Hello Andrew,

I am running an analysis on 66 subjects whose data are collected from 4 different scanning sites. I am including the four scanning places as nuisance factors, as well as the mean framewise displacement. The subjects are divided in only two groups.
I have organized the design matrix as: [site1 site2 site3 site4 MFD 1 group1 group2], where '1' is constant for all subjects. 

I wanted to confirm I am understanding the contrast right. If I have no assumptions about the data, my contrast should be [0,0,0,0,0,0,1,1] and the type of test should be F-test. However, if I want to make some assumptions (e.g. grounp1>group2), my contrast should be [0,0,0,0,0,0,1,-1] and the type should be t-test. So, by marking the 0s I am indicating the first 6 values of each row are nuisance factors that should be regressed out of the data and the last two values are the groups.

Could you provide some help on if I am doing this correctly? 

Thank you in advance.

Best Regards,

-Ana