Furthermore, the way you have set it up is a paired t-test. Follow the unpaired t-test in the wiki. Hope that helps. Cheers, Andreas Von: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Colin Hawco <[log in to unmask]> Antworten an: FSL - FMRIB's Software Library <[log in to unmask]> Datum: Dienstag, 15. März 2016 17:48 An: <[log in to unmask]> Betreff: Re: [FSL] design matrix for testing A=B vs A!=B You are committing a statistically fallacy here, by trying to say A and B are equal. You cannot demonstrate that with that contrast. If p < 0.05 we reject the null hypothesis that A and B are EQUAL. If p > 0.05, all we can say is that we are not certain that any difference between A and B is a true population difference for our probability level. You cannot really show two groups are equal based on a traditional t-test. In fact that is very tricky to do. The best you can do with this approach is show they are not STATISTICALLY different at a given threshold. Colin Hawco, PhD Neuranalysis Consulting Neuroimaging analysis and consultation www.neuranalysis.com <http://www.neuranalysis.com> [log in to unmask] From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Qasim Bukhari Sent: March-15-16 12:30 PM To: [log in to unmask] Subject: [FSL] design matrix for testing A=B vs A!=B Dear FSL experts I was running a study, and just wanted to make sure that my design matrix is correct I want to test whether my group A is equal to group B or not(both having 8 subjects). Null hypothesis is that it is NOT equal, and I want to prove it false. (that means if A and B are equal I m happy) Should these be my mat. file 1 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 1 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 1 -1 1 0 0 0 0 0 0 0 -1 0 1 0 0 0 0 0 0 -1 0 0 1 0 0 0 0 0 -1 0 0 0 1 0 0 0 0 -1 0 0 0 0 1 0 0 0 -1 0 0 0 0 0 1 0 0 -1 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 1 and con file 1 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 Would the design matrices remain the same if I reverse my null hypothesis ? That means to make the null hypothesis that both groups are same (optimal result that we disprove it). What would be the change in the design matrix then? I think I m doing something wrong, if anyone can help in this, I ll be grateful ? Thanks and kind regards, Qasim