Hello,

I want to run a whole brain cortical thickness analysis and I will like to confirm some steps.

a) for correcting for multiple comparison, I want to use both Monte Carlo and permutations in order to compare the difference. Are these the right commands?

Monte Carlo : mri_glmfit-sim --glmdir lh.name.glmdir --sim mc-z 5000 2 mc-z.abs.2 --sm-sign abs --cwp 0.05 --overwrite

Permutation: mri_glmfit-sim --glmdir lh.name.glmdir --sim perm 5000 2 permcsd --sim-sign abs --cwp 0.05 --perm-resid --overwrite

b) I have 2 groups and a contrast of (1 -1 0 0) representing where group 1> group 2 removing the effect of age. If I correct for multiple comparisons using abs and while visualizing my result the color map for the surviving clusters is blue , this means areas where group 1 < group 2. If the color map for the surviving clusters is red/yellow, this means areas where group 1> group 2.

Thank you.

Best,

Paul

Sent from my BlackBerry 10 smartphone.