Centre for Youth Mental Health - Research Publications
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ItemNo Preview AvailableAccommodating site variation in neuroimaging data using normative and hierarchical Bayesian models(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2022-10-29)The potential of normative modeling to make individualized predictions from neuroimaging data has enabled inferences that go beyond the case-control approach. However, site effects are often confounded with variables of interest in a complex manner and can bias estimates of normative models, which has impeded the application of normative models to large multi-site neuroimaging data sets. In this study, we suggest accommodating for these site effects by including them as random effects in a hierarchical Bayesian model. We compared the performance of a linear and a non-linear hierarchical Bayesian model in modeling the effect of age on cortical thickness. We used data of 570 healthy individuals from the ABIDE (autism brain imaging data exchange) data set in our experiments. In addition, we used data from individuals with autism to test whether our models are able to retain clinically useful information while removing site effects. We compared the proposed single stage hierarchical Bayesian method to several harmonization techniques commonly used to deal with additive and multiplicative site effects using a two stage regression, including regressing out site and harmonizing for site with ComBat, both with and without explicitly preserving variance caused by age and sex as biological variation of interest, and with a non-linear version of ComBat. In addition, we made predictions from raw data, in which site has not been accommodated for. The proposed hierarchical Bayesian method showed the best predictive performance according to multiple metrics. Beyond that, the resulting z-scores showed little to no residual site effects, yet still retained clinically useful information. In contrast, performance was particularly poor for the regression model and the ComBat model in which age and sex were not explicitly modeled. In all two stage harmonization models, predictions were poorly scaled, suffering from a loss of more than 90% of the original variance. Our results show the value of hierarchical Bayesian regression methods for accommodating site variation in neuroimaging data, which provides an alternative to harmonization techniques. While the approach we propose may have broad utility, our approach is particularly well suited to normative modeling where the primary interest is in accurate modeling of inter-subject variation and statistical quantification of deviations from a reference model.
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ItemSite effects how-to and when: An overview of retrospective techniques to accommodate site effects in multi-site neuroimaging analyses(FRONTIERS MEDIA SA, 2022-10-31)Site differences, or systematic differences in feature distributions across multiple data-acquisition sites, are a known source of heterogeneity that may adversely affect large-scale meta- and mega-analyses of independently collected neuroimaging data. They influence nearly all multi-site imaging modalities and biomarkers, and methods to compensate for them can improve reliability and generalizability in the analysis of genetics, omics, and clinical data. The origins of statistical site effects are complex and involve both technical differences (scanner vendor, head coil, acquisition parameters, imaging processing) and differences in sample characteristics (inclusion/exclusion criteria, sample size, ancestry) between sites. In an age of expanding international consortium research, there is a growing need to disentangle technical site effects from sample characteristics of interest. Numerous statistical and machine learning methods have been developed to control for, model, or attenuate site effects - yet to date, no comprehensive review has discussed the benefits and drawbacks of each for different use cases. Here, we provide an overview of the different existing statistical and machine learning methods developed to remove unwanted site effects from independently collected neuroimaging samples. We focus on linear mixed effect models, the ComBat technique and its variants, adjustments based on image quality metrics, normative modeling, and deep learning approaches such as generative adversarial networks. For each method, we outline the statistical foundation and summarize strengths and weaknesses, including their assumptions and conditions of use. We provide information on software availability and comment on the ease of use and the applicability of these methods to different types of data. We discuss validation and comparative reports, mention caveats and provide guidance on when to use each method, depending on context and specific research questions.
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ItemNo Preview AvailableBrainhack: Developing a culture of open, inclusive, community-driven neuroscience(CELL PRESS, 2021-06-02)Brainhack is an innovative meeting format that promotes scientific collaboration and education in an open, inclusive environment. This NeuroView describes the myriad benefits for participants and the research community and how Brainhacks complement conventional formats to augment scientific progress.
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ItemCharting brain growth and aging at high spatial precision(eLIFE SCIENCES PUBL LTD, 2022-02-01)Defining reference models for population variation, and the ability to study individual deviations is essential for understanding inter-individual variability and its relation to the onset and progression of medical conditions. In this work, we assembled a reference cohort of neuroimaging data from 82 sites (N=58,836; ages 2-100) and used normative modeling to characterize lifespan trajectories of cortical thickness and subcortical volume. Models are validated against a manually quality checked subset (N=24,354) and we provide an interface for transferring to new data sources. We showcase the clinical value by applying the models to a transdiagnostic psychiatric sample (N=1985), showing they can be used to quantify variability underlying multiple disorders whilst also refining case-control inferences. These models will be augmented with additional samples and imaging modalities as they become available. This provides a common reference platform to bind results from different studies and ultimately paves the way for personalized clinical decision-making.
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ItemIndividual deviations from normative models of brain structure in a large cross-sectional schizophrenia cohort(SPRINGERNATURE, 2021-07)The heterogeneity of schizophrenia has defied efforts to derive reproducible and definitive anatomical maps of structural brain changes associated with the disorder. We aimed to map deviations from normative ranges of brain structure for individual patients and evaluate whether the loci of individual deviations recapitulated group-average brain maps of schizophrenia pathology. For each of 48 white matter tracts and 68 cortical regions, normative percentiles of variation in fractional anisotropy (FA) and cortical thickness (CT) were established using diffusion-weighted and structural MRI from healthy adults (n = 195). Individuals with schizophrenia (n = 322) were classified as either within the normative range for healthy individuals of the same age and sex (5-95% percentiles), infra-normal (<5% percentile) or supra-normal (>95% percentile). Repeating this classification for each tract and region yielded a deviation map for each individual. Compared to the healthy comparison group, the schizophrenia group showed widespread reductions in FA and CT, involving virtually all white matter tracts and cortical regions. Paradoxically, however, no more than 15-20% of patients deviated from the normative range for any single tract or region. Furthermore, 79% of patients showed infra-normal deviations for at least one locus (healthy individuals: 59 ± 2%, p < 0.001). Thus, while infra-normal deviations were common among patients, their anatomical loci were highly inconsistent between individuals. Higher polygenic risk for schizophrenia associated with a greater number of regions with infra-normal deviations in CT (r = -0.17, p = 0.006). We conclude that anatomical loci of schizophrenia-related changes are highly heterogeneous across individuals to the extent that group-consensus pathological maps are not representative of most individual patients. Normative modeling can aid in parsing schizophrenia heterogeneity and guiding personalized interventions.
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ItemSelective screening imaging of the aortoiliac arterial system in kidney transplant candidates with non-contrast pelvic computed tomography.(Wiley, 2021-07)Non-contrast pelvic computed tomography (CT) can detect severe iliac artery calcifications that present technical contraindications to kidney transplantation (TCT). We screened 454 asymptomatic patients with a history of any of the following: hemodialysis >10 years, diabetes mellitus >20 years, coronary artery disease (CAD) with percutaneous or surgical interventions, carotid disease, diabetes with below-/above-knee amputations, and heart-kidney transplantation candidacy. Patients with normal dorsalis pedis and/or tibialis posterior pulses were not screened. A total of 8.4% had severe calcifications with TCT; CT determined laterality for implantation in 13.9%. No patients with the following characteristics were classified as TCT: age <40 years, hemodialysis >10 years, carotid arterial disease, prior lower extremity amputation, or heart-kidney transplantation candidacy. CAD was associated with TCT in univariate though not multivariate analysis. Limiting screening to patients >40 years, with DM >20 years, or with CAD, 9.8% had a TCT and CT determined transplant laterality in 14.2%. Screening for severe iliac artery calcifications is useful for selected kidney transplantation candidates over age 40. It can assist with laterality choice or surgeon determination of TCT. Cost and radiation exposure risks should be weighed against the morbidity risks from unnecessary surgery.