Dataset Information

Enhancing reproducibility in developmental EEG research: BIDS, cluster-based permutation tests, and effect sizes.

ABSTRACT: Developmental research using electroencephalography (EEG) offers valuable insights in brain processes early in life, but at the same time, applying this sensitive technique to young children who are often non-compliant and have short attention spans comes with practical limitations. It is thus of particular importance to optimally use the limited resources to advance our understanding of development through reproducible and replicable research practices. Here, we describe methodological approaches that help maximize the reproducibility of developmental EEG research. We discuss how to transform EEG data into the standardized Brain Imaging Data Structure (BIDS) which organizes data according to the FAIR data sharing principles. We provide a tutorial on how to use cluster-based permutation testing to analyze developmental EEG data. This versatile test statistic solves the multiple comparison problem omnipresent in EEG analysis and thereby substantially decreases the risk of reporting false discoveries. Finally, we describe how to quantify effect sizes, in particular of cluster-based permutation results. Reporting effect sizes conveys a finding's impact and robustness which in turn informs future research. To demonstrate these methodological approaches to data organization, analysis and report, we use a publicly accessible infant EEG dataset and provide a complete copy of the analysis code.

SUBMITTER: Meyer M

PROVIDER: S-EPMC8607163 | biostudies-literature | 2021 Dec

REPOSITORIES: biostudies-literature

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Enhancing reproducibility in developmental EEG research: BIDS, cluster-based permutation tests, and effect sizes.

Meyer Marlene M Lamers Didi D Kayhan Ezgi E Hunnius Sabine S Oostenveld Robert R

Developmental cognitive neuroscience 20211112

Developmental research using electroencephalography (EEG) offers valuable insights in brain processes early in life, but at the same time, applying this sensitive technique to young children who are often non-compliant and have short attention spans comes with practical limitations. It is thus of particular importance to optimally use the limited resources to advance our understanding of development through reproducible and replicable research practices. Here, we describe methodological approach ...[more]

PMID: 34801856

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Project description:BackgroundTime series analysis is critical for understanding brain signals and their relationship to behavior and cognition. Cluster-based permutation tests (CBPT) are commonly used to analyze a variety of electrophysiological signals including EEG, MEG, ECoG, and sEEG data without a priori assumptions about specific temporal effects. However, two major limitations of CBPT include the inability to directly analyze experiments with multiple fixed effects and the inability to account for random effects (e.g. variability across subjects). Here, we propose a flexible multi-step hypothesis testing strategy using CBPT with Linear Mixed Effects Models (LMEs) and Generalized Linear Mixed Effects Models (GLMEs) that can be applied to a wide range of experimental designs and data types.MethodsWe first evaluate the statistical robustness of LMEs and GLMEs using simulated data distributions. Second, we apply a multi-step hypothesis testing strategy to analyze ERPs and broadband power signals extracted from human ECoG recordings collected during a simple image viewing experiment with image category and novelty as fixed effects. Third, we assess the statistical power differences between analyzing signals with CBPT using LMEs compared to CBPT using separate t-tests run on each fixed effect through simulations that emulate broadband power signals. Finally, we apply CBPT using GLMEs to high-gamma burst data to demonstrate the extension of the proposed method to the analysis of nonlinear data.ResultsFirst, we found that LMEs and GLMEs are robust statistical models. In simple simulations LMEs produced highly congruent results with other appropriately applied linear statistical models, but LMEs outperformed many linear statistical models in the analysis of "suboptimal" data and maintained power better than analyzing individual fixed effects with separate t-tests. GLMEs also performed similarly to other nonlinear statistical models. Second, in real world human ECoG data, LMEs performed at least as well as separate t-tests when applied to predefined time windows or when used in conjunction with CBPT. Additionally, fixed effects time courses extracted with CBPT using LMEs from group-level models of pseudo-populations replicated latency effects found in individual category-selective channels. Third, analysis of simulated broadband power signals demonstrated that CBPT using LMEs was superior to CBPT using separate t-tests in identifying time windows with significant fixed effects especially for small effect sizes. Lastly, the analysis of high-gamma burst data using CBPT with GLMEs produced results consistent with CBPT using LMEs applied to broadband power data.ConclusionsWe propose a general approach for statistical analysis of electrophysiological data using CBPT in conjunction with LMEs and GLMEs. We demonstrate that this method is robust for experiments with multiple fixed effects and applicable to the analysis of linear and nonlinear data. Our methodology maximizes the statistical power available in a dataset across multiple experimental variables while accounting for hierarchical random effects and controlling FWER across fixed effects. This approach substantially improves power and accuracy leading to better reproducibility. Additionally, CBPT using LMEs and GLMEs can be used to analyze individual channels or pseudo-population data for the comparison of functional or anatomical groups of data.

Project description:BackgroundMediation analysis can be used to evaluate the effect of an exposure on an outcome acting through an intermediate variable or mediator. For studies with small sample sizes, permutation testing may be useful in evaluating the indirect effect (i.e., the effect of exposure on the outcome through the mediator) while maintaining the appropriate type I error rate. For mediation analysis in studies with small sample sizes, existing permutation testing methods permute the residuals under the full or alternative model, but have not been evaluated under situations where covariates are included. In this article, we consider and evaluate two additional permutation approaches for testing the indirect effect in mediation analysis based on permutating the residuals under the reduced or null model which allows for the inclusion of covariates.MethodsSimulation studies were used to empirically evaluate the behavior of these two additional approaches: (1) the permutation test of the Indirect Effect under Reduced Models (IERM) and (2) the Permutation Supremum test under Reduced Models (PSRM). The performance of these methods was compared to the standard permutation approach for mediation analysis, the permutation test of the Indirect Effect under Full Models (IEFM). We evaluated the type 1 error rates and power of these methods in the presence of covariates since mediation analysis assumes no unmeasured confounders of the exposure-mediator-outcome relationships.ResultsThe proposed PSRM approach maintained type I error rates below nominal levels under all conditions, while the proposed IERM approach exhibited grossly inflated type I rates in many conditions and the standard IEFM exhibited inflated type I error rates under a small number of conditions. Power did not differ substantially between the proposed PSRM approach and the standard IEFM approach.ConclusionsThe proposed PSRM approach is recommended over the existing IEFM approach for mediation analysis in studies with small sample sizes.

Dataset Information

Enhancing reproducibility in developmental EEG research: BIDS, cluster-based permutation tests, and effect sizes.

Publications

Enhancing reproducibility in developmental EEG research: BIDS, cluster-based permutation tests, and effect sizes.

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