underlying the individual differences in the AB. We found that AB magnitude correlated with the executive control functioning of working memory (WM) in behavior, which was fully mediated by T1 performance. Structural variations in the right temporoparietal junction (rTPJ) and its intrinsic functional connectivity with the left inferior frontal junction (lIFJ) accounted for the individual differences in the AB, which was moderated by the executive control of working memory. Disrupting the function of the lIFJ attenuated the AB deficit. Our findings clarified the neural correlates of the individual differences in the AB and elucidated its relationship with the consolidation-driven inhibitory control process.

Structural and Functional Brain Parameters Related to Cognitive Performance Across Development: Replication and Extension of the Parieto-Frontal Integration Theory in a Single Sample

The parieto-frontal integration theory (PFIT) identified a fronto-parietal network of regions where individual differences in brain parameters most strongly relate to cognitive performance. PFIT was supported and extended in adult samples, but not in youths or within single-scanner well-powered multimodal studies. We performed multimodal neuroimaging in 1601 youths age 8-22 on the same 3-Tesla scanner with contemporaneous neurocognitive assessment, measuring volume, gray matter density (GMD), mean diffusivity (MD), cerebral blood flow (CBF), resting-state functional magnetic resonance imaging measures of the amplitude of low frequency fluctuations (ALFFs) and regional homogeneity (ReHo), and activation to a working memory and a social cognition task. Across age and sex groups, better performance was associated with higher volumes, greater GMD, lower MD, lower CBF, higher ALFF and ReHo, and greater activation for the working memory task in PFIT regions. However, additional cortical, striatal, limbic, and cerebellar regions showed comparable effects, hence PFIT needs expansion into an extended PFIT (ExtPFIT) network incorporating nodes that support motivation and affect. Associations of brain parameters became stronger with advancing age group from childhood to adolescence to young adulthood, effects occurring earlier in females. This ExtPFIT network is developmentally fine-tuned, optimizing abundance and integrity of neural tissue while maintaining a low resting energy state.

Connectome-Based Predictive Modeling of Creativity Anxiety

While a recent upsurge in the application of neuroimaging methods to creative cognition has yielded encouraging progress toward understanding the neural underpinnings of creativity, the neural basis of barriers to creativity are as yet unexplored. Here, we report the first investigation into the neural correlates of one such recently identified barrier to creativity: anxiety specific to creative thinking, or creativity anxiety (Daker et al., 2019). We employed a machine-learning technique for exploring relations between functional connectivity and behavior (connectome-based predictive modeling; CPM) to investigate the functional connections underlying creativity anxiety. Using whole-brain resting-state functional connectivity data, we identified a network of connections or "edges" that predicted individual differences in creativity anxiety, largely comprising connections within and between regions of the executive and default networks and the limbic system. We then found that the edges related to creativity anxiety identified in one sample generalize to predict creativity anxiety in an independent sample. We additionally found evidence that the network of edges related to creativity anxiety were largely distinct from those found in previous work to be related to divergent creative ability (Beaty et al., 2018). In addition to being the first work on the neural correlates of creativity anxiety, this research also included the development of a new Chinese-language version of the Creativity Anxiety Scale, and demonstrated that key behavioral findings from the initial work on creativity anxiety are replicable across cultures and languages.

The Constrained Network-Based Statistic: A New Level of Inference for Neuroimaging

Neuroimaging research aimed at dissecting the network organization of the brain is poised to flourish under major initiatives, but converging evidence suggests more accurate inferential procedures are needed to promote discovery. Inference is typically performed at the cluster level with a network-based statistic (NBS) that boosts power by leveraging known dependence within the local neighborhood. However, existing NBS methods overlook another important form of dependence-shared membership in large-scale brain networks. Here, we propose a new level of inference that pools information within predefined large-scale networks: the Constrained Network-Based Statistic (cNBS). We evaluated sensitivity and specificity of cNBS against existing standard NBS and threshold-free NBS by resampling task data from the largest openly available fMRI database: the Human Connectome Project. cNBS was most sensitive to effect sizes below medium, which accounts for the majority of ground truth effects. In contrast, threshold-free NBS was most sensitive to higher effect sizes. Ground truth maps showed grouping of effects within large-scale networks, supporting the relevance of cNBS. All methods controlled FWER as intended. In summary, cNBS is a promising new level of inference for promoting more valid inference, a critical step towards more reproducible discovery in neuroscience.

Predictive modeling of neurobehavioral state and trait variation across development

A key goal of human neurodevelopmental research is to map neural and behavioral trajectories across both health and disease. A growing number of developmental consortia have begun to address this gap by providing open access to cross-sectional and longitudinal 'big data' repositories. However, it remains challenging to develop models that enable prediction of both within-subject and between-subject neurodevelopmental variation. Here, we present a conceptual and analytical perspective of two essential ingredients for mapping neurodevelopmental trajectories: state and trait components of variance. We focus on mapping variation across a range of neural and behavioral measurements and consider concurrent alterations of state and trait variation across development. We present a quantitative framework for combining both state- and trait-specific sources of neurobehavioral variation across development. Specifically, we argue that non-linear mixed growth models that leverage state and trait components of variance and consider environmental factors are necessary to comprehensively map brain-behavior relationships. We discuss this framework in the context of mapping language neurodevelopmental changes in early childhood, with an emphasis on measures of functional connectivity and their reliability for establishing robust neurobehavioral relationships. The ultimate goal is to statistically unravel developmental trajectories of neurobehavioral relationships that involve a combination of individual differences and age-related changes.

From Description to Explanation: Integrating Across Multiple Levels of Analysis to Inform Neuroscientific Accounts of Dimensional Personality Pathology

Dimensional approaches to psychiatric nosology are rapidly transforming the way researchers and clinicians conceptualize personality pathology, leading to a growing interest in describing how individuals differ from one another. Yet, in order to successfully prevent and treat personality pathology, it is also necessary to explain the sources of these individual differences. The emerging field of personality neuroscience is well-positioned to guide the transition from description to explanation within personality pathology research. However, establishing comprehensive, mechanistic accounts of personality pathology will require personality neuroscientists to move beyond atheoretical studies that link trait differences to neural correlates without considering the algorithmic processes that are carried out by those correlates. We highlight some of the dangers we see in overpopulating personality neuroscience with brain-trait associational studies and offer a series of recommendations for personality neuroscientists seeking to build explanatory theories of personality pathology.

Topographic organization of the human subcortex unveiled with functional connectivity gradients

Brain atlases are fundamental to understanding the topographic organization of the human brain, yet many contemporary human atlases cover only the cerebral cortex, leaving the subcortex a terra incognita. We use functional MRI (fMRI) to map the complex topographic organization of the human subcortex, revealing large-scale connectivity gradients and new areal boundaries. We unveil four scales of subcortical organization that recapitulate well-known anatomical nuclei at the coarsest scale and delineate 27 new bilateral regions at the finest. Ultrahigh field strength fMRI corroborates and extends this organizational structure, enabling the delineation of finer subdivisions of the hippocampus and the amygdala, while task-evoked fMRI reveals a subtle subcortical reorganization in response to changing cognitive demands. A new subcortical atlas is delineated, personalized to represent individual differences and used to uncover reproducible brain-behavior relationships. Linking cortical networks to subcortical regions recapitulates a task-positive to task-negative axis. This new atlas enables holistic connectome mapping and characterization of cortico-subcortical connectivity.

Predicting intelligence from brain gray matter volume

A positive association between brain size and intelligence is firmly established, but whether region-specific anatomical differences contribute to general intelligence remains an open question. Results from voxel-based morphometry (VBM) - one of the most widely used morphometric methods - have remained inconclusive so far. Here, we applied cross-validated machine learning-based predictive modeling to test whether out-of-sample prediction of individual intelligence scores is possible on the basis of voxel-wise gray matter volume. Features were derived from structural magnetic resonance imaging data (N = 308) using (a) a purely data-driven method (principal component analysis) and (b) a domain knowledge-based approach (atlas parcellation). When using relative gray matter (corrected for total brain size), only the atlas-based approach provided significant prediction, while absolute gray matter (uncorrected) allowed for above-chance prediction with both approaches. Importantly, in all significant predictions, the absolute error was relatively high, i.e., greater than ten IQ points, and in the atlas-based models, the predicted IQ scores varied closely around the sample mean. This renders the practical value even of statistically significant prediction results questionable. Analyses based on the gray matter of functional brain networks yielded significant predictions for the fronto-parietal network and the cerebellum. However, the mean absolute errors were not reduced in contrast to the global models, suggesting that general intelligence may be related more to global than region-specific differences in gray matter volume. More generally, our study highlights the importance of predictive statistical analysis approaches for clarifying the neurobiological bases of intelligence and provides important suggestions for future research using predictive modeling.

How Tasks Change Whole-Brain Functional Organization to Reveal Brain-Phenotype Relationships

Functional connectivity (FC) calculated from task fMRI data better reveals brain-phenotype relationships than rest-based FC, but how tasks have this effect is unknown. In over 700 individuals performing seven tasks, we use psychophysiological interaction (PPI) and predictive modeling analyses to demonstrate that task-induced changes in FC successfully predict phenotype, and these changes are not simply driven by task activation. Activation, however, is useful for prediction only if the in-scanner task is related to the predicted phenotype. To further characterize these predictive FC changes, we develop and apply an inter-subject PPI analysis. We find that moderate, but not high, task-induced consistency of the blood-oxygen-level-dependent (BOLD) signal across individuals is useful for prediction. Together, these findings demonstrate that in-scanner tasks have distributed, phenotypically relevant effects on brain functional organization, and they offer a framework to leverage both task activation and FC to reveal the neural bases of complex human traits, symptoms, and behaviors.

Toward a "treadmill test" for cognition: Improved prediction of general cognitive ability from the task activated brain

General cognitive ability (GCA) refers to a trait-like ability that contributes to performance across diverse cognitive tasks. Identifying brain-based markers of GCA has been a longstanding goal of cognitive and clinical neuroscience. Recently, predictive modeling methods have emerged that build whole-brain, distributed neural signatures for phenotypes of interest. In this study, we employ a predictive modeling approach to predict GCA based on fMRI task activation patterns during the N-back working memory task as well as six other tasks in the Human Connectome Project dataset (n = 967), encompassing 15 task contrasts in total. We found tasks are a highly effective basis for prediction of GCA: The 2-back versus 0-back contrast achieved a 0.50 correlation with GCA scores in 10-fold cross-validation, and 13 out of 15 task contrasts afforded statistically significant prediction of GCA. Additionally, we found that task contrasts that produce greater frontoparietal activation and default mode network deactivation-a brain activation pattern associated with executive processing and higher cognitive demand-are more effective in the prediction of GCA. These results suggest a picture analogous to treadmill testing for cardiac function: Placing the brain in a more cognitively demanding task state significantly improves brain-based prediction of GCA.

Predicting Biological Gender and Intelligence From fMRI via Dynamic Functional Connectivity

OBJECTIVE

This paper explores the predictive capability of dynamic functional connectivity extracted from functional magnetic resonance imaging (fMRI) of the human brain, in contrast to static connectivity used in past research.

METHODS

Several state-of-the-art features extracted from static functional connectivity of the brain are employed to predict biological gender and intelligence using publicly available Human Connectome Project (HCP) database. Next, a novel tensor parallel factor (PARAFAC) decomposition model is proposed to decompose sequence of dynamic connectivity matrices into common connectivity components that are orthonormal to each other, common time-courses, and corresponding distinct subject-wise weights. The subject-wise loading of the components are employed to predict biological gender and intelligence using a random forest classifier (respectively, regressor) using 5-fold cross-validation.

RESULTS

The results demonstrate that dynamic functional connectivity can indeed classify biological gender with a high accuracy (0.94, where male identification accuracy was 0.87 and female identification accuracy was 0.97). It can also predict intelligence with less normalized mean square error (0.139 for fluid intelligence and 0.031 for fluid ability metrics) compared with other functional connectivity measures (the nearest mean square error were 0.147 and 0.037 for fluid intelligence and fluid ability metrics, respectively, using static connectivity approaches).

CONCLUSION

Our work is an important milestone for the understanding of non-stationary behavior of hemodynamic blood-oxygen level dependent (BOLD) signal in brain and how they are associated with biological gender and intelligence.

SIGNIFICANCE

The paper demonstrates that dynamic behavior of brain can contribute substantially towards forming a fingerprint of biological gender and intelligence.

Connectome-based models can predict early symptom improvement in major depressive disorder

BACKGROUND

Major depressive disorder (MDD) is a debilitating mental illness with more than 50% of patients not achieving an adequate response using first-line treatments. Reliable models that predict antidepressant treatment outcome are needed to guide clinical decision making. We aimed to build predictive models of treatment improvement for MDD patients using machine learning approaches based on fMRI resting-state functional connectivity patterns.

METHODS

Resting-state fMRI data were acquired from 192 untreated MDD patients at recruitment, and their severity of depression was assessed by Hamilton Rating Scale for Depression (HAMD) at baseline. Patients were given medication after the initial MR scan and their symptoms were monitored through HAMD for a period of six months. Connectome-based predictive modeling (CPM) algorithms were implemented to predict the improvement in HAMD score at one month from resting-state connectivity at baseline. Additionally, by selectively combining the features from all leave-one-out iterations in the model building stage, we created a consensus model that could be generalized to predict improvement in HAMD score in samples of non-overlapping subjects at different time points.

RESULTS

Using baseline functional connectivity, CPM successfully predicted symptom improvement of depression at one month. In addition, a consensus 'MDD improvement model' could predict symptom improvement for novel individuals at the two-week, one-month, two-month and three-month time points after antidepressant treatment.

CONCLUSIONS

Individual pre-treatment functional brain networks contain meaningful information that can be gleaned to build predictors of treatment outcome. The identified MDD improvement networks could be an appropriate biomarker for predicting individual therapeutic response of antidepressant treatment. Replication and validation using other large datasets will be a key next step before these models can be used in clinical practice.

Toward Addiction Prediction: An Overview of Cross-Validated Predictive Modeling Findings and Considerations for Future Neuroimaging Research

Substance use is a leading cause of disability and death worldwide. Despite the existence of evidence-based treatments, clinical outcomes are highly variable across individuals, and relapse rates following treatment remain high. Within this context, methods to identify individuals at particular risk for unsuccessful treatment (i.e., limited within-treatment abstinence), or for relapse following treatment, are needed to improve outcomes. Cumulatively, the literature generally supports the hypothesis that individual differences in brain function and structure are linked to differences in treatment outcomes, although anatomical loci and directions of associations have differed across studies. However, this work has almost entirely used methods that may overfit the data, leading to inflated effect size estimates and reduced likelihood of reproducibility in novel clinical samples. In contrast, cross-validated predictive modeling (i.e., machine learning) approaches are designed to overcome limitations of traditional approaches by focusing on individual differences and generalization to novel subjects (i.e., cross-validation), thereby increasing the likelihood of replication and potential translation to novel clinical settings. Here, we review recent studies using these approaches to generate brain-behavior models of treatment outcomes in addictions and provide recommendations for further work using these methods.

Toward Robust Anxiety Biomarkers: A Machine Learning Approach in a Large-Scale Sample

BACKGROUND

The field of psychiatry has long sought biomarkers that can objectively diagnose patients, predict treatment response, or identify individuals at risk of illness onset. However, reliable psychiatric biomarkers have yet to emerge. The recent application of machine learning techniques to develop neuroimaging-based biomarkers has yielded promising preliminary results. However, much of the work in this domain has not met best practice standards from the field of machine learning. This is especially true for studies of anxiety, creating uncertainty about the potential for anxiety biomarker development.

METHODS

We applied machine learning tools to predict trait anxiety from neuroimaging measurements in humans. Using publicly available data from the Brain Genomics Superstruct Project, we compared a suite of neuroimaging-based machine learning models predicting anxiety within a discovery sample (n = 531, 307 women) via k-fold cross-validation, and we tested the final model (a stacked model incorporating region-to-region functional connectivity, amygdala seed-to-voxel connectivity, and volumetric and cortical thickness data) in a held-out, unseen test sample (n = 348, 209 women).

RESULTS

Though the best model was able to predict anxiety within the discovery sample (cross-validated R2 of .06, permutation test p < .001), the generalization test within the holdout sample failed (R2 of -.04, permutation test p > .05).

CONCLUSIONS

In this study, we did not find evidence of a generalizable anxiety biomarker. However, we encourage other researchers to investigate this topic, utilizing large samples and proper methodology, to clarify the potential of neuroimaging-based anxiety biomarkers.

Identification of a brain fingerprint for overweight and obesity

The brain plays a central role in the pathophysiology of overweight and obesity. Connectome-based Predictive Modeling (CPM) is a newly developed, data-driven approach that exploits whole-brain functional connectivity to predict a behavior or trait that varies across individuals. We used CPM to determine whether brain "fingerprints" evoked during milkshake consumption could be isolated for common measures of adiposity in 67 adults with overweight and obesity. We found that CPM captures more variance in waist circumference than either percent body fat or BMI, the most frequently used measures to assess brain correlates of obesity. In a post-hoc analysis, we were also able to derive a largely separable functional connectivity network predicting fasting blood insulin. These findings suggest that, in individuals with overweight and obesity, brain network patterns may be more tightly coupled to waist circumference than BMI or percent body fat and that adiposity and glucose tolerance are associated with distinct maps, pointing to dissociable central pathophysiological phenotypes for obesity and diabetes.

GEFF: Graph embedding for functional fingerprinting

It has been well established that Functional Connectomes (FCs), as estimated from functional MRI (fMRI) data, have an individual fingerprint that can be used to identify an individual from a population (subject-identification). Although identification rate is high when using resting-state FCs, other tasks show moderate to low values. Furthermore, identification rate is task-dependent, and is low when distinct cognitive states, as captured by different fMRI tasks, are compared. Here we propose an embedding framework, GEFF (Graph Embedding for Functional Fingerprinting), based on group-level decomposition of FCs into eigenvectors. GEFF creates an eigenspace representation of a group of subjects using one or more task FCs (Learning Stage). In the Identification Stage, we compare new instances of FCs from the Learning subjects within this eigenspace (validation dataset). The validation dataset contains FCs either from the same tasks as the Learning dataset or from the remaining tasks that were not included in Learning. Assessment of validation FCs within the eigenspace results in significantly increased subject-identification rates for all fMRI tasks tested and potentially task-independent fingerprinting process. It is noteworthy that combining resting-state with one fMRI task for GEFF Learning Stage covers most of the cognitive space for subject identification. Thus, while designing an experiment, one could choose a task fMRI to ask a specific question and combine it with resting-state fMRI to extract maximum subject differentiability using GEFF. In addition to subject-identification, GEFF was also used for identification of cognitive states, i.e. to identify the task associated to a given FC, regardless of the subject being already in the Learning dataset or not (subject-independent task-identification). In addition, we also show that eigenvectors from the Learning Stage can be characterized as task- and subject-dominant, subject-dominant or neither, using two-way ANOVA of their corresponding loadings, providing a deeper insight into the extent of variance in functional connectivity across individuals and cognitive states.

Earliest amyloid and tau deposition modulate the influence of limbic networks during closed-loop hippocampal downregulation

Research into hippocampal self-regulation abilities may help determine the clinical significance of hippocampal hyperactivity throughout the pathophysiological continuum of Alzheimer's disease. In this study, we aimed to identify the effects of amyloid-β peptide 42 (amyloid-β42) and phosphorylated tau on the patterns of functional connectomics involved in hippocampal downregulation. We identified 48 cognitively unimpaired participants (22 with elevated CSF amyloid-β peptide 42 levels, 15 with elevated CSF phosphorylated tau levels, mean age of 62.705 ± 4.628 years), from the population-based 'Alzheimer's and Families' study, with baseline MRI, CSF biomarkers, APOE genotyping and neuropsychological evaluation. We developed a closed-loop, real-time functional MRI neurofeedback task with virtual reality and tailored it for training downregulation of hippocampal subfield cornu ammonis 1 (CA1). Neurofeedback performance score, cognitive reserve score, hippocampal volume, number of apolipoprotein ε4 alleles and sex were controlled for as confounds in all cross-sectional analyses. First, using voxel-wise multiple regression analysis and controlling for CSF biomarkers, we identified the effect of healthy ageing on eigenvector centrality, a measure of each voxel's overall influence based on iterative whole-brain connectomics, during hippocampal CA1 downregulation. Then, controlling for age, we identified the effects of abnormal CSF amyloid-β42 and phosphorylated tau levels on eigenvector centrality during hippocampal CA1 downregulation. Across subjects, our main findings during hippocampal downregulation were: (i) in the absence of abnormal biomarkers, age correlated with eigenvector centrality negatively in the insula and midcingulate cortex, and positively in the inferior temporal gyrus; (ii) abnormal CSF amyloid-β42 (<1098) correlated negatively with eigenvector centrality in the anterior cingulate cortex and primary motor cortex; and (iii) abnormal CSF phosphorylated tau levels (>19.2) correlated with eigenvector centrality positively in the ventral striatum, anterior cingulate and somatosensory cortex, and negatively in the precuneus and orbitofrontal cortex. During resting state functional MRI, similar eigenvector centrality patterns in the cingulate had previously been associated to CSF biomarkers in mild cognitive impairment and dementia patients. Using the developed closed-loop paradigm, we observed such patterns, which are characteristic of advanced disease stages, during a much earlier presymptomatic phase. In the absence of CSF biomarkers, our non-invasive, interactive, adaptive and gamified neuroimaging procedure may provide important information for clinical prognosis and monitoring of therapeutic efficacy. We have released the developed paradigm and analysis pipeline as open-source software to facilitate replication studies.

Cerebellar-cortical function and connectivity during sensorimotor behavior in aging FMR1 gene premutation carriers

•

FMR1 premutation carriers show increased variability in motor control.

•

Premutation carriers show reduced extrastriate activation during motor behavior.

•

Premutation carriers show reduced extrastriate-cerebellar functional connectivity.

•

Reduced extrastriate-cerebellar functional connectivity is related to motor issues.

Introduction

Premutation carriers of the FMR1 gene are at risk of developing fragile X-associated tremor/ataxia syndrome (FXTAS), a neurodegenerative disease characterized by motor, cognitive, and psychiatric decline as well as cerebellar and cerebral white matter pathology. Several studies have documented preclinical sensorimotor issues in aging premutation carriers, but the extent to which sensorimotor brain systems are affected and may represent early indicators of atypical neurodegeneration has not been determined.

Materials and methods

Eighteen healthy controls and 16 FMR1 premutation carriers (including five with possible, probable, or definite FXTAS) group-matched on age, sex, and handedness completed a visually guided precision gripping task with their right hand during fMRI. During the test, they used a modified pinch grip to press at 60% of their maximum force against a custom fiber-optic transducer. Participants viewed a horizontal white force bar that moved upward with increased force and downward with decreased force and a static target bar that was red during rest and turned green to cue the participant to begin pressing at the beginning of each trial. Participants were instructed to press so that the white force bar stayed as steady as possible at the level of the green target bar. Trials were 2-sec in duration and alternated with 2-sec rest periods. Five 24-sec blocks consisting of six trials were presented. Participants’ reaction time, the accuracy of their force relative to the target force, and the variability of their force accuracy across trials were examined. BOLD signal change and task-based functional connectivity (FC) were examined during force vs. rest.

Results

Relative to healthy controls, premutation carriers showed increased trial-to-trial variability of force output, though this was specific to younger premutation carriers in our sample. Relative to healthy controls, premutation carriers also showed reduced extrastriate activation during force relative to rest. FC between ipsilateral cerebellar Crus I and extrastriate cortex was reduced in premutation carriers compared to controls. Reduced Crus I-extrastriate FC was related to increased force accuracy variability in premutation carriers. Increased reaction time was associated with more severe clinically rated neurological abnormalities.

Conclusions

Findings of reduced activation in extrastriate cortex and reduced Crus I-extrastriate FC implicate deficient visual feedback processing and reduced cerebellar modulation of corrective motor commands. Our results are consistent with documented cerebellar pathology and visual-spatial processing in FXTAS and pre-symptomatic premutation carriers, and suggest FC alterations of cerebellar-cortical networks during sensorimotor behavior may represent a “prodromal” feature associated with FXTAS degeneration.

Distinct patterns of thought mediate the link between brain functional connectomes and well-being

Ongoing thought patterns constitute important aspects of both healthy and abnormal human cognition. However, the neural mechanisms behind these daily experiences and their contribution to well-being remain a matter of debate. Here, using resting-state fMRI and retrospective thought sampling in a large neurotypical cohort (n = 211), we identified two distinct patterns of thought, broadly describing the participants' current concerns and future plans, that significantly explained variability in the individual functional connectomes. Consistent with the view that ongoing thoughts are an emergent property of multiple neural systems, network-based analysis highlighted the central importance of both unimodal and transmodal cortices in the generation of these experiences. Importantly, while state-dependent current concerns predicted better psychological health, mediating the effect of functional connectomes, trait-level future plans were related to better social health, yet with no mediatory influence. Collectively, we show that ongoing thoughts can influence the link between brain physiology and well-being.

Behavioral and Neural Signatures of Working Memory in Childhood

Working memory function changes across development and varies across individuals. The patterns of behavior and brain function that track individual differences in working memory during human development, however, are not well understood. Here, we establish associations between working memory, other cognitive abilities, and functional MRI (fMRI) activation in data from over 11,500 9- to 10-year-old children (both sexes) enrolled in the Adolescent Brain Cognitive Development (ABCD) Study, an ongoing longitudinal study in the United States. Behavioral analyses reveal robust relationships between working memory, short-term memory, language skills, and fluid intelligence. Analyses relating out-of-scanner working memory performance to memory-related fMRI activation in an emotional n-back task demonstrate that frontoparietal activity during a working memory challenge indexes working memory performance. This relationship is domain specific, such that fMRI activation related to emotion processing during the emotional n-back task, inhibitory control during a stop-signal task (SST), and reward processing during a monetary incentive delay (MID) task does not track memory abilities. Together, these results inform our understanding of individual differences in working memory in childhood and lay the groundwork for characterizing the ways in which they change across adolescence.SIGNIFICANCE STATEMENT Working memory is a foundational cognitive ability that changes over time and varies across individuals. Here, we analyze data from over 11,500 9- to 10-year-olds to establish relationships between working memory, other cognitive abilities, and frontoparietal brain activity during a working memory challenge, but not during other cognitive challenges. Our results lay the groundwork for assessing longitudinal changes in working memory and predicting later academic and other real-world outcomes.

Cortical electrophysiological evidence for individual-specific temporal organization of brain functional networks

The human brain has been demonstrated to rapidly and continuously form and dissolve networks on a subsecond timescale, offering effective and essential substrates for cognitive processes. Understanding how the dynamic organization of brain functional networks on a subsecond level varies across individuals is, therefore, of great interest for personalized neuroscience. However, it remains unclear whether features of such rapid network organization are reliably unique and stable in single subjects and, therefore, can be used in characterizing individual networks. Here, we used two sets of 5‐min magnetoencephalography (MEG) resting data from 39 healthy subjects over two consecutive days and modeled the spontaneous brain activity as recurring networks fast shifting between each other in a coordinated manner. MEG cortical maps were obtained through source reconstruction using the beamformer method and subjects' temporal structure of recurring networks was obtained via the Hidden Markov Model. Individual organization of dynamic brain activity was quantified with the features of the network‐switching pattern (i.e., transition probability and mean interval time) and the time‐allocation mode (i.e., fractional occupancy and mean lifetime). Using these features, we were able to identify subjects from the group with significant accuracies (~40% on average in 0.5–48 Hz). Notably, the default mode network displayed a distinguishable pattern, being the least frequently visited network with the longest duration for each visit. Together, we provide initial evidence suggesting that the rapid dynamic temporal organization of brain networks achieved in electrophysiology is intrinsic and subject specific.

Network connectivity predicts language processing in healthy adults

Brain imaging has been used to predict language skills during development and neuropathology but its accuracy in predicting language performance in healthy adults has been poorly investigated. To address this shortcoming, we studied the ability to predict reading accuracy and single‐word comprehension scores from rest‐ and task‐based functional magnetic resonance imaging (fMRI) datasets of 424 healthy adults. Using connectome‐based predictive modeling, we identified functional brain networks with >400 edges that predicted language scores and were reproducible in independent data sets. To simplify these complex models we identified the overlapping edges derived from the three task‐fMRI sessions (language, working memory, and motor tasks), and found 12 edges for reading recognition and 11 edges for vocabulary comprehension that accounted for 20% of the variance of these scores, both in the training sample and in the independent sample. The overlapping edges predominantly emanated from language areas within the frontoparietal and default‐mode networks, with a strong precuneus prominence. These findings identify a small subset of edges that accounted for a significant fraction of the variance in language performance that might serve as neuromarkers for neuromodulation interventions to improve language performance or for presurgical planning to minimize language impairments.

Multi-Hypergraph Learning-Based Brain Functional Connectivity Analysis in fMRI Data

Recently, a hypergraph constructed from functional magnetic resonance imaging (fMRI) was utilized to explore brain functional connectivity networks (FCNs) for the classification of neurodegenerative diseases. Each edge of a hypergraph (called hyperedge) can connect any number of brain regions-of-interest (ROIs) instead of only two ROIs, and thus characterizes high-order relations among multiple ROIs that cannot be uncovered by a simple graph in the traditional graph based FCN construction methods. Unlike the existing hypergraph based methods where all hyperedges are assumed to have equal weights and only certain topological features are extracted from the hypergraphs, we propose a hypergraph learning based method for FCN construction in this paper. Specifically, we first generate hyperedges from fMRI time series based on sparse representation, then employ hypergraph learning to adaptively learn hyperedge weights, and finally define a hypergraph similarity matrix to represent the FCN. In our proposed method, weighting hyperedges results in better discriminative FCNs across subjects, and the defined hypergraph similarity matrix can better reveal the overall structure of brain network than using those hypergraph topological features. Moreover, we propose a multi-hypergraph learning based method by integrating multi-paradigm fMRI data, where the hyperedge weights associated with each fMRI paradigm are jointly learned and then a unified hypergraph similarity matrix is computed to represent the FCN. We validate the effectiveness of the proposed method on the Philadelphia Neurodevelopmental Cohort dataset for the classification of individuals' learning ability from three paradigms of fMRI data. Experimental results demonstrate that our proposed approach outperforms the traditional graph based methods (i.e., Pearson's correlation and partial correlation with the graphical Lasso) and the existing unweighted hypergraph based methods, which sheds light on how to optimize estimation of FCNs for cognitive and behavioral study.

Intrinsic neural circuitry of depression in adolescent females

BACKGROUND

Adolescence is characterized by affective and cognitive changes that increase vulnerability to depression, especially in females. Neurodevelopmental models attribute adolescent depression to abnormal responses in amygdala, striatum, and prefrontal cortex (PFC). We examined whether the strength of functional brain networks involving these regions predicts depression symptoms in adolescent females.

METHODS

In this longitudinal study, we recorded resting-state functional connectivity (RSFC) in 174 adolescent females. Using a cross-validation strategy, we related RSFC profiles that included (a) a network consisting of amygdala, striatum, and PFC (within-circuit model), (b) connectivity of this network to the whole brain (extended-circuit model), and (c) a network consisting of the entire brain (whole-brain model) to depression symptoms assessed concurrently and 18 months later.

RESULTS

In testing subsets, the within-circuit RSFC profiles were associated with depression symptoms concurrently and 18 months later, while the extended-circuit and whole-brain model did not explain any additional variance in depression symptoms. Connectivity related to anterior cingulate and ventromedial prefrontal cortex contributed most to the association.

CONCLUSIONS

Our results demonstrate that RSFC-based brain networks that include amygdala, striatum, and PFC are stable neural signatures of concurrent and future depression symptoms, representing a significant step toward identifying the neural mechanism of depression in adolescence.

Model-Based and Model-Free Analyses of the Neural Correlates of Tongue Movements

The tongue performs movements in all directions to subserve its diverse functions in chewing, swallowing, and speech production. Using task-based functional MRI in a group of 17 healthy young participants, we studied (1) potential differences in the cerebral control of frontal (protrusion), horizontal (side to side), and vertical (elevation) tongue movements and (2) inter-individual differences in tongue motor control. To investigate differences between different tongue movements, we performed voxel-wise multiple linear regressions. To investigate inter-individual differences, we applied a novel approach, spatio-temporal filtering of independent components. For this approach, individual functional data were decomposed into spatially independent components and corresponding time courses using independent component analysis. A temporal filter (correlation with the expected brain response) was used to identify independent components time-locked to the tongue motor tasks. A spatial filter (cross-correlation with established neurofunctional systems) was used to identify brain activity not time-locked to the tasks. Our results confirm the importance of an extended bilateral cortical and subcortical network for the control of tongue movements. Frontal (protrusion) tongue movements, highly overlearned movements related to speech production, showed less activity in the frontal and parietal lobes compared to horizontal (side to side) and vertical (elevation) movements and greater activity in the left frontal and temporal lobes compared to vertical movements (cluster-forming threshold of Z > 3.1, cluster significance threshold of p < 0.01, corrected for multiple comparisons). The investigation of inter-individual differences revealed a component representing the tongue primary sensorimotor cortex time-locked to the task in all participants. Using the spatial filter, we found the default mode network in 16 of 17 participants, the left fronto-parietal network in 16, the right fronto-parietal network in 8, and the executive control network in four participants (Pearson's r > 0.4 between neurofunctional systems and individual components). These results demonstrate that spatio-temporal filtering of independent components allows to identify individual brain activity related to a specific task and also structured spatiotemporal processes representing known neurofunctional systems on an individual basis. This novel approach may be useful for the assessment of individual patients and results may be related to individual clinical, behavioral, and genetic information.

Individualized perturbation of the human connectome reveals reproducible biomarkers of network dynamics relevant to cognition

Large-scale brain networks are often described using resting-state functional magnetic resonance imaging (fMRI). However, the blood oxygenation level-dependent (BOLD) signal provides an indirect measure of neuronal firing and reflects slow-evolving hemodynamic activity that fails to capture the faster timescale of normal physiological function. Here we used fMRI-guided transcranial magnetic stimulation (TMS) and simultaneous electroencephalography (EEG) to characterize individual brain dynamics within discrete brain networks at high temporal resolution. TMS was used to induce controlled perturbations to individually defined nodes of the default mode network (DMN) and the dorsal attention network (DAN). Source-level EEG propagation patterns were network-specific and highly reproducible across sessions 1 month apart. Additionally, individual differences in high-order cognitive abilities were significantly correlated with the specificity of TMS propagation patterns across DAN and DMN, but not with resting-state EEG dynamics. Findings illustrate the potential of TMS-EEG perturbation-based biomarkers to characterize network-level individual brain dynamics at high temporal resolution, and potentially provide further insight on their behavioral significance.

Gender Differences in Connectome-based Predictions of Individualized Intelligence Quotient and Sub-domain Scores

Scores on intelligence tests are strongly predictive of various important life outcomes. However, the gender discrepancy on intelligence quotient (IQ) prediction using brain imaging variables has not been studied. To this aim, we predicted individual IQ scores for males and females separately using whole-brain functional connectivity (FC). Robust predictions of intellectual capabilities were achieved across three independent data sets (680 subjects) and two intelligence measurements (IQ and fluid intelligence) using the same model within each gender. Interestingly, we found that intelligence of males and females were underpinned by different neurobiological correlates, which are consistent with their respective superiority in cognitive domains (visuospatial vs verbal ability). In addition, the identified FC patterns are uniquely predictive on IQ and its sub-domain scores only within the same gender but neither for the opposite gender nor on the IQ-irrelevant measures such as temperament traits. Moreover, females exhibit significantly higher IQ predictability than males in the discovery cohort. This findings facilitate our understanding of the biological basis of intelligence by demonstrating that intelligence is underpinned by a variety of complex neural mechanisms that engage an interacting network of regions-particularly prefrontal-parietal and basal ganglia-whereas the network pattern differs between genders.

Spontaneous network activity <35 ​Hz accounts for variability in stimulus-induced gamma responses

Gamma activity is thought to serve several cognitive processes, including attention and memory. Even for the simplest stimulus, the occurrence of gamma activity is highly variable, both within and between individuals. The sources of this variability, however, are largely unknown. In this paper, we address one possible cause: the cross-frequency influence of spontaneous, whole-brain network activity on visual stimulus processing. By applying Hidden Markov modelling to MEG data, we reveal that the trial-averaged gamma response to a moving grating depends on the individual network dynamics, inferred from slower brain activity (<35 ​Hz) in the absence of stimulation (resting-state and task baseline). In addition, we demonstrate that modulations of network activity in task baseline influence the gamma response on the level of trials. In summary, our results reveal a cross-frequency and cross-session association between gamma responses induced by visual stimulation and spontaneous network activity. These findings underline the dependency of visual stimulus processing on the individual, functional network architecture.

Functional connectivity predicts changes in attention observed across minutes, days, and months

The ability to sustain attention differs across people and changes within a single person over time. Although recent work has demonstrated that patterns of functional brain connectivity predict individual differences in sustained attention, whether these same patterns capture fluctuations in attention within individuals remains unclear. Here, across five independent studies, we demonstrate that the sustained attention connectome-based predictive model (CPM), a validated model of sustained attention function, generalizes to predict attentional state from data collected across minutes, days, weeks, and months. Furthermore, the sustained attention CPM is sensitive to within-subject state changes induced by propofol as well as sevoflurane, such that individuals show functional connectivity signatures of stronger attentional states when awake than when under deep sedation and light anesthesia. Together, these results demonstrate that fluctuations in attentional state reflect variability in the same functional connectivity patterns that predict individual differences in sustained attention.

Deep neural networks and kernel regression achieve comparable accuracies for functional connectivity prediction of behavior and demographics

There is significant interest in the development and application of deep neural networks (DNNs) to neuroimaging data. A growing literature suggests that DNNs outperform their classical counterparts in a variety of neuroimaging applications, yet there are few direct comparisons of relative utility. Here, we compared the performance of three DNN architectures and a classical machine learning algorithm (kernel regression) in predicting individual phenotypes from whole-brain resting-state functional connectivity (RSFC) patterns. One of the DNNs was a generic fully-connected feedforward neural network, while the other two DNNs were recently published approaches specifically designed to exploit the structure of connectome data. By using a combined sample of almost 10,000 participants from the Human Connectome Project (HCP) and UK Biobank, we showed that the three DNNs and kernel regression achieved similar performance across a wide range of behavioral and demographic measures. Furthermore, the generic feedforward neural network exhibited similar performance to the two state-of-the-art connectome-specific DNNs. When predicting fluid intelligence in the UK Biobank, performance of all algorithms dramatically improved when sample size increased from 100 to 1000 subjects. Improvement was smaller, but still significant, when sample size increased from 1000 to 5000 subjects. Importantly, kernel regression was competitive across all sample sizes. Overall, our study suggests that kernel regression is as effective as DNNs for RSFC-based behavioral prediction, while incurring significantly lower computational costs. Therefore, kernel regression might serve as a useful baseline algorithm for future studies.

Development of structure-function coupling in human brain networks during youth

The human brain is organized into a hierarchy of functional systems that evolve in childhood and adolescence to support the dynamic control of attention and behavior. However, it remains unknown how developing white-matter architecture supports coordinated fluctuations in neural activity underlying cognition. We document marked remodeling of structure–function coupling in youth, which aligns with cortical hierarchies of functional specialization and evolutionary expansion. Further, we demonstrate that structure–function coupling in rostrolateral prefrontal cortex supports age-related improvements in executive ability. These findings have broad relevance for accounts of experience-dependent plasticity in healthy development and abnormal development associated with neuropsychiatric illness.

The protracted development of structural and functional brain connectivity within distributed association networks coincides with improvements in higher-order cognitive processes such as executive function. However, it remains unclear how white-matter architecture develops during youth to directly support coordinated neural activity. Here, we characterize the development of structure–function coupling using diffusion-weighted imaging and n-back functional MRI data in a sample of 727 individuals (ages 8 to 23 y). We found that spatial variability in structure–function coupling aligned with cortical hierarchies of functional specialization and evolutionary expansion. Furthermore, hierarchy-dependent age effects on structure–function coupling localized to transmodal cortex in both cross-sectional data and a subset of participants with longitudinal data (n = 294). Moreover, structure–function coupling in rostrolateral prefrontal cortex was associated with executive performance and partially mediated age-related improvements in executive function. Together, these findings delineate a critical dimension of adolescent brain development, whereby the coupling between structural and functional connectivity remodels to support functional specialization and cognition.

A decade of test-retest reliability of functional connectivity: A systematic review and meta-analysis

BACKGROUND

Once considered mere noise, fMRI-based functional connectivity has become a major neuroscience tool in part due to early studies demonstrating its reliability. These fundamental studies revealed only the tip of the iceberg; over the past decade, many test-retest reliability studies have continued to add nuance to our understanding of this complex topic. A summary of these diverse and at times contradictory perspectives is needed.

OBJECTIVES

We aimed to summarize the existing knowledge regarding test-retest reliability of functional connectivity at the most basic unit of analysis: the individual edge level. This entailed (1) a meta-analytic estimate of reliability and (2) a review of factors influencing reliability.

METHODS

A search of Scopus was conducted to identify studies that estimated edge-level test-retest reliability. To facilitate comparisons across studies, eligibility was restricted to studies measuring reliability via the intraclass correlation coefficient (ICC). The meta-analysis included a random effects pooled estimate of mean edge-level ICC, with studies nested within datasets. The review included a narrative summary of factors influencing edge-level ICC.

RESULTS

From an initial pool of 212 studies, 44 studies were identified for the qualitative review and 25 studies for quantitative meta-analysis. On average, individual edges exhibited a "poor" ICC of 0.29 (95% CI = 0.23 to 0.36). The most reliable measurements tended to involve: (1) stronger, within-network, cortical edges, (2) eyes open, awake, and active recordings, (3) more within-subject data, (4) shorter test-retest intervals, (5) no artifact correction (likely due in part to reliable artifact), and (6) full correlation-based connectivity with shrinkage.

CONCLUSION

This study represents the first meta-analysis and systematic review investigating test-retest reliability of edge-level functional connectivity. Key findings suggest there is room for improvement, but care should be taken to avoid promoting reliability at the expense of validity. By pooling existing knowledge regarding this key facet of accuracy, this study supports broader efforts to improve inferences in the field.

Task-induced brain connectivity promotes the detection of individual differences in brain-behavior relationships

Although both resting and task-induced functional connectivity (FC) have been used to characterize the human brain and cognitive abilities, the potential of task-induced FCs in individualized prediction for out-of-scanner cognitive traits remains largely unexplored. A recent study Greene et al. (2018) predicted the fluid intelligence scores using FCs derived from rest and multiple task conditions, suggesting that task-induced brain state manipulation improved prediction of individual traits. Here, using a large dataset incorporating fMRI data from rest and 7 distinct task conditions, we replicated the original study by employing a different machine learning approach, and applying the method to predict two reading comprehension-related cognitive measures. Consistent with their findings, we found that task-based machine learning models often outperformed rest-based models. We also observed that combining multi-task fMRI improved prediction performance, yet, integrating the more fMRI conditions can not necessarily ensure better predictions. Compared with rest, the predictive FCs derived from language and working memory tasks were highlighted with more predictive power in predominantly default mode and frontoparietal networks. Moreover, prediction models demonstrated high stability to be generalizable across distinct cognitive states. Together, this replication study highlights the benefit of using task-based FCs to reveal brain-behavior relationships, which may confer more predictive power and promote the detection of individual differences of connectivity patterns underlying relevant cognitive traits, providing strong evidence for the validity and robustness of the original findings.