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I want to do a comparative analysis within different acquisition from the same subject (and later between different subjects). I have 100 volumes for each acquisition. My protocol is 5 blocks of 30 sec each alternatively of rest (subject in rest position) and active (ankle dorsi-flexion), beginning from rest. I did a design matrix with 200 scans (100 for the first acquisition and 100 for the second one) with two condition. the first condition is the protocol of the fist acquisition, the second the protocol of the second acquisiton, the last column is the constant one (see my design matrix attached). if I put a contrast vector of 1 -1 0 I should get the difference of the two activation maps, isn't it?? because it doesn't seem to work... is this the right way to do the comparison between two activation maps or is there a better method??