Results of repeated-measures MANOVA on the projected IQMs.

We did not find an effect of the site nor an effect of defacing on the principal components extracted from the IQMs. However, applying the IQMs standardization and PCA separately per site mitigated the site effects, revealing a defacing bias. Despite being significant, the defacing bias is associated with a negligible effect size. Effect size is reported as partial η2 () and was computed with the function F_to_η2 from the R package effectsize [46], which implements the formula given in Equation D in S1 Text with df = numDF and df_error = denDF. pFDR corresponds to p-values controlled for false discovery rate (FDR).