Increased power by harmonizing structural MRI site differences with the ComBat batch adjustment method in ENIGMA

Atlas of Gray Matter Volume Differences Across Psychiatric Conditions: A Systematic Review With a Novel Meta-Analysis That Considers Co-Occurring Disorders

BACKGROUND

Regional gray matter volume (GMV) differences between individuals with mental disorders and comparison participants may be confounded by co-occurring disorders. To disentangle disorder-specific GMV correlates, we conducted a large-scale multidisorder meta-analysis using a novel approach that explicitly models co-occurring disorders.

METHODS

We systematically reviewed voxel-based morphometry studies indexed in PubMed and Scopus up to January 2023 that compared adults with major mental disorders (anorexia nervosa, schizophrenia spectrum, anxiety, bipolar, major depressive, obsessive-compulsive, and posttraumatic stress disorders plus attention-deficit/hyperactivity, autism spectrum, and borderline personality disorders) with comparison participants. Two authors independently extracted data and assessed quality using the Newcastle-Ottawa Scale. We derived GMV correlates for each disorder using: 1) a multidisorder meta-analysis that accounted for all co-occurring mental disorders simultaneously and 2) separate standard meta-analyses for each disorder in which co-occurring disorders were ignored. We assessed the alterations' extent, intensity (effect size), and specificity (interdisorder correlations and transdiagnostic alterations) for both approaches.

RESULTS

We included 433 studies (499 datasets) involving 19,718 patients and 16,441 comparison participants (51% female, ages 20-67 years). We provide GMV correlate maps for each disorder using both approaches. The novel approach, which accounted for co-occurring disorders, produced GMV correlates that were more focal and disorder specific (less correlated across disorders and fewer transdiagnostic abnormalities).

CONCLUSIONS

This work offers the most comprehensive atlas of GMV correlates across major mental disorders. Modeling co-occurring disorders yielded more specific correlates, supporting this approach's validity. The atlas NIfTI maps are available online.

ComBatLS: A Location- and Scale-Preserving Method for Multi-Site Image Harmonization

Recent study has leveraged massive datasets and advanced harmonization methods to construct normative models of neuroanatomical features and benchmark individuals' morphology. However, current harmonization tools do not preserve the effects of biological covariates including sex and age on features' variances; this failure may induce error in normative scores, particularly when such factors are distributed unequally across sites. Here, we introduce a new extension of the popular ComBat harmonization method, ComBatLS, that preserves biological variance in features' locations and scales. We use UK Biobank data to show that ComBatLS robustly replicates individuals' normative scores better than other ComBat methods when subjects are assigned to sex-imbalanced synthetic "sites." Additionally, we demonstrate that ComBatLS significantly reduces sex biases in normative scores compared to traditional methods. Finally, we show that ComBatLS successfully harmonizes consortium data collected across over 50 studies. R implementation of ComBatLS is available at https://github.com/andy1764/ComBatFamily.

Distinct brain atrophy progression subtypes underlie phenoconversion in isolated REM sleep behaviour disorder

BACKGROUND

Synucleinopathies include a spectrum of disorders varying in features and severity, including idiopathic/isolated REM sleep behaviour disorder (iRBD), Parkinson's disease (PD), and dementia with Lewy bodies (DLB). Distinct brain atrophy patterns may already be seen in iRBD; however, how brain atrophy begins and progresses remains unclear.

METHODS

A multicentric cohort of 1276 participants (451 polysomnography-confirmed iRBD, 142 PD with probable RBD, 87 DLB, and 596 controls) underwent T1-weighted MRI and longitudinal clinical assessments. Brain atrophy was quantified using vertex-based cortical surface reconstruction and volumetric segmentation. The unsupervised machine learning algorithm, Subtype and Stage Inference (SuStaIn), was used to reconstruct spatiotemporal patterns of brain atrophy progression.

FINDINGS

SuStaIn identified two distinct subtypes of brain atrophy progression: 1) a "cortical-first" subtype, with atrophy beginning in the frontal lobes and involving the subcortical structures at later stages; and 2) a "subcortical-first" subtype, with atrophy beginning in the limbic areas and involving cortical structures at later stages. Both cortical- and subcortical-first subtypes were associated with a higher rate of increase in MDS-UPDRS-III scores over time, but cognitive decline was subtype-specific, being associated with advancing stages in patients classified as cortical-first but not subcortical-first. Classified patients were more likely to phenoconvert over time compared to stage 0/non-classified patients. Among the 88 patients with iRBD who phenoconverted during follow-up, those classified within the cortical-first subtype had a significantly increased likelihood of developing DLB compared to PD, unlike those classified within the subcortical-first subtype.

INTERPRETATION

There are two distinct atrophy progression subtypes in iRBD, with the cortical-first subtype linked to an increased likelihood of developing DLB, while both subtypes were associated with worsening parkinsonian motor features. This underscores the potential utility of subtype identification and staging for monitoring disease progression and patient selection for trials.

FUNDING

This study was supported by grants to S.R. from Alzheimer Society Canada (0000000082) and by Parkinson Canada (PPG-2023-0000000122). The work performed in Montreal was supported by the Canadian Institutes of Health Research (CIHR), the Fonds de recherche du Québec - Santé (FRQS), and the W. Garfield Weston Foundation. The work performed in Oxford was funded by Parkinson's UK (J-2101) and the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC). The work performed in Prague was funded by the Czech Health Research Council (grant NU21-04-00535) and by The National Institute for Neurological Research (project number LX22NPO5107), financed by the European Union - Next Generation EU. The work performed in Newcastle was funded by the NIHR Newcastle BRC based at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University. The work performed in Paris was funded by grants from the Programme d'investissements d'avenir (ANR-10-IAIHU-06), the Paris Institute of Neurosciences - IHU (IAIHU-06), the Agence Nationale de la Recherche (ANR-11-INBS-0006), Électricité de France (Fondation d'Entreprise EDF), the EU Joint Programme-Neurodegenerative Disease Research (JPND) for the Control-PD Project (Cognitive Propagation in Prodromal Parkinson's disease), the Fondation Thérèse et René Planiol, the Fonds Saint-Michel; by unrestricted support for research on Parkinson's disease from Energipole (M. Mallart) and the Société Française de Médecine Esthétique (M. Legrand); and by a grant from the Institut de France to Isabelle Arnulf (for the ALICE Study). The work performed in Sydney was supported by a Dementia Team Grant from the National Health and Medical Research Council (#1095127). The work performed in Cologne was funded by the Else Kröner-Fresenius-Stiftung (grant number 2019_EKES.02), the Köln Fortune Program, Faculty of Medicine, University of Cologne, and the "Netzwerke 2021 Program (Ministry of Culture and Science of Northrhine Westphalia State). The work performed in Aarhus was supported by funding from the Lundbeck Foundation, Parkinsonforeningen (The Danish Parkinson Association), and the Jascha Foundation.

Burst of gyrification in the human brain after birth

Gyrification, the intricate folding of the brain's cortex, begins mid-gestation and surges dramatically throughout the perinatal period. Yet, a critical factor has been largely overlooked in neurodevelopmental research: the profound impact of birth on brain structure. Leveraging the largest known perinatal MRI dataset-819 sessions spanning 21 to 45 postconceptional weeks-we reveal a burst in gyrification immediately following birth (~37 weeks post-conception), amounting to half the entire gyrification expansion occurring during the fetal period. Using state-of-the-art, homogenized imaging processing tools across varied acquisition protocols, and applying a regression discontinuity design approach that is novel to neuroimaging, we provide the first evidence of a sudden, birth-triggered shift in cortical development. Investigation of additional cortical features confirms that this effect is uniquely confined to gyrification. This finding sheds light onto the understanding of early brain development, suggesting that the neurobiological consequences of birth may hold significant behavioral and physiological relevance.

Lifespan reference curves for harmonizing multi-site regional brain white matter metrics from diffusion MRI

Age-related white matter (WM) microstructure maturation and decline occur throughout the human lifespan, complementing the process of gray matter development and degeneration. Here, we create normative lifespan reference curves for global and regional WM microstructure by harmonizing diffusion MRI (dMRI)-derived data from ten public datasets (N = 40,898 subjects; age: 3-95 years; 47.6% male). We tested three harmonization methods on regional diffusion tensor imaging (DTI) based fractional anisotropy (FA), a metric of WM microstructure, extracted using the ENIGMA-DTI pipeline. ComBat-GAM harmonization provided multi-study trajectories most consistent with known WM maturation peaks. Lifespan FA reference curves were validated with test-retest data and used to assess the effect of the ApoE4 risk factor for dementia in WM across the lifespan. We found significant associations between ApoE4 and FA in WM regions associated with neurodegenerative disease even in healthy individuals across the lifespan, with regional age-by-genotype interactions. Our lifespan reference curves and tools to harmonize new dMRI data to the curves are publicly available as eHarmonize ( https://github.com/ahzhu/eharmonize ).

Rethinking MRI as a measurement device through modular and portable pipelines

The premise of MRI as a reliable measurement device is limited by proprietary barriers and inconsistent implementations, which prevent the establishment of measurement uncertainties. As a result, biomedical studies that rely on these methods are plagued by systematic variance, undermining the perceived promise of quantitative imaging biomarkers (QIBs) and hindering their clinical translation. This review explores the added value of open-source measurement pipelines in minimizing variability sources that would otherwise remain unknown. First, we introduce a tiered benchmarking framework (from black-box to glass-box) that exposes how opacity at different workflow stages propagates measurement uncertainty. Second, we provide a concise glossary to promote consistent terminology for strategies that enhance reproducibility before acquisition or enable valid post-hoc pooling of QIBs. Building on this foundation, we present two illustrative measurement workflows that decouple workflow logic from the orchestration of computational processes in an MRI measurement pipeline, rooted in the core principles of modularity and portability. Designed as accessible entry points for implementation, these examples serve as practical guides, helping users adapt the frameworks to their specific needs and facilitating collaboration. Through critical evaluation of existing approaches, we discuss how standardized workflows can help identify outstanding challenges in translating glass-box frameworks into clinical scanner environments. Ultimately, achieving this goal will require coordinated efforts from QIB developers, regulators, industry partners, and clinicians alike.

Transdiagnostic Neurobiology of Social Cognition and Individual Variability as Measured by Fractional Amplitude of Low-Frequency Fluctuation in Autism and Schizophrenia Spectrum Disorders

BACKGROUND

Fractional amplitude of low-frequency fluctuation (fALFF) is a validated measure of resting-state spontaneous brain activity. Previous fALFF findings in autism and schizophrenia spectrum disorders (SSDs) have been highly heterogeneous. We aimed to use fALFF in a large sample of typically developing control (TDC), autistic, and SSD participants to explore group differences and relationships with inter-individual variability of fALFF maps and social cognition.

METHODS

FALFF from 495 participants (185 TDC, 68 autism, and 242 SSD) was computed using functional magnetic resonance imaging as signal power within two frequency bands (i.e., slow-4 and slow-5), normalized by the power in the remaining frequency spectrum. Permutation analysis of linear models was employed to investigate the relationship of fALFF with diagnostic groups, higher-level social cognition, and lower-level social cognition. Each participant's average distance of fALFF map to all others was defined as a variability score, with higher scores indicating less typical maps.

RESULTS

Lower fALFF in the visual and higher fALFF in the frontal regions were found in both SSD and autistic participants compared with TDCs. Limited differences were observed between autistic and SSD participants in the cuneus regions only. Associations between slow-4 fALFF and higher-level social cognitive scores across the whole sample were observed in the lateral occipitotemporal and temporoparietal junction. Individual variability within the autism and SSD groups was also significantly higher compared with TDC.

CONCLUSIONS

Similar patterns of fALFF and individual variability in autism and SSD suggest some common neurobiological features across these related heterogeneous conditions.

Atypical hierarchical brain connectivity in autism: Insights from stepwise causal analysis using Liang information flow

Autism spectrum disorder (ASD) is associated with atypical brain connectivity, yet its hierarchical organization remains underexplored. In this study, we applied the Liang information flow method to analyze stepwise causal functional connectivity in ASD, offering a novel approach to understanding how different brain networks interact. Using resting-state fMRI data from ASD individuals and healthy controls, we observed significant alterations in both positive and negative causal connections across the ventral attention network, limbic network, frontal-parietal network, and default mode network. These disruptions were detected at multiple hierarchical levels, indicating changes in communication patterns across brain regions. By leveraging features of hierarchical causal connectivity, we achieved high classification accuracy between ASD and healthy individuals. Additionally, changes in network node degrees were found to correlate with ASD clinical symptoms, particularly social and communication behaviors. Our findings provide new insights into disrupted hierarchical brain connectivity in ASD and demonstrate the potential of this approach for distinguishing ASD from typical development.

Site effects in multisite fetal brain MRI: morphological insights into early brain development

OBJECTIVE

To evaluate multisite effects on fetal brain MRI. Specifically, to identify crucial acquisition factors affecting fetal brain structural measurements and developmental patterns, while assessing the effectiveness of existing harmonization methods in mitigating site effects.

MATERIALS AND METHODS

Between May 2017 and March 2022, T2-weighted fast spin-echo sequences in-utero MRI were performed on healthy fetuses from retrospectively recruited pregnant volunteers on four different scanners at four sites. A generalized additive model (GAM) was used to quantitatively assess site effects, including field strength (FS), manufacturer (M), in-plane resolution (R), and slice thickness (ST), on subcortical volume and cortical morphological measurements, including cortical thickness, curvature, and sulcal depth. Growth models were selected to elucidate the developmental trajectories of these morphological measurements. Welch's test was performed to evaluate the influence of site effects on developmental trajectories. The comBat-GAM harmonization method was applied to mitigate site-related biases.

RESULTS

The final analytic sample consisted of 340 MRI scans from 218 fetuses (mean GA, 30.1 weeks ± 4.4 [range, 21.7-40 weeks]). GAM results showed that lower FS and lower spatial resolution led to overestimations in selected brain regions of subcortical volumes and cortical morphological measurements. Only the peak cortical thickness in developmental trajectories was significantly influenced by the effects of FS and R. Notably, ComBat-GAM harmonization effectively removed site effects while preserving developmental patterns.

CONCLUSION

Our findings pinpointed the key acquisition factors in in-utero fetal brain MRI and underscored the necessity of data harmonization when pooling multisite data for fetal brain morphology investigations.

KEY POINTS

Question How do specific site MRI acquisition factors affect fetal brain imaging? Finding Lower FS and spatial resolution overestimated subcortical volumes and cortical measurements. Cortical thickness in developmental trajectories was influenced by FS and in-plane resolution. Clinical relevance This study provides important guidelines for the fetal MRI community when scanning fetal brains and underscores the necessity of data harmonization of cross-center fetal studies.

Beyond case-control study in neuroimaging for psychiatric disorders: Harmonizing and utilizing the brain images from multiple sites

Recent magnetic resonance imaging (MRI) research has advanced our understanding of brain pathophysiology in psychiatric disorders. This progress necessitates re-evaluation of the diagnostic system for psychiatric disorders based on MRI-based biomarkers, with implications for precise clinical diagnosis and optimal therapeutics. To achieve this goal, large-scale multi-site studies are essential to develop a standardized MRI database, with the analysis of several thousands of images and the incorporation of new data. A critical challenge in these studies is to minimize sampling and measurement biases in MRI studies to accurately capture the diversity of disease-derived biomarkers. Various techniques have been employed to consolidate datasets from multiple sites in case-control studies. Traveling subject harmonization stands out as a powerful tool that can differentiate measurement bias from sample variety and sampling bias. A non-linear statistical model for a normative trajectory across the lifespan also strengthens the database to mitigate sampling bias from known factors such as age and sex. These approaches can enhance the alterations between psychiatric disorders and integrate new data and follow-up scans into existing life-course trajectory, enhancing the reliability of machine learning classification and subtyping. Although this approach has been developed using T1-weighted structural image features, future research may extend this framework to other modalities and measures. The required sample size and methodological establishment are needed for future investigations, leading to novel insights into the brain pathophysiology of psychiatric disorders and the development of optimal therapeutics for bedside clinical applications. Sharing big data and their findings also need to be considered.

Neural basis for individual differences in the attention-enhancing effects of methylphenidate

Stimulant drugs that boost dopamine, like methylphenidate (MP), enhance attention and are effective treatments for attention-deficit hyperactivity disorder (ADHD). Yet there is large individual variation in attentional capacity and response to MP. It is unclear whether this variation is driven by individual differences in relative density of dopamine receptor subtypes, magnitude of dopamine increases induced by MP, or both. Here, we extensively characterized the brain dopamine system with positron emission tomography (PET) imaging (including striatal dopamine D1 and D2/3 receptor availability and MP-induced dopamine increases) and measured attention task-evoked fMRI brain activity in two separate sessions (placebo and 60 mg oral MP; single-blind, counterbalanced) in 37 healthy adults. A network of lateral frontoparietal and visual cortices was sensitive to increasing attentional (and working memory) load, whose activity positively correlated with performance across individuals (partial r = 0.474, P = 0.008; controlling for age). MP-induced change in activity within this network correlated with MP-induced change in performance (partial r = 0.686, P < 0.001). The ratio of D1-to-D2/3 receptors in dorsomedial caudate positively correlated with baseline attentional network activity and negatively correlated with MP-induced changes in activity (all pFWE < 0.02). MP-induced changes in attentional load network activity mediated the association between D1-to-D2/3 ratio and MP-induced improvements in performance (mediation estimate = 23.20 [95%CI: -153.67 -81.79], P = 0.004). MP attention-boosting effects were not linked to the magnitude of striatal dopamine increases, but rather showed dependence on an individual's baseline receptor density. Individuals with lower D1-to-D2/3 ratios tended to have lower frontoparietal activity during sustained attention and experienced greater improvement in brain function and task performance with MP.

ENIGMA-Meditation: Worldwide Consortium for Neuroscientific Investigations of Meditation Practices

Meditation is a family of ancient and contemporary contemplative mind-body practices that can modulate psychological processes, awareness, and mental states. Over the last 40 years, clinical science has manualized meditation practices and designed various meditation interventions that have shown therapeutic efficacy for disorders including depression, pain, addiction, and anxiety. Over the past decade, neuroimaging has been used to examine the neuroscientific basis of meditation practices, effects, states, and outcomes for clinical and nonclinical populations. However, the generalizability and replicability of current neuroscientific models of meditation have not yet been established, because they are largely based on small datasets entrenched with heterogeneity along several domains of meditation (e.g., practice types, meditation experience, clinical disorder targeted), experimental design, and neuroimaging methods (e.g., preprocessing, analysis, task-based, resting-state, structural magnetic resonance imaging). These limitations have precluded a nuanced and rigorous neuroscientific phenotyping of meditation practices and their potential benefits. Here, we present ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis)-Meditation, the first worldwide collaborative consortium for neuroscientific investigations of meditation practices. ENIGMA-Meditation will enable systematic meta- and mega-analyses of globally distributed neuroimaging datasets of meditation using shared, standardized neuroimaging methods and tools to improve statistical power and generalizability. Through this powerful collaborative framework, existing neuroscientific accounts of meditation practices can be extended to generate novel and rigorous neuroscientific insights that account for multidomain heterogeneity. ENIGMA-Meditation will inform neuroscientific mechanisms that underlie therapeutic action of meditation practices on psychological and cognitive attributes, thereby advancing the field of meditation and contemplative neuroscience.

A generalizable normative deep autoencoder for brain morphological anomaly detection: application to the multi-site StratiBip dataset on bipolar disorder in an external validation framework

The heterogeneity of psychiatric disorders makes researching disorder-specific neurobiological markers an ill-posed problem. Here, we face the need for disease stratification models by presenting a generalizable multivariate normative modelling framework for characterizing brain morphology, applied to bipolar disorder (BD). We used deep autoencoders in an anomaly detection framework, combined for the first time with a confounder removal step that integrates training and external validation. The model was trained with healthy control (HC) data from the human connectome project and applied to multi-site external data of HC and BD individuals. We found that brain deviating scores were greater, more heterogeneous, and with increased extreme values in the BD group, with volumes prominently from the basal ganglia, hippocampus, and adjacent regions emerging as significantly deviating. Similarly, individual brain deviating maps based on modified z scores expressed higher abnormalities occurrences, but their overall spatial overlap was lower compared to HCs. Our generalizable framework enabled the identification of brain deviating patterns differing between the subject and the group levels, a step forward towards the development of more effective and personalized clinical decision support systems and patient stratification in psychiatry.

Abnormal Functional Connectivity of the Primary Sensory Network in Autism Spectrum Disorder: Sex Differences, Early Overdevelopment, and Clinical Significance

INTRODUCTION

Primary sensory processing is atypical in patients with autism spectrum disorder (ASD) and affects daily functioning. However, the functional connectivity (FC) patterns of primary networks in ASD have not been systematically investigated.

METHODS

Primary networks were defined as four regions of interest (ROIs) in each brain hemisphere. We analyzed ROI-wise FC in 105 individuals with ASD and 132 typically developing (TD) participants from Autism Brain Imaging Data Exchange I. We calculated the correlation between abnormal FC and clinical scores. Additionally, data from 53 individuals with ASD from our laboratory's two-site dataset were used to validate the results and assess the effects of sex and age on FC consistency.

RESULTS

Regarding the ROI-wise connectivity, significant group differences in FC emerged in several regional pairs, particularly in the primary auditory and somatosensory regions. Abnormal brain regions correlated with clinical symptoms. As age increased, abnormal FC had an initial fast and then slowing development trend, and the abnormal FC in females was higher than that in males. The two-site dataset results were consistent with those of the multisite dataset in assessing the influence of age and sex on FC.

CONCLUSION

Abnormal FC exists in the primary sensory cortex of patients with ASD, which correlates with clinical outcomes and may cause impairments in advanced cognitive functions. In addition, the primary sensory cortex of patients with ASD may undergo excessive growth in the early stages and demonstrate imbalanced development according to sex. These findings may help identify new biomarkers for ASD.

The Psychosis MRI Shared Data Resource (Psy-ShareD)

Neuroimaging research in the field of schizophrenia and other psychotic disorders has sought to investigate neuroanatomical markers, relative to healthy control groups. In recent decades, a large number of structural magnetic resonance imaging (MRI) studies have been funded and undertaken, but their small sample sizes and heterogeneous methods have led to inconsistencies across findings. To tackle this, efforts have been made to combine datasets across studies and sites. While notable recent multicentre initiatives and the resulting meta- and mega-analytical outputs have progressed the field, efforts have generally been restricted to MRI scans in one or two illness stages, often overlook patient heterogeneity, and study populations have rarely been globally representative of the diversity of patients who experience psychosis. Furthermore, access to these datasets is often restricted to consortia members who can contribute data, likely from research institutions located in high-income countries. The Psychosis MRI Shared Data Resource (Psy-ShareD) is a new open access structural MRI data sharing partnership that will host pre-existing structural T1-weighted MRI data collected across multiple sites worldwide, including the Global South. MRI T1 data included in Psy-ShareD will be available in image and feature-level formats, having been harmonised using state-of-the-art approaches. All T1 data will be linked to demographic and illness-related (diagnosis, symptoms, medication status) measures, and in a number of datasets, IQ and cognitive data, and medication history will also be available, allowing subgroup and dimensional analyses. Psy-ShareD will be free-to-access for all researchers. Importantly, comprehensive data catalogues, scientific support and training resources will be available to facilitate use by early career researchers and build capacity in the field. We are actively seeking new collaborators to contribute further T1 data. Collaborators will benefit in terms of authorships, as all publications arising from Psy-ShareD will include data contributors as authors.

Classification of Major Depressive Disorder Using Vertex-Wise Brain Sulcal Depth, Curvature, and Thickness with a Deep and a Shallow Learning Model

Major depressive disorder (MDD) is a complex psychiatric disorder that affects the lives of hundreds of millions of individuals around the globe. Even today, researchers debate if morphological alterations in the brain are linked to MDD, likely due to the heterogeneity of this disorder. The application of deep learning tools to neuroimaging data, capable of capturing complex non-linear patterns, has the potential to provide diagnostic and predictive biomarkers for MDD. However, previous attempts to demarcate MDD patients and healthy controls (HC) based on segmented cortical features via linear machine learning approaches have reported low accuracies. In this study, we used globally representative data from the ENIGMA-MDD working group containing 7,012 participants from 30 sites (N=2,772 MDD and N=4,240 HC), which allows a comprehensive analysis with generalizable results. Based on the hypothesis that integration of vertex-wise cortical features can improve classification performance, we evaluated the classification of a DenseNet and a Support Vector Machine (SVM), with the expectation that the former would outperform the latter. As we analyzed a multi-site sample, we additionally applied the ComBat harmonization tool to remove potential nuisance effects of site. We found that both classifiers exhibited close to chance performance (balanced accuracy DenseNet: 51%; SVM: 53%), when estimated on unseen sites. Slightly higher classification performance (balanced accuracy DenseNet: 58%; SVM: 55%) was found when the cross-validation folds contained subjects from all sites, indicating site effect. In conclusion, the integration of vertex-wise morphometric features and the use of the non-linear classifier did not lead to the differentiability between MDD and HC. Our results support the notion that MDD classification on this combination of features and classifiers is unfeasible. Future studies are needed to determine whether more sophisticated integration of information from other MRI modalities such as fMRI and DWI will lead to a higher performance in this diagnostic task.

Subgroups of cognitive impairments in schizophrenia characterized by executive function and their morphological features: a latent profile analysis study

BACKGROUND

The heterogeneity of cognitive impairments in schizophrenia has been widely observed. However, reliable cognitive boundaries to differentiate the subgroups remain elusive. The key challenge for cognitive subtyping is applying an integrated and standardized cognitive assessment and understanding the subgroup-specific neurobiological mechanisms. The present study endeavors to explore cognitive subgroups and identify their morphological features.

METHODS

A total of 920 schizophrenia patients and 169 healthy controls were recruited. MATRICS Consensus Cognitive Battery was applied to assess cognitive performance and recognize cognitive subgroups through latent profile and latent transition analysis. Cortical thickness and gray matter volume were employed for the morphological features across subgroups.

RESULTS

Four reproducible cognitive subgroups were identified, including multidomain-intact, executive-preserved, executive-deteriorated, and multidomain-deteriorated subgroup. After 12 weeks of follow-up, the cognitive characteristics of three out of the four subgroups kept stability, except for multidomain-deteriorated subgroup in which 48.8% of patients with improved cognition transited into the executive-deteriorated subgroup. Across subgroups, significant gradient features of brain structure were exhibited in fronto-temporal regions, hippocampus, and insula. Compared to healthy controls, multidomain-intact subgroup showed the most intact cognition and morphology, and multidomain-deteriorated subgroup with youngest age showed morphological decline in extensive regions. The remaining two subgroups showed intermediate cognitive performance, but could be distinguished by executive function and morphological differences in posterior cingulate cortex.

CONCLUSIONS

Our study provides novel insights into the heterogeneity of cognitive impairments in schizophrenia and the morphological features from cross-sectional and longitudinal levels, which could advance our understanding of complex cognition-morphology relationships and guide personalized interventions.

Decomposing the Brain in Autism: Linking Behavioral Domains to Neuroanatomical Variation and Genomic Underpinnings

BACKGROUND

Autism is accompanied by highly individualized patterns of neurodevelopmental differences in brain anatomy. This variability makes the neuroanatomy of autism inherently difficult to describe at the group level. Here, we examined interindividual neuroanatomical differences using a dimensional approach that decomposed the domains of social communication and interaction (SCI), restricted and repetitive behaviors (RRBs), and atypical sensory processing (ASP) within a neurodiverse study population. Moreover, we aimed to link the resulting neuroanatomical patterns to specific molecular underpinnings.

METHODS

Neurodevelopmental differences in cortical thickness (CT) and surface area (SA) were correlated with SCI, RRB, and ASP domain scores by regression of a general linear model in a large neurodiverse sample of 288 autistic individuals and 140 nonautistic individuals, ages 6 to 30 years, recruited within the European Autism Interventions Longitudinal European Autism Project (EU-AIMS LEAP). The domain-specific patterns of neuroanatomical variability were subsequently correlated with cortical gene expression profiles via the Allen Human Brain Atlas.

RESULTS

Across groups, behavioral variations in SCI, RRBs, and ASP were associated with interindividual differences in CT and SA in partially non-overlapping frontoparietal, temporal, and occipital networks. These domain-specific imaging patterns were enriched for genes that 1) are differentially expressed in autism, 2) mediate typical brain development, and 3) are associated with specific cortical cell types. Many of these genes were implicated in pathways governing synaptic structure and function.

CONCLUSIONS

Our study corroborates the close relationship between neuroanatomical variation and interindividual differences in autism-related symptoms and traits within the general framework of neurodiversity and links domain-specific patterns of neuroanatomical differences to putative molecular underpinnings.

Assessment of ComBat Harmonization Performance on Structural Magnetic Resonance Imaging Measurements

Data aggregation across multiple research centers is gaining importance in the context of MRI research, driving diverse high-dimensional datasets to form large-scale heterogeneous sample, increasing statistical power and relevance of machine learning and deep learning algorithm. Site-related effects have been demonstrated to introduce bias in MRI features and confound subsequent analyses. Although Combating Batch (ComBat) technique has been recently reported to successfully harmonize multi-scale neuroimaging features, its performance assessments are still limited and largely based on qualitative visualizations and statistical analyses. In this study, we stand out by using a robust cross-validation approach to assess ComBat performances applied on volume- and surface-based measures acquired across three sites. A machine learning approach based on Multi-Class Gaussian Process Classifier was applied to predict imaging site based on raw and harmonized brain features, providing quantitative insights into ComBat effectiveness, and verifying the association between biological covariates and harmonized brain features. Our findings showed differences in terms of ComBat performances across measures of regional brain morphology, demonstrating tissue specific site effect modeling. ComBat adjustment of site effects also varied across regional level of each specific volume-based and surface-based measures. ComBat effectively eliminates unwanted data site-related variability, by maintaining or even enhancing data association with biological factors. Of note, ComBat has demonstrated flexibility and robustness of application on unseen independent gray matter volume data from the same sites.

Structural and functional correlates of olfactory reward processing in behavioral variant frontotemporal dementia

The behavioral variant of frontotemporal dementia (bvFTD) includes symptoms that reflect altered pursuit of rewards, including food, alcohol, and money. Little is known, however, about how these reward changes relate to atrophy and functional connectivity within reward-related regions. The goal of this study was to examine the structural and functional correlates of valence perception for olfactory rewards in 24 patients with bvFTD. Regression analysis of resting-state brain functional connectivity indicated that more positive valence ratings of olfactory stimuli were predicted by ventral pallidum connectivity to other reward circuit regions, particularly functional connectivity between ventral pallidum and bilateral anterior cingulate cortex/ventromedial prefrontal cortex. Structural analysis showed that atrophy of the anterior cingulate cortex was also significantly associated with perceiving stimuli as more rewarding. Finally, there was a significant interaction between ventral pallidum connectivity and atrophy of the anterior cingulate cortex. More specifically, the ventral pallidum connectivity had a greater effect on the positive perception of olfactory stimuli in the setting of low anterior cingulate cortex volume. These findings indicate that atrophy and functional connectivity within reward-relevant regions exert independent and interacting effects on the perception of pleasantness in bvFTD, potentially due to changes in hedonic "liking" signals.

Neuroimaging Insights into Brain Mechanisms of Early-onset Restrictive Eating Disorders

Background

Early-onset restrictive eating disorders (rEO-ED) encompass a heterogeneous group of conditions, including early-onset anorexia nervosa (EO-AN) and avoidant restrictive food intake disorders (ARFID). Almost nothing is known about the consequences of rEO-ED on brain development.

Methods

We performed the largest comparison of MRI-derived brain features in children and early adolescents (<13 years) with EO-AN (n=124), ARFID (n=50), and typically developing individuals (TD, n=112).

Results

Despite similar body mass index (BMI) distributions, EO-AN and ARFID showed divergent structural patterns, suggesting independent brain mechanisms. Half the regional brain measures were correlated with BMI in EO-AN and none in ARFID, indicating a partial mediation of EO-AN signal by BMI. EO-AN was associated with a widespread pattern of thinner cortex, while underweight ARFID patients exhibited smaller surface area and subcortical volumes than TD.

Conclusion

Future studies will be required to partition the contribution of low BMI vs. ED mechanisms in neurodevelopmental disorders.

Transdiagnostic alterations in white matter microstructure associated with suicidal thoughts and behaviours in the ENIGMA Suicidal Thoughts and Behaviours consortium

Previous studies have suggested that alterations in white matter (WM) microstructure are implicated in suicidal thoughts and behaviours (STBs). However, findings of diffusion tensor imaging (DTI) studies have been inconsistent. In this large-scale mega-analysis conducted by the ENIGMA Suicidal Thoughts and Behaviours (ENIGMA-STB) consortium, we examined WM alterations associated with STBs. Data processing was standardised across sites, and resulting WM microstructure measures (fractional anisotropy, axial diffusivity, mean diffusivity and radial diffusivity) for 25 WM tracts were pooled across 40 cohorts. We compared these measures among individuals with a psychiatric diagnosis and lifetime history of suicide attempt (n=652; mean age=35.4±14.7; female=71.8%), individuals with a psychiatric diagnosis but no STB (i.e., clinical controls; n=1871; mean age=34±14.8; female=59.8%), and individuals with no mental disorder diagnosis and no STB (i.e., healthy controls; n=642; mean age=29.6±13.1; female=62.9%). We also compared these measures among individuals with recent suicidal ideation (n=714; mean age=36.3±15.3; female=66.1%), clinical controls (n=1184; mean age=36.8±15.6; female=63.1%), and healthy controls (n=1240; mean age= 31.6±15.5; female=61.0%). We found subtle but statistically significant effects, such as lower fractional anisotropy associated with a history of suicide attempt, over and above the effect of psychiatric diagnoses. These effects were strongest in the corona radiata, thalamic radiation, fornix/stria terminalis, corpus callosum and superior longitudinal fasciculus. Effect sizes were small (Cohen's d < 0.25). Recent suicidal ideation was not associated with alterations in WM microstructure. This large-scale coordinated mega-analysis revealed subtle regional and global alterations in WM microstructure in individuals with a history of suicide attempt. Longitudinal studies are needed to confirm whether these alterations are a risk factor for suicidal behaviour.

Current best practices and future opportunities for reproducible findings using large-scale neuroimaging in psychiatry

Research into the brain basis of psychopathology is challenging due to the heterogeneity of psychiatric disorders, extensive comorbidities, underdiagnosis or overdiagnosis, multifaceted interactions with genetics and life experiences, and the highly multivariate nature of neural correlates. Therefore, increasingly larger datasets that measure more variables in larger cohorts are needed to gain insights. In this review, we present current "best practice" approaches for using existing databases, collecting and sharing new repositories for big data analyses, and future directions for big data in neuroimaging and psychiatry with an emphasis on contributing to collaborative efforts and the challenges of multi-study data analysis.

Hearing Function Moderates Age-Related Differences in Brain Morphometry in the HCP Aging Cohort

There are well-established relationships between aging and neurodegenerative changes, and between aging and hearing loss. The goal of this study was to determine how structural brain aging is influenced by hearing loss. Human Connectome Project Aging data were analyzed, including T1-weighted Magnetic Resonance Imaging (MRI) and Words in noise (WIN) thresholds (n = 623). Freesurfer extracted gray and white matter volume, and cortical thickness, area, and curvature. Linear regression models targeted (1) interactions between age and WIN threshold and (2) correlations with WIN threshold adjusted for age, both corrected for false discovery rate (pFDR < 0.05). WIN threshold moderated age-related increase in volume in bilateral inferior lateral ventricles, with a higher threshold associated with increased age-related ventricle expansion. Age-related differences in the occipital cortex also increased with higher WIN thresholds. When controlling for age, high WIN threshold was correlated with reduced cortical thickness in Heschl's gyrus, calcarine sulcus, and other sensory regions, and reduced temporal lobe white matter. Older volunteers with poorer hearing and cognitive scores had the lowest volume in left parahippocampal white matter. These results suggest that better hearing is associated with reduced age-related differences in medial temporal lobe, while better hearing at any age is associated with greater cortical tissue in auditory and other sensory regions. Future longitudinal studies are needed to assess the causal nature of these relationships, but these results indicate interventions that preserve or protect hearing function may combat some neurodegenerative changes in aging.

Quantitative MRI Measures and Cognitive Function in People With Drug-Resistant Juvenile Myoclonic Epilepsy

BACKGROUND AND OBJECTIVES

Neuroimaging studies have so far identified structural changes in individuals with juvenile myoclonic epilepsy (JME) when compared with controls. However, the underlying mechanisms of drug-resistant JME remain unknown. In this study, we aimed at characterizing the structural underpinnings of drug-resistant JME using MRI-derived cortical morphologic markers.

METHODS

In this prospective cross-sectional 2-center study, T1-weighted MRI and neuropsychological measures of verbal memory and executive function were obtained in individuals with drug-resistant and drug-responsive JME recruited from epilepsy outpatient clinics and healthy controls. We performed vertexwise measurements of cortical thickness, surface area, and local gyrification index (LGI). Vertexwise group comparisons were corrected for multiple comparisons at a familywise error (FWE) of 0.05. The neuropsychological profile of disease subgroups was analyzed through principal component analysis.

RESULTS

We studied 42 individuals with drug-resistant JME (mean age 29 ± 11 years, 50% female), 37 with drug-responsive JME (mean age 34 ± 10, years, 59% female), and 71 healthy controls (mean age 21 ± 9 years, 61% female). Surface area was increased in participants with drug-resistant JME in the left temporal lobe (Cohen d = 0.82 [-0.52 to -1.12], pFWE < 0.05) when compared with the drug-responsive group. Although no cortical thickness changes were observed between disease subgroups, drug-resistant and drug-sensitive participants showed discrete cortical thinning against controls (Cohen d = -0.42 [-0.83 to -0.01], pFWE < 0.05; Cohen d = -0.57 [-1.03 to -0.11], pFWE < 0.05, respectively). LGI was increased in the left temporal and occipital lobes in drug-resistant participants (Cohen d = 0.60 [0.34-0.86], pFWE < 0.05) when contrasting against drug-sensitive participants, but not controls. The composite executive function score was reduced in drug-resistant individuals compared with controls and drug-sensitive individuals (-1.74 [-2.58 to -0.90], p < 0.001 and -1.29 [-2.25 to -0.33], p < 0.01, respectively). Significant correlations were observed between executive function impairment and increased surface area in the precuneus and medial prefrontal regions (r = -0.79, pFWE < 0.05) in participants with drug-resistant JME.

DISCUSSION

We identified a developmental phenotype in individuals with drug-resistant JME characterized by changes in cortical surface area and folding complexity, the extent of which correlates with executive dysfunction. No association was observed between cortical thickness and disease severity. Our findings support a neurodevelopmental basis for drug resistance and cognitive impairment in JME.

3D CNN for neuropsychiatry: Predicting Autism with interpretable Deep Learning applied to minimally preprocessed structural MRI data

Predictive modeling approaches are enabling progress toward robust and reproducible brain-based markers of neuropsychiatric conditions by leveraging the power of multivariate analyses of large datasets. While deep learning (DL) offers another promising avenue to further advance progress, there are challenges related to implementation in 3D (best for MRI) and interpretability. Here, we address these challenges and describe an interpretable predictive pipeline for inferring Autism diagnosis using 3D DL applied to minimally processed structural MRI scans. We trained 3D DL models to predict Autism diagnosis using the openly available ABIDE I and II datasets (n = 1329, split into training, validation, and test sets). Importantly, we did not perform transformation to template space, to reduce bias and maximize sensitivity to structural alterations associated with Autism. Our models attained predictive accuracies equivalent to those of previous machine learning (ML) studies, while side-stepping the time- and resource-demanding requirement to first normalize data to a template. Our interpretation step, which identified brain regions that contributed most to accurate inference, revealed regional Autism-related alterations that were highly consistent with the literature, encompassing a left-lateralized network of regions supporting language processing. We have openly shared our code and models to enable further progress towards remaining challenges, such as the clinical heterogeneity of Autism and site effects, and to enable the extension of our method to other neuropsychiatric conditions.

Bridging big data in the ENIGMA consortium to combine non-equivalent cognitive measures

Investigators in neuroscience have turned to Big Data to address replication and reliability issues by increasing sample size. These efforts unveil new questions about how to integrate data across distinct sources and instruments. The goal of this study was to link scores across common auditory verbal learning tasks (AVLTs). This international secondary analysis aggregated multisite raw data for AVLTs across 53 studies totaling 10,505 individuals. Using the ComBat-GAM algorithm, we isolated and removed the component of memory scores associated with site effects while preserving instrumental effects. After adjustment, a continuous item response theory model used multiple memory items of varying difficulty to estimate each individual's latent verbal learning ability on a single scale. Equivalent raw scores across AVLTs were then found by linking individuals through the ability scale. Harmonization reduced total cross-site score variance by 37% while preserving meaningful memory effects. Age had the largest impact on scores overall (- 11.4%), while race/ethnicity variable was not significant (p > 0.05). The resulting tools were validated on dually administered tests. The conversion tool is available online so researchers and clinicians can convert memory scores across instruments. This work demonstrates that global harmonization initiatives can address reproducibility challenges across the behavioral sciences.

Modeling the impact of MRI acquisition bias on structural connectomes: Harmonizing structural connectomes

One way to increase the statistical power and generalizability of neuroimaging studies is to collect data at multiple sites or merge multiple cohorts. However, this usually comes with site-related biases due to the heterogeneity of scanners and acquisition parameters, negatively impacting sensitivity. Brain structural connectomes are not an exception: Being derived from T1-weighted and diffusion-weighted magnetic resonance images, structural connectivity is impacted by differences in imaging protocol. Beyond minimizing acquisition parameter differences, removing bias with postprocessing is essential. In this work we create, from the exhaustive Human Connectome Project Young Adult dataset, a resampled dataset of different b-values and spatial resolutions, modeling a cohort scanned across multiple sites. After demonstrating the statistical impact of acquisition parameters on connectivity, we propose a linear regression with explicit modeling of b-value and spatial resolution, and validate its performance on separate datasets. We show that b-value and spatial resolution affect connectivity in different ways and that acquisition bias can be reduced using a linear regression informed by the acquisition parameters while retaining interindividual differences and hence boosting fingerprinting performance. We also demonstrate the generative potential of our model, and its generalization capability in an independent dataset reflective of typical acquisition practices in clinical settings.

A generalizable normative deep autoencoder for brain morphological anomaly detection: application to the multi-site StratiBip dataset on bipolar disorder in an external validation framework

The heterogeneity of psychiatric disorders makes researching disorder-specific neurobiological markers an ill-posed problem. Here, we face the need for disease stratification models by presenting a generalizable multivariate normative modelling framework for characterizing brain morphology, applied to bipolar disorder (BD). We employed deep autoencoders in an anomaly detection framework, combined with a confounder removal step integrating training and external validation. The model was trained with healthy control (HC) data from the human connectome project and applied to multi-site external data of HC and BD individuals. We found that brain deviating scores were greater, more heterogeneous, and with increased extreme values in the BD group, with volumes prominently from the basal ganglia, hippocampus and adjacent regions emerging as significantly deviating. Similarly, individual brain deviating maps based on modified z scores expressed higher abnormalities occurrences, but their overall spatial overlap was lower compared to HCs. Our generalizable framework enabled the identification of subject- and group-level brain normative-deviating patterns, a step forward towards the development of more effective and personalized clinical decision support systems and patient stratification in psychiatry.

Influences of RASopathies on Neuroanatomical Variation in Children

BACKGROUND

RASopathies are a group of disorders characterized by pathogenic mutations in the Ras/mitogen-activated protein kinase (Ras/MAPK) signaling pathway. Distinct pathogenic variants in genes encoding proteins in the Ras/MAPK pathway cause Noonan syndrome (NS) and neurofibromatosis type 1 (NF1), which are associated with increased risk for autism spectrum disorder and attention-deficit/hyperactivity disorder.

METHODS

This study examined the effect of RASopathies (NS and NF1) on human neuroanatomy, specifically on surface area (SA), cortical thickness (CT), and subcortical volumes. Using vertex-based analysis for cortical measures and Desikan region of interest parcellation for subcortical volumes, we compared structural T1-weighted images of children with RASopathies (n = 91, mean age = 8.81 years, SD = 2.12) to those of sex- and age-matched typically developing children (n = 74, mean age = 9.07 years, SD = 1.77).

RESULTS

Compared with typically developing children, RASopathies had convergent effects on SA and CT, exhibiting increased SA in the precentral gyrus, decreased SA in occipital regions, and thinner CT in the precentral gyrus. RASopathies exhibited divergent effects on subcortical volumes, with syndrome-specific influences from NS and NF1. Overall, children with NS showed decreased volumes in striatal and thalamic structures, and children with NF1 displayed increased volumes in the hippocampus, amygdala, and thalamus.

CONCLUSIONS

Our study reveals the converging and diverging neuroanatomical effects of RASopathies on human neurodevelopment. The convergence of cortical effects on SA and CT indicates a shared influence of Ras/MAPK hyperactivation on the human brain. Therefore, considering these measures as objective outcome indicators for targeted treatments is imperative.

A worldwide study of white matter microstructural alterations in people living with Parkinson's disease

The progression of Parkinson's disease (PD) is associated with microstructural alterations in neural pathways, contributing to both motor and cognitive decline. However, conflicting findings have emerged due to the use of heterogeneous methods in small studies. Here we performed a large diffusion MRI study in PD, integrating data from 17 cohorts worldwide, to identify stage-specific profiles of white matter differences. Diffusion-weighted MRI data from 1654 participants diagnosed with PD (age: 20-89 years; 33% female) and 885 controls (age: 19-84 years; 47% female) were analyzed using the ENIGMA-DTI protocol to evaluate white matter microstructure. Skeletonized maps of fractional anisotropy (FA) and mean diffusivity (MD) were compared across Hoehn and Yahr (HY) disease groups and controls to reveal the profile of white matter alterations at different stages. We found an enhanced, more widespread pattern of microstructural alterations with each stage of PD, with eventually lower FA and higher MD in almost all regions of interest: Cohen's d effect sizes reached d = -1.01 for FA differences in the fornix at PD HY Stage 4/5. The early PD signature in HY stage 1 included higher FA and lower MD across the entire white matter skeleton, in a direction opposite to that typical of other neurodegenerative diseases. FA and MD were associated with motor and non-motor clinical dysfunction. While overridden by degenerative changes in the later stages of PD, early PD is associated with paradoxically higher FA and lower MD in PD, consistent with early compensatory changes associated with the disorder.

Cortical structure and subcortical volumes in conduct disorder: a coordinated analysis of 15 international cohorts from the ENIGMA-Antisocial Behavior Working Group

BACKGROUND

Conduct disorder is associated with the highest burden of any mental disorder in childhood, yet its neurobiology remains unclear. Inconsistent findings limit our understanding of the role of brain structure alterations in conduct disorder. This study aims to identify the most robust and replicable brain structural correlates of conduct disorder.

METHODS

The ENIGMA-Antisocial Behavior Working Group performed a coordinated analysis of structural MRI data from 15 international cohorts. Eligibility criteria were a mean sample age of 18 years or less, with data available on sex, age, and diagnosis of conduct disorder, and at least ten participants with conduct disorder and ten typically developing participants. 3D T1-weighted MRI brain scans of all participants were pre-processed using ENIGMA-standardised protocols. We assessed group differences in cortical thickness, surface area, and subcortical volumes using general linear models, adjusting for age, sex, and total intracranial volume. Group-by-sex and group-by-age interactions, and DSM-subtype comparisons (childhood-onset vs adolescent-onset, and low vs high levels of callous-unemotional traits) were investigated. People with lived experience of conduct disorder were not involved in this study.

FINDINGS

We collated individual participant data from 1185 young people with conduct disorder (339 [28·6%] female and 846 [71·4%] male) and 1253 typically developing young people (446 [35·6%] female and 807 [64·4%] male), with a mean age of 13·5 years (SD 3·0; range 7-21). Information on race and ethnicity was not available. Relative to typically developing young people, the conduct disorder group had lower surface area in 26 cortical regions and lower total surface area (Cohen's d 0·09-0·26). Cortical thickness differed in the caudal anterior cingulate cortex (d 0·16) and the banks of the superior temporal sulcus (d -0·13). The conduct disorder group also had smaller amygdala (d 0·13), nucleus accumbens (d 0·11), thalamus (d 0·14), and hippocampus (d 0·12) volumes. Most differences remained significant after adjusting for ADHD comorbidity or intelligence quotient. No group-by-sex or group-by-age interactions were detected. Few differences were found between DSM-defined conduct disorder subtypes. However, individuals with high callous-unemotional traits showed more widespread differences compared with controls than those with low callous-unemotional traits.

INTERPRETATION

Our findings provide robust evidence of subtle yet widespread brain structural alterations in conduct disorder across subtypes and sexes, mostly in surface area. These findings provide further evidence that brain alterations might contribute to conduct disorder. Greater consideration of this under-recognised disorder is needed in research and clinical practice.

FUNDING

Academy of Medical Sciences and Economic and Social Research Council.

Structural white matter abnormalities in Schizophrenia and associations with neurocognitive performance and symptom severity

Schizophrenia is associated with robust white matter (WM) abnormalities but influences of potentially confounding variables and relationships with cognitive performance and symptom severity remain to be fully determined. This study was designed to evaluate WM abnormalities based on diffusion tensor imaging (DTI) in individuals with schizophrenia, and their relationships with cognitive performance and symptom severity. Data from individuals with schizophrenia (SZ; n=138, mean age±SD=39.02±11.82; 105 males) and healthy controls (HC; n=143, mean age±SD=37.07±10.84; 102 males) were collected as part of the Function Biomedical Informatics Research Network Phase 3 study. Fractional anisotropy (FA), axial diffusivity (AD), radial diffusivity (RD), and mean diffusivity (MD) were compared between individuals with schizophrenia and healthy controls, and their relationships with neurocognitive performance and symptomatology assessed. Individuals with SZ had significantly lower FA in forceps minor and the left inferior fronto-occipital fasciculus compared to HC. FA in several tracts were associated with speed of processing and attention/vigilance and the severity of the negative symptom alogia. This study suggests that regional WM abnormalities are fundamentally involved in the pathophysiology of schizophrenia and may contribute to cognitive performance deficits and symptom expression observed in schizophrenia.

Exploring the potential of representation and transfer learning for anatomical neuroimaging: Application to psychiatry

The perspective of personalized medicine for brain disorders requires efficient learning models for anatomical neuroimaging-based prediction of clinical conditions. There is now a consensus on the benefit of deep learning (DL) in addressing many medical imaging tasks, such as image segmentation. However, for single-subject prediction problems, recent studies yielded contradictory results when comparing DL with Standard Machine Learning (SML) on top of classical feature extraction. Most existing comparative studies were limited in predicting phenotypes of little clinical interest, such as sex and age, and using a single dataset. Moreover, they conducted a limited analysis of the employed image pre-processing and feature selection strategies. This paper extensively compares DL and SML prediction capacity on five multi-site problems, including three increasingly complex clinical applications in psychiatry namely schizophrenia, bipolar disorder, and Autism Spectrum Disorder (ASD) diagnosis. To compensate for the relative scarcity of neuroimaging data on these clinical datasets, we also evaluate three pre-training strategies for transfer learning from brain imaging of the general healthy population: self-supervised learning, generative modeling and supervised learning with age. Overall, we find similar performance between randomly initialized DL and SML for the three clinical tasks and a similar scaling trend for sex prediction. This was replicated on an external dataset. We also show highly correlated discriminative brain regions between DL and linear ML models in all problems. Nonetheless, we demonstrate that self-supervised pre-training on large-scale healthy population imaging datasets (N≈10k), along with Deep Ensemble, allows DL to learn robust and transferable representations to smaller-scale clinical datasets (N≤1k). It largely outperforms SML on 2 out of 3 clinical tasks both in internal and external test sets. These findings suggest that the improvement of DL over SML in anatomical neuroimaging mainly comes from its capacity to learn meaningful and useful abstract representations of the brain anatomy, and it sheds light on the potential of transfer learning for personalized medicine in psychiatry.

ComBatLS: A location- and scale-preserving method for multi-site image harmonization

Recent work has leveraged massive datasets and advanced harmonization methods to construct normative models of neuroanatomical features and benchmark individuals' morphology. However, current harmonization tools do not preserve the effects of biological covariates including sex and age on features' variances; this failure may induce error in normative scores, particularly when such factors are distributed unequally across sites. Here, we introduce a new extension of the popular ComBat harmonization method, ComBatLS, that preserves biological variance in features' locations and scales. We use UK Biobank data to show that ComBatLS robustly replicates individuals' normative scores better than other ComBat methods when subjects are assigned to sex-imbalanced synthetic "sites". Additionally, we demonstrate that ComBatLS significantly reduces sex biases in normative scores compared to traditional methods. Finally, we show that ComBatLS successfully harmonizes consortium data collected across over 50 studies. R implementation of ComBatLS is available at https://github.com/andy1764/ComBatFamily.

Multimodal Neuroimaging Summary Scores as Neurobiological Markers of Psychosis

BACKGROUND AND HYPOTHESIS

Structural brain alterations are well-established features of schizophrenia but they do not effectively predict disease/disease risk. Similar to polygenic risk scores in genetics, we integrated multifactorial aspects of brain structure into a summary "Neuroscore" and examined its potential as a marker of disease.

STUDY DESIGN

We extracted measures from T1-weighted scans and diffusion tensor imaging (DTI) models from three studies with schizophrenia and healthy individuals. We calculated individual-level summary scores (Neuroscores) for T1-weighted and DTI measures and a combined score (Multimodal Neuroscore-MM). We assessed each score's ability to differentiate schizophrenia cases from controls and its relationship to clinical symptomatology, intelligence quotient (IQ), and medication dosage. We assessed Neuroscore specificity by performing all analyses in a more inclusive psychosis sample and by using scores generated from MDD effect sizes.

STUDY RESULTS

All Neuroscores significantly differentiated schizophrenia cases from controls (T1 d = 0.56, DTI d = 0.29, MM d = 0.64) to a greater degree than individual brain regions. Higher Neuroscores (ie, increased liability) were associated with lower IQ (T1 β = -0.26, DTI β = -0.15, MM β = -0.30). Higher T1-weighted Neuroscores were associated with higher positive and negative symptom severity (Positive β = 0.21, Negative β = 0.16); Higher Multimodal Neuroscores were associated with higher positive symptom severity (β = 0.30). SZ Neuroscores outperformed MDD Neuroscores in predicting IQ (T1: z = 3.5, q = 0.0007; MM: z = 1.8, q = 0.05).

CONCLUSIONS

Neuroscores are a step toward leveraging widespread structural brain alterations in psychosis to identify robust neurobiological markers of disease. Future studies will assess ways to improve neuroscore calculation, including developing the optimal methods to calculate neuroscores and considering disorder overlap.

Transdiagnostic Neurobiology of Social Cognition and Individual Variability as Measured by Fractional Amplitude of Low-Frequency Fluctuation in Schizophrenia and Autism Spectrum Disorders

Fractional amplitude of low-frequency fluctuation (fALFF) is a validated measure of resting-state spontaneous brain activity. Previous fALFF findings in autism and schizophrenia spectrum disorders (ASDs and SSDs) have been highly heterogeneous. We aimed to use fALFF in a large sample of typically developing control (TDC), ASD and SSD participants to explore group differences and relationships with inter-individual variability of fALFF maps and social cognition. fALFF from 495 participants (185 TDC, 68 ASD, and 242 SSD) was computed using functional magnetic resonance imaging as signal power within two frequency bands (i.e., slow-4 and slow-5), normalized by the power in the remaining frequency spectrum. Permutation analysis of linear models was employed to investigate the relationship of fALFF with diagnostic groups, higher-level social cognition, and lower-level social cognition. Each participant's average distance of fALFF map to all others was defined as a variability score, with higher scores indicating less typical maps. Lower fALFF in the visual and higher fALFF in the frontal regions were found in both SSD and ASD participants compared with TDCs. Limited differences were observed between ASD and SSD participants in the cuneus regions only. Associations between slow-4 fALFF and higher-level social cognitive scores across the whole sample were observed in the lateral occipitotemporal and temporoparietal junction. Individual variability within the ASD and SSD groups was also significantly higher compared with TDC. Similar patterns of fALFF and individual variability in ASD and SSD suggest some common neurobiological deficits across these related heterogeneous conditions.

Sex Differences in the Brain's White Matter Microstructure during Development assessed using Advanced Diffusion MRI Models

Typical sex differences in white matter (WM) microstructure during development are incompletely understood. Here we evaluated sex differences in WM microstructure during typical brain development using a sample of neurotypical individuals across a wide developmental age (N=239, aged 5-22 years). We used the conventional diffusion-weighted MRI (dMRI) model, diffusion tensor imaging (DTI), and two advanced dMRI models, the tensor distribution function (TDF) and neurite orientation dispersion density imaging (NODDI) to assess WM microstructure. WM microstructure exhibited significant, regionally consistent sex differences across the brain during typical development. Additionally, the TDF model was most sensitive in detecting sex differences. These findings highlight the importance of considering sex in neurodevelopmental research and underscore the value of the advanced TDF model.

Consortium Profile: The Methylation, Imaging and NeuroDevelopment (MIND) Consortium

Epigenetic processes, such as DNA methylation, show potential as biological markers and mechanisms underlying gene-environment interplay in the prediction of mental health and other brain-based phenotypes. However, little is known about how peripheral epigenetic patterns relate to individual differences in the brain itself. An increasingly popular approach to address this is by combining epigenetic and neuroimaging data; yet, research in this area is almost entirely comprised of cross-sectional studies in adults. To bridge this gap, we established the Methylation, Imaging and NeuroDevelopment (MIND) Consortium, which aims to bring a developmental focus to the emerging field of Neuroimaging Epigenetics by (i) promoting collaborative, adequately powered developmental research via multi-cohort analyses; (ii) increasing scientific rigor through the establishment of shared pipelines and open science practices; and (iii) advancing our understanding of DNA methylation-brain dynamics at different developmental periods (from birth to emerging adulthood), by leveraging data from prospective, longitudinal pediatric studies. MIND currently integrates 15 cohorts worldwide, comprising (repeated) measures of DNA methylation in peripheral tissues (blood, buccal cells, and saliva) and neuroimaging by magnetic resonance imaging across up to five time points over a period of up to 21 years (Npooled DNAm = 11,299; Npooled neuroimaging = 10,133; Npooled combined = 4,914). By triangulating associations across multiple developmental time points and study types, we hope to generate new insights into the dynamic relationships between peripheral DNA methylation and the brain, and how these ultimately relate to neurodevelopmental and psychiatric phenotypes.

Principal component analysis as an efficient method for capturing multivariate brain signatures of complex disorders-ENIGMA study in people with bipolar disorders and obesity

Multivariate techniques better fit the anatomy of complex neuropsychiatric disorders which are characterized not by alterations in a single region, but rather by variations across distributed brain networks. Here, we used principal component analysis (PCA) to identify patterns of covariance across brain regions and relate them to clinical and demographic variables in a large generalizable dataset of individuals with bipolar disorders and controls. We then compared performance of PCA and clustering on identical sample to identify which methodology was better in capturing links between brain and clinical measures. Using data from the ENIGMA-BD working group, we investigated T1-weighted structural MRI data from 2436 participants with BD and healthy controls, and applied PCA to cortical thickness and surface area measures. We then studied the association of principal components with clinical and demographic variables using mixed regression models. We compared the PCA model with our prior clustering analyses of the same data and also tested it in a replication sample of 327 participants with BD or schizophrenia and healthy controls. The first principal component, which indexed a greater cortical thickness across all 68 cortical regions, was negatively associated with BD, BMI, antipsychotic medications, and age and was positively associated with Li treatment. PCA demonstrated superior goodness of fit to clustering when predicting diagnosis and BMI. Moreover, applying the PCA model to the replication sample yielded significant differences in cortical thickness between healthy controls and individuals with BD or schizophrenia. Cortical thickness in the same widespread regional network as determined by PCA was negatively associated with different clinical and demographic variables, including diagnosis, age, BMI, and treatment with antipsychotic medications or lithium. PCA outperformed clustering and provided an easy-to-use and interpret method to study multivariate associations between brain structure and system-level variables. PRACTITIONER POINTS: In this study of 2770 Individuals, we confirmed that cortical thickness in widespread regional networks as determined by principal component analysis (PCA) was negatively associated with relevant clinical and demographic variables, including diagnosis, age, BMI, and treatment with antipsychotic medications or lithium. Significant associations of many different system-level variables with the same brain network suggest a lack of one-to-one mapping of individual clinical and demographic factors to specific patterns of brain changes. PCA outperformed clustering analysis in the same data set when predicting group or BMI, providing a superior method for studying multivariate associations between brain structure and system-level variables.

Gradient Matching Federated Domain Adaptation for Brain Image Classification

Federated learning has shown its unique advantages in many different tasks, including brain image analysis. It provides a new way to train deep learning models while protecting the privacy of medical image data from multiple sites. However, previous studies suggest that domain shift across different sites may influence the performance of federated models. As a solution, we propose a gradient matching federated domain adaptation (GM-FedDA) method for brain image classification, aiming to reduce domain discrepancy with the assistance of a public image dataset and train robust local federated models for target sites. It mainly includes two stages: 1) pretraining stage; we propose a one-common-source adversarial domain adaptation (OCS-ADA) strategy, i.e., adopting ADA with gradient matching loss to pretrain encoders for reducing domain shift at each target site (private data) with the assistance of a common source domain (public data) and 2) fine-tuning stage; we develop a gradient matching federated (GM-Fed) fine-tuning method for updating local federated models pretrained with the OCS-ADA strategy, i.e., pushing the optimization direction of a local federated model toward its specific local minimum by minimizing gradient matching loss between sites. Using fully connected networks as local models, we validate our method with the diagnostic classification tasks of schizophrenia and major depressive disorder based on multisite resting-state functional MRI (fMRI), respectively. Results show that the proposed GM-FedDA method outperforms other commonly used methods, suggesting the potential of our method in brain imaging analysis and other fields, which need to utilize multisite data while preserving data privacy.

SAN: Mitigating spatial covariance heterogeneity in cortical thickness data collected from multiple scanners or sites

In neuroimaging studies, combining data collected from multiple study sites or scanners is becoming common to increase the reproducibility of scientific discoveries. At the same time, unwanted variations arise by using different scanners (inter-scanner biases), which need to be corrected before downstream analyses to facilitate replicable research and prevent spurious findings. While statistical harmonization methods such as ComBat have become popular in mitigating inter-scanner biases in neuroimaging, recent methodological advances have shown that harmonizing heterogeneous covariances results in higher data quality. In vertex-level cortical thickness data, heterogeneity in spatial autocorrelation is a critical factor that affects covariance heterogeneity. Our work proposes a new statistical harmonization method called spatial autocorrelation normalization (SAN) that preserves homogeneous covariance vertex-level cortical thickness data across different scanners. We use an explicit Gaussian process to characterize scanner-invariant and scanner-specific variations to reconstruct spatially homogeneous data across scanners. SAN is computationally feasible, and it easily allows the integration of existing harmonization methods. We demonstrate the utility of the proposed method using cortical thickness data from the Social Processes Initiative in the Neurobiology of the Schizophrenia(s) (SPINS) study. SAN is publicly available as an R package.

Using brain structural neuroimaging measures to predict psychosis onset for individuals at clinical high-risk

Machine learning approaches using structural magnetic resonance imaging (sMRI) can be informative for disease classification, although their ability to predict psychosis is largely unknown. We created a model with individuals at CHR who developed psychosis later (CHR-PS+) from healthy controls (HCs) that can differentiate each other. We also evaluated whether we could distinguish CHR-PS+ individuals from those who did not develop psychosis later (CHR-PS-) and those with uncertain follow-up status (CHR-UNK). T1-weighted structural brain MRI scans from 1165 individuals at CHR (CHR-PS+, n = 144; CHR-PS-, n = 793; and CHR-UNK, n = 228), and 1029 HCs, were obtained from 21 sites. We used ComBat to harmonize measures of subcortical volume, cortical thickness and surface area data and corrected for non-linear effects of age and sex using a general additive model. CHR-PS+ (n = 120) and HC (n = 799) data from 20 sites served as a training dataset, which we used to build a classifier. The remaining samples were used external validation datasets to evaluate classifier performance (test, independent confirmatory, and independent group [CHR-PS- and CHR-UNK] datasets). The accuracy of the classifier on the training and independent confirmatory datasets was 85% and 73% respectively. Regional cortical surface area measures-including those from the right superior frontal, right superior temporal, and bilateral insular cortices strongly contributed to classifying CHR-PS+ from HC. CHR-PS- and CHR-UNK individuals were more likely to be classified as HC compared to CHR-PS+ (classification rate to HC: CHR-PS+, 30%; CHR-PS-, 73%; CHR-UNK, 80%). We used multisite sMRI to train a classifier to predict psychosis onset in CHR individuals, and it showed promise predicting CHR-PS+ in an independent sample. The results suggest that when considering adolescent brain development, baseline MRI scans for CHR individuals may be helpful to identify their prognosis. Future prospective studies are required about whether the classifier could be actually helpful in the clinical settings.

Sex Differences in the Brain's White Matter Microstructure during Development assessed using Advanced Diffusion MRI Models

Typical sex differences in white matter (WM) microstructure during development are incompletely understood. Here we evaluated sex differences in WM microstructure during typical brain development using a sample of neurotypical individuals across a wide developmental age (N=239, aged 5-22 years). We used the conventional diffusion-weighted MRI (dMRI) model, diffusion tensor imaging (DTI), and two advanced dMRI models, the tensor distribution function (TDF) and neurite orientation dispersion density imaging (NODDI) to assess WM microstructure. WM microstructure exhibited significant, regionally consistent sex differences across the brain during typical development. Additionally, the TDF model was most sensitive in detecting sex differences. These findings highlight the importance of considering sex in neurodevelopmental research and underscore the value of the advanced TDF model.

Childhood trauma moderates schizotypy-related brain morphology: analyses of 1182 healthy individuals from the ENIGMA schizotypy working group

BACKGROUND

Schizotypy represents an index of psychosis-proneness in the general population, often associated with childhood trauma exposure. Both schizotypy and childhood trauma are linked to structural brain alterations, and it is possible that trauma exposure moderates the extent of brain morphological differences associated with schizotypy.

METHODS

We addressed this question using data from a total of 1182 healthy adults (age range: 18-65 years old, 647 females/535 males), pooled from nine sites worldwide, contributing to the Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Schizotypy working group. All participants completed both the Schizotypal Personality Questionnaire Brief version (SPQ-B), and the Childhood Trauma Questionnaire (CTQ), and underwent a 3D T1-weighted brain MRI scan from which regional indices of subcortical gray matter volume and cortical thickness were determined.

RESULTS

A series of multiple linear regressions revealed that differences in cortical thickness in four regions-of-interest were significantly associated with interactions between schizotypy and trauma; subsequent moderation analyses indicated that increasing levels of schizotypy were associated with thicker left caudal anterior cingulate gyrus, right middle temporal gyrus and insula, and thinner left caudal middle frontal gyrus, in people exposed to higher (but not low or average) levels of childhood trauma. This was found in the context of morphological changes directly associated with increasing levels of schizotypy or increasing levels of childhood trauma exposure.

CONCLUSIONS

These results suggest that alterations in brain regions critical for higher cognitive and integrative processes that are associated with schizotypy may be enhanced in individuals exposed to high levels of trauma.

The contribution of first-episode illness characteristics and cumulative antipsychotic usage to progressive structural brain changes over a long-term follow-up in schizophrenia

Exposure to antipsychotics as well as certain first-episode illness characteristics have been associated with greater gray matter (GM) deficits in the early phase of schizophrenia. Whether the first-episode illness characteristics affect the long-term progression of the structural brain changes remain unexplored. We therefore assessed the role of first-episode illness characteristics and life-time antipsychotic use in relation to long-term structural brain GM changes in schizophrenia. Individuals with schizophrenia (SZ, n = 29) and non-psychotic controls (n = 61) from the Northern Finland Birth Cohort 1966 underwent structural MRI at the ages of 34 (baseline) and 43 (follow-up) years. At follow-up, the average duration of illness was 19.8 years. Voxel-based morphometry was used to assess the effects of predictors on longitudinal GM changes in schizophrenia-relevant brain areas. Younger age of onset (AoO), higher cumulative antipsychotic dose and severity of symptoms were associated with greater GM deficits in the SZ group at follow-up. None of the first-episode illness characteristics were associated with longitudinal GM changes during 9-year follow-up period. We conclude that a younger AoO and high life-time antipsychotic use may contribute to progression of structural brain changes in schizophrenia. Apart from AoO, other first-episode illness characteristics may not contribute to longitudinal GM changes in midlife.

SAN: mitigating spatial covariance heterogeneity in cortical thickness data collected from multiple scanners or sites

In neuroimaging studies, combining data collected from multiple study sites or scanners is becoming common to increase the reproducibility of scientific discoveries. At the same time, unwanted variations arise by using different scanners (inter-scanner biases), which need to be corrected before downstream analyses to facilitate replicable research and prevent spurious findings. While statistical harmonization methods such as ComBat have become popular in mitigating inter-scanner biases in neuroimaging, recent methodological advances have shown that harmonizing heterogeneous covariances results in higher data quality. In vertex-level cortical thickness data, heterogeneity in spatial autocorrelation is a critical factor that affects covariance heterogeneity. Our work proposes a new statistical harmonization method called SAN (Spatial Autocorrelation Normalization) that preserves homogeneous covariance vertex-level cortical thickness data across different scanners. We use an explicit Gaussian process to characterize scanner-invariant and scanner-specific variations to reconstruct spatially homogeneous data across scanners. SAN is computationally feasible, and it easily allows the integration of existing harmonization methods. We demonstrate the utility of the proposed method using cortical thickness data from the Social Processes Initiative in the Neurobiology of the Schizophrenia(s) (SPINS) study. SAN is publicly available as an R package.

Lifespan reference curves for harmonizing multi-site regional brain white matter metrics from diffusion MRI

Age-related white matter (WM) microstructure maturation and decline occur throughout the human lifespan, complementing the process of gray matter development and degeneration. Here, we create normative lifespan reference curves for global and regional WM microstructure by harmonizing diffusion MRI (dMRI)-derived data from ten public datasets (N = 40,898 subjects; age: 3-95 years; 47.6% male). We tested three harmonization methods on regional diffusion tensor imaging (DTI) based fractional anisotropy (FA), a metric of WM microstructure, extracted using the ENIGMA-DTI pipeline. ComBat-GAM harmonization provided multi-study trajectories most consistent with known WM maturation peaks. Lifespan FA reference curves were validated with test-retest data and used to assess the effect of the ApoE4 risk factor for dementia in WM across the lifespan. We found significant associations between ApoE4 and FA in WM regions associated with neurodegenerative disease even in healthy individuals across the lifespan, with regional age-by-genotype interactions. Our lifespan reference curves and tools to harmonize new dMRI data to the curves are publicly available as eHarmonize (https://github.com/ahzhu/eharmonize).