HI,

I have a set of 10 controls, 10 patients in category 1 and 10 patients in category 2. I am interested in comparing difference between functional connectivity using CONN.

I defined 4 2nd level covariates in Set Up steps as following:
controls as 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
category1 as 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 
category2 as 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1
category12 as 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

Now in second-level analysis steps, somehow for following two comparisons, I am getting very different results:

(1) For controls > category12, I selected controls and category12 and defined contrast as 1 -1
(2) For controls > category1 and category 2, I selected controls, category1 and category 2 and defined contrast as 1 -1 -1

Shouldn't both of these contrasts give me identical results as I am averaging over category 1 and category 2 in (2) above which is similar as category12?

I would really appreciate any help.

Thanks.