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?
Thanks a lot for your help.
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