Jeanette,
My apologies, I should have said runA - RunB. I actually have 3 runs in total, each being a slightly different task. So yes, this is why I am trying to run the third level analysis.
To summarize what I have done:
1st level: Ran each run for each subject
2nd level: Did a within group analysis for each group (Control, 24 participants and MCI, 16 participants) which contained 5 contrasts of interest
3rd level: Where the problem is. I am trying to get results for each 2nd level contrast, using a Con - MCI and MCI - Con contrasts.
-Carlos
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