Dear SPM-Experts,
I have set up a full factorial model on the second level in which I compare two groups (factor 1) and two time points: pre vs post (factor 2).
I was wondering whether the contrast images for factor 2 can stem from the same first-level GLM? Specifically, there, I modelled the pre- and post-session within one GLM and defined various contrasts already on the first level, for instance, differential contrast pre vs. post (1 -1 and other regressors 0), mean activity pre (1 0), mean activity post (0 1). For the second-level full factorial model , I guess I would use then the mean activity pre (1 0) and mean activity post (0 1) contrast images from the first level as inputs (for the two levels of factor 2).
Alternatively, one could run two first-level GLMs - one for only the pre session, and one for only the post-session, and then use those mean activity contrast images for the second-level model.
However, I would prefer the first option, because then one could already compare the pre vs. post activity on the first-level. This way one could also use this difference contrast on the second level and run for instance a simple two-sample t-test, comparing the two groups.
I hope that my prefered variant is also fine for the full factorial model. Or is the alternative variant (separate first-level models for pre and post) preferable? And if so, why? I am not completely sure if these two variants should produce the same or similar results anyway. My intuition is yes, but on the other hand, when modeling both pre- and post-session in one model the mean baseline activity to which, for instance, pre-activity-only is compared, is quite different (because it also includes post-activity) then when keeping them separate.
Maybe someone can help. Thanks a lot!
Stefan
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