Hi Erin,
> Is it possible, using 3dLME to specify the model so that I can investigate the effect
> of patient status after accounting for any potential effect of scanner (pre- or
> post-upgrade)?
Sure, you can add the scanner as a categorical variable.
> Would I need to change my SS calculation to Type I/sequential and then enter
> scanner first in my model specification?
This is controversial issue. Some people prefer type I, but the problem is that it's sensitive to the order (or position) of each variable in the model. You can try both type I and III, and see how much they differ.
Gang