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Hi Louis, Thanks for sending. Using this design, for the group comparisons the contrasts should be: *1 -1 0* *1 0 -1* *0 1 -1* *-1 1 0* *-1 0 1**0 -1 1* These are all 6 possible differences (in both directions. The F-test would use any two of these, provided that all 3 groups are represented. It could be the first and the second, for example. The design.fts would then be: */NumWaves 6/NumContrasts 1/Matrix1 1 0 0 0 0* Regarding the extraction of FA for some ROIs, see the commands fslstats and fslmeants. All the best, Anderson On 22 November 2017 at 22:27, S.J. Li <[log in to unmask]> wrote: > Hi > Sorry, that is actually my design.con file > I mistype into matrix > > I have 3 groups > group1: number=19 > group2: number=18 > group3: number=27 > > design.con > > /ContrastName1 Group 1 > /ContrastName2 Group 2 > /ContrastName3 Group 3 > /NumWaves 3 > /NumContrasts 3 > /PPheights 1.000000e+00 1.000000e+00 1.000000e+00 > /RequiredEffect 0.909 0.934 0.762 > > /Matrix > 1.000000e+00 0.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > > design.mat > > /NumWaves 3 > /NumPoints 64 > /PPheights 1.000000e+00 1.000000e+00 1.000000e+00 > > /Matrix > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 1.000000e+00 0.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 1.000000e+00 0.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > 0.000000e+00 0.000000e+00 1.000000e+00 > > design.fts > > /NumWaves 3 > /NumContrasts 1 > > /Matrix > 1 1 1 > > I have one more question is that how do I extract the FA value in the > specific brain region (have significantly difference) for creating the > table to compare? > > Thank you very much! > > Louis >