Fig. 3.

Distributions of left superior frontal cortical thickness residuals across scanners before harmonization (A), after cross-sectional ComBat (B), and after longitudinal ComBat (REML method) (C). Residuals are derived from linear mixed effects models including explanatory variables baseline age, sex, diagnosis, time, diagnosis × time interaction, and a subject-level random intercept. Scanners are ordered left to right by increasing residual means (red dots). Kenward-Roger (KR) test for additive scanner effects and Fligner-Killeen (FK) test for multiplicative scanner effects were significant for unharmonized and cross-sectional ComBat-harmonized data, but not for longitudinal ComBat harmonized data, confirming that longitudinal ComBat successfully removed scanner effects.