I am setting up a dual regression for a within subjects design and would like to add in an additional covariate.  The scans are pooled from two different scanners (although each subject had both of their scans on the same scanner).  When looking at the ICA components, a couple components have a marked difference within the group of subjects that correlates to which scanner the data was collected on.  So, we would like to include scanner as a nuisance covariate in our paired t-test.  When setting up my design, I receive an error message that states:  “Warning – design matrix uses different groups (for different variances), but these do not contain “separable” EVs for the different groups (it is necessary that, for each EV, only one of the groups has non-zero values). “  It seems to allow me to continue, but I wanted to verify that the results that I will get will be valid.

Thanks in advance,

Rachel