Thanks so much for your response, Anderson.
Here is a new design matrix and contrast matrix. There are 4 groups (patient time 1 (PT1), healthy control time 1 (HC1), patient time 2 (PT2), and healthy control time 2 (HC2). Some subjects have only 1 session of resting state data, some subjects have 2 sessions. Therefore, this time, we used the multi-session, multi-subject (repeated measures analysis) example as a template. We didn’t use the GUI, since with 174 subjects, it seemed like it makes more sense to use a script to design the matrix. Since the scans come from 3 different studies, we have a covariate representing the study, which is in the last column.
The contrast matrix is designed to compare PT2 and PT2 (represented by 1) against HC1 and HC2 (represented by -1).
We really appreciate your input with this!! Please let us know if we are still constructing the matrix incorrectly.
Thank you again,
Alex
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