ComBat Harmonization With and Without Empirical Bayes Estimation for Resting-State Functional Connectivity in Pediatric Mild Traumatic Brain Injury: a CARE4Kids Study

ComBat is commonly used to mitigate batch effects in multi-site neuroimaging studies. Although empirical bayes estimation is a key component of ComBat, its impact on resting-state functional connectivity measures, including site effect reductions and preservation of original within-site variability remains underexplored. Empirical bayes estimation was evaluated on functional connectivity in adolescents with mild TBI. Resting-state fMRI data were collected from 144 adolescents across six sites participating in the CARE4Kids study. Functional connectivity was computed over resting state networks defined using Seitzman parcellation. ComBat with and without empirical bayes estimation was assessed by quantifying: (1) site variability based on one-way ANOVA, (2) within-site consistency before and after harmonization (intraclass correlation coefficient), (3) age correlations, and (4) site effects of the principal components. All networks demonstrated significant moderate-to-large site effects (all p  < 0.001) before harmonization. Harmonization without empirical bayes yielded low residual site effect sizes, whereas empirical bayes harmonization yielded low-to-medium site effects. Within-site consistency between the data before and after harmonization was consistently excellent when using empirical bayes estimation. Harmonization without empirical bayes was excellent across sites with higher sample sizes (n ≥ 13), but moderate-to-excellent for smaller sites (n ≤ 12). Both approaches improved age associations across connections involving the default mode and dorsal attention networks and reduced site effects in the first principal component ( p  > 0.05). ComBat with or without empirical bayes effectively removes site variability while preserving age in functional connectivity measures, however, empirical bayes estimation better preserves the original within-site variability.