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You need to use "-e" option to define the exchangeability between the two time points. -e design.grp If the first 50 points are from your first time points, the second 50 points are from your second data points. Here is the example design.grp for randomise. The two scans are from the same subject. Thus, they might be correlated. You need to count for that. Otherwise, program will have problem with TFCE correction. It happened to me before. design.grp: should be the 1 2 3 .. 50 1 2 3 ... 50 >>> SUBSCRIBE FSL Jay <[log in to unmask]> 11/15/2011 9:10 AM >>> Hello, I am trying to run randomise for repeated measures on baseline (50 scans) and followup data( 50 scans) as a paired analyses. In my design matrix , i have first 3 columns to model group, time, interaction followed by 50 columns to model the categorical effect. Hence, the size of design matrix is (100 X 53). I have attached the design matrix (design.mat). When i run randomise on my TBSS data using this design matrix, i get the following Warning ( i have pasted the terminal text below ). For some reason tfce is not able to handle it. Can you please explain why and what is the work around for this situation? ============================================================================ FIU-iMac08:stats jay$ randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 --T2 -V randomise options: -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -n 5000 --T2 -V Loading Data: Data loaded 9.32066e+28 permutations required for exhaustive test of t-test 1 Doing 5000 random permutations Starting permutation 1 (Unpermuted data) Starting permutation 2 Warning: tfce has detected a large number of integral steps. This operation may require a great deal of time to complete. ============================================================================ Regards Jay