Identifying reproducible individual differences in childhood functional brain networks: An ABCD study

DeepComBat: A statistically motivated, hyperparameter-robust, deep learning approach to harmonization of neuroimaging data

Neuroimaging data acquired using multiple scanners or protocols are increasingly available. However, such data exhibit technical artifacts across batches which introduce confounding and decrease reproducibility. This is especially true when multi-batch data are analyzed using complex downstream models which are more likely to pick up on and implicitly incorporate batch-related information. Previously proposed image harmonization methods have sought to remove these batch effects; however, batch effects remain detectable in the data after applying these methods. We present DeepComBat, a deep learning harmonization method based on a conditional variational autoencoder and the ComBat method. DeepComBat combines the strengths of statistical and deep learning methods in order to account for the multivariate relationships between features while simultaneously relaxing strong assumptions made by previous deep learning harmonization methods. As a result, DeepComBat can perform multivariate harmonization while preserving data structure and avoiding the introduction of synthetic artifacts. We apply this method to cortical thickness measurements from a cognitive-aging cohort and show DeepComBat qualitatively and quantitatively outperforms existing methods in removing batch effects while preserving biological heterogeneity. Additionally, DeepComBat provides a new perspective for statistically motivated deep learning harmonization methods.

Threat- and reward-related brain circuitry, perceived stress, and anxiety in adolescents during the COVID-19 pandemic: a longitudinal investigation

The Coronavirus disease (COVID-19) pandemic led to heightened anxiety in adolescents. The basolateral amygdala (BLA) and the nucleus accumbens (NAcc) are implicated in response to stress and may contribute to anxiety. The role of threat- and reward-related circuitry in adolescent anxiety during the COVID-19 pandemic, however, is not clear. Ninety-nine adolescents underwent resting-state fMRI ∼1 year before the pandemic. Following shelter-in-place orders, adolescents reported their perceived stress and, 1 month later, their anxiety. Generalized multivariate analyses identified BLA and NAcc seed-based whole-brain functional connectivity maps with perceived stress. In the resulting significant clusters, we examined the association between seed-based connectivityand subsequent anxiety. Perceived stress was associated with bilateral BLA and NAcc connectivity across distributed clusters that included prefrontal, limbic, temporal, and cerebellar regions. Several NAcc connectivity clusters located in ventromedial prefrontal, parahippocampal, and temporal cortices were positively associated with anxiety; NAcc connectivity with the inferior frontal gyrus was negatively associated. BLA connectivity was not associated with anxiety. These results underscore the integrative role of the NAcc in responding to acute stressors and its relation to anxiety in adolescents. Elucidating the involvement of subcortical-cortical circuitry in adolescents' capacity to respond adaptively to environmental challenges can inform treatment for anxiety-related disorders.

Comparing the stability and reproducibility of brain-behavior relationships found using canonical correlation analysis and partial least squares within the ABCD sample

Canonical correlation analysis (CCA) and partial least squares correlation (PLS) detect linear associations between two data matrices by computing latent variables (LVs) having maximal correlation (CCA) or covariance (PLS). This study compared the similarity and generalizability of CCA- and PLS-derived brain-behavior relationships. Data were accessed from the baseline Adolescent Brain Cognitive Development (ABCD) dataset (N > 9,000, 9-11 years). The brain matrix consisted of cortical thickness estimates from the Desikan-Killiany atlas. Two phenotypic scales were examined separately as the behavioral matrix; the Child Behavioral Checklist (CBCL) subscale scores and NIH Toolbox performance scores. Resampling methods were used to assess significance and generalizability of LVs. LV1 for the CBCL brain relationships was found to be significant, yet not consistently stable or reproducible, across CCA and PLS models (singular value: CCA = .13, PLS = .39, p < .001). LV1 for the NIH brain relationships showed similar relationships between CCA and PLS and was found to be stable and reproducible (singular value: CCA = .21, PLS = .43, p < .001). The current study suggests that stability and reproducibility of brain-behavior relationships identified by CCA and PLS are influenced by the statistical characteristics of the phenotypic measure used when applied to a large population-based pediatric sample.

Population-level normative models reveal race- and socioeconomic-related variability in cortical thickness of threat neurocircuitry

The inequitable distribution of economic resources and exposure to adversity between racial groups contributes to mental health disparities within the United States. Consideration of the potential neurodevelopmental consequences, however, has been limited particularly for neurocircuitry known to regulate the emotional response to threat. Characterizing the consequences of inequity on threat neurocircuitry is critical for robust and generalizable neurobiological models of psychiatric illness. Here we use data from the Adolescent Brain and Cognitive Development Study 4.0 release to investigate the contributions of individual and neighborhood-level economic resources and exposure to discrimination. We investigate the potential appearance of race-related differences using both standard methods and through population-level normative modeling. We show that, in a sample of white and Black adolescents, racial inequities in socioeconomic factors largely contribute to the appearance of race-related differences in cortical thickness of threat neurocircuitry. The race-related differences are preserved through the use of population-level models and such models also preserve associations between cortical thickness and specific socioeconomic factors. The present findings highlight that such socioeconomic inequities largely underlie race-related differences in brain morphology. The present findings provide important new insight for the generation of generalizable neurobiological models of psychiatric illness.

Two common and distinct forms of variation in human functional brain networks

The cortex has a characteristic layout with specialized functional areas forming distributed large-scale networks. However, substantial work shows striking variation in this organization across people, which relates to differences in behavior. While most previous work treats individual differences as linked to boundary shifts between the borders of regions, here we show that cortical 'variants' also occur at a distance from their typical position, forming ectopic intrusions. Both 'border' and 'ectopic' variants are common across individuals, but differ in their location, network associations, properties of subgroups of individuals, activations during tasks, and prediction of behavioral phenotypes. Border variants also track significantly more with shared genetics than ectopic variants, suggesting a closer link between ectopic variants and environmental influences. This work argues that these two dissociable forms of variation-border shifts and ectopic intrusions-must be separately accounted for in the analysis of individual differences in cortical systems across people.

Predicting high-level visual areas in the absence of task fMRI

The ventral visual stream is organized into units, or functional regions of interest (fROIs), specialized for processing high-level visual categories. Task-based fMRI scans ("localizers") are typically used to identify each individual's nuanced set of fROIs. The unique landscape of an individual's functional activation may rely in large part on their specialized connectivity patterns; recent studies corroborate this by showing that connectivity can predict individual differences in neural responses. We focus on the ventral visual stream and ask: how well can an individual's resting state functional connectivity localize their fROIs for face, body, scene, and object perception? And are the neural processors for any particular visual category better predicted by connectivity than others, suggesting a tighter mechanistic relationship between connectivity and function? We found, among 18 fROIs predicted from connectivity for each subject, all but one were selective for their preferred visual category. Defining an individual's fROIs based on their connectivity patterns yielded regions that were more selective than regions identified from previous studies or atlases in nearly all cases. Overall, we found that in the absence of a domain-specific localizer task, a 10-min resting state scan can be reliably used for defining these fROIs.

The default mode network is associated with changes in internalizing and externalizing problems differently in adolescent boys and girls

Internalizing and externalizing problems that emerge during adolescence differentially increase boys' and girls' risk for developing psychiatric disorders. It is not clear, however, whether there are sex differences in the intrinsic functional architecture of the brain that underlie changes in the severity of internalizing and externalizing problems in adolescents. Using resting-state fMRI data and self-reports of behavioral problems obtained from 128 adolescents (73 females; 9-14 years old) at two timepoints, we conducted multivoxel pattern analysis to identify resting-state functional connectivity markers at baseline that predict changes in the severity of internalizing and externalizing problems in boys and girls 2 years later. We found sex-differentiated involvement of the default mode network in changes in internalizing and externalizing problems. Whereas changes in internalizing problems were associated with the dorsal medial subsystem in boys and with the medial temporal subsystem in girls, changes in externalizing problems were predicted by hyperconnectivity between core nodes of the DMN and frontoparietal network in boys and hypoconnectivity between the DMN and affective networks in girls. Our results suggest that different neural mechanisms predict changes in internalizing and externalizing problems in adolescent boys and girls and offer insights concerning mechanisms that underlie sex differences in the expression of psychopathology in adolescence.

A precision functional atlas of personalized network topography and probabilities

Although the general location of functional neural networks is similar across individuals, there is vast person-to-person topographic variability. To capture this, we implemented precision brain mapping functional magnetic resonance imaging methods to establish an open-source, method-flexible set of precision functional network atlases-the Masonic Institute for the Developing Brain (MIDB) Precision Brain Atlas. This atlas is an evolving resource comprising 53,273 individual-specific network maps, from more than 9,900 individuals, across ages and cohorts, including the Adolescent Brain Cognitive Development study, the Developmental Human Connectome Project and others. We also generated probabilistic network maps across multiple ages and integration zones (using a new overlapping mapping technique, Overlapping MultiNetwork Imaging). Using regions of high network invariance improved the reproducibility of executive function statistical maps in brain-wide associations compared to group average-based parcellations. Finally, we provide a potential use case for probabilistic maps for targeted neuromodulation. The atlas is expandable to alternative datasets with an online interface encouraging the scientific community to explore and contribute to understanding the human brain function more precisely.

Dissociation of Reliability, Heritability, and Predictivity in Coarse- and Fine-Scale Functional Connectomes during Development

The functional connectome supports information transmission through the brain at various spatial scales, from exchange between broad cortical regions to finer-scale, vertex-wise connections that underlie specific information processing mechanisms. In adults, while both the coarse- and fine-scale functional connectomes predict cognition, the fine scale can predict up to twice the variance as the coarse-scale functional connectome. Yet, past brain-wide association studies, particularly using large developmental samples, focus on the coarse connectome to understand the neural underpinnings of individual differences in cognition. Using a large cohort of children (age 9-10 years; n = 1,115 individuals; both sexes; 50% female, including 170 monozygotic and 219 dizygotic twin pairs and 337 unrelated individuals), we examine the reliability, heritability, and behavioral relevance of resting-state functional connectivity computed at different spatial scales. We use connectivity hyperalignment to improve access to reliable fine-scale (vertex-wise) connectivity information and compare the fine-scale connectome with the traditional parcel-wise (coarse scale) functional connectomes. Though individual differences in the fine-scale connectome are more reliable than those in the coarse-scale, they are less heritable. Further, the alignment and scale of connectomes influence their ability to predict behavior, whereby some cognitive traits are equally well predicted by both connectome scales, but other, less heritable cognitive traits are better predicted by the fine-scale connectome. Together, our findings suggest there are dissociable individual differences in information processing represented at different scales of the functional connectome which, in turn, have distinct implications for heritability and cognition.

A precision neuroscience approach to estimating reliability of neural responses during emotion processing: Implications for task-fMRI

Recent work demonstrating low test-retest reliability of neural activation during fMRI tasks raises questions about the utility of task-based fMRI for the study of individual variation in brain function. Two possible sources of the instability in task-based BOLD signal over time are noise or measurement error in the instrument, and meaningful variation across time within-individuals in the construct itself-brain activation elicited during fMRI tasks. Examining the contribution of these two sources of test-retest unreliability in task-evoked brain activity has far-reaching implications for cognitive neuroscience. If test-retest reliability largely reflects measurement error, it suggests that task-based fMRI has little utility in the study of either inter- or intra-individual differences. On the other hand, if task-evoked BOLD signal varies meaningfully over time, it would suggest that this tool may yet be well suited to studying intraindividual variation. We parse these sources of variance in BOLD signal in response to emotional cues over time and within-individuals in a longitudinal sample with 10 monthly fMRI scans. Test-retest reliability was low, reflecting a lack of stability in between-person differences across scans. In contrast, within-person, within-session internal consistency of the BOLD signal was higher, and within-person fluctuations across sessions explained almost half the variance in voxel-level neural responses. Additionally, monthly fluctuations in neural response to emotional cues were associated with intraindividual variation in mood, sleep, and exposure to stressors. Rather than reflecting trait-like differences across people, neural responses to emotional cues may be more reflective of intraindividual variation over time. These patterns suggest that task-based fMRI may be able to contribute to the study of individual variation in brain function if more attention is given to within-individual variation approaches, psychometrics-beginning with improving reliability beyond the modest estimates observed here, and the validity of task fMRI beyond the suggestive associations reported here.

Brain Imaging in Routine Psychiatric Practice

Technologies in the 21st century provide increasingly detailed and accurate maps of brain structure and function. So why don't psychiatrists order brain imaging on all our patients? Here we briefly review major neuroimaging methods and some of their findings in psychiatry. As clinicians and neuroimaging researchers, we are eager to bring brain imaging into daily clinical practice. However, to be clinically useful, any test in medicine must demonstrate adequate test statistics, and show proven benefits that outweigh its risks and costs. In 2024, beyond certain limited circumstances, we have no imaging tests that can meet those standards to provide diagnosis or guide treatment. This cold fact explains why for most psychiatric patients, neuroimaging is not currently recommended by professional organizations or the National Institute of Mental Health.

Resting state network connectivity is associated with cognitive flexibility performance in youth in the Adolescent Brain Cognitive Development Study

Cognitive flexibility is an executive functioning skill that develops in childhood, and when impaired, has transdiagnostic implications for psychiatric disorders. To identify how intrinsic neural architecture at rest is linked to cognitive flexibility performance, we used the data-driven method of independent component analysis (ICA) to investigate resting state networks (RSNs) and their whole-brain connectivity associated with levels of cognitive flexibility performance in children. We hypothesized differences by cognitive flexibility performance in RSN connectivity strength in cortico-striatal circuitry, which would manifest via the executive control network, right and left frontoparietal networks (FPN), salience network, default mode network (DMN), and basal ganglia network. We selected participants from the Adolescent Brain Cognitive Development (ABCD) Study who scored at the 25th, ("CF-Low"), 50th ("CF-Average"), or 75th percentiles ("CF-High") on a cognitive flexibility task, were early to middle puberty, and did not exhibit significant psychopathology (n = 967, 47.9% female; ages 9-10). We conducted whole-brain ICA, identifying 14 well-characterized RSNs. Groups differed in connectivity strength in the right FPN, anterior DMN, and posterior DMN. Planned comparisons indicated CF-High had stronger connectivity between right FPN and supplementary motor/anterior cingulate than CF-Low. CF-High had more anti-correlated connectivity between anterior DMN and precuneus than CF-Average. CF-Low had stronger connectivity between posterior DMN and supplementary motor/anterior cingulate than CF-Average. Post-hoc correlations with reaction time by trial type demonstrated significant associations with connectivity. In sum, our results suggest childhood cognitive flexibility performance is associated with DMN and FPN connectivity strength at rest, and that there may be optimal levels of connectivity associated with task performance that vary by network.

Cognitive deficits and altered functional brain network organization in pediatric brain tumor patients

Survivors of pediatric brain tumors experience significant cognitive deficits from their diagnosis and treatment. The exact mechanisms of cognitive injury are poorly understood, and validated predictors of long-term cognitive outcome are lacking. Resting state functional magnetic resonance imaging allows for the study of the spontaneous fluctuations in bulk neural activity, providing insight into brain organization and function. Here, we evaluated cognitive performance and functional network architecture in pediatric brain tumor patients. Forty-nine patients (7-18 years old) with a primary brain tumor diagnosis underwent resting state imaging during regularly scheduled clinical visits. All patients were tested with a battery of cognitive assessments. Extant data from 139 typically developing children were used as controls. We found that obtaining high-quality imaging data during routine clinical scanning was feasible. Functional network organization was significantly altered in patients, with the largest disruptions observed in patients who received propofol sedation. Awake patients demonstrated significant decreases in association network segregation compared to controls. Interestingly, there was no difference in the segregation of sensorimotor networks. With a median follow-up of 3.1 years, patients demonstrated cognitive deficits in multiple domains of executive function. Finally, there was a weak correlation between decreased default mode network segregation and poor picture vocabulary score. Future work with longer follow-up, longitudinal analyses, and a larger cohort will provide further insight into this potential predictor.

Substructure of the brain's Cingulo-Opercular network

The Cingulo-Opercular network (CON) is an executive network of the human brain that regulates actions. CON is composed of many widely distributed cortical regions that are involved in top-down control over both lower-level (i.e., motor) and higher-level (i.e., cognitive) functions, as well as in processing of painful stimuli. Given the topographical and functional heterogeneity of the CON, we investigated whether subnetworks within the CON support separable aspects of action control. Using precision functional mapping (PFM) in 15 participants with > 5 hours of resting state functional connectivity (RSFC) and task data, we identified three anatomically and functionally distinct CON subnetworks within each individual. These three distinct subnetworks were linked to Decisions, Actions, and Feedback (including pain processing), respectively, in convergence with a meta-analytic task database. These Decision, Action and Feedback subnetworks represent pathways by which the brain establishes top-down goals, transforms those goals into actions, implemented as movements, and processes critical action feedback such as pain.

Variability in Cognitive Task Performance in Early Adolescence Is Associated With Stronger Between-Network Anticorrelation and Future Attention Problems

Background

Intraindividual variability (IIV) during cognitive task performance is a key behavioral index of attention and a consistent marker of attention-deficit/hyperactivity disorder. In adults, lower IIV has been associated with anticorrelation between the default mode network (DMN) and dorsal attention network (DAN)-thought to underlie effective allocation of attention. However, whether these behavioral and neural markers of attention are 1) associated with each other and 2) can predict future attention-related deficits has not been examined in a developmental, population-based cohort.

Methods

We examined relationships at the baseline visit between IIV on 3 cognitive tasks, DMN-DAN anticorrelation, and parent-reported attention problems using data from the Adolescent Brain Cognitive Development (ABCD) Study (N = 11,878 participants, ages 9 to 10 years, female = 47.8%). We also investigated whether behavioral and neural markers of attention at baseline predicted attention problems 1, 2, and 3 years later.

Results

At baseline, greater DMN-DAN anticorrelation was associated with lower IIV across all 3 cognitive tasks (B = 0.22 to 0.25). Older age at baseline was associated with stronger DMN-DAN anticorrelation and lower IIV (B = -0.005 to -0.0004). Weaker DMN-DAN anticorrelation and IIV were cross-sectionally associated with attention problems (B = 1.41 to 7.63). Longitudinally, lower IIV at baseline was associated with less severe attention problems 1 to 3 years later, after accounting for baseline attention problems (B = 0.288 to 0.77).

Conclusions

The results suggest that IIV in early adolescence is associated with worsening attention problems in a representative cohort of U.S. youth. Attention deficits in early adolescence may be important for understanding and predicting future cognitive and clinical outcomes.

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

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

Stability, change, and reliable individual differences in electroencephalography measures: a lifespan perspective on progress and opportunities

Electroencephalographic (EEG) methods have great potential to serve both basic and clinical science approaches to understand individual differences in human neural function. Importantly, the psychometric properties of EEG data, such as internal consistency and test-retest reliability, constrain their ability to differentiate individuals successfully. Rapid and recent technological and computational advancements in EEG research make it timely to revisit the topic of psychometric reliability in the context of individual difference analyses. Moreover, pediatric and clinical samples provide some of the most salient and urgent opportunities to apply individual difference approaches, but the changes these populations experience over time also provide unique challenges from a psychometric perspective. Here we take a developmental neuroscience perspective to consider progress and new opportunities for parsing the reliability and stability of individual differences in EEG measurements across the lifespan. We first conceptually map the different profiles of measurement reliability expected for different types of individual difference analyses over the lifespan. Next, we summarize and evaluate the state of the field's empirical knowledge and need for testing measurement reliability, both internal consistency and test-retest reliability, across EEG measures of power, event-related potentials, nonlinearity, and functional connectivity across ages. Finally, we highlight how standardized pre-processing software for EEG denoising and empirical metrics of individual data quality may be used to further improve EEG-based individual differences research moving forward. We also include recommendations and resources throughout that individual researchers can implement to improve the utility and reproducibility of individual differences analyses with EEG across the lifespan.

A shared neural basis underlying psychiatric comorbidity

Recent studies proposed a general psychopathology factor underlying common comorbidities among psychiatric disorders. However, its neurobiological mechanisms and generalizability remain elusive. In this study, we used a large longitudinal neuroimaging cohort from adolescence to young adulthood (IMAGEN) to define a neuropsychopathological (NP) factor across externalizing and internalizing symptoms using multitask connectomes. We demonstrate that this NP factor might represent a unified, genetically determined, delayed development of the prefrontal cortex that further leads to poor executive function. We also show this NP factor to be reproducible in multiple developmental periods, from preadolescence to early adulthood, and generalizable to the resting-state connectome and clinical samples (the ADHD-200 Sample and the Stratify Project). In conclusion, we identify a reproducible and general neural basis underlying symptoms of multiple mental health disorders, bridging multidimensional evidence from behavioral, neuroimaging and genetic substrates. These findings may help to develop new therapeutic interventions for psychiatric comorbidities.

DeepComBat: A Statistically Motivated, Hyperparameter-Robust, Deep Learning Approach to Harmonization of Neuroimaging Data

Neuroimaging data from multiple batches (i.e. acquisition sites, scanner manufacturer, datasets, etc.) are increasingly necessary to gain new insights into the human brain. However, multi-batch data, as well as extracted radiomic features, exhibit pronounced technical artifacts across batches. These batch effects introduce confounding into the data and can obscure biological effects of interest, decreasing the generalizability and reproducibility of findings. This is especially true when multi-batch data is used alongside complex downstream analysis models, such as machine learning methods. Image harmonization methods seeking to remove these batch effects are important for mitigating these issues; however, significant multivariate batch effects remain in the data following harmonization by current state-of-the-art statistical and deep learning methods. We present DeepCombat, a deep learning harmonization method based on a conditional variational autoencoder architecture and the ComBat harmonization model. DeepCombat learns and removes subject-level batch effects by accounting for the multivariate relationships between features. Additionally, DeepComBat relaxes a number of strong assumptions commonly made by previous deep learning harmonization methods and is empirically robust across a wide range of hyperparameter choices. We apply this method to neuroimaging data from a large cognitive-aging cohort and find that DeepCombat outperforms existing methods, as assessed by a battery of machine learning methods, in removing scanner effects from cortical thickness measurements while preserving biological heterogeneity. Additionally, DeepComBat provides a new perspective for statistically-motivated deep learning harmonization methods.

How can graph theory inform the dual-stream model of speech processing? a resting-state fMRI study of post-stroke aphasia

The dual-stream model of speech processing has been proposed to represent the cortical networks involved in speech comprehension and production. Although it is arguably the prominent neuroanatomical model of speech processing, it is not yet known if the dual-stream model represents actual intrinsic functional brain networks. Furthermore, it is unclear how disruptions after a stroke to the functional connectivity of the dual-stream model's regions are related to specific types of speech production and comprehension impairments seen in aphasia. To address these questions, in the present study, we examined two independent resting-state fMRI datasets: (1) 28 neurotypical matched controls and (2) 28 chronic left-hemisphere stroke survivors with aphasia collected at another site. Structural MRI, as well as language and cognitive behavioral assessments, were collected. Using standard functional connectivity measures, we successfully identified an intrinsic resting-state network amongst the dual-stream model's regions in the control group. We then used both standard functional connectivity analyses and graph theory approaches to determine how the functional connectivity of the dual-stream network differs in individuals with post-stroke aphasia, and how this connectivity may predict performance on clinical aphasia assessments. Our findings provide strong evidence that the dual-stream model is an intrinsic network as measured via resting-state MRI, and that weaker functional connectivity of the hub nodes of the dual-stream network defined by graph theory methods, but not overall average network connectivity, is weaker in the stroke group than in the control participants. Also, the functional connectivity of the hub nodes predicted specific types of impairments on clinical assessments. In particular, the relative strength of connectivity of the right hemisphere's homologues of the left dorsal stream hubs to the left dorsal hubs versus right ventral stream hubs is a particularly strong predictor of post-stroke aphasia severity and symptomology.

Less is more: balancing noise reduction and data retention in fMRI with data-driven scrubbing

Functional MRI (fMRI) data may be contaminated by artifacts arising from a myriad of sources, including subject head motion, respiration, heartbeat, scanner drift, and thermal noise. These artifacts cause deviations from common distributional assumptions, introduce spatial and temporal outliers, and reduce the signal-to-noise ratio of the data-all of which can have negative consequences for the accuracy and power of downstream statistical analysis. Scrubbing is a technique for excluding fMRI volumes thought to be contaminated by artifacts and generally comes in two flavors. Motion scrubbing based on subject head motion-derived measures is popular but suffers from a number of drawbacks, among them the need to choose a threshold, a lack of generalizability to multiband acquisitions, and high rates of censoring of individual volumes and entire subjects. Alternatively, data-driven scrubbing methods like DVARS are based on observed noise in the processed fMRI timeseries and may avoid some of these issues. Here we propose "projection scrubbing", a novel data-driven scrubbing method based on a statistical outlier detection framework and strategic dimension reduction, including independent component analysis (ICA), to isolate artifactual variation. We undertake a comprehensive comparison of motion scrubbing with data-driven projection scrubbing and DVARS. We argue that an appropriate metric for the success of scrubbing is maximal data retention subject to reasonable performance on typical benchmarks such as the validity, reliability, and identifiability of functional connectivity. We find that stringent motion scrubbing yields worsened validity, worsened reliability, and produced small improvements to fingerprinting. Meanwhile, data-driven scrubbing methods tend to yield greater improvements to fingerprinting while not generally worsening validity or reliability. Importantly, however, data-driven scrubbing excludes a fraction of the number of volumes or entire sessions compared to motion scrubbing. The ability of data-driven fMRI scrubbing to improve data retention without negatively impacting the quality of downstream analysis has major implications for sample sizes in population neuroscience research.

Polyneuro risk scores capture widely distributed connectivity patterns of cognition

Resting-state functional connectivity (RSFC) is a powerful tool for characterizing brain changes, but it has yet to reliably predict higher-order cognition. This may be attributed to small effect sizes of such brain-behavior relationships, which can lead to underpowered, variable results when utilizing typical sample sizes (N∼25). Inspired by techniques in genomics, we implement the polyneuro risk score (PNRS) framework - the application of multivariate techniques to RSFC data and validation in an independent sample. Utilizing the Adolescent Brain Cognitive Development® cohort split into two datasets, we explore the framework's ability to reliably capture brain-behavior relationships across 3 cognitive scores - general ability, executive function, learning & memory. The weight and significance of each connection is assessed in the first dataset, and a PNRS is calculated for each participant in the second. Results support the PNRS framework as a suitable methodology to inspect the distribution of connections contributing towards behavior, with explained variance ranging from 1.0 % to 21.4 %. For the outcomes assessed, the framework reveals globally distributed, rather than localized, patterns of predictive connections. Larger samples are likely necessary to systematically identify the specific connections contributing towards complex outcomes. The PNRS framework could be applied translationally to identify neurologically distinct subtypes of neurodevelopmental disorders.

Using synthetic MR images for distortion correction

Functional MRI (fMRI) data acquired using echo-planar imaging (EPI) are highly distorted by magnetic field inhomogeneities. Distortion and differences in image contrast between EPI and T1-weighted and T2-weighted (T1w/T2w) images makes their alignment a challenge. Typically, field map data are used to correct EPI distortions. Alignments achieved with field maps can vary greatly and depends on the quality of field map data. However, many public datasets lack field map data entirely. Additionally, reliable field map data is often difficult to acquire in high-motion pediatric or developmental cohorts. To address this, we developed Synth, a software package for distortion correction and cross-modal image registration that does not require field map data. Synth combines information from T1w and T2w anatomical images to construct an idealized undistorted synthetic image with similar contrast properties to EPI data. This synthetic image acts as an effective reference for individual-specific distortion correction. Using pediatric (ABCD: Adolescent Brain Cognitive Development) and adult (MSC: Midnight Scan Club; HCP: Human Connectome Project) data, we demonstrate that Synth performs comparably to field map distortion correction approaches, and often outperforms them. Field map-less distortion correction with Synth allows accurate and precise registration of fMRI data with missing or corrupted field map information.

Maturation of large-scale brain systems over the first month of life

The period immediately after birth is a critical developmental window, capturing rapid maturation of brain structure and a child's earliest experiences. Large-scale brain systems are present at delivery, but how these brain systems mature during this narrow window (i.e. first weeks of life) marked by heightened neuroplasticity remains uncharted. Using multivariate pattern classification techniques and functional connectivity magnetic resonance imaging, we detected robust differences in brain systems related to age in newborns (n = 262; R2 = 0.51). Development over the first month of life occurred brain-wide, but differed and was more pronounced in brain systems previously characterized as developing early (i.e. sensorimotor networks) than in those characterized as developing late (i.e. association networks). The cingulo-opercular network was the only exception to this organizing principle, illuminating its early role in brain development. This study represents a step towards a normative brain "growth curve" that could be used to identify atypical brain maturation in infancy.

Comparing the stability and reproducibility of brain-behaviour relationships found using Canonical Correlation Analysis and Partial Least Squares within the ABCD Sample

Introduction

Canonical Correlation Analysis (CCA) and Partial Least Squares Correlation (PLS) detect associations between two data matrices based on computing a linear combination between the two matrices (called latent variables; LVs). These LVs maximize correlation (CCA) and covariance (PLS). These different maximization criteria may render one approach more stable and reproducible than the other when working with brain and behavioural data at the population-level. This study compared the LVs which emerged from CCA and PLS analyses of brain-behaviour relationships from the Adolescent Brain Cognitive Development (ABCD) dataset and examined their stability and reproducibility.

Methods

Structural T1-weighted imaging and behavioural data were accessed from the baseline Adolescent Brain Cognitive Development dataset (N > 9000, ages = 9-11 years). The brain matrix consisted of cortical thickness estimates in different cortical regions. The behavioural matrix consisted of 11 subscale scores from the parent-reported Child Behavioral Checklist (CBCL) or 7 cognitive performance measures from the NIH Toolbox. CCA and PLS models were separately applied to the brain-CBCL analysis and brain-cognition analysis. A permutation test was used to assess whether identified LVs were statistically significant. A series of resampling statistical methods were used to assess stability and reproducibility of the LVs.

Results

When examining the relationship between cortical thickness and CBCL scores, the first LV was found to be significant across both CCA and PLS models (singular value: CCA = .13, PLS = .39, p < .001). LV1 from the CCA model found that covariation of CBCL scores was linked to covariation of cortical thickness. LV1 from the PLS model identified decreased cortical thickness linked to lower CBCL scores. There was limited evidence of stability or reproducibility of LV1 for both CCA and PLS. When examining the relationship between cortical thickness and cognitive performance, there were 6 significant LVs for both CCA and PLS (p < .01). The first LV showed similar relationships between CCA and PLS and was found to be stable and reproducible (singular value: CCA = .21, PLS = .43, p < .001).

Conclusion

CCA and PLS identify different brain-behaviour relationships with limited stability and reproducibility when examining the relationship between cortical thickness and parent-reported behavioural measures. However, both methods identified relatively similar brain-behaviour relationships that were stable and reproducible when examining the relationship between cortical thickness and cognitive performance. The results of the current study suggest that stability and reproducibility of brain-behaviour relationships identified by CCA and PLS are influenced by characteristics of the analyzed sample and the included behavioural measurements when applied to a large pediatric dataset.

A cognitive process modeling framework for the ABCD study stop-signal task

The Adolescent Brain Cognitive Development (ABCD) Study is a longitudinal neuroimaging study of unprecedented scale that is in the process of following over 11,000 youth from middle childhood though age 20. However, a design feature of the study's stop-signal task violates "context independence", an assumption critical to current non-parametric methods for estimating stop-signal reaction time (SSRT), a key measure of inhibitory ability in the study. This has led some experts to call for the task to be changed and for previously collected data to be used with caution. We present a cognitive process modeling framework, the RDEX-ABCD model, that provides a parsimonious explanation for the impact of this design feature on "go" stimulus processing and successfully accounts for key behavioral trends in the ABCD data. Simulation studies using this model suggest that failing to account for the context independence violations in the ABCD design can lead to erroneous inferences in several realistic scenarios. However, we demonstrate that RDEX-ABCD effectively addresses these violations and can be used to accurately measure SSRT along with an array of additional mechanistic parameters of interest (e.g., attention to the stop signal, cognitive efficiency), advancing investigators' ability to draw valid and nuanced inferences from ABCD data. AVAILABILITY OF DATA AND MATERIALS: Data from the ABCD Study are available through the NIH Data Archive (NDA): nda.nih.gov/abcd. Code for all analyses featured in this study is openly available on the Open Science Framework (OSF): osf.io/2h8a7/.

General psychopathology factor (p-factor) prediction using resting-state functional connectivity and a scanner-generalization neural network

The general psychopathology factor (p-factor) represents shared variance across mental disorders based on psychopathologic symptoms. The Adolescent Brain Cognitive Development (ABCD) Study offers an unprecedented opportunity to investigate functional networks (FNs) from functional magnetic resonance imaging (fMRI) associated with the psychopathology of an adolescent cohort (n > 10,000). However, the heterogeneities associated with the use of multiple sites and multiple scanners in the ABCD Study need to be overcome to improve the prediction of the p-factor using fMRI. We proposed a scanner-generalization neural network (SGNN) to predict the individual p-factor by systematically reducing the scanner effect for resting-state functional connectivity (RSFC). We included 6905 adolescents from 18 sites whose fMRI data were collected using either Siemens or GE scanners. The p-factor was estimated based on the Child Behavior Checklist (CBCL) scores available in the ABCD study using exploratory factor analysis. We evaluated the Pearson's correlation coefficients (CCs) for p-factor prediction via leave-one/two-site-out cross-validation (LOSOCV/LTSOCV) and identified important FNs from the weight features (WFs) of the SGNN. The CCs were higher for the SGNN than for alternative models when using both LOSOCV (0.1631 ± 0.0673 for the SGNN vs. 0.1497 ± 0.0710 for kernel ridge regression [KRR]; p < 0.05 from a two-tailed paired t-test) and LTSOCV (0.1469 ± 0.0381 for the SGNN vs. 0.1394 ± 0.0359 for KRR; p = 0.01). It was found that (a) the default-mode and dorsal attention FNs were important for p-factor prediction, and (b) the intra-visual FN was important for scanner generalization. We demonstrated the efficacy of our novel SGNN model for p-factor prediction while simultaneously eliminating scanner-related confounding effects for RSFC.

Challenges for machine learning in clinical translation of big data imaging studies

Combining deep learning image analysis methods and large-scale imaging datasets offers many opportunities to neuroscience imaging and epidemiology. However, despite these opportunities and the success of deep learning when applied to a range of neuroimaging tasks and domains, significant barriers continue to limit the impact of large-scale datasets and analysis tools. Here, we examine the main challenges and the approaches that have been explored to overcome them. We focus on issues relating to data availability, interpretability, evaluation, and logistical challenges and discuss the problems that still need to be tackled to enable the success of "big data" deep learning approaches beyond research.

The Age of Reason: Functional Brain Network Development during Childhood

Human childhood is characterized by dramatic changes in the mind and brain. However, little is known about the large-scale intrinsic cortical network changes that occur during childhood because of methodological challenges in scanning young children. Here, we overcome this barrier by using sophisticated acquisition and analysis tools to investigate functional network development in children between the ages of 4 and 10 years ([Formula: see text]; 50 female, 42 male). At multiple spatial scales, age is positively associated with brain network segregation. At the system level, age was associated with segregation of systems involved in attention from those involved in abstract cognition, and with integration among attentional and perceptual systems. Associations between age and functional connectivity are most pronounced in visual and medial prefrontal cortex, the two ends of a gradient from perceptual, externally oriented cortex to abstract, internally oriented cortex. These findings suggest that both ends of the sensory-association gradient may develop early, in contrast to the classical theories that cortical maturation proceeds from back to front, with sensory areas developing first and association areas developing last. More mature patterns of brain network architecture, controlling for age, were associated with better visuospatial reasoning abilities. Our results suggest that as cortical architecture becomes more specialized, children become more able to reason about the world and their place in it.SIGNIFICANCE STATEMENT Anthropologists have called the transition from early to middle childhood the "age of reason", when children across cultures become more independent. We employ cutting-edge neuroimaging acquisition and analysis approaches to investigate associations between age and functional brain architecture in childhood. Age was positively associated with segregation between cortical systems that process the external world and those that process abstract phenomena like the past, future, and minds of others. Surprisingly, we observed pronounced development at both ends of the sensory-association gradient, challenging the theory that sensory areas develop first and association areas develop last. Our results open new directions for research into how brains reorganize to support rapid gains in cognitive and socioemotional skills as children reach the age of reason.

Bayesian multisource data integration for explainable brain-behavior analysis

Different data sources can provide complementary information. Moving from a simple approach based on using one data source at a time to a systems approach that integrates multiple data sources provides an opportunity to understand complex brain disorders or cognitive processes. We propose a data fusion method, called Bayesian Multisource Data Integration, to model the interactions among data sources and behavioral variables. The proposed method generates representations from data sources and uses Bayesian network modeling to associate representations with behavioral variables. The generated Bayesian network is transparent and easy to understand. Bayesian inference is used to understand how the perturbation of representation is related to behavioral changes. The proposed method was assessed on the simulated data and data from the Adolescent Brain Cognitive Development study. For the Adolescent Brain Cognitive Development study, we found diffusion tensor imaging and resting-state functional magnetic resonance imaging were synergistic in understanding the fluid intelligence composite and the total score composite in healthy youth (9-11 years of age).

Use of connectotyping on task functional MRI data reveals dynamic network level cross talking during task performance

Task-based functional MRI (fMRI) has greatly improved understanding of brain functioning, enabling the identification of brain areas associated with specific cognitive operations. Traditional analyses are limited to associating activation patterns in particular regions with specific cognitive operation, largely ignoring regional cross-talk or dynamic connectivity, which we propose is crucial for characterization of brain function in the context of task fMRI. We use connectotyping, which efficiently models functional brain connectivity to reveal the progression of temporal brain connectivity patterns in task fMRI. Connectotyping was employed on data from twenty-four participants (12 male, mean age 24.8 years, 2.57 std. dev) who performed a widely spaced event-related fMRI word vs. pseudoword decision task, where stimuli were presented every 20 s. After filtering for movement, we ended up with 15 participants that completed each trial and had enough usable data for our analyses. Connectivity matrices were calculated per participant across time for each stimuli type. A Repeated Measures ANOVA applied on the connectotypes was used to characterize differences across time for words and pseudowords. Our group level analyses found significantly different dynamic connectivity patterns during word vs. pseudoword processing between the Fronto-Parietal and Cingulo-Parietal Systems, areas involved in cognitive task control, memory retrieval, and semantic processing. Our findings support the presence of dynamic changes in functional connectivity during task execution and that such changes can be characterized using connectotyping but not with traditional Pearson’s correlations.

Person-specific and precision neuroimaging: Current methods and future directions

Most neuroimaging studies of brain function analyze data in normalized space to identify regions of common activation across participants. These studies treat interindividual differences in brain organization as noise, but this approach can obscure important information about the brain's functional architecture. Recently, a number of studies have adopted a person-specific approach that aims to characterize these individual differences and explore their reliability and implications for behavior. A subset of these studies has taken a precision imaging approach that collects multiple hours of data from each participant to map brain function on a finer scale. In this review, we provide a broad overview of how person-specific and precision imaging techniques have used resting-state measures to examine individual differences in the brain's organization and their impact on behavior, followed by how task-based activity continues to add detail to these discoveries. We argue that person-specific and precision approaches demonstrate substantial promise in uncovering new details of the brain's functional organization and its relationship to behavior in many areas of cognitive neuroscience. We also discuss some current limitations in this new field and some new directions it may take.

Accounting for motion in resting-state fMRI: What part of the spectrum are we characterizing in autism spectrum disorder?

The exclusion of high-motion participants can reduce the impact of motion in functional Magnetic Resonance Imaging (fMRI) data. However, the exclusion of high-motion participants may change the distribution of clinically relevant variables in the study sample, and the resulting sample may not be representative of the population. Our goals are two-fold: 1) to document the biases introduced by common motion exclusion practices in functional connectivity research and 2) to introduce a framework to address these biases by treating excluded scans as a missing data problem. We use a study of autism spectrum disorder in children without an intellectual disability to illustrate the problem and the potential solution. We aggregated data from 545 children (8-13 years old) who participated in resting-state fMRI studies at Kennedy Krieger Institute (173 autistic and 372 typically developing) between 2007 and 2020. We found that autistic children were more likely to be excluded than typically developing children, with 28.5% and 16.1% of autistic and typically developing children excluded, respectively, using a lenient criterion and 81.0% and 60.1% with a stricter criterion. The resulting sample of autistic children with usable data tended to be older, have milder social deficits, better motor control, and higher intellectual ability than the original sample. These measures were also related to functional connectivity strength among children with usable data. This suggests that the generalizability of previous studies reporting naïve analyses (i.e., based only on participants with usable data) may be limited by the selection of older children with less severe clinical profiles because these children are better able to remain still during an rs-fMRI scan. We adapt doubly robust targeted minimum loss based estimation with an ensemble of machine learning algorithms to address these data losses and the resulting biases. The proposed approach selects more edges that differ in functional connectivity between autistic and typically developing children than the naïve approach, supporting this as a promising solution to improve the study of heterogeneous populations in which motion is common.

Predicting the future of neuroimaging predictive models in mental health

Predictive modeling using neuroimaging data has the potential to improve our understanding of the neurobiology underlying psychiatric disorders and putatively information interventions. Accordingly, there is a plethora of literature reviewing published studies, the mathematics underlying machine learning, and the best practices for using these approaches. As our knowledge of mental health and machine learning continue to evolve, we instead aim to look forward and "predict" topics that we believe will be important in current and future studies. Some of the most discussed topics in machine learning, such as bias and fairness, the handling of dirty data, and interpretable models, may be less familiar to the broader community using neuroimaging-based predictive modeling in psychiatry. In a similar vein, transdiagnostic research and targeting brain-based features for psychiatric intervention are modern topics in psychiatry that predictive models are well-suited to tackle. In this work, we target an audience who is a researcher familiar with the fundamental procedures of machine learning and who wishes to increase their knowledge of ongoing topics in the field. We aim to accelerate the utility and applications of neuroimaging-based predictive models for psychiatric research by highlighting and considering these topics. Furthermore, though not a focus, these ideas generalize to neuroimaging-based predictive modeling in other clinical neurosciences and predictive modeling with different data types (e.g., digital health data).

Adolescent development of multiscale structural wiring and functional interactions in the human connectome

Adolescence is a time of profound changes in the physical wiring and function of the brain. Here, we analyzed structural and functional brain network development in an accelerated longitudinal cohort spanning 14 to 25 y (n = 199). Core to our work was an advanced in vivo model of cortical wiring incorporating MRI features of corticocortical proximity, microstructural similarity, and white matter tractography. Longitudinal analyses assessing age-related changes in cortical wiring identified a continued differentiation of multiple corticocortical structural networks in youth. We then assessed structure-function coupling using resting-state functional MRI measures in the same participants both via cross-sectional analysis at baseline and by studying longitudinal change between baseline and follow-up scans. At baseline, regions with more similar structural wiring were more likely to be functionally coupled. Moreover, correlating longitudinal structural wiring changes with longitudinal functional connectivity reconfigurations, we found that increased structural differentiation, particularly between sensory/unimodal and default mode networks, was reflected by reduced functional interactions. These findings provide insights into adolescent development of human brain structure and function, illustrating how structural wiring interacts with the maturation of macroscale functional hierarchies.

Neurobiological, familial and genetic risk factors for dimensional psychopathology in the Adolescent Brain Cognitive Development study

BACKGROUND

Adolescence is a key period for brain development and the emergence of psychopathology. The Adolescent Brain Cognitive Development (ABCD) study was created to study the biopsychosocial factors underlying healthy and pathological brain development during this period, and comprises the world's largest youth cohort with neuroimaging, family history and genetic data.

METHODS

We examined 9856 unrelated 9-to-10-year-old participants in the ABCD study drawn from 21 sites across the United States, of which 7662 had multimodal magnetic resonance imaging scans passing quality control, and 4447 were non-Hispanic white and used for polygenic risk score analyses. Using data available at baseline, we associated eight 'syndrome scale scores' from the Child Behavior Checklist-summarizing anxious/depressed symptoms, withdrawn/depressed symptoms, somatic complaints, social problems, thought problems, attention problems, rule-breaking behavior, and aggressive behavior-with resting-state functional and structural brain magnetic resonance imaging measures; eight indicators of family history of psychopathology; and polygenic risk scores for major depression, bipolar disorder, schizophrenia, attention deficit hyperactivity disorder (ADHD) and anorexia nervosa. As a sensitivity analysis, we excluded participants with clinically significant (>97th percentile) or borderline (93rd-97th percentile) scores for each dimension.

RESULTS

Most Child Behavior Checklist dimensions were associated with reduced functional connectivity within one or more of four large-scale brain networks-default mode, cingulo-parietal, dorsal attention, and retrosplenial-temporal. Several dimensions were also associated with increased functional connectivity between the default mode, dorsal attention, ventral attention and cingulo-opercular networks. Conversely, almost no global or regional brain structural measures were associated with any of the dimensions. Every family history indicator was associated with every dimension. Major depression polygenic risk was associated with six of the eight dimensions, whereas ADHD polygenic risk was exclusively associated with attention problems and externalizing behavior (rule-breaking and aggressive behavior). Bipolar disorder, schizophrenia and anorexia nervosa polygenic risk were not associated with any of the dimensions. Many associations remained statistically significant even after excluding participants with clinically significant or borderline psychopathology, suggesting that the same risk factors that contribute to clinically significant psychopathology also contribute to continuous variation within the clinically normal range.

CONCLUSIONS

This study codifies neurobiological, familial and genetic risk factors for dimensional psychopathology across a population-scale cohort of community-dwelling preadolescents. Future efforts are needed to understand how these multiple modalities of risk intersect to influence trajectories of psychopathology into late adolescence and adulthood.

Shared and unique brain network features predict cognitive, personality, and mental health scores in the ABCD study

How individual differences in brain network organization track behavioral variability is a fundamental question in systems neuroscience. Recent work suggests that resting-state and task-state functional connectivity can predict specific traits at the individual level. However, most studies focus on single behavioral traits, thus not capturing broader relationships across behaviors. In a large sample of 1858 typically developing children from the Adolescent Brain Cognitive Development (ABCD) study, we show that predictive network features are distinct across the domains of cognitive performance, personality scores and mental health assessments. On the other hand, traits within each behavioral domain are predicted by similar network features. Predictive network features and models generalize to other behavioral measures within the same behavioral domain. Although tasks are known to modulate the functional connectome, predictive network features are similar between resting and task states. Overall, our findings reveal shared brain network features that account for individual variation within broad domains of behavior in childhood.

Neurobiological antecedents of multisite pain in children

ABSTRACT

Altered brain structure and function is evident in adults with multisite chronic pain. Although many such adults trace their pain back to childhood, it has been difficult to disentangle whether central nervous system alterations precede or are consequences of chronic pain. If the former is true, aberrant brain activity may identify children vulnerable to developing chronic pain later in life. We examined structural and functional brain magnetic resonance imaging metrics in a subset of children from the first 2 assessments of the Adolescent Brain and Cognitive Development Study. Children (aged 9-10) who were pain free at baseline and then developed multisite pain 1 year later (n = 115) were matched to control children who were pain free at both timepoints (n = 230). We analyzed brain structure (cortical thickness and gray matter volume) and function (spontaneous neural activity and functional connectivity). Results were deemed significant at the cluster level P < 0.05 false discovery rate corrected for multiple comparisons. At baseline, children who subsequently developed multisite pain had increased neural activity in superior parietal /primary somatosensory and motor cortices and decreased activity in the medial prefrontal cortex. They also exhibited stronger functional connectivity between the salience network, somatosensory, and default mode network regions. No significant differences in the brain structure were observed. Increased neural activity and functional connectivity between brain regions, consistent to that seen in adults with chronic pain, exist in children before developing multisite pain. These findings may represent a neural vulnerability to developing future chronic pain.

Privacy-preserving harmonization via distributed ComBat

Challenges in clinical data sharing and the need to protect data privacy have led to the development and popularization of methods that do not require directly transferring patient data. In neuroimaging, integration of data across multiple institutions also introduces unwanted biases driven by scanner differences. These scanner effects have been shown by several research groups to severely affect downstream analyses. To facilitate the need of removing scanner effects in a distributed data setting, we introduce distributed ComBat, an adaptation of a popular harmonization method for multivariate data that borrows information across features. We present our fast and simple distributed algorithm and show that it yields equivalent results using data from the Alzheimer's Disease Neuroimaging Initiative. Our method enables harmonization while ensuring maximal privacy protection, thus facilitating a broad range of downstream analyses in functional and structural imaging studies.

Reproducible brain-wide association studies require thousands of individuals

Magnetic resonance imaging (MRI) has transformed our understanding of the human brain through well-replicated mapping of abilities to specific structures (for example, lesion studies) and functions1-3 (for example, task functional MRI (fMRI)). Mental health research and care have yet to realize similar advances from MRI. A primary challenge has been replicating associations between inter-individual differences in brain structure or function and complex cognitive or mental health phenotypes (brain-wide association studies (BWAS)). Such BWAS have typically relied on sample sizes appropriate for classical brain mapping4 (the median neuroimaging study sample size is about 25), but potentially too small for capturing reproducible brain-behavioural phenotype associations5,6. Here we used three of the largest neuroimaging datasets currently available-with a total sample size of around 50,000 individuals-to quantify BWAS effect sizes and reproducibility as a function of sample size. BWAS associations were smaller than previously thought, resulting in statistically underpowered studies, inflated effect sizes and replication failures at typical sample sizes. As sample sizes grew into the thousands, replication rates began to improve and effect size inflation decreased. More robust BWAS effects were detected for functional MRI (versus structural), cognitive tests (versus mental health questionnaires) and multivariate methods (versus univariate). Smaller than expected brain-phenotype associations and variability across population subsamples can explain widespread BWAS replication failures. In contrast to non-BWAS approaches with larger effects (for example, lesions, interventions and within-person), BWAS reproducibility requires samples with thousands of individuals.

The positive-negative mode link between brain connectivity, demographics and behaviour: a pre-registered replication of Smith et al. (2015)

In mental health research, it has proven difficult to find measures of brain function that provide reliable indicators of mental health and well-being, including susceptibility to mental health disorders. Recently, a family of data-driven analyses have provided such reliable measures when applied to large, population-level datasets. In the current pre-registered replication study, we show that the canonical correlation analysis (CCA) methods previously developed using resting-state magnetic resonance imaging functional connectivity and subject measures (SMs) of cognition and behaviour from healthy adults are also effective in measuring well-being (a 'positive-negative axis') in an independent developmental dataset. Our replication was successful in two out of three of our pre-registered criteria, such that a primary CCA mode's weights displayed a significant positive relationship and explained a significant amount of variance in both functional connectivity and SMs. The only criterion that was not successful was that compared to other modes the magnitude of variance explained by the primary CCA mode was smaller than predicted, a result that could indicate a developmental trajectory of a primary mode. This replication establishes a signature neurotypical relationship between connectivity and phenotype, opening new avenues of research in neuroscience with clear clinical applications.

Measurement matters: An individual differences examination of family socioeconomic factors, latent dimensions of children's experiences, and resting state functional brain connectivity in the ABCD sample

The variation in experiences between high and low-socioeconomic status contexts are posited to play a crucial role in shaping the developing brain and may explain differences in child outcomes. Yet, examinations of SES and brain development have largely been limited to distal proxies of these experiences (e.g., income comparisons). The current study sought to disentangle the effects of multiple socioeconomic indices and dimensions of more proximal experiences on resting-state functional connectivity (rsFC) in a sample of 7834 youth (aged 9-10 years) from the Adolescent Brain Cognitive Development (ABCD) study. We applied moderated nonlinear factor analysis (MNLFA) to establish measurement invariance among three latent environmental dimensions of experience (material/economic deprivation, caregiver social support, and psychosocial threat). Results revealed measurement biases as a function of child age, sex, racial group, family income, and parental education, which were statistically adjusted in the final MNLFA scores. Mixed-effects models demonstrated that socioeconomic indices and psychosocial threat differentially predicted variation in frontolimbic networks, and threat statistically moderated the association between income and connectivity between the dorsal and ventral attention networks. Findings illuminate the importance of reducing measurement biases to gain a more socioculturally-valid understanding of the complex and nuanced links between socioeconomic context, children's experiences, and neurodevelopment.

Scan Once, Analyse Many: Using Large Open-Access Neuroimaging Datasets to Understand the Brain

We are now in a time of readily available brain imaging data. Not only are researchers now sharing data more than ever before, but additionally large-scale data collecting initiatives are underway with the vision that many future researchers will use the data for secondary analyses. Here I provide an overview of available datasets and some example use cases. Example use cases include examining individual differences, more robust findings, reproducibility-both in public input data and availability as a replication sample, and methods development. I further discuss a variety of considerations associated with using existing data and the opportunities associated with large datasets. Suggestions for further readings on general neuroimaging and topic-specific discussions are also provided.

Functional brain network community structure in childhood: Unfinished territories and fuzzy boundaries

Adult cortex is organized into distributed functional communities. Yet, little is known about community architecture of children’s brains. Here, we uncovered the community structure of cortex in childhood using fMRI data from 670 children aged 9–11 years (48% female, replication sample n = 544, 56% female) from the Adolescent Brain and Cognitive Development study. We first applied a data-driven community detection approach to cluster cortical regions into communities, then employed a generative model-based approach called the weighted stochastic block model to further probe community interactions. Children showed similar community structure to adults, as defined by Yeo and colleagues in 2011, in early-developing sensory and motor communities, but differences emerged in transmodal areas. Children have more cortical territory in the limbic community, which is involved in emotion processing, than adults. Regions in association cortex interact more flexibly across communities, creating uncertainty for the model-based assignment algorithm, and perhaps reflecting cortical boundaries that are not yet solidified. Uncertainty was highest for cingulo-opercular areas involved in flexible deployment of cognitive control. Activation and deactivation patterns during a working memory task showed that both the data-driven approach and a set of adult communities statistically capture functional organization in middle childhood. Collectively, our findings suggest that community boundaries are not solidified by middle childhood.

Mitigating site effects in covariance for machine learning in neuroimaging data

To acquire larger samples for answering complex questions in neuroscience, researchers have increasingly turned to multi‐site neuroimaging studies. However, these studies are hindered by differences in images acquired across multiple sites. These effects have been shown to bias comparison between sites, mask biologically meaningful associations, and even introduce spurious associations. To address this, the field has focused on harmonizing data by removing site‐related effects in the mean and variance of measurements. Contemporaneously with the increase in popularity of multi‐center imaging, the use of machine learning (ML) in neuroimaging has also become commonplace. These approaches have been shown to provide improved sensitivity, specificity, and power due to their modeling the joint relationship across measurements in the brain. In this work, we demonstrate that methods for removing site effects in mean and variance may not be sufficient for ML. This stems from the fact that such methods fail to address how correlations between measurements can vary across sites. Data from the Alzheimer's Disease Neuroimaging Initiative is used to show that considerable differences in covariance exist across sites and that popular harmonization techniques do not address this issue. We then propose a novel harmonization method called Correcting Covariance Batch Effects (CovBat) that removes site effects in mean, variance, and covariance. We apply CovBat and show that within‐site correlation matrices are successfully harmonized. Furthermore, we find that ML methods are unable to distinguish scanner manufacturer after our proposed harmonization is applied, and that the CovBat‐harmonized data retain accurate prediction of disease group.

Associated functional network development and language abilities in children

During childhood, the brain is gradually converging to the efficient functional architecture observed in adults. How the brain's functional architecture evolves with age, particularly in young children, is however, not well understood. We examined the functional connectivity of the core language regions, in association with cortical growth and language abilities, in 175 young children in the age range of 4 to 9 years. We analyzed the brain's developmental changes using resting-state functional and T1-weighted structural magnetic resonance imaging data. The results showed increased functional connectivity strength with age between the pars triangularis of the left inferior frontal gyrus and left temporoparietal regions (cohen's d = 0.54, CI: 0.24 - 0.84), associated with children's language abilities. Stronger functional connectivity between bilateral prefrontal and temporoparietal regions was associated with better language abilities regardless of age. In addition, the stronger functional connectivity between the left inferior frontal and temporoparietal regions was associated with larger surface area and thinner cortical thickness in these regions, which in turn was associated with superior language abilities. Thus, using functional and structural brain indices, coupled with behavioral measures, we elucidate the association of functional language network development, language ability, and cortical growth, thereby adding to our understanding of the neural basis of language acquisition in young children.

Brain-wide functional connectivity patterns support general cognitive ability and mediate effects of socioeconomic status in youth

General cognitive ability (GCA) is an individual difference dimension linked to important academic, occupational, and health-related outcomes and its development is strongly linked to differences in socioeconomic status (SES). Complex abilities of the human brain are realized through interconnections among distributed brain regions, but brain-wide connectivity patterns associated with GCA in youth, and the influence of SES on these connectivity patterns, are poorly understood. The present study examined functional connectomes from 5937 9- and 10-year-olds in the Adolescent Brain Cognitive Development (ABCD) multi-site study. Using multivariate predictive modeling methods, we identified whole-brain functional connectivity patterns linked to GCA. In leave-one-site-out cross-validation, we found these connectivity patterns exhibited strong and statistically reliable generalization at 19 out of 19 held-out sites accounting for 18.0% of the variance in GCA scores (cross-validated partial η²). GCA-related connections were remarkably dispersed across brain networks: across 120 sets of connections linking pairs of large-scale networks, significantly elevated GCA-related connectivity was found in 110 of them, and differences in levels of GCA-related connectivity across brain networks were notably modest. Consistent with prior work, socioeconomic status was a strong predictor of GCA in this sample, and we found that distributed GCA-related brain connectivity patterns significantly statistically mediated this relationship (mean proportion mediated: 15.6%, p < 2 × 10^-16). These results demonstrate that socioeconomic status and GCA are related to broad and diffuse differences in functional connectivity architecture during early adolescence, potentially suggesting a mechanism through which socioeconomic status influences cognitive development.

Linking irritability and functional brain networks: A transdiagnostic case for expanding consideration of development and environment in RDoC

The National Institute of Mental Health Research Domain Criteria (RDoC) framework promotes the dimensional and transdiagnostic operationalization of psychopathology, but consideration of the neurodevelopmental foundations of mental health problems requires deeper examination. Irritability, the dispositional tendency to angry emotion that has both mood and behavioral elements, is dimensional, transdiagnostic, and observable early in life-a promising target for the identification of early neural indicators or risk factors for psychopathology. Here, we examine functional brain networks linked to irritability from preschool to adulthood and discuss how development and early experience may influence these neural substrates. Functional connectivity measured with fMRI varies according to irritability and indicates the atypical coordination of several functional networks involved in emotion generation, emotion perception, attention, internalization, and cognitive control. We lay out an agenda to improve our understanding and detection of atypical brain:behavior patterns through advances in the characterization of both functional networks and irritability as well as the consideration and operationalization of developmental and early life environmental influences on this pathway.

What have we really learned from functional connectivity in clinical populations?

Functional connectivity (FC), or the statistical interdependence of blood-oxygen dependent level (BOLD) signals between brain regions using fMRI, has emerged as a widely used tool for probing functional abnormalities in clinical populations due to the promise of the approach across conceptual, technical, and practical levels. With an already vast and steadily accumulating neuroimaging literature on neurodevelopmental, psychiatric, and neurological diseases and disorders in which FC is a primary measure, we aim here to provide a high-level synthesis of major concepts that have arisen from FC findings in a manner that cuts across different clinical conditions and sheds light on overarching principles. We highlight that FC has allowed us to discover the ubiquity of intrinsic functional networks across virtually all brains and clarify typical patterns of neurodevelopment over the lifespan. This understanding of typical FC maturation with age has provided important benchmarks against which to evaluate divergent maturation in early life and degeneration in late life. This in turn has led to the important insight that many clinical conditions are associated with complex, distributed, network-level changes in the brain, as opposed to solely focal abnormalities. We further emphasize the important role that FC studies have played in supporting a dimensional approach to studying transdiagnostic clinical symptoms and in enhancing the multimodal characterization and prediction of the trajectory of symptom progression across conditions. We highlight the unprecedented opportunity offered by FC to probe functional abnormalities in clinical conditions where brain function could not be easily studied otherwise, such as in disorders of consciousness. Lastly, we suggest high priority areas for future research and acknowledge critical barriers associated with the use of FC methods, particularly those related to artifact removal, data denoising and feasibility in clinical contexts.

Precision Functional Mapping of the Subcortex and Cerebellum

Human functional brain networks can be reliably characterized within individuals using precision functional mapping. This approach entails the collection of large quantities of functional magnetic resonance imaging (fMRI) data from each individual subject. Studies employing precision functional mapping in the cerebral cortex have found that individuals manifest unique representations of functional brain networks around a central tendency described by previous group average approaches. We recently extended precision functional mapping to the subcortex and cerebellum, which has revealed several novel organizational principles within these structures. Here, we detail these principles and provide insights into how precision functional mapping of subcortical structures and the cerebellum may become clinically translatable.