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Dear Meera, > I have a somewhat (basic) question regarding 2nd level analyses. I have been conducting my analyses such that at first level I'll specify my contrasts (i.e., task vs baseline), and then at 2nd level I run a t test entering "1" when defining my contrast. I heard once that it is better to run only main effects at 1st level, and specify your actual contrasts at 2nd level (though I can't remember the rationale for this). > > I'm just wondering if anyone has any insight into this (e.g., is the activation more robust in one case versus another), and why it would make a difference when you specify your contrast. If you specify the contrasts appropriately, there shouldn't be any difference. See, for example: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;4d2421a6.1109 to see this in regard to a paired-samples t-test vs. a one-sample t-test on difference images. The significance of the result depends on the effect size (how big a difference is), the error, and the degrees of freedom. If you specify a 2nd-level contrast incorrectly—for example, not accounting for subjects in the design matrix—you can artificially (inappropriately) inflate your degrees of freedom, and thus get a "more significant" result. There has been quite a bit of discussion on the list about 2nd-level ANOVAs and appropriate error partitioning, if you're interested. But certainly for common cases of comparing 2 conditions using a t-test, it's fairly straightforward, and doesn't matter one way or the other. Hope this helps! Best regards, Jonathan -- Dr. Jonathan Peelle Department of Neurology University of Pennsylvania 3 West Gates 3400 Spruce Street Philadelphia, PA 19104 USA http://jonathanpeelle.net/