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Dear FSL experts, I am not sure how to set-up our design matrix for the following study. We have a 3x2x2x2 desing: Task difficulty (3 levels, within-subject) Patient group (2 levels, between-subject) Genotype (2 levels, between-subject) Treatment (2 levels, within-subject, applied in different scanning sessions) At the first level, we model load per run. At the second level, we combine runs per load level. At the third level, we include the other three factors resulting in the following shortenend design matrix (only 1 subject per cell): group P1-G1-T1 P1-G2-T1 P2-G1-T1 P2-G2-T1 P1-G1-T2 P1-G2-T2 P2-G1-T2 P2-G2-T2 1 1 0 0 0 0 0 0 0 2 0 1 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 4 0 0 0 1 0 0 0 0 1 0 0 0 0 1 0 0 0 2 0 0 0 0 0 1 0 0 3 0 0 0 0 0 0 1 0 4 0 0 0 0 0 0 0 1 Would this be the correct model? We would also like to include a covariate modeling whether treatment 1 or 2 was applied in the first or the second scanning session. If we do so by using 1 for order 1 and 2 for the other order in a 9th EV, the following error message occurs: Waring - desing matrix uses different groups (for different variances) but these do not contain "separable" EVs for the different groups. What would be the correct way to do this? Or would be a better option to do separate analyses for treatment a the third level and to model the treatment factor at a fourth level? Thank you very much for help, Claudia