External Email - Use Caution
Dear Kersten,
Thank you for your answer, I have some follow-up questions to the first two points before I can move on.
1) Regarding family-relation, since three random effects may not work, did you mean that a simpler model with 2 random effects (intercept and family ID, thus leaving out slope which I assume is time from baseline) would work? While forgetting family ID is an option, it would be a model that may attract criticism.
2) Regarding multiple comparison correction, I understand how to perform the procedure you suggested (second option) to simply calculate the corrected p threshold using pcor = -log10(pth) and then use pcor as threshold for the sig.mgh. However after running FDR2: [detvtx,sided_pval,pth] = lme_mass_FDR2(F_lhstats.pval,F_lhstats.sgn,lhcortex,0.05,0);
While detvtx is not empty (a few vertexes survived) and the pth value is calculated to 1.00000e-30 and therefore pcor to 30. This doesn’t seem right. What is also strange is that I saw a few times a more reasonable pth in the range of e-5 using the exact same data and procedure. I cannot replicate this in the same analysis in R2021, now I only get the e-30 (I only tried left cortex thickness so far).
Best, Julian