Brain parcellation selection: An overlooked decision point with meaningful effects on individual differences in resting-state functional connectivity

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

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

The future of psychophysiology, then and now

Since its founding in 1973, Biological Psychology has showcased and provided invaluable support to psychophysiology, a field that has grown and changed enormously. This article discusses some constancies that have remained fundamental to the journal and to the field as well as some important trends. Some aspects of our science have not received due consideration, affecting not only the generalizability of our findings but the way we develop and evaluate our research questions and the potential of our field to contribute to the common good. The article offers a number of predictions and recommendations for the next period of growth of psychophysiology.

Investigating Associations Between Maternal Behavior and the Development of Functional Connectivity During the Transition From Late Childhood to Early Adolescence

BACKGROUND

Parenting behavior is thought to affect child brain development, with implications for mental health. However, longitudinal studies that use whole-brain approaches are lacking. In this study, we investigated associations between parenting behavior, age-related changes in whole-brain functional connectivity, and psychopathology symptoms in children and adolescents.

METHODS

Two hundred forty (126 female) children underwent resting-state functional magnetic resonance imaging at up to two time points, providing a total of 398 scans covering the age range 8 to 13 years. Parenting behavior was self-reported at baseline. Parenting factors (positive parenting, inattentive parenting, and harsh and inconsistent discipline) were identified based on a factor analysis of self-report parenting questionnaires. Longitudinal measures of child internalizing and externalizing symptoms were collected. Network-based R-statistics was used to identify associations between parenting and age-related changes in functional connectivity.

RESULTS

Higher maternal inattentive behavior was associated with lower decreases in connectivity over time, particularly between regions of the ventral attention and default mode networks and frontoparietal and default mode networks. However, this association was not significant after strict correction for multiple comparisons.

CONCLUSIONS

While results should be considered preliminary, they suggest that inattentive parenting may be associated with a reduction in the normative pattern of increased network specialization that occurs with age. This may reflect a delayed development of functional connectivity.

The significance of structural rich club hubs for the processing of hierarchical stimuli

The brain's structural network follows a hierarchy that is described as rich club (RC) organization, with RC hubs forming the well-interconnected top of this hierarchy. In this study, we tested whether RC hubs are involved in the processing of hierarchically higher structures in stimulus sequences. Moreover, we explored the role of previously suggested cortical gradients along anterior-posterior and medial-lateral axes throughout the frontal cortex. To this end, we conducted a functional magnetic resonance imaging (fMRI) experiment and presented participants with blocks of digit sequences that were structured on different hierarchically nested levels. We additionally collected diffusion weighted imaging data of the same subjects to identify RC hubs. This classification then served as the basis for a region of interest analysis of the fMRI data. Moreover, we determined structural network centrality measures in areas that were found as activation clusters in the whole-brain fMRI analysis. Our findings support the previously found anterior and medial shift for processing hierarchically higher structures of stimuli. Additionally, we found that the processing of hierarchically higher structures of the stimulus structure engages RC hubs more than for lower levels. Areas involved in the functional processing of hierarchically higher structures were also more likely to be part of the structural RC and were furthermore more central to the structural network. In summary, our results highlight the potential role of the structural RC organization in shaping the cortical processing hierarchy.

A multi-sample evaluation of the measurement structure and function of the modified monetary incentive delay task in adolescents

Interpreting the neural response elicited during task functional magnetic resonance imaging (fMRI) remains a challenge in neurodevelopmental research. The monetary incentive delay (MID) task is an fMRI reward processing task that is extensively used in the literature. However, modern psychometric tools have not been used to evaluate measurement properties of the MID task fMRI data. The current study uses data for a similar task design across three adolescent samples (N = 346 [Agemean 12.0; 44 % Female]; N = 97 [19.3; 58 %]; N = 112 [20.2; 38 %]) to evaluate multiple measurement properties of fMRI responses on the MID task. Confirmatory factor analysis (CFA) is used to evaluate an a priori theoretical model for the task and its measurement invariance across three samples. Exploratory factor analysis (EFA) is used to identify the data-driven measurement structure across the samples. CFA results suggest that the a priori model is a poor representation of these MID task fMRI data. Across the samples, the data-driven EFA models consistently identify a six-to-seven factor structure with run and bilateral brain region factors. This factor structure is moderately-to-highly congruent across the samples. Altogether, these findings demonstrate a need to evaluate theoretical frameworks for popular fMRI task designs to improve our understanding and interpretation of brain-behavior associations.

Graph Learning for Cortical Parcellation from Tensor Decompositions of Resting-State fMRI

Cortical parcellation has long been a cornerstone in the field of neuroscience, enabling the cerebral cortex to be partitioned into distinct, non-overlapping regions that facilitate the interpretation and comparison of complex neuroscientific data. In recent years, these parcellations have frequently been based on the use of resting-state fMRI (rsfMRI) data. In parallel, methods such as independent components analysis have long been used to identify large-scale functional networks with significant spatial overlap between networks. Despite the fact that both forms of decomposition make use of the same spontaneous brain activity measured with rsfMRI, a gap persists in establishing a clear relationship between disjoint cortical parcellations and brain-wide networks. To address this, we introduce a novel parcellation framework that integrates NASCAR, a three-dimensional tensor decomposition method that identifies a series of functional brain networks, with state-of-the-art graph representation learning to produce cortical parcellations that represent near-homogeneous functional regions that are consistent with these brain networks. Further, through the use of the tensor decomposition, we avoid the limitations of traditional approaches that assume statistical independence or orthogonality in defining the underlying networks. Our findings demonstrate that these parcellations are comparable or superior to established atlases in terms of homogeneity of the functional connectivity across parcels, task contrast alignment, and architectonic map alignment. Our methodological pipeline is highly automated, allowing for rapid adaptation to new datasets and the generation of custom parcellations in just minutes, a significant advancement over methods that require extensive manual input. We describe this integrated approach, which we refer to as Untamed, as a tool for use in the fields of cognitive and clinical neuroscientific research. Parcellations created from the Human Connectome Project dataset using Untamed, along with the code to generate atlases with custom parcel numbers, are publicly available at https://untamed-atlas.github.io.

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.

Should one go for individual- or group-level brain parcellations? A deep-phenotyping benchmark

The analysis and understanding of brain characteristics often require considering region-level information rather than voxel-sampled data. Subject-specific parcellations have been put forward in recent years, as they can adapt to individual brain organization and thus offer more accurate individual summaries than standard atlases. However, the price to pay for adaptability is the lack of group-level consistency of the data representation. Here, we investigate whether the good representations brought by individualized models are merely an effect of circular analysis, in which individual brain features are better represented by subject-specific summaries, or whether this carries over to new individuals, i.e., whether one can actually adapt an existing parcellation to new individuals and still obtain good summaries in these individuals. For this, we adapt a dictionary-learning method to produce brain parcellations. We use it on a deep-phenotyping dataset to assess quantitatively the patterns of activity obtained under naturalistic and controlled-task-based settings. We show that the benefits of individual parcellations are substantial, but that they vary a lot across brain systems.

Homological landscape of human brain functional sub-circuits

Human whole-brain functional connectivity networks have been shown to exhibit both local/quasilocal (e.g., set of functional sub-circuits induced by node or edge attributes) and non-local (e.g., higher-order functional coordination patterns) properties. Nonetheless, the non-local properties of topological strata induced by local/quasilocal functional sub-circuits have yet to be addressed. To that end, we proposed a homological formalism that enables the quantification of higher-order characteristics of human brain functional sub-circuits. Our results indicated that each homological order uniquely unravels diverse, complementary properties of human brain functional sub-circuits. Noticeably, the H 1 homological distance between rest and motor task were observed at both whole-brain and sub-circuit consolidated level which suggested the self-similarity property of human brain functional connectivity unraveled by homological kernel. Furthermore, at the whole-brain level, the rest-task differentiation was found to be most prominent between rest and different tasks at different homological orders: i) Emotion task H 0 , ii) Motor task H 1 , and iii) Working memory task H 2 . At the functional sub-circuit level, the rest-task functional dichotomy of default mode network is found to be mostly prominent at the first and second homological scaffolds. Also at such scale, we found that the limbic network plays a significant role in homological reconfiguration across both task- and subject- domain which sheds light to subsequent Investigations on the complex neuro-physiological role of such network. From a wider perspective, our formalism can be applied, beyond brain connectomics, to study non-localized coordination patterns of localized structures stretching across complex network fibers.

Can hubs of the human connectome be identified consistently with diffusion MRI?

Recent years have seen a surge in the use of diffusion MRI to map connectomes in humans, paralleled by a similar increase in processing and analysis choices. Yet these different steps and their effects are rarely compared systematically. Here, in a healthy young adult population (n = 294), we characterized the impact of a range of analysis pipelines on one widely studied property of the human connectome: its degree distribution. We evaluated the effects of 40 pipelines (comparing common choices of parcellation, streamline seeding, tractography algorithm, and streamline propagation constraint) and 44 group-representative connectome reconstruction schemes on highly connected hub regions. We found that hub location is highly variable between pipelines. The choice of parcellation has a major influence on hub architecture, and hub connectivity is highly correlated with regional surface area in most of the assessed pipelines (ρ > 0.70 in 69% of the pipelines), particularly when using weighted networks. Overall, our results demonstrate the need for prudent decision-making when processing diffusion MRI data, and for carefully considering how different processing choices can influence connectome organization.

Limbic network co-localization predicts pharmacoresistance in dysplasia-related epilepsy

To evaluate the role of focal cortical dysplasia co-localization to cortical functional networks in the development of pharmacoresistance. One hundred thirty-six focal cortical dysplasia patients with 3.0 T or 1.5 T MRI were identified from clinical databases at Children's National Hospital. Clinico-radio-pathologic factors and network co-localization were determined. Using binomial logistic regression, limbic network co-localization (odds ratio 4.164 95% confidence interval 1.02-17.08, p = 0.048), and focal to bilateral tonic-clonic seizures (4.82, 1.30-18.03, p = 0.019) predicted pharmacoresistance. These findings provide clinicians with markers to identify patients with focal cortical dysplasia-related epilepsy at high risk of developing pharmacoresistance and should facilitate earlier epilepsy surgical evaluation.

Optimizing network neuroscience computation of individual differences in human spontaneous brain activity for test-retest reliability

A rapidly emerging application of network neuroscience in neuroimaging studies has provided useful tools to understand individual differences in intrinsic brain function by mapping spontaneous brain activity, namely intrinsic functional network neuroscience (ifNN). However, the variability of methodologies applied across the ifNN studies-with respect to node definition, edge construction, and graph measurements-makes it difficult to directly compare findings and also challenging for end users to select the optimal strategies for mapping individual differences in brain networks. Here, we aim to provide a benchmark for best ifNN practices by systematically comparing the measurement reliability of individual differences under different ifNN analytical strategies using the test-retest design of the Human Connectome Project. The results uncovered four essential principles to guide ifNN studies: (1) use a whole brain parcellation to define network nodes, including subcortical and cerebellar regions; (2) construct functional networks using spontaneous brain activity in multiple slow bands; and (3) optimize topological economy of networks at individual level; and (4) characterize information flow with specific metrics of integration and segregation. We built an interactive online resource of reliability assessments for future ifNN (https://ibraindata.com/research/ifNN).

Functional connectomics in depression: insights into therapies

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

Enhancing precision in human neuroscience

Human neuroscience has always been pushing the boundary of what is measurable. During the last decade, concerns about statistical power and replicability - in science in general, but also specifically in human neuroscience - have fueled an extensive debate. One important insight from this discourse is the need for larger samples, which naturally increases statistical power. An alternative is to increase the precision of measurements, which is the focus of this review. This option is often overlooked, even though statistical power benefits from increasing precision as much as from increasing sample size. Nonetheless, precision has always been at the heart of good scientific practice in human neuroscience, with researchers relying on lab traditions or rules of thumb to ensure sufficient precision for their studies. In this review, we encourage a more systematic approach to precision. We start by introducing measurement precision and its importance for well-powered studies in human neuroscience. Then, determinants for precision in a range of neuroscientific methods (MRI, M/EEG, EDA, Eye-Tracking, and Endocrinology) are elaborated. We end by discussing how a more systematic evaluation of precision and the application of respective insights can lead to an increase in reproducibility in human neuroscience.

Interpreting and validating complexity and causality in lesion-symptom prognoses

This paper considers the steps needed to generate pragmatic and interpretable lesion-symptom mappings that can be used for clinically reliable prognoses. The novel contributions are 3-fold. We first define and inter-relate five neurobiological and five methodological constraints that need to be accounted for when interpreting lesion-symptom associations and generating synthetic lesion data. The first implication is that, because of these constraints, lesion-symptom mapping needs to focus on probabilistic relationships between Lesion and Symptom, with Lesion as a multivariate spatial pattern, Symptom as a time-dependent behavioural profile and evidence that Lesion raises the probability of Symptom. The second implication is that in order to assess the strength of probabilistic causality, we need to distinguish between causal lesion sites, incidental lesion sites, spared but dysfunctional sites and intact sites, all of which might affect the accuracy of the predictions and prognoses generated. We then formulate lesion-symptom mappings in logical notations, including combinatorial rules, that are then used to evaluate and better understand complex brain-behaviour relationships. The logical and theoretical framework presented applies to any type of neurological disorder but is primarily discussed in relationship to stroke damage. Accommodating the identified constraints, we discuss how the 1965 Bradford Hill criteria for inferring probabilistic causality, post hoc, from observed correlations in epidemiology-can be applied to lesion-symptom mapping in stroke survivors. Finally, we propose that rather than rely on post hoc evaluation of how well the causality criteria have been met, the neurobiological and methodological constraints should be addressed, a priori, by changing the experimental design of lesion-symptom mappings and setting up an open platform to share and validate the discovery of reliable and accurate lesion rules that are clinically useful.

Multimodal neuroimaging in post-COVID syndrome and correlation with cognition

Brain changes have been reported in the first weeks after SARS-CoV-2 infection. However, limited literature exists about brain alterations in post-COVID syndrome, a condition increasingly associated with cognitive impairment. The present study aimed to evaluate brain functional and structural alterations in patients with post-COVID syndrome, and assess whether these brain alterations were related to cognitive dysfunction. Eighty-six patients with post-COVID syndrome and 36 healthy controls were recruited and underwent neuroimaging acquisition and a comprehensive neuropsychological assessment. Cognitive and neuroimaging examinations were performed 11 months after the first symptoms of SARS-CoV-2. Whole-brain functional connectivity analysis was performed. Voxel-based morphometry was performed to evaluate grey matter volume, and diffusion tensor imaging was carried out to analyse white-matter alterations. Correlations between cognition and brain changes were conducted and Bonferroni corrected. Post-COVID syndrome patients presented with functional connectivity changes, characterized by hypoconnectivity between left and right parahippocampal areas, and between bilateral orbitofrontal and cerebellar areas compared to controls. These alterations were accompanied by reduced grey matter volume in cortical, limbic and cerebellar areas, and alterations in white matter axial and mean diffusivity. Grey matter volume loss showed significant associations with cognitive dysfunction. These cognitive and brain alterations were more pronounced in hospitalized patients compared to non-hospitalized patients. No associations with vaccination status were found. The present study shows persistent structural and functional brain abnormalities 11 months after the acute infection. These changes are associated with cognitive dysfunction and contribute to a better understanding of the pathophysiology of the post-COVID syndrome.

The elusive metric of lesion load

One of the widely used metrics in lesion-symptom mapping is lesion load that codes the amount of damage to a given brain region of interest. Lesion load aims to reduce the complex 3D lesion information into a feature that can reflect both site of damage, defined by the location of the region of interest, and size of damage within that region of interest. Basically, the process of estimation of lesion load converts a voxel-based lesion map into a region-based lesion map, with regions defined as atlas-based or data-driven spatial patterns. Here, after examining current definitions of lesion load, four methodological issues are discussed: (1) lesion load is agnostic to the location of damage within the region of interest, and it disregards damage outside the region of interest, (2) lesion load estimates are prone to errors introduced by the uncertainty in lesion delineation, spatial warping of the lesion/region, and binarization of the lesion/region, (3) lesion load calculation depends on brain parcellation selection, and (4) lesion load does not necessarily reflect a white matter disconnection. Overall, lesion load, when calculated in a robust way, can serve as a clinically-useful feature for explaining and predicting post-stroke outcome and recovery.

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.

Right amygdala-right precuneus connectivity is associated with childhood trauma in major depression patients and healthy controls

The present study investigated the effect of childhood trauma (CT) on amygdala and hippocampus functional connectivity (FC) and the association with clinical presentations of major depressive disorder (MDD). Participants included 73 MDD patients (42 with moderate-to-severe CT and 31 with no or low CT) and 64 healthy controls (HC; 30 with moderate-to-severe CT and 34 with no or low CT). Seed-based whole-brain resting-state FC analyses were performed with seeds located in amygdala and hippocampus. Individuals with moderate-to-severe CT, irrespective of MDD diagnosis, had decreased right amygdala-right precuneus connectivity compared to those with no or low CT. Right amygdala-right precuneus connectivity was significantly correlated with physical and social trait anhedonia in MDD. Mediation effects of this FC on relationship between CT (specifically neglect but not abuse) and trait anhedonia in MDD were significant. MDD patients demonstrated increased right amygdala-left middle frontal gyrus FC, decreased right amygdala-right medial superior frontal gyrus (mSFG) FC and decreased right hippocampus-bilateral mSFG FC relative to HC. Findings highlight the effect of CT on right amygdala-right precuneus FC irrespective of MDD diagnosis. FC of right amygdala-right precuneus may be involved in the mechanism linking CT and depression through its association with trait anhedonia.

Cingulate-Prefrontal Connectivity During Dynamic Cognitive Control Mediates Association Between p Factor and Adaptive Functioning in a Transdiagnostic Pediatric Sample

BACKGROUND

Covariation among psychiatric symptoms is being actively pursued for transdiagnostic dimensions of psychopathology with predictive utility. A superordinate dimension, the p factor, reflects overall psychopathology burden and has support from genetic and neuroimaging correlates. However, the neurocognitive correlates that link an elevated p factor to maladaptive outcomes are unknown. We tested the mediating potential of dynamic adjustments in cognitive control rooted in functional connections anchored by the dorsal anterior cingulate cortex (dACC) in a transdiagnostic pediatric sample.

METHODS

A multiple mediation model tested the association between the p factor (derived by principal component analysis of Child Behavior Checklist syndrome scales) and outcome measured with the Vineland Adaptive Behavior Scale-II in 89 children ages 8 to 13 years (23 female) with a variety of primary neurodevelopmental diagnoses who underwent functional magnetic resonance imaging during a socioaffective Stroop-like task with eye gaze as distractor. Mediators included functional connectivity of frontoparietal- and salience network-affiliated dACC seeds during conflict adaptation.

RESULTS

Higher p factor scores were related to worse adaptive functioning. This effect was partially mediated by conflict adaptation-dependent functional connectivity between the frontoparietal network-affiliated dACC seed and the right dorsolateral prefrontal cortex. Post hoc follow-up indicated that the p factor was related to all Vineland Adaptive Behaviors Scale-II domains; the association was strongest for socialization followed by daily living skills and then communication. Mediation results remained significant for socialization only.

CONCLUSIONS

Higher psychopathology burden was associated with worse adaptive functioning in early adolescence. This association was mediated by weaker dACC-dorsolateral prefrontal cortex functional connectivity underlying modulation of cognitive control in response to contextual contingencies. Our results contribute to the identification of transdiagnostic and developmentally relevant neurocognitive endophenotypes of psychopathology.

Considering dynamic nature of the brain: the clinical importance of connectivity variability in machine learning classification and prediction

The brain connectivity of resting-state fMRI (rs-fMRI) represents an intrinsic state of brain architecture, and it has been used as a useful neural marker for detecting psychiatric conditions as well as for predicting psychosocial characteristics. However, most studies using brain connectivity have focused more on the strength of functional connectivity over time (static-FC) but less attention to temporal characteristics of connectivity changes (FC-variability). The primary goal of the current study was to investigate the effectiveness of using the FC-variability in classifying an individual's pathological characteristics from others and predicting psychosocial characteristics. In addition, the current study aimed to prove that benefits of the FC-variability are reliable across various analysis procedures. To this end, three open public large resting-state fMRI datasets including individuals with Autism Spectrum Disorder (ABIDE; N = 1249), Schizophrenia disorder (COBRE; N = 145), and typical development (NKI; N = 672) were utilized for the machine learning (ML) classification and prediction based on their static-FC and the FC-variability metrics. To confirm the robustness of FC-variability utility, we benchmarked the ML classification and prediction with various brain parcellations and sliding window parameters. As a result, we found that the ML performances were significantly improved when the ML included FC-variability features in classifying pathological populations from controls (e.g., individuals with autism spectrum disorder vs. typical development) and predicting psychiatric severity (e.g., score of autism diagnostic observation schedule), regardless of parcellation selection and sliding window size. Additionally, the ML performance deterioration was significantly prevented with FC-variability features when excessive features were inputted into the ML models, yielding more reliable results. In conclusion, the current finding proved the usefulness of the FC-variability and its reliability.

Relations Between Executive Functioning and Internalizing Symptoms Vary as a Function of Frontoparietal-amygdala Resting State Connectivity

The prefrontal cortex and the frontoparietal network are associated with a variety of regulatory behaviors. Functional connections between these brain regions and the amygdala are implicated in risk for anxiety disorders. The prefrontal cortex and frontoparietal network are also linked to executive functioning, or behaviors that help orient action towards higher order goals. Where much research has been focused on deleterious effects of under-controlled behavior, a body of work suggests that over-controlled behavior may also pose a risk for internalizing problems. Indeed, while work suggests that high levels of attention shifting may still be protective against internalizing problems, there is evidence that high levels of inhibitory control may be a risk factor for socioemotional difficulties. In the ABCD sample, which offers large sample sizes as well as sociodemographic diversity, we test the interaction between frontoparietal network-amygdala resting state functional connectivity and executive functioning behaviors on longitudinal changes in internalizing symptoms from approximately 10 to 12 years of age. We found that higher proficiency in attention shifting indeed predicts fewer internalizing behaviors over time. In addition, higher proficiency in inhibitory control predicts fewer internalizing symptoms over time, but only for children showing resting state connectivity moderately above the sample average between the frontoparietal network and amygdala. This finding supports the idea that top-down control may not be adaptive for all children, and relations between executive functioning and anxiety risk may vary as a function of trait-level regulation.

The Role of School Environment in Brain Structure, Connectivity, and Mental Health in Children: A Multimodal Investigation

BACKGROUND

Much work has been dedicated to understanding the effects of adverse home environments on brain development. While the school social and learning environment plays a role in child development, little work has been done to investigate the impact of the school environment on the developing brain. The goal of the present study was to examine associations between the school environment, brain structure and connectivity, and mental health.

METHODS

In this preregistered study we investigated these questions in a large sample of adolescents (9-10 years of age) from the Adolescent Brain Cognitive Development (ABCD) Study. We examined the association between school environment and gray matter (n = 10,435) and white matter (n = 10,770) structure and functional connectivity (n = 9528). We then investigated multivariate relationships between school-associated brain measures and mental health.

RESULTS

School environment was associated with connectivity of the auditory and retrosplenial temporal network as well as of higher-order cognitive networks like the cingulo-opercular, default mode, ventral attention, and frontoparietal networks. Multivariate analyses revealed that connectivity of the cingulo-opercular and default mode networks was also associated with mental health.

CONCLUSIONS

Findings shed light on the neural mechanisms through which favorable school environments may contribute to positive mental health outcomes in children. Our findings have implications for interventions targeted at promoting positive youth functioning through improving school environments.

Systematic evaluation of machine learning algorithms for neuroanatomically-based age prediction in youth

Application of machine learning (ML) algorithms to structural magnetic resonance imaging (sMRI) data has yielded behaviorally meaningful estimates of the biological age of the brain (brain-age). The choice of the ML approach in estimating brain-age in youth is important because age-related brain changes in this age-group are dynamic. However, the comparative performance of the available ML algorithms has not been systematically appraised. To address this gap, the present study evaluated the accuracy (mean absolute error [MAE]) and computational efficiency of 21 machine learning algorithms using sMRI data from 2105 typically developing individuals aged 5-22 years from five cohorts. The trained models were then tested in two independent holdout datasets, one comprising 4078 individuals aged 9-10 years and another comprising 594 individuals aged 5-21 years. The algorithms encompassed parametric and nonparametric, Bayesian, linear and nonlinear, tree-based, and kernel-based models. Sensitivity analyses were performed for parcellation scheme, number of neuroimaging input features, number of cross-validation folds, number of extreme outliers, and sample size. Tree-based models and algorithms with a nonlinear kernel performed comparably well, with the latter being especially computationally efficient. Extreme Gradient Boosting (MAE of 1.49 years), Random Forest Regression (MAE of 1.58 years), and Support Vector Regression (SVR) with Radial Basis Function (RBF) Kernel (MAE of 1.64 years) emerged as the three most accurate models. Linear algorithms, with the exception of Elastic Net Regression, performed poorly. Findings of the present study could be used as a guide for optimizing methodology when quantifying brain-age in youth.

Mediating effect of pubertal stages on the family environment and neurodevelopment: An open-data replication and multiverse analysis of an ABCD Study®

Increasing evidence demonstrates that environmental factors meaningfully impact the development of the brain (Hyde et al., 2020; McEwen and Akil, 2020). Recent work from the Adolescent Brain Cognitive Development (ABCD) Study^® suggests that puberty may indirectly account for some association between the family environment and brain structure and function (Thijssen et al., 2020). However, a limited number of large studies have evaluated what, how, and why environmental factors impact neurodevelopment. When these topics are investigated, there is typically inconsistent operationalization of variables between studies which may be measuring different aspects of the environment and thus different associations in the analytic models. Multiverse analyses (Steegen et al., 2016) are an efficacious technique for investigating the effect of different operationalizations of the same construct on underlying interpretations. While one of the assets of Thijssen et al. (2020) was its large sample from the ABCD data, the authors used an early release that contained 38% of the full ABCD sample. Then, the analyses used several 'researcher degrees of freedom' (Gelman and Loken, 2014) to operationalize key independent, mediating and dependent variables, including but not limited to, the use of a latent factor of preadolescents' environment comprised of different subfactors, such as parental monitoring and child-reported family conflict. While latent factors can improve reliability of constructs, the nuances of each subfactor and measure that comprise the environment may be lost, making the latent factors difficult to interpret in the context of individual differences. This study extends the work of Thijssen et al. (2020) by evaluating the extent to which the analytic choices in their study affected their conclusions. In Aim 1, using the same variables and models, we replicate findings from the original study using the full sample in Release 3.0. Then, in Aim 2, using a multiverse analysis we extend findings by considering nine alternative operationalizations of family environment, three of puberty, and five of brain measures (total of 135 models) to evaluate the impact on conclusions from Aim 1. In these results, 90% of the directions of effects and 60% of the p-values (e.g. p > .05 and p < .05) across effects were comparable between the two studies. However, raters agreed that only 60% of the effects had replicated. Across the multiverse analyses, there was a degree of variability in beta estimates across the environmental variables, and lack of consensus between parent reported and child reported pubertal development for the indirect effects. This study demonstrates the challenge in defining which effects replicate, the nuance across environmental variables in the ABCD data, and the lack of consensus across parent and child reported puberty scales in youth.

Coordinated cortical thickness alterations across six neurodevelopmental and psychiatric disorders

Neuropsychiatric disorders are increasingly conceptualized as overlapping spectra sharing multi-level neurobiological alterations. However, whether transdiagnostic cortical alterations covary in a biologically meaningful way is currently unknown. Here, we studied co-alteration networks across six neurodevelopmental and psychiatric disorders, reflecting pathological structural covariance. In 12,024 patients and 18,969 controls from the ENIGMA consortium, we observed that co-alteration patterns followed normative connectome organization and were anchored to prefrontal and temporal disease epicenters. Manifold learning revealed frontal-to-temporal and sensory/limbic-to-occipitoparietal transdiagnostic gradients, differentiating shared illness effects on cortical thickness along these axes. The principal gradient aligned with a normative cortical thickness covariance gradient and established a transcriptomic link to cortico-cerebello-thalamic circuits. Moreover, transdiagnostic gradients segregated functional networks involved in basic sensory, attentional/perceptual, and domain-general cognitive processes, and distinguished between regional cytoarchitectonic profiles. Together, our findings indicate that shared illness effects occur in a synchronized fashion and along multiple levels of hierarchical cortical organization.

Data-Driven Clustering of Functional Signals Reveals Gradients in Processing Both within the Anterior Hippocampus and across Its Long Axis

A particularly elusive puzzle concerning the hippocampus is how the structural differences along its long anteroposterior axis might beget meaningful functional differences, particularly in terms of the granularity of information processing. One measure posits to quantify this granularity by calculating the average statistical independence of the BOLD signal across neighboring voxels, or intervoxel similarity (IVS), and has shown the anterior hippocampus to process coarser-grained information than the posterior hippocampus. This measure, however, has yielded opposing results in studies of developmental and healthy aging samples, which also varied in fMRI acquisition parameters and hippocampal parcellation methods. To reconcile these findings, we measured IVS across two separate resting-state fMRI acquisitions and compared the results across many of the most widely used parcellation methods in a large young-adult sample of male and female humans (Acquisition 1, N = 233; Acquisition 2, N = 176). Finding conflicting results across acquisitions and parcellations, we reasoned that a data-driven approach to hippocampal parcellation is necessary. To this end, we implemented a group masked independent components analysis to identify functional subunits of the hippocampus, most notably separating the anterior hippocampus into separate anterior-medial, anterior-lateral, and posteroanterior-lateral components. Measuring IVS across these components revealed a decrease in IVS along the medial-lateral axis of the anterior hippocampus but an increase from anterior to posterior. We conclude that intervoxel similarity is deeply affected by parcellation and that grounding one's parcellation in a functionally informed approach might allow for a more complex and reliable characterization of the hippocampus.SIGNIFICANCE STATEMENT Processing information along hierarchical scales of granularity is critical for many of the feats of cognition considered most human. Recently, the changes in structure, cortical connectivity, and apparent functional properties across parcels of the hippocampal long axis have been hypothesized to underlie this hierarchical gradient in information processing. We show here, however, that the choice of parcellation method itself drastically affects one particular measure of granularity across the hippocampus and that a functionally informed approach to parcellation reveals gradients both within the anterior hippocampus and in nonlinear form across the long axis. These results point to the issue of parcellation as a critical one in the study of the hippocampus and reorient interpretation of existing results.

Heterogeneity in PFC-amygdala connectivity in middle childhood, and concurrent interrelations with inhibitory control and anxiety symptoms

The prefrontal cortex (PFC) is a key brain area in considering adaptive regulatory behaviors. This includes regulatory projections to regions of the limbic system such as the amygdala, where the nature of functional connections may confer lower risk for anxiety disorders. The PFC is also associated with behaviors like executive functioning. Inhibitory control is a behavior encompassed by executive functioning and is generally viewed favorably for adaptive socioemotional development. Yet, some research suggests that high levels of inhibitory control may actually be a risk factor for some maladaptive developmental outcomes, like anxiety disorders. In a sample of 51 children ranging from 7 to 9 years old, we examined resting state functional connectivity between regions of the PFC and the amygdala. We used Subgrouping Group Iterative Multiple Model Estimation (S-GIMME) to identify and characterize data-driven subgroups of individuals with similar networks of connectivity between these brain regions. Generated subgroups were collapsed into children characterized by the presence or absence of recovered connections between the PFC and amygdala. For subsets of children with available data (N = 38-44), we then tested whether inhibitory control, as measured by a stop signal task, moderated the relation between these subgroups and child-reported anxiety symptoms. We found an inverse relation between stop-signal reaction times and reported count of anxiety symptoms when covarying for connectivity group, suggesting that greater inhibitory control was actually related to greater anxiety symptoms, but only when accounting for patterns of PFC-amygdala connectivity. These data suggest that there is a great deal of heterogeneity in the nature of functional connections between the PFC and amygdala during this stage of development. The findings also provide support for the notion of high levels of inhibitory control as a risk factor for anxiety, but trait-level biopsychosocial factors may be important to consider in assessing the nature of risk.

Evaluation of functional MRI-based human brain parcellation: a review

Brain parcellations play a crucial role in the analysis of brain imaging data sets, as they can significantly affect the outcome of the analysis. In recent years, several novel approaches for constructing MRI-based brain parcellations have been developed with promising results. In the absence of ground truth, several evaluation approaches have been used to evaluate currently available brain parcellations. In this article, we review and critique methods used for evaluating functional brain parcellations constructed using fMRI data sets. We also describe how some of these evaluation methods have been used to estimate the optimal parcellation granularity. We provide a critical discussion of the current approach to the problem of identifying the optimal brain parcellation that is suited for a given neuroimaging study. We argue that the criteria for an optimal brain parcellation must depend on the application the parcellation is intended for. We describe a teleological approach to the evaluation of brain parcellations, where brain parcellations are evaluated in different contexts and optimal brain parcellations for each context are identified separately. We conclude by discussing several directions for further research that would result in improved evaluation strategies.

Age-related change in task-evoked amygdala-prefrontal circuitry: A multiverse approach with an accelerated longitudinal cohort aged 4-22 years

The amygdala and its connections with medial prefrontal cortex (mPFC) play central roles in the development of emotional processes. While several studies have suggested that this circuitry exhibits functional changes across the first two decades of life, findings have been mixed - perhaps resulting from differences in analytic choices across studies. Here we used multiverse analyses to examine the robustness of task-based amygdala-mPFC function findings to analytic choices within the context of an accelerated longitudinal design (4-22 years-old; N = 98; 183 scans; 1-3 scans/participant). Participants recruited from the greater Los Angeles area completed an event-related emotional face (fear, neutral) task. Parallel analyses varying in preprocessing and modeling choices found that age-related change estimates for amygdala reactivity were more robust than task-evoked amygdala-mPFC functional connectivity to varied analytical choices. Specification curves indicated evidence for age-related decreases in amygdala reactivity to faces, though within-participant changes in amygdala reactivity could not be differentiated from between-participant differences. In contrast, amygdala-mPFC functional connectivity results varied across methods much more, and evidence for age-related change in amygdala-mPFC connectivity was not consistent. Generalized psychophysiological interaction (gPPI) measurements of connectivity were especially sensitive to whether a deconvolution step was applied. Our findings demonstrate the importance of assessing the robustness of findings to analysis choices, although the age-related changes in our current work cannot be overinterpreted given low test-retest reliability. Together, these findings highlight both the challenges in estimating developmental change in longitudinal cohorts and the value of multiverse approaches in developmental neuroimaging for assessing robustness of results.

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.

Associations among Household and Neighborhood Socioeconomic Disadvantages, Resting-state Frontoamygdala Connectivity, and Internalizing Symptoms in Youth

Exposure to socioeconomic disadvantages (SED) can have negative impacts on mental health, yet SED are a multifaceted construct and the precise processes by which SED confer deleterious effects are less clear. Using a large and diverse sample of preadolescents (ages 9-10 years at baseline, n = 4038, 49% female) from the Adolescent Brain Cognitive Development Study, we examined associations among SED at both household (i.e., income-needs and material hardship) and neighborhood (i.e., area deprivation and neighborhood unsafety) levels, frontoamygdala resting-state functional connectivity, and internalizing symptoms at baseline and 1-year follow-up. SED were positively associated with internalizing symptoms at baseline and indirectly predicted symptoms 1 year later through elevated symptoms at baseline. At the household level, youth in households characterized by higher disadvantage (i.e., lower income-to-needs ratio) exhibited more strongly negative frontoamygdala coupling, particularly between the bilateral amygdala and medial OFC (mOFC) regions within the frontoparietal network. Although more strongly positive amygdala-mOFC coupling was associated with higher levels of internalizing symptoms at baseline and 1-year follow-up, it did not mediate the association between income-to-needs ratio and internalizing symptoms. However, at the neighborhood level, amygdala-mOFC functional coupling moderated the effect of neighborhood deprivation on internalizing symptoms. Specifically, higher neighborhood deprivation was associated with higher internalizing symptoms for youth with more strongly positive connectivity, but not for youth with more strongly negative connectivity, suggesting a potential buffering effect. Findings highlight the importance of capturing multilevel socioecological contexts in which youth develop to identify youth who are most likely to benefit from early interventions.

Neural heterogeneity underlying late adolescent motivational processing is linked to individual differences in behavioral sensation seeking

Adolescent risk-taking, including sensation seeking (SS), is often attributed to developmental changes in connectivity among brain regions implicated in cognitive control and reward processing. Despite considerable scientific and popular interest in this neurodevelopmental framework, there are few empirical investigations of adolescent functional connectivity, let alone examinations of its links to SS behavior. The studies that have been done focus on mean-based approaches and leave unanswered questions about individual differences in neurodevelopment and behavior. The goal of this paper is to take a person-specific approach to the study of adolescent functional connectivity during a continuous motivational state, and to examine links between connectivity and self-reported SS behavior in 104 adolescents (M_Age  = 19.3; SD_Age  = 1.3). Using Group Iterative Multiple Model Estimation (GIMME), person-specific connectivity during two neuroimaging runs of a monetary incentive delay task was estimated among 12 a priori brain regions of interest representing reward, cognitive, and salience networks. Two data-driven subgroups were detected, a finding that was consistent between both neuroimaging runs, but associations with SS were only found in the first run, potentially reflecting neural habituation in the second run. Specifically, the subgroup that had unique connections between reward-related regions had greater SS and showed a distinctive relation between connectivity strength in the reward regions and SS. These findings provide novel evidence for heterogeneity in adolescent brain-behavior relations by showing that subsets of adolescents have unique associations between neural motivational processing and SS. Findings have broader implications for future work on reward processing, as they demonstrate that brain-behavior relations may attenuate across runs.

Altered brain network topology in children with auditory processing disorder: A resting-state multi-echo fMRI study

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A graph-theoretical approach was used to assess the functional topology in APD.

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Brain networks in APD are similarly integrated and segregated compared to HCs.

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Children with APD have different hub organization.

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Significant group differences were found in the PC measure in the bilateral STG.

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Regional differences observed within the DMN indicate multimodal roles in APD.

Children with auditory processing disorder (APD) experience hearing difficulties, particularly in the presence of competing sounds, despite having normal audiograms. There is considerable debate on whether APD symptoms originate from bottom-up (e.g., auditory sensory processing) and/or top-down processing (e.g., cognitive, language, memory). A related issue is that little is known about whether functional brain network topology is altered in APD. Therefore, we used resting-state functional magnetic resonance imaging data to investigate the functional brain network organization of 57 children from 8 to 14 years old, diagnosed with APD (n = 28) and without hearing difficulties (healthy control, HC; n = 29). We applied complex network analysis using graph theory to assess the whole-brain integration and segregation of functional networks and brain hub architecture. Our results showed children with APD and HC have similar global network properties –i.e., an average of all brain regions– and modular organization. Still, the APD group showed different hub architecture in default mode-ventral attention, somatomotor and frontoparietal-dorsal attention modules. At the nodal level –i.e., single-brain regions–, we observed decreased participation coefficient (PC – a measure quantifying the diversity of between-network connectivity) in auditory cortical regions in APD, including bilateral superior temporal gyrus and left middle temporal gyrus. Beyond auditory regions, PC was also decreased in APD in bilateral posterior temporo-occipital cortices, left intraparietal sulcus, and right posterior insular cortex. Correlation analysis suggested a positive association between PC in the left parahippocampal gyrus and the listening-in-spatialized-noise -sentences task where APD children were engaged in auditory perception. In conclusion, our findings provide evidence of altered brain network organization in children with APD, specific to auditory networks, and shed new light on the neural systems underlying children's listening difficulties.