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Dear Walter, > How do construct the design matrix in this case > > 4 subjects, 3x2 = 6 conditions in 3 runs for every subject > > time course for conditions > session 1: 1 2 1 2 1 2 1 2 1 2 1 2 1 > 2: 3 4 3 4 3 4 3 4 3 4 3 4 3 > 3: 5 6 5 6 5 6 5 6 5 6 5 6 5 > 4: 1 2 1 2 1 2 1 2 1 2 1 2 1 > 5: 3 4 3 4 3 4 3 4 3 4 3 4 3 > 6: > etc > 12: 5 6 5 6 5 6 5 6 5 6 5 6 5 > > Goal: how to specify the to-be-tested contrasts C1>C2, C2>C1, C3>C4, > C4>C3, C5>C6 and C6>C5 for the group? > Why should there be 48 elements in the contrast vectors? > What are the elements? I would imagine that you have specified 4 subjects (i.e. sessions - S) with 12 effects per session. These may be the 6 conditions (C) with two regressors per condition (a and b) (a box car and its derivative?). If this is the case and the columns correspond to: S1C1a S1C1b S1C2a S1C2b ... S2C1a S2C1b.....S4C6a S4C6b Contrast weights testing for the average effect (over these subjects) of C1 > C2 would look like: 1 0 -1 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 0 0 0.... With best wishes - Karl %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%