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I have had some trouble setting up a comparison between resting scans that I believe is due to how I am setting up my model. 

I have 2 groups of participants. All participants were scanned before receiving 1 of 2 randomly selected treatments. Then they were scanned again afterwards. 

My biggest question is how to set up the explanatory variables. I had originally set them to empty and then tried to compare the participants in a higher level analysis but was unable. 

The main thing I would like to do is run a paired t-test between the two groups. But I strongly feel I am setting up the lvl 1 analyses up incorrectly.