Hi, 
I have 24 conditions from first level analysis , the first 8 are response to stimuli#1 and second 8 stimuli#2 and last 8 to stimuli#3. In order to do PPI analysis and compare stimuli effect I put the first 8 on the left and second 8 on the right side to form P but the result of this is very different from when I merged this 8 conditions from the beginning and run first level for 3 conditions(stimuli) . I wonder if there is any explanation or recommendation to this kind of analysis. The reason of having 24 conditions is that we add more details to be more flexible in creating contrasts. for example stimuli#1, hard, positive, level1 and so on.
BR