I'm a bit confused about how to set up my group analysis. I have 3 subjects with 5 sessions each.
Each session had 2 runs, A and B. I want to do a contrast between A and B.
My intuition is to set up a second level analysis for condition A with an EV for each subject (i.e. 1
group, 3 EVs). Then a separate second level analysis for condition B. Then I'd do a third level
analysis to compare the group A activation versus group B activation.
However, the second level analysis generates a .gfeat directory, but the group analysis requests a
.feat directory. It's not clear to me what the input to my third level analysis should be (assuming
my intuition was correct in the first place).
Also, someone else (an SPM user) suggested that I should do the A-B contrast as a first level
analysis and bring the contrast up to the second level analysis for the group. Doesn't this assume
equal variance across A and B?