Jeanette,
Correct. This is exactly what I have done that is giving me the original error message I described.
I will also try that design you mentioned when I get a chance. There are actually 5 contrasts that I am specifying. I guess I will just run them in different analyses since that design matrix will be way too large.
When you mentions pairs in this case it seems that you mean pairs of runs not pairs of subjects, correct? As I mentioned before, I have 24 controls and 16 MCI.
Thanks
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