Fig. 2.

Site-specific cortical thickness averaged across regions. Non-harmonized (A), ComBat harmonized (B), and ComBat-GAM harmonized (C) data in participants with PTSD. Non-harmonized (D), ComBat harmonized (E), and ComBat-GAM harmonized (F) data in trauma-exposed controls. The order of sites in the figure is consistent with the order of site names in the legend from top to bottom to facilitate with interpretation. Compared to non-harmonized data, ComBat and ComBat-GAM lead to smaller differences between site-specific data and the mean values averaged across sites, and they do not change the site-specific standard deviations for cortical thickness. The effects of harmonization by LME models cannot be shown here because data harmonization and statistical analyses are inseparable in LME methods. Mean cortical thickness averaged across regions is shown to minimize regional biases. The boxplots were made using the default settings of the R ggplot2 function geom_boxplot(). The lower and upper hinges correspond to the first and third quartiles (the 25th and 75th percentiles). The upper whisker extends from the hinge to the largest value no further than 1.5 * IQR from the hinge (where IQR is the inter-quartile range, or distance between the first and third quartiles). The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR of the hinge. Data beyond the end of the whiskers are called “outlying” points and are plotted individually.