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Dear Ou, > I am trying to follow the instructions (http://www.fmrib.ox.ac.uk/fsl/tbss/index.html) to analyze my DTI data. Everything works fine until the voxelwise statistics: > > design_ttest2 design 7 11 > randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask –d design.mat -t design.con -n 500 --T2 –V > > Suppose I have 18 subjects, 7 are controls and 11 are patients. The design_ttest2 command above generated design.mat and design.con to do the statistics, and the randomise command did the t-test of the two groups. > > However, the 18 subjects I have are actually from 3 groups, each group has 6 subjects. I would like to see if there is any difference between groups 1 and 2, 2 and 3, and 1 and 3. In this case, how should I set the design.mat and design.con files, and how should I use the randomise command? the design_ttest2 script just creates a couple of very simple files specifying a design matrix and contrasts to look for A>B and B>A for the two-sample t-test case. For more complicated designs (yours is a one-way ANOVA) you can either use the Glm tool (glm_gui on a Mac) or you can have a look at the files created by design_ttest2 and from those it should be fairly clear how to change them for your case. If you are not familiar with GLM designs I suggest you read up on 2nd level designs on the Feat help pages (http://www.fmrib.ox.ac.uk/fsl/feat5/detail.html#higher) before you proceed. Good luck Jesper