Dear Freesurfer experts,


I'm having troubles when setting a permutation test, I'm making  group comparisons, but I'm introducing the Age, and cortical thickness as niusance variables (as previously recommended).

It seems that permutations only work for orthogonal matrices, does this means that I cannot set any niusance variable?


If so, this is telling me that I can run the command with the flag "--perm-force", and I'm wondering, which would be the implications of force to run the permutations with niusance variables?


Many thanks in advance,
Gabriel