[Freesurfer] mri_glmfit-sim

Hi,

I have 3 beginner questions about the use of mri_glmfit-sim

1. Under what type of circumstances should I run mri_glmfit-sim with permutation simulations?  2. The voxel threshold of 0.01 (cache 2) is used a lot. Is this too lenient in cortical thickness comparisons?  3. About the sign of the test (abs, neg, pos): is a one-tailed sign justified if I have an hypothesis? If the uncorrected (mri_glmfit) test shows a significant difference in one direction but not the other, am I justified to use pos/neg (instead of abs) in the mri_glmfit-sim stage and explicitly state that in the manuscript?

Thanks. Hope to learn more. Have a good week.

Cheers, Shane