Cluster failure or power failure? Evaluating sensitivity in cluster-level inference

The effects of childhood adversity: Two specific neural patterns

Childhood adversity (CA) is associated with an elevated risk of psychopathology across the lifespan and altered brain functions are thought to play an important role in linking CA to mental vulnerability. Previous research has proposed that CA generally influences emotion processing and particularly affects reward processing and cognitive control, yet convergent evidence for CA-related neural and functional networks underlying these processes remains to be fully understood. To investigate the impact of CA on functional brain activations, the present study performed Activation Likelihood Estimation (ALE) analyses across neuroimaging studies involving three task domains: emotion processing, cognitive control, and reward processing. ALE results revealed two significant CA-related convergences of activation in the left amygdala and insula. To better understand and characterize the functions of these ALE-derived clusters, we applied the Meta-Analytic Connectivity Modeling (MACM) approach to identify co-activation maps, and the functional decoding approach to reveal cluster-related psychological processes. Results demonstrated two distinct neural and functional networks in CA: an amygdala-centered emotion processing network and an insula-centered somatomotor processing network. These specific neural patterns indicate the effect of CA on multiple neural and functional networks engaged in sensory-motor and emotion processing functions. Our results provide insights into the neurobiological embedding associated with CA.

Bias in data-driven replicability analysis of univariate brain-wide association studies

Recent studies have used big neuroimaging datasets to answer an important question: how many subjects are required for reproducible brain-wide association studies? These data-driven approaches could be considered a framework for testing the reproducibility of several neuroimaging models and measures. Here we test part of this framework, namely estimates of statistical errors of univariate brain-behaviour associations obtained from resampling large datasets with replacement. We demonstrate that reported estimates of statistical errors are largely a consequence of bias introduced by random effects when sampling with replacement close to the full sample size. We show that future meta-analyses can largely avoid these biases by only resampling up to 10% of the full sample size. We discuss implications that reproducing mass-univariate association studies requires tens-of-thousands of participants, urging researchers to adopt other methodological approaches.

Functional and structural connectivity of the subregions of the amygdala in ADHD children with or without ODD

OBJECTIVES

The current study aimed to investigate the structural and functional connectivity of the subregions of the amygdala in children with Attention Deficit/Hyperactivity Disorder (ADHD) only or comorbid with Oppositional Defiant Disorder (ODD).

METHODS

A total of 354 children with ADHD-only, 161 children with ADHD and ODD (ADHD + ODD), and 100 healthy controls were enrolled. The Child Behavior Checklist (CBCL) and the Behavior Rating Inventory of Executive Function (BRIEF) were filled out by caregivers. Analysis of covariance (ANCOVA) was performed to test group-wise differences in these behavioral measures. A subsample comprising 209 participants underwent a resting-state functional MRI scan and a diffusion-weighted imaging (DWI) scan. Functional connectivity and structural connectivity were calculated using bilateral subregions of the Amygdala as seeds. Between-group voxel-wise comparisons were conducted.

RESULTS

The ADHD + ODD group had more anxious/depressed moods, more delinquent and aggressive behaviors, more emotional control problems, and more inhibition deficits than the ADHD-only group (all PBonferroni-corrected < 0.05). Compared with the control and ADHD + ODD groups, the ADHD-only group displayed increased FC strength between the amygdala subregions and the left caudate, left putamen, and frontal cortex. Regarding structural connectivity (SC), the ADHD-only group demonstrated higher streamline density in the left internal capsule, corpus callosum, and the right superior corona radiata. The altered SC was associated with emotional problems in children with ADHD, while the altered FC was associated with other ADHD-related clinical features.

CONCLUSIONS

Altered structural and functional connectivity of the subregions of the amygdala in children with ADHD compared with their healthy counterparts were respectively associated with ADHD-related behavioral and emotional problems.

CLINICAL TRIAL NUMBER

not applicable.

Polyconnectomic Scoring of Functional Connectivity Patterns Across Eight Neuropsychiatric and Three Neurodegenerative Disorders

BACKGROUND

Neuropsychiatric and neurodegenerative disorders involve diverse changes in brain functional connectivity. As an alternative to approaches that search for specific mosaic patterns of affected connections and networks, we used polyconnectomic scoring to quantify disorder-related whole-brain connectivity signatures into interpretable, personalized scores.

METHODS

The polyconnectomic score (PCS) measures the extent to which an individual's functional connectivity mirrors the whole-brain circuitry characteristics of a trait. We computed PCSs for 8 neuropsychiatric conditions (attention-deficit/hyperactivity disorder, anxiety-related disorders, autism spectrum disorder, obsessive-compulsive disorder, bipolar disorder, major depressive disorder, schizoaffective disorder, and schizophrenia) and 3 neurodegenerative conditions (Alzheimer's disease, frontotemporal dementia, and Parkinson's disease) across 22 datasets with resting-state functional magnetic resonance imaging data from 10,667 individuals (5325 patients, 5342 control participants). We also examined PCSs in 26,673 individuals from the population-based UK Biobank cohort.

RESULTS

PCSs were consistently higher in out-of-sample patients across 6 of the 8 neuropsychiatric and across all 3 investigated neurodegenerative disorders ([minimum, maximum]: area under the receiver operating characteristic curve = [0.55, 0.73], false discovery rate-corrected p [pFDR] = [1.8 × 10-16, 4.5 × 10-2]). Individuals with elevated PCS levels for neuropsychiatric conditions exhibited higher neuroticism (pFDR < 9.7 × 10-5), lower cognitive performance (pFDR < 5.3 × 10-5), and lower general well-being (pFDR < 9.7 × 10-4).

CONCLUSIONS

Our findings reveal generalizable whole-brain connectivity alterations in brain disorders. Polyconnectomic scoring effectively aggregates disorder-related signatures across the entire brain into an interpretable, participant-specific metric. A toolbox is provided for PCS computation.

Topological cluster statistic (TCS): Toward structural connectivity-guided fMRI cluster enhancement

Functional magnetic resonance imaging (fMRI) studies most commonly use cluster-based inference to detect local changes in brain activity. Insufficient statistical power and disproportionate false-positive rates reportedly hinder optimal inference. We propose a structural connectivity-guided clustering framework, called topological cluster statistic (TCS), that enhances sensitivity by leveraging white matter anatomical connectivity information. TCS harnesses multimodal information from diffusion tractography and functional imaging to improve task fMRI activation inference. Compared to conventional approaches, TCS consistently improves power over a wide range of effects. This improvement results in a 10%-50% increase in local sensitivity with the greatest gains for medium-sized effects. TCS additionally enables inspection of underlying anatomical networks and thus uncovers knowledge regarding the anatomical underpinnings of brain activation. This novel approach is made available in the PALM software to facilitate usability. Given the increasing recognition that activation reflects widespread, coordinated processes, TCS provides a way to integrate the known structure underlying widespread activations into neuroimaging analyses moving forward.

Seeing more than the Tip of the Iceberg: Approaches to Subthreshold Effects in Functional Magnetic Resonance Imaging of the Brain

Many functional magnetic resonance imaging (fMRI) studies and presurgical mapping applications rely on mass-univariate inference with subsequent multiple comparison correction. Statistical results are frequently visualized as thresholded statistical maps. This approach has inherent limitations including the risk of drawing overly-selective conclusions based only on selective results passing such thresholds. This article gives an overview of both established and newly emerging scientific approaches to supplement such conventional analyses by incorporating information about subthreshold effects with the aim to improve interpretation of findings or leverage a wider array of information. Topics covered include neuroimaging data visualization, p-value histogram analysis and the related Higher Criticism approach for detecting rare and weak effects. Further examples from multivariate analyses and dedicated Bayesian approaches are provided.

Precision fMRI and cluster-failure in the individual brain

Advances in neuroimaging acquisition protocols and denoising techniques, along with increasing magnetic field strengths, have dramatically improved the temporal signal-to-noise ratio (tSNR) in functional magnetic resonance imaging (fMRI). This permits spatial resolution with submillimeter voxel sizes and ultrahigh temporal resolution and opens a route toward performing precision fMRI in the brains of individuals. Yet ultrahigh spatial and temporal resolution comes at a cost: it reduces tSNR and, therefore, the sensitivity to the blood oxygen level-dependent (BOLD) effect and other functional contrasts across the brain. Here we investigate the potential of various smoothing filters to improve BOLD sensitivity while preserving the spatial accuracy of activated clusters in single-subject analysis. We introduce adaptive-weight smoothing with optimized metrics (AWSOM), which addresses this challenge extremely well. AWSOM employs a local inference approach that is as sensitive as cluster-corrected inference of data smoothed with large Gaussian kernels, but it preserves spatial details across multiple tSNR levels. This is essential for examining whole-brain fMRI data because tSNR varies across the entire brain, depending on the distance of a brain region from the receiver coil, the type of setup, acquisition protocol, preprocessing, and resolution. We found that cluster correction in single subjects results in inflated family-wise error and false positive rates. AWSOM effectively suppresses false positives while remaining sensitive even to small clusters of activated voxels. Furthermore, it preserves signal integrity, that is, the relative activation strength of significant voxels, making it a valuable asset for a wide range of fMRI applications. Here we demonstrate these features and make AWSOM freely available to the research community for download.

From Maps to Models: A Survey on the Reliability of Small Studies of Task-Based fMRI

Task-based functional magnetic resonance imaging is a powerful tool for studying brain function, but neuroimaging research produces ongoing concerns regarding small-sample studies and how to interpret them. Although it is well understood that larger samples are preferable, many situations require researchers to make judgments from small studies, including reviewing the existing literature, analyzing pilot data, or assessing subsamples. Quantitative guidance on how to make these judgments remains scarce. To address this, we leverage the Human Connectome Project's Young Adult dataset to survey various analyses-from regional activation maps to predictive models. We find that, for some classic analyses such as detecting regional activation or cluster peak location, studies with as few as 40 subjects are adequate, although this depends crucially on effect sizes. For predictive modeling, similar sizes can be adequate for detecting whether features are predictable, but at least an order of magnitude more (at least hundreds) may be required for developing consistent predictions. These results offer valuable insights for designing and interpreting fMRI studies, emphasizing the importance of considering effect size, sample size, and analysis approach when assessing the reliability of findings. We hope that this survey serves as a reference for identifying which kinds of research questions can be reliably answered with small-scale studies.

Social Cognition and Functional Connectivity in Early and Chronic Schizophrenia

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

A mediation approach in resting-state connectivity between the medial prefrontal cortex and anterior cingulate in mild cognitive impairment

Mild cognitive impairment (MCI) is recognized as the prodromal phase of dementia, a condition that can be either maintained or reversed through timely medical interventions to prevent cognitive decline. Considerable studies using functional magnetic resonance imaging (fMRI) have indicated that altered activity in the medial prefrontal cortex (mPFC) serves as an indicator of various cognitive stages of aging. However, the impacts of intrinsic functional connectivity in the mPFC as a mediator on cognitive performance in individuals with and without MCI have not been fully understood. In this study, we recruited 42 MCI patients and 57 healthy controls, assessing their cognitive abilities and functional brain connectivity patterns through neuropsychological evaluations and resting-state fMRI, respectively. The MCI patients exhibited poorer performance on multiple neuropsychological tests compared to the healthy controls. At the neural level, functional connectivity between the mPFC and the anterior cingulate cortex (ACC) was significantly weaker in the MCI group and correlated with multiple neuropsychological test scores. The result of the mediation analysis further demonstrated that functional connectivity between the mPFC and ACC notably mediated the relationship between the MCI and semantic fluency performance. These findings suggest that altered mPFC-ACC connectivity may have a plausible causal influence on cognitive decline and provide implications for early identifications of neurodegenerative diseases and precise monitoring of disease progression.

Neural correlates of inattention in adults with ADHD

In the last two decades, numerous magnetic resonance imaging (MRI) studies have examined differences in cortical structure between individuals with Attention-Deficit/Hyperactivity Disorder (ADHD) and healthy controls. These studies primarily emphasized alterations in gray matter volume (GMV) and cortical thickness (CT). Still, the scientific literature is notably scarce in regard to investigating associations of cortical structure with ADHD psychopathology, specifically inattention within adults with ADHD. The present study aimed to elucidate neurobiological underpinnings of inattention beyond GMV and CT by including cortical gyrification, sulcal depth, and fractal dimension. Building upon the Comparison of Methylphenidate and Psychotherapy in Adult ADHD Study (COMPAS), cortical structure parameters were investigated using 141 T1-weighted anatomical scans of adult patients with ADHD. All brain structural analyses were performed using the threshold-free cluster enhancement (TFCE) approach and the Computational Anatomy Toolbox (CAT12) integrated into the Statistical Parametric Mapping Software (Matlab Version R2021a). Results revealed significant correlations of inattention in multiple brain regions. Cortical gyrification was negatively correlated, whereas cortical thickness and fractal dimension were positively associated with inattention. The clusters showed widespread distribution across the cerebral cortex, with both hemispheres affected. The cortical regions most prominently affected included the precuneus, para-, pre-, and postcentral gyri, superior parietal lobe, and posterior cingulate cortex. This study highlights the importance of cortical alterations in attentional processes in adults with ADHD. Further research in this area is warranted to elucidate intricacies of inattention in adults with ADHD to potentially enhance diagnostic accuracy and inform personalized treatment strategies.

Study design features increase replicability in cross-sectional and longitudinal brain-wide association studies

Brain-wide association studies (BWAS) are a fundamental tool in discovering brain-behavior associations. Several recent studies showed that thousands of study participants are required for good replicability of BWAS because the standardized effect sizes (ESs) are much smaller than the reported standardized ESs in smaller studies. Here, we perform analyses and meta-analyses of a robust effect size index using 63 longitudinal and cross-sectional magnetic resonance imaging studies from the Lifespan Brain Chart Consortium (77,695 total scans) to demonstrate that optimizing study design is critical for increasing standardized ESs and replicability in BWAS. A meta-analysis of brain volume associations with age indicates that BWAS with larger variability in covariate have larger reported standardized ES. In addition, the longitudinal studies we examined reported systematically larger standardized ES than cross-sectional studies. Analyzing age effects on global and regional brain measures from the United Kingdom Biobank and the Alzheimer's Disease Neuroimaging Initiative, we show that modifying longitudinal study design through sampling schemes improves the standardized ESs and replicability. Sampling schemes that improve standardized ESs and replicability include increasing between-subject age variability in the sample and adding a single additional longitudinal measurement per subject. To ensure that our results are generalizable, we further evaluate these longitudinal sampling schemes on cognitive, psychopathology, and demographic associations with structural and functional brain outcome measures in the Adolescent Brain and Cognitive Development dataset. We demonstrate that commonly used longitudinal models can, counterintuitively, reduce standardized ESs and replicability. The benefit of conducting longitudinal studies depends on the strengths of the between- versus within-subject associations of the brain and non-brain measures. Explicitly modeling between- versus within-subject effects avoids averaging the effects and allows optimizing the standardized ESs for each separately. Together, these results provide guidance for study designs that improve the replicability of BWAS.

Resting-state amygdala subregion and precuneus connectivity provide evidence for a dimensional approach to studying social anxiety disorder

Social anxiety disorder (SAD) is a prevalent and disabling mental health condition, characterized by excessive fear and anxiety in social situations. Resting-state functional magnetic resonance imaging (fMRI) paradigms have been increasingly used to understand the neurobiological underpinnings of SAD in the absence of threat-related stimuli. Previous studies have primarily focused on the role of the amygdala in SAD. However, the amygdala consists of functionally and structurally distinct subregions, and recent studies have highlighted the importance of investigating the role of these subregions independently. Using multiband fMRI, we analyzed resting-state data from 135 participants (42 SAD, 93 healthy controls). By employing voxel-wise permutation testing, we examined group differences of fMRI connectivity and associations between fMRI connectivity and social anxiety symptoms to further investigate the classification of SAD as a categorical or dimensional construct. Seed-to-whole brain functional connectivity analysis using multiple 'seeds' including the amygdala and its subregions and the precuneus, revealed no statistically significant group differences. However, social anxiety severity was significantly negatively correlated with functional connectivity of the precuneus - perigenual anterior cingulate cortex and positively correlated with functional connectivity of the amygdala (specifically the superficial subregion) - parietal/cerebellar areas. Our findings demonstrate clear links between symptomatology and brain connectivity in the absence of diagnostic differences, with evidence of amygdala subregion-specific alterations. The observed brain-symptom associations did not include disturbances in the brain's fear circuitry (i.e., disturbances in connectivity between amygdala - prefrontal regions) likely due to the absence of threat-related stimuli.

Brain-phenotype predictions can survive across diverse real-world data

Recent work suggests that machine learning models predicting psychiatric treatment outcomes based on clinical data may fail when applied to unharmonized samples. Neuroimaging predictive models offer the opportunity to incorporate neurobiological information, which may be more robust to dataset shifts. Yet, among the minority of neuroimaging studies that undertake any form of external validation, there is a notable lack of attention to generalization across dataset-specific idiosyncrasies. Research settings, by design, remove the between-site variations that real-world and, eventually, clinical applications demand. Here, we rigorously test the ability of a range of predictive models to generalize across three diverse, unharmonized samples: the Philadelphia Neurodevelopmental Cohort (n=1291), the Healthy Brain Network (n=1110), and the Human Connectome Project in Development (n=428). These datasets have high inter-dataset heterogeneity, encompassing substantial variations in age distribution, sex, racial and ethnic minority representation, recruitment geography, clinical symptom burdens, fMRI tasks, sequences, and behavioral measures. We demonstrate that reproducible and generalizable brain-behavior associations can be realized across diverse dataset features with sample sizes in the hundreds. Results indicate the potential of functional connectivity-based predictive models to be robust despite substantial inter-dataset variability. Notably, for the HCPD and HBN datasets, the best predictions were not from training and testing in the same dataset (i.e., cross-validation) but across datasets. This result suggests that training on diverse data may improve prediction in specific cases. Overall, this work provides a critical foundation for future work evaluating the generalizability of neuroimaging predictive models in real-world scenarios and clinical settings.

UNRAVELing the synergistic effects of psilocybin and environment on brain-wide immediate early gene expression in mice

The effects of context on the subjective experience of serotonergic psychedelics have not been fully examined in human neuroimaging studies, partly due to limitations of the imaging environment. Here, we administered saline or psilocybin to mice in their home cage or an enriched environment, immunofluorescently-labeled brain-wide c-Fos, and imaged iDISCO+ cleared tissue with light sheet fluorescence microscopy (LSFM) to examine the impact of environmental context on psilocybin-elicited neural activity at cellular resolution. Voxel-wise analysis of c-Fos-immunofluorescence revealed clusters of neural activity associated with main effects of context and psilocybin-treatment, which were validated with c-Fos+ cell density measurements. Psilocybin increased c-Fos expression in subregions of the neocortex, caudoputamen, central amygdala, and parasubthalamic nucleus while it decreased c-Fos in the hypothalamus, cortical amygdala, striatum, and pallidum in a predominantly context-independent manner. To gauge feasibility of future mechanistic studies on ensembles activated by psilocybin, we confirmed activity- and Cre-dependent genetic labeling in a subset of these neurons using TRAP2+/-;Ai14+ mice. Network analyses treating each psilocybin-sensitive cluster as a node indicated that psilocybin disrupted co-activity between highly correlated regions, reduced brain modularity, and dramatically attenuated intermodular co-activity. Overall, our results indicate that main effects of context and psilocybin were robust, widespread, and reorganized network architecture, whereas context×psilocybin interactions were surprisingly sparse.

Competing neural representations of choice shape evidence accumulation in humans

Making adaptive choices in dynamic environments requires flexible decision policies. Previously, we showed how shifts in outcome contingency change the evidence accumulation process that determines decision policies. Using in silico experiments to generate predictions, here we show how the cortico-basal ganglia-thalamic (CBGT) circuits can feasibly implement shifts in decision policies. When action contingencies change, dopaminergic plasticity redirects the balance of power, both within and between action representations, to divert the flow of evidence from one option to another. When competition between action representations is highest, the rate of evidence accumulation is the lowest. This prediction was validated in in vivo experiments on human participants, using fMRI, which showed that (1) evoked hemodynamic responses can reliably predict trial-wise choices and (2) competition between action representations, measured using a classifier model, tracked with changes in the rate of evidence accumulation. These results paint a holistic picture of how CBGT circuits manage and adapt the evidence accumulation process in mammals.

Hemispheric contributions toward interoception and emotion recognition in left-vs right-semantic dementia

BACKGROUND

The hemispheric contributions toward interoception, the perception of internal bodily cues, and emotion recognition remains unclear. Semantic dementia cases with either left-dominant (i.e., left-SD) or right-dominant (i.e., right-SD) anterior temporal lobe atrophy experience emotion recognition difficulties, however, little is known about interoception in these syndromes. Here, we hypothesised that right-SD would show worse interoception and emotion recognition due to right-dominant atrophy.

METHODS

Thirty-five participants (8 left-SD; 6 right-SD; 21 controls) completed a monitoring task. Participants pressed a button when they: (1) felt their heartbeat, without pulse measurement (Interoception); or (2) heard a recorded heartbeat (Exteroception-control). Simultaneous ECG was recorded. Accuracy was calculated by comparing the event frequency (i.e., heartbeat or sound) to response frequency. Emotion recognition was assessed via the Facial Affect Selection Task. Voxel-based morphometry analyses identified neural correlates of interoception and emotion recognition.

RESULTS

Right-SD showed worse interoception than controls and left-SD (both p's < 0.001). Both patient groups showed worse emotion recognition than controls (right-SD: p < .001; left-SD: p = .018), and right-SD showed worse emotion recognition than left-SD (p = .003). Regression analyses revealed that worse emotion recognition was predicted by right-SD (p = .002), left-SD (p = .005), and impaired interoception (p = .004). Interoception and emotion were associated with the integrity of right-lateralised structures including the insula, temporal pole, thalamus, superior temporal gyrus, and hippocampus.

CONCLUSION

Our study provides the first evidence for impaired interoception in right-SD, suggesting that impaired emotion recognition in this syndrome is driven by inaccurate internal monitoring. Further we identified a common neurobiological basis for interoception and emotion in the right hemisphere.

Reproducibility in Neuroimaging Analysis: Challenges and Solutions

Recent years have marked a renaissance in efforts to increase research reproducibility in psychology, neuroscience, and related fields. Reproducibility is the cornerstone of a solid foundation of fundamental research-one that will support new theories built on valid findings and technological innovation that works. The increased focus on reproducibility has made the barriers to it increasingly apparent, along with the development of new tools and practices to overcome these barriers. Here, we review challenges, solutions, and emerging best practices with a particular emphasis on neuroimaging studies. We distinguish 3 main types of reproducibility, discussing each in turn. Analytical reproducibility is the ability to reproduce findings using the same data and methods. Replicability is the ability to find an effect in new datasets, using the same or similar methods. Finally, robustness to analytical variability refers to the ability to identify a finding consistently across variation in methods. The incorporation of these tools and practices will result in more reproducible, replicable, and robust psychological and brain research and a stronger scientific foundation across fields of inquiry.

Cortico-cerebellar audio-motor regions coordinate self and other in musical joint action

Joint music performance requires flexible sensorimotor coordination between self and other. Cognitive and sensory parameters of joint action-such as shared knowledge or temporal (a)synchrony-influence this coordination by shifting the balance between self-other segregation and integration. To investigate the neural bases of these parameters and their interaction during joint action, we asked pianists to play on an MR-compatible piano, in duet with a partner outside of the scanner room. Motor knowledge of the partner's musical part and the temporal compatibility of the partner's action feedback were manipulated. First, we found stronger activity and functional connectivity within cortico-cerebellar audio-motor networks when pianists had practiced their partner's part before. This indicates that they simulated and anticipated the auditory feedback of the partner by virtue of an internal model. Second, we observed stronger cerebellar activity and reduced behavioral adaptation when pianists encountered subtle asynchronies between these model-based anticipations and the perceived sensory outcome of (familiar) partner actions, indicating a shift towards self-other segregation. These combined findings demonstrate that cortico-cerebellar audio-motor networks link motor knowledge and other-produced sounds depending on cognitive and sensory factors of the joint performance, and play a crucial role in balancing self-other integration and segregation.

Statistical power in network neuroscience

Network neuroscience has emerged as a leading method to study brain connectivity. The success of these investigations is dependent not only on approaches to accurately map connectivity but also on the ability to detect real effects in the data - that is, statistical power. We review the state of statistical power in the field and discuss sample size, effect size, measurement error, and network topology as key factors that influence the power of brain connectivity investigations. We use the term 'differential power' to describe how power can vary between nodes, edges, and graph metrics, leaving traces in both positive and negative connectome findings. We conclude with strategies for working with, rather than around, power in connectivity studies.

UNRAVELing the synergistic effects of psilocybin and environment on brain-wide immediate early gene expression in mice

The effects of context on the subjective experience of serotonergic psychedelics have not been fully examined in human neuroimaging studies, partly due to limitations of the imaging environment. Here, we administered saline or psilocybin to mice in their home cage or an enriched environment, immunofluorescently-labeled brain-wide c-Fos, and imaged cleared tissue with light sheet microscopy to examine the impact of context on psilocybin-elicited neural activity at cellular resolution. Voxel-wise analysis of c-Fos-immunofluorescence revealed differential neural activity, which we validated with c-Fos + cell density measurements. Psilocybin increased c-Fos expression in the neocortex, caudoputamen, central amygdala, and parasubthalamic nucleus and decreased c-Fos in the hypothalamus, cortical amygdala, striatum, and pallidum. Main effects of context and psilocybin-treatment were robust, widespread, and spatially distinct, whereas interactions were surprisingly sparse.

Non-conscious processing of fear faces: a function of the implicit self-concept of anxiety

BACKGROUND

Trait anxiety refers to a stable tendency to experience fears and worries across many situations. High trait anxiety is a vulnerability factor for the development of psychopathologies. Self-reported trait anxiety appears to be associated with an automatic processing advantage for threat-related information. Self-report measures assess aspects of the explicit self-concept of anxiety. Indirect measures can tap into the implicit self-concept of anxiety.

METHODS

We examined automatic brain responsiveness to non-conscious threat as a function of trait anxiety using functional magnetic resonance imaging. Besides a self-report instrument, we administered the Implicit Association Test (IAT) to assess anxiety. We used a gender-decision paradigm presenting brief (17 ms) and backward-masked facial expressions depicting disgust and fear.

RESULTS

Explicit trait anxiety was not associated with brain responsiveness to non-conscious threat. However, a relation of the implicit self-concept of anxiety with masked fear processing in the thalamus, precentral gyrus, and lateral prefrontal cortex was observed.

CONCLUSIONS

We provide evidence that a measure of the implicit self-concept of anxiety is a valuable predictor of automatic neural responses to threat in cortical and subcortical areas. Hence, implicit anxiety measures could be a useful addition to explicit instruments. Our data support the notion that the thalamus may constitute an important neural substrate in biased non-conscious processing in anxiety.

Spatially-enhanced clusterwise inference for testing and localizing intermodal correspondence

With the increasing availability of neuroimaging data from multiple modalities-each providing a different lens through which to study brain structure or function-new techniques for comparing, integrating, and interpreting information within and across modalities have emerged. Recent developments include hypothesis tests of associations between neuroimaging modalities, which can be used to determine the statistical significance of intermodal associations either throughout the entire brain or within anatomical subregions or functional networks. While these methods provide a crucial foundation for inference on intermodal relationships, they cannot be used to answer questions about where in the brain these associations are most pronounced. In this paper, we introduce a new method, called CLEAN-R, that can be used both to test intermodal correspondence throughout the brain and also to localize this correspondence. Our method involves first adjusting for the underlying spatial autocorrelation structure within each modality before aggregating information within small clusters to construct a map of enhanced test statistics. Using structural and functional magnetic resonance imaging data from a subsample of children and adolescents from the Philadelphia Neurodevelopmental Cohort, we conduct simulations and data analyses where we illustrate the high statistical power and nominal type I error levels of our method. By constructing an interpretable map of group-level correspondence using spatially-enhanced test statistics, our method offers insights beyond those provided by earlier methods.

Behavioral and brain functional characteristics of children with Attention-Deficit/Hyperactivity disorder and anxiety trait

The current study aimed to explore the behavioral, daily-life executive functional, and brain functional connectivity patterns in children with attention-deficit/hyperactivity disorder (ADHD) and anxiety. A total of 246 children with non-comorbid ADHD and 91 healthy controls (HCs) participated in the current study, among whom 175 subjects went through resting-state functional magnetic resonance imaging (fMRI) scans. The ADHD participants were divided into two subgroups: ADHD with a high level of anxiety (ADHD + ANX) and ADHD with a low level of anxiety (ADHD-ANX). The Child Behavior Checklist (CBCL) and the Behavior Rating Inventory of Executive Function (BRIEF) were used to capture the behavioral and daily-life executive functional characteristics. Independent component analysis with dual regression models was applied to the fMRI data. All statistical models were estimated with age and sex as covariates. Compared with the ADHD-ANX group, the ADHD + ANX group showed more withdrawn, somatic, social, thought, attention, delinquent, and aggressive problems (all corrected p < 0.05). The ADHD + ANX group also displayed more impaired emotional control and working memory than the ADHD-ANX (all corrected p < 0.05). The ADHD-ANX group, but not the ADHD + ANX group, showed elevated functional connectivity within the default mode network compared with the HC group. The mean function connectivity within the default mode network significantly mediated the correlation between anxiety level and attention problems. In sum, anxiety in children with ADHD was associated with more social, emotional, and behavioral problems, more impaired daily-life executive function, and altered brain function. Our work provides important information on the heterogeneity of ADHD.

Evaluation of thresholding methods for activation likelihood estimation meta-analysis via large-scale simulations

In recent neuroimaging studies, threshold-free cluster enhancement (TFCE) gained popularity as a sophisticated thresholding method for statistical inference. It was shown to feature higher sensitivity than the frequently used approach of controlling the cluster-level family-wise error (cFWE) and it does not require setting a cluster-forming threshold at voxel level. Here, we examined the applicability of TFCE to a widely used method for coordinate-based neuroimaging meta-analysis, Activation Likelihood Estimation (ALE), by means of large-scale simulations. We created over 200,000 artificial meta-analysis datasets by independently varying the total number of experiments included and the amount of spatial convergence across experiments. Next, we applied ALE to all datasets and compared the performance of TFCE to both voxel-level and cluster-level FWE correction approaches. All three multiple-comparison correction methods yielded valid results, with only about 5% of the significant clusters being based on spurious convergence, which corresponds to the nominal level the methods were controlling for. On average, TFCE's sensitivity was comparable to that of cFWE correction, but it was slightly worse for a subset of parameter combinations, even after TFCE parameter optimization. cFWE yielded the largest significant clusters, closely followed by TFCE, while voxel-level FWE correction yielded substantially smaller clusters, showcasing its high spatial specificity. Given that TFCE does not outperform the standard cFWE correction but is computationally much more expensive, we conclude that employing TFCE for ALE cannot be recommended to the general user.

Parsimonious model for mass-univariate vertexwise analysis

Purpose: Covariance between gray-matter measurements can reflect structural or functional brain networks though it has also been shown to be influenced by confounding factors (e.g., age, head size, and scanner), which could lead to lower mapping precision (increased size of associated clusters) and create distal false positives associations in mass-univariate vertexwise analyses. Approach: We evaluated this concern by performing state-of-the-art mass-univariate analyses (general linear model, GLM) on traits simulated from real vertex-wise gray matter data (including cortical and subcortical thickness and surface area). We contrasted the results with those from linear mixed models (LMMs), which have been shown to overcome similar issues in omics association studies. Results: We showed that when performed on a large sample ( N = 8662 , UK Biobank), GLMs yielded greatly inflated false positive rate (cluster false discovery rate > 0.6 ). We showed that LMMs resulted in more parsimonious results: smaller clusters and reduced false positive rate but at a cost of increased computation. Next, we performed mass-univariate association analyses on five real UKB traits (age, sex, BMI, fluid intelligence, and smoking status) and LMM yielded fewer and more localized associations. We identified 19 significant clusters displaying small associations with age, sex, and BMI, which suggest a complex architecture of at least dozens of associated areas with those phenotypes. Conclusions: The published literature could contain a large proportion of redundant (possibly confounded) associations that are largely prevented using LMMs. The parsimony of LMMs results from controlling for the joint effect of all vertices, which prevents local and distal redundant associations from reaching significance.

Improving power in functional magnetic resonance imaging by moving beyond cluster-level inference

Inference in neuroimaging typically occurs at the level of focal brain areas or circuits. Yet, increasingly, well-powered studies paint a much richer picture of broad-scale effects distributed throughout the brain, suggesting that many focal reports may only reflect the tip of the iceberg of underlying effects. How focal versus broad-scale perspectives influence the inferences we make has not yet been comprehensively evaluated using real data. Here, we compare sensitivity and specificity across procedures representing multiple levels of inference using an empirical benchmarking procedure that resamples task-based connectomes from the Human Connectome Project dataset (∼1,000 subjects, 7 tasks, 3 resampling group sizes, 7 inferential procedures). Only broad-scale (network and whole brain) procedures obtained the traditional 80% statistical power level to detect an average effect, reflecting >20% more statistical power than focal (edge and cluster) procedures. Power also increased substantially for false discovery rate- compared with familywise error rate-controlling procedures. The downsides are fairly limited; the loss in specificity for broad-scale and FDR procedures was relatively modest compared to the gains in power. Furthermore, the broad-scale methods we introduce are simple, fast, and easy to use, providing a straightforward starting point for researchers. This also points to the promise of more sophisticated broad-scale methods for not only functional connectivity but also related fields, including task-based activation. Altogether, this work demonstrates that shifting the scale of inference and choosing FDR control are both immediately attainable and can help remedy the issues with statistical power plaguing typical studies in the field.

Empirical facts from search for replicable associations between cortical thickness and psychometric variables in healthy adults

The study of associations between inter-individual differences in brain structure and behaviour has a long history in psychology and neuroscience. Many associations between psychometric data, particularly intelligence and personality measures and local variations of brain structure have been reported. While the impact of such reported associations often goes beyond scientific communities, resonating in the public mind, their replicability is rarely evidenced. Previously, we have shown that associations between psychometric measures and estimates of grey matter volume (GMV) result in rarely replicated findings across large samples of healthy adults. However, the question remains if these observations are at least partly linked to the multidetermined nature of the variations in GMV, particularly within samples with wide age-range. Therefore, here we extended those evaluations and empirically investigated the replicability of associations of a broad range of psychometric variables and cortical thickness in a large cohort of healthy young adults. In line with our observations with GMV, our current analyses revealed low likelihood of significant associations and their rare replication across independent samples. We here discuss the implications of these findings within the context of accumulating evidence of the general poor replicability of structural-brain-behaviour associations, and more broadly of the replication crisis.

CLEAN: Leveraging spatial autocorrelation in neuroimaging data in clusterwise inference

While clusterwise inference is a popular approach in neuroimaging that improves sensitivity, current methods do not account for explicit spatial autocorrelations because most use univariate test statistics to construct cluster-extent statistics. Failure to account for such dependencies could result in decreased reproducibility. To address methodological and computational challenges, we propose a new powerful and fast statistical method called CLEAN (Clusterwise inference Leveraging spatial Autocorrelations in Neuroimaging). CLEAN computes multivariate test statistics by modelling brain-wise spatial autocorrelations, constructs cluster-extent test statistics, and applies a refitting-free resampling approach to control false positives. We validate CLEAN using simulations and applications to the Human Connectome Project. This novel method provides a new direction in neuroimaging that paces with advances in high-resolution MRI data which contains a substantial amount of spatial autocorrelation.

Characterization of Hemodynamic Alterations in Schizophrenia and Bipolar Disorder and Their Effect on Resting-State fMRI Functional Connectivity

Common and distinct neural bases of Schizophrenia (SZ) and bipolar disorder (BP) have been explored using resting-state fMRI (rs-fMRI) functional connectivity (FC). However, fMRI is an indirect measure of neural activity, which is a convolution of the hemodynamic response function (HRF) and latent neural activity. The HRF, which models neurovascular coupling, varies across the brain within and across individuals, and is altered in many psychiatric disorders. Given this background, this study had three aims: quantifying HRF aberrations in SZ and BP, measuring the impact of such HRF aberrations on FC group differences, and exploring the genetic basis of HRF aberrations. We estimated voxel-level HRFs by deconvolving rs-fMRI data obtained from SZ (N = 38), BP (N = 19), and matched healthy controls (N = 35). We identified HRF group differences (P < .05, FDR corrected) in many regions previously implicated in SZ/BP, with mediodorsal, habenular, and central lateral nuclei of the thalamus exhibiting HRF differences in all pairwise group comparisons. Thalamus seed-based FC analysis revealed that ignoring HRF variability results in false-positive and false-negative FC group differences, especially in insula, superior frontal, and lingual gyri. HRF was associated with DRD2 gene expression (P < .05, 1.62 < |Z| < 2.0), as well as with medication dose (P < .05, 1.75 < |Z| < 3.25). In this first study to report HRF aberrations in SZ and BP, we report the possible modulatory effect of dopaminergic signalling on HRF, and the impact that HRF variability can have on FC studies in clinical samples. To mitigate the impact of HRF variability on FC group differences, we suggest deconvolution during data preprocessing.

A protocol for working with open-source neuroimaging datasets

Large, publicly available neuroimaging datasets are becoming increasingly common, but their use presents challenges because of insufficient knowledge of the tool options for data processing and proper data organization. Here, we describe a protocol to lessen these barriers. We describe the steps for the search and download of the open-source dataset. We detail the steps for proper data management and practical guidelines for data analysis. Finally, we give instructions for data and result sharing on public repositories and preprint services. For complete details on the use and execution of this profile, please refer to Horien et al. (2021).

Associations of sleep measures with neural activations accompanying fear conditioning and extinction learning and memory in trauma-exposed individuals

STUDY OBJECTIVES

Sleep disturbances increase risk of posttraumatic stress disorder (PTSD). Sleep effects on extinction may contribute to such risk. Neural activations to fear extinction were examined in trauma-exposed participants and associated with sleep variables.

METHODS

Individuals trauma-exposed within the past 2 years (N = 126, 63 PTSD) completed 2 weeks actigraphy and sleep diaries, three nights ambulatory polysomnography and a 2-day fMRI protocol with Fear-Conditioning, Extinction-Learning and, 24 h later, Extinction-Recall phases. Activations within the anterior cerebrum and regions of interest (ROI) were examined within the total, PTSD-diagnosed and trauma-exposed control (TEC) groups. Sleep variables were used to predict activations within groups and among total participants. Family wise error was controlled at p < 0.05 using nonparametric analysis with 5,000 permutations.

RESULTS

Initially, Fear Conditioning activated broad subcortical and cortical anterior-cerebral regions. Within-group analyses showed: (1) by end of Fear Conditioning activations decreased in TEC but not PTSD; (2) across Extinction Learning, TEC activated medial prefrontal areas associated with emotion regulation whereas PTSD did not; (3) beginning Extinction Recall, PTSD activated this emotion-regulatory region whereas TEC did not. However, the only between-group contrast reaching significance was greater activation of a hippocampal ROI in TEC at Extinction Recall. A greater number of sleep variables were associated with cortical activations in separate groups versus the entire sample and in PTSD versus TEC.

CONCLUSIONS

PTSD nonsignificantly delayed extinction learning relative to TEC possibly increasing vulnerability to pathological anxiety. The influence of sleep integrity on brain responses to threat and extinction may be greater in more symptomatic individuals.

Signatures of life course socioeconomic conditions in brain anatomy

Socioeconomic status (SES) plays a significant role in health and disease. At the same time, early-life conditions affect neural function and structure, suggesting the brain may be a conduit for the biological embedding of SES. Here, we investigate the brain anatomy signatures of SES in a large-scale population cohort aged 45-85 years. We assess both gray matter morphometry and tissue properties indicative of myelin content. Higher life course SES is associated with increased volume in several brain regions, including postcentral and temporal gyri, cuneus, and cerebellum. We observe more widespread volume differences and higher myelin content in the sensorimotor network but lower myelin content in the temporal lobe associated with childhood SES. Crucially, childhood SES differences persisted in adult brains even after controlling for adult SES, highlighting the unique contribution of early-life conditions to brain anatomy, independent of later changes in SES. These findings inform on the biological underpinnings of social inequality, particularly as they pertain to early-life conditions.

Neural Coding of Visual Objects Rapidly Reconfigures to Reflect Subtrial Shifts in Attentional Focus

Every day, we respond to the dynamic world around us by choosing actions to meet our goals. Flexible neural populations are thought to support this process by adapting to prioritize task-relevant information, driving coding in specialized brain regions toward stimuli and actions that are currently most important. Accordingly, human fMRI shows that activity patterns in frontoparietal cortex contain more information about visual features when they are task-relevant. However, if this preferential coding drives momentary focus, for example, to solve each part of a task in turn, it must reconfigure more quickly than we can observe with fMRI. Here, we used multivariate pattern analysis of magnetoencephalography data to test for rapid reconfiguration of stimulus information when a new feature becomes relevant within a trial. Participants saw two displays on each trial. They attended to the shape of a first target then the color of a second, or vice versa, and reported the attended features at a choice display. We found evidence of preferential coding for the relevant features in both trial phases, even as participants shifted attention mid-trial, commensurate with fast subtrial reconfiguration. However, we only found this pattern of results when the stimulus displays contained multiple objects and not in a simpler task with the same structure. The data suggest that adaptive coding in humans can operate on a fast, subtrial timescale, suitable for supporting periods of momentary focus when complex tasks are broken down into simpler ones, but may not always do so.

Lateral Prefrontal Cortex Is a Hub for Music Production from Structural Rules to Movements

Complex sequential behaviors, such as speaking or playing music, entail flexible rule-based chaining of single acts. However, it remains unclear how the brain translates abstract structural rules into movements. We combined music production with multimodal neuroimaging to dissociate high-level structural and low-level motor planning. Pianists played novel musical chord sequences on a muted MR-compatible piano by imitating a model hand on screen. Chord sequences were manipulated in terms of musical harmony and context length to assess structural planning, and in terms of fingers used for playing to assess motor planning. A model of probabilistic sequence processing confirmed temporally extended dependencies between chords, as opposed to local dependencies between movements. Violations of structural plans activated the left inferior frontal and middle temporal gyrus, and the fractional anisotropy of the ventral pathway connecting these two regions positively predicted behavioral measures of structural planning. A bilateral frontoparietal network was instead activated by violations of motor plans. Both structural and motor networks converged in lateral prefrontal cortex, with anterior regions contributing to musical structure building, and posterior areas to movement planning. These results establish a promising approach to study sequence production at different levels of action representation.

Mapping cortico-subcortical sensitivity to 4 Hz amplitude modulation depth in human auditory system with functional MRI

Temporal modulations in the envelope of acoustic waveforms at rates around 4 Hz constitute a strong acoustic cue in speech and other natural sounds. It is often assumed that the ascending auditory pathway is increasingly sensitive to slow amplitude modulation (AM), but sensitivity to AM is typically considered separately for individual stages of the auditory system. Here, we used blood oxygen level dependent (BOLD) fMRI in twenty human subjects (10 male) to measure sensitivity of regional neural activity in the auditory system to 4 Hz temporal modulations. Participants were exposed to AM noise stimuli varying parametrically in modulation depth to characterize modulation-depth effects on BOLD responses. A Bayesian hierarchical modeling approach was used to model potentially nonlinear relations between AM depth and group-level BOLD responses in auditory regions of interest (ROIs). Sound stimulation activated the auditory brainstem and cortex structures in single subjects. BOLD responses to noise exposure in core and belt auditory cortices scaled positively with modulation depth. This finding was corroborated by whole-brain cluster-level inference. Sensitivity to AM depth variations was particularly pronounced in the Heschl's gyrus but also found in higher-order auditory cortical regions. None of the sound-responsive subcortical auditory structures showed a BOLD response profile that reflected the parametric variation in AM depth. The results are compatible with the notion that early auditory cortical regions play a key role in processing low-rate modulation content of sounds in the human auditory system.

Taking the 4D Nature of fMRI Data Into Account Promises Significant Gains in Data Completion

Functional magnetic resonance imaging (fMRI) is a powerful, noninvasive tool that has significantly contributed to the understanding of the human brain. FMRI data provide a sequence of whole-brain volumes over time and hence are inherently four dimensional (4D). Missing data in fMRI experiments arise from image acquisition limits, susceptibility and motion artifacts or during confounding noise removal. Hence, significant brain regions may be excluded from the data, which can seriously undermine the quality of subsequent analyses due to the significant number of missing voxels. We take advantage of the four dimensional (4D) nature of fMRI data through a tensor representation and introduce an effective algorithm to estimate missing samples in fMRI data. The proposed Riemannian nonlinear spectral conjugate gradient (RSCG) optimization method uses tensor train (TT) decomposition, which enables compact representations and provides efficient linear algebra operations. Exploiting the Riemannian structure boosts algorithm performance significantly, as evidenced by the comparison of RSCG-TT with state-of-the-art stochastic gradient methods, which are developed in the Euclidean space. We thus provide an effective method for estimating missing brain voxels and, more importantly, clearly show that taking the full 4D structure of fMRI data into account provides important gains when compared with three-dimensional (3D) and the most commonly used two-dimensional (2D) representations of fMRI data.

Considering Hemispheric Specialization in Emotional Face Processing: An Eye Tracking Study in Left- and Right-Lateralised Semantic Dementia

Face processing relies on a network of occipito-temporal and frontal brain regions. Temporal regions are heavily involved in looking at and processing emotional faces; however, the contribution of each hemisphere to this process remains under debate. Semantic dementia (SD) is a rare neurodegenerative brain condition characterized by anterior temporal lobe atrophy, which is either predominantly left- (left-SD) or right-lateralised (right-SD). This syndrome therefore provides a unique lesion model to understand the role of laterality in emotional face processing. Here, we investigated facial scanning patterns in 10 left-SD and 6 right-SD patients, compared to 22 healthy controls. Eye tracking was recorded via a remote EyeLink 1000 system, while participants passively viewed fearful, happy, and neutral faces over 72 trials. Analyses revealed that right-SD patients had more fixations to the eyes than controls in the Fear (p = 0.04) condition only. Right-SD patients also showed more fixations to the eyes than left-SD patients in all conditions: Fear (p = 0.01), Happy (p = 0.008), and Neutral (p = 0.04). In contrast, no differences between controls and left-SD patients were observed for any emotion. No group differences were observed for fixations to the mouth, or the whole face. This study is the first to examine patterns of facial scanning in left- versus right- SD, demonstrating more of a focus on the eyes in right-SD. Neuroimaging analyses showed that degradation of the right superior temporal sulcus was associated with increased fixations to the eyes. Together these results suggest that right lateralised brain regions of the face processing network are involved in the ability to efficiently utilise changeable cues from the face.

Moderated t-tests for group-level fMRI analysis

In recent years, there has been significant criticism of functional magnetic resonance imaging (fMRI) studies with small sample sizes. The argument is that such studies have low statistical power, as well as reduced likelihood for statistically significant results to be true effects. The prevalence of these studies has led to a situation where a large number of published results are not replicable and likely false. Despite this growing body of evidence, small sample fMRI studies continue to be regularly performed; likely due to the high cost of scanning. In this report we investigate the use of a moderated t-statistic for performing group-level fMRI analysis to help alleviate problems related to small sample sizes. The proposed approach, implemented in the popular R-package LIMMA (linear models for microarray data), has found wide usage in the genomics literature for dealing with similar issues. Utilizing task-based fMRI data from the Human Connectome Project (HCP), we compare the performance of the moderated t-statistic with the standard t-statistic, as well as the pseudo t-statistic commonly used in non-parametric fMRI analysis. We find that the moderated t-test significantly outperforms both alternative approaches for studies with sample sizes less than 40 subjects. Further, we find that the results were consistent both when using voxel-based and cluster-based thresholding. We also introduce an R-package, LIMMI (linear models for medical images), that provides a quick and convenient way to apply the method to fMRI data.

A guide to the measurement and interpretation of fMRI test-retest reliability

The test-retest reliability of functional neuroimaging data has recently been a topic of much discussion. Despite early conflicting reports, converging reports now suggest that test-retest reliability is poor for standard univariate measures-namely, voxel- and region-level task-based activation and edge-level functional connectivity. To better understand the implications of these recent studies requires understanding the nuances of test-retest reliability as commonly measured by the intraclass correlation coefficient (ICC). Here we provide a guide to the measurement and interpretation of test-retest reliability in functional neuroimaging and review major findings in the literature. We highlight the importance of making choices that improve reliability so long as they do not diminish validity, pointing to the potential of multivariate approaches that improve both. Finally, we discuss the implications of recent reports of low test-retest reliability in the context of ongoing work in the field.

The role of the left and right inferior frontal gyrus in processing metaphoric and unrelated co-speech gestures

Gestures are an integral part of in-person conversations and complement the meaning of the speech they accompany. The neural processing of co-speech gestures is supported by a mostly left-lateralized network of fronto-temporal regions. However, in contrast to iconic gestures, metaphoric as well as unrelated gestures have been found to more strongly engage the left and right inferior frontal gyrus (IFG), respectively. With this study, we conducted the first systematic comparison of all three types of gestures and resulting potential laterality effects. During collection of functional imaging data, 74 subjects were presented with 5 s videos of abstract speech with related metaphoric gestures, concrete speech with related iconic gestures and concrete speech with unrelated gestures. They were asked to judge whether the content of the speech and gesture matched or not. Differential contrasts revealed that both abstract related and concrete unrelated compared to concrete related stimuli elicited stronger activation of the bilateral IFG. Analyses of lateralization indices for IFG activation further showed a left hemispheric dominance for metaphoric gestures and a right hemispheric dominance for unrelated gestures. Our results give support to the hypothesis that the bilateral IFG is activated specifically when processing load for speech-gesture combinations is high. In addition, laterality effects indicate a stronger involvement of the right IFG in mismatch detection and conflict processing, whereas the left IFG performs the actual integration of information from speech and gesture.

Improving the sensitivity of cluster-based statistics for functional magnetic resonance imaging data

Because of the high dimensionality of neuroimaging data, identifying a statistical test that is both valid and maximally sensitive is an important challenge. Here, we present a combination of two approaches for functional magnetic resonance imaging (fMRI) data analysis that together result in substantial improvements of the sensitivity of cluster‐based statistics. The first approach is to create novel cluster definitions that optimize sensitivity to plausible effect patterns. The second is to adopt a new approach to combine test statistics with different sensitivity profiles, which we call the min(p) method. These innovations are made possible by using the randomization inference framework. In this article, we report on a set of simulations and analyses of real task fMRI data that demonstrate (a) that the proposed methods control the false‐alarm rate, (b) that the sensitivity profiles of cluster‐based test statistics vary depending on the cluster defining thresholds and cluster definitions, and (c) that the min(p) method for combining these test statistics results in a drastic increase of sensitivity (up to fivefold), compared to existing fMRI analysis methods. This increase in sensitivity is not at the expense of the spatial specificity of the inference.

Beyond language impairment: Profiles of apathy in primary progressive aphasia

Primary progressive aphasia (PPA) is characterised by predominant language and communication impairment. However, behavioural changes, such as apathy, are increasingly recognised. Apathy is defined as a reduction in motivation and goal-directed behaviour. Recent theoretical models have suggested that apathy can be delineated into multiple dimensions: executive apathy (i.e., deficits in maintaining goals and organisation), emotional apathy (i.e., emotional blunting and indifference) and initiation apathy (i.e., reduced self-initiation). Whether the nature of apathy differs between clinical variants of PPA, and across early and late disease stages, remains to be established. Here, carers/informants of 20 semantic variant PPA (svPPA), 15 non-fluent variant PPA (nfvPPA), 16 logopenic variant PPA (lvPPA) and 25 healthy older controls completed the Dimensional Apathy Scale to quantify executive, emotional and initiation apathy. Voxel-based morphometry was used to identify associations between dimensions of apathy and regions of grey matter intensity decrease. Our behavioural results showed greater executive and initiation apathy in late svPPA than in late nfvPPA patients, while late svPPA had greater emotional apathy than both late nfvPPA and late lvPPA groups. Executive and initiation apathy were significantly higher than premorbid levels in all PPA subtypes, while elevated emotional apathy was only seen in early and late svPPA. Distinct neural correlates were identified across apathy dimensions. Executive apathy correlated with grey matter intensity of the left dorsolateral prefrontal and inferior parietal cortices; emotional apathy with the left medial prefrontal, insular and cerebellar regions; and initiation apathy with right parietal areas. Our findings are the first to reveal evidence of the dimensional nature of apathy in PPA, with different clinical signatures observed for each subtype. From a clinical standpoint, these results will inform the development of targeted interventions for specific aspects of apathy which emerge in PPA.

Decoding with confidence: Statistical control on decoder maps

In brain imaging, decoding is widely used to infer relationships between brain and cognition, or to craft brain-imaging biomarkers of pathologies. Yet, standard decoding procedures do not come with statistical guarantees, and thus do not give confidence bounds to interpret the pattern maps that they produce. Indeed, in whole-brain decoding settings, the number of explanatory variables is much greater than the number of samples, hence classical statistical inference methodology cannot be applied. Specifically, the standard practice that consists in thresholding decoding maps is not a correct inference procedure. We contribute a new statistical-testing framework for this type of inference. To overcome the statistical inefficiency of voxel-level control, we generalize the Family Wise Error Rate (FWER) to account for a spatial tolerance δ, introducing the δ-Family Wise Error Rate (δ-FWER). Then, we present a decoding procedure that can control the δ-FWER: the Ensemble of Clustered Desparsified Lasso (EnCluDL), a procedure for multivariate statistical inference on high-dimensional structured data. We evaluate the statistical properties of EnCluDL with a thorough empirical study, along with three alternative procedures including decoder map thresholding. We show that EnCluDL exhibits the best recovery properties while ensuring the expected statistical control.

Confidence Sets for Cohen's d effect size images

Current statistical inference methods for task-fMRI suffer from two fundamental limitations. First, the focus is solely on detection of non-zero signal or signal change, a problem that is exacerbated for large scale studies (e.g. UK Biobank, N=40,000+) where the 'null hypothesis fallacy' causes even trivial effects to be determined as significant. Second, for any sample size, widely used cluster inference methods only indicate regions where a null hypothesis can be rejected, without providing any notion of spatial uncertainty about the activation. In this work, we address these issues by developing spatial Confidence Sets (CSs) on clusters found in thresholded Cohen's d effect size images. We produce an upper and lower CS to make confidence statements about brain regions where Cohen's d effect sizes have exceeded and fallen short of a non-zero threshold, respectively. The CSs convey information about the magnitude and reliability of effect sizes that is usually given separately in a t-statistic and effect estimate map. We expand the theory developed in our previous work on CSs for %BOLD change effect maps (Bowring et al., 2019) using recent results from the bootstrapping literature. By assessing the empirical coverage with 2D and 3D Monte Carlo simulations resembling fMRI data, we find our method is accurate in sample sizes as low as N=60. We compute Cohen's d CSs for the Human Connectome Project working memory task-fMRI data, illustrating the brain regions with a reliable Cohen's d response for a given threshold. By comparing the CSs with results obtained from a traditional statistical voxelwise inference, we highlight the improvement in activation localization that can be gained with the Confidence Sets.

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

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