Hello Matthew, Thank you for your prompt reply. I tried running my analysis the way you suggested and got the following error. my 4d file which i am using as my regressor is T2. I used tbss_non_FA pointing them to a folder with T2 files in it and eventually got all_B0.nii in stats folder which i am using the following command. My design matrix looks as following Group EV 1 EV 2 EV 3 1 1 0 1 1 1 0 1 1 1 0 1 1 1 0 1 1 1 0 1 2 0 1 1 2 0 1 1 2 0 1 1 2 0 1 1 2 0 1 1 randomise -i all_FA_skeletonised -o tbss_with_T2 -m mean_FA_skeleton_mask -d designT2.mat -t designT2.con -n 500 --vxf=all_B0.nii --vxl=3 Am I doing something wrong here ? randomise options: -i all_FA_skeletonised -o tbss_with_T2 -m mean_FA_skeleton_mask -d designT2.mat -t designT2.con -n 500 --vxf=all_B0.nii --vxl=3 Loading Data: ***************************************************** Loading voxelwise ev: all_B0.nii for EV 3 Data loaded 3.23088e+13 permutations required for exhaustive test of t-test 1 Doing 500 random permutations Warning! No output options selected. Outputing raw tstat only Starting permutation 1 (Unpermuted data) 3.23088e+13 permutations required for exhaustive test of t-test 2 Doing 500 random permutations Warning! No output options selected. Outputing raw tstat only Starting permutation 1 (Unpermuted data) Finished, exiting. Kindly suggest Thank you Sincerely, Ankit Master