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Dear FS experts,
Instead of using mri_glmfit-sim, I am trying to implement a customized multiple comparison correction algorithm using permutation. Before I implement my own, I want to make sure my permutation idea is correct. So I was looking at how mri_glmfit-sim does the permutation. The link here http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has a simple description for how to do permutation, but I don't quite understand the 1st step: Permute the design matrix. To me, permute the design matrix means permute the matrix rows here, but still hard to understand why permuting matrix rows does the trick. Anyway, I will not use any design matrix in my customized implementation, so it does not matter for now. My problem can be described as follows: if I have a ROI (a label file) on fsaverage, and I have a test subject and a group of control subjects whose thickness values on every vertex in this label are all known. (The test subject and control subjects are all using fsaverage reference space). I want to compare this test subject's thickness within the ROI to a control group of subjects (within the same ROI). This is a multiple-comparison problem, so I want to use permutation to get less FP rate. My question is: How do I permute the test subject's points and control subjects' points in ROI? My understanding is that: for each point in the label, I randomly re-assign all (1+n) values from (1+n) subjects to these (n+1) subjects (where n is the number of subjects in control group). And when all points in the label are done, this is only 1 permutation. I will need at least 1000 times of permutation to get the comparison statistics. Is my understanding right? Thank you! Xiao