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Hi Anderson, Thanks for the answer.... For the question 1) you said: >> It can happen: TFCE uses not only the height (that is symmetric around zero for both contrasts) but also the spatial distribution (that is not symmetric). So, it differs. So, what could be the signification of this for the results I obtained? Also: I performed an experience with 4 repeated measures (condition 1, condition 2, condition 3, condition 4) over 2 groups (control and test). So I want to examine: 1) the time effect in the control group 2) the time effect in the test group 3) the timeXgroup interaction... How could I build my design matrix in FSL. I have look at the FEAT-UserGuide and GLM-FslWiki but all examples deal with 2 or 3 measures Thanks in advance Arsene ________________________________ Von: FSL - FMRIB's Software Library <[log in to unmask]> im Auftrag von Anderson M. Winkler <[log in to unmask]> Gesendet: Mittwoch, 31. Mai 2017 02:23 An: [log in to unmask] Betreff: Re: [FSL] Trouble with Two-Sample Paired T-test results using randomise TFCE Hi Arsene, Please see below: On 29 May 2017 at 19:14, Henri Longin <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear all, I'm performing a two-Sample Paired T-test VBM using a statistical analysis with randomise TFCE. 1) Results obtained by estimating the 2 paired differences A-B and B-A showed to be different from each other (what was expected) but one was not the opposite of the other: why? It can happen: TFCE uses not only the height (that is symmetric around zero for both contrasts) but also the spatial distribution (that is not symmetric). So, it differs. 2) More generally, how can one optimally choose the number of permutations in randomise TFCE? There is no rule for this. More permutations make the p-values more reliable. The default in randomise is 5000 and it's ok to stay with that. All the best, Anderson Thanks in advance Arsene