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A question: are there two subjects in each group (G1, G2, G3)? Or one subject in each group with two scans? Demean: (http://mumford.fmripower.org/mean_centering/) For two subjects case: G1 G2 G3 CNI_1 CNI_2 1 0 0 -0.667 -9.333 1 0 0 0.333 12.667 0 1 0 0.333 1.667 0 1 0 -0.667 -6.337 0 0 1 0.333 10.667 0 0 1 0.333 -9.333 For one subject case: You'd better get the average FA map from the two scans. Then use the following design matrix: G1 G2 G3 CNI_1 CNI_2 1 0 0 -0.167 1.5 0 1 0 -0.167 -3 0 0 1 0.333 1.5 Contrast1: 1 -1 0 0 0 Contrast2: 1 0 -1 0 0 Contrast3: 0 1 -1 0 0 Yingying From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of R Duke Sent: Wednesday, May 16, 2012 3:13 PM To: [log in to unmask] Subject: [FSL] Randomise Contrast Dear FSL Experts, I have a question regarding my Randomise design matrix. I have three groups (G1, G2, G3) and two covariates of no interest (CNI). I am interested in between group FA differences and feel that I should control for my two covariates of no interest. Given this information I was wondering if the design matrix I have listed below is correct? G1 G2 G3 CNI_1_G1 CNI_1_G2 CNI_1_G3 CNI_2_G1 CNI_2_G2 CNI_2_G3 1 0 0 1 0 0 22 0 0 1 0 0 2 0 0 44 0 0 0 1 0 0 2 0 0 33 0 0 1 0 0 1 0 0 25 0 0 0 1 0 0 2 0 0 42 0 0 1 0 0 2 0 0 22 Contrast1: 1 -1 0 0 0 0 0 0 (give me voxels where FA for G1 > FA for G2) Contrast2: 1 0 -1 0 0 0 0 0 0 (give me voxels where FA for G1 > FA for G3) Contrast3: 0 1 -1 0 0 0 0 0 0 (give me voxels where FA for G2 > FA for G3) I was also wondering if this design controls for within or between group variance? In other words, what happens if I put my two covariates of no interest in only 2 columns (just listing the covariate of no interest across each group in two columns - one column for CNI_1 across all groups and one column for CNI_2 across all groups)? Would this be controlling for between group differences? Cheers!