Hi, FSL experts,

I am a beginner with FSL.  Previously I asked one question on the independent t-test with FSL (e.g., patients, healthy controls). Two experts suggested me simply using the "1" as "Group" for both patients and healthy controls. I agree as if I used "1" for one group and "2" as the other group, I did not observe any effects between the groups. I was thinking that this FSL approach is different from the common behavioral data analysis. 

Now I want to do the paired t-test (the same patients were tested two times, before the treatment, and after the treatment). My quick thought is that of course, I should use the "1" as group for both sessions ("before" session and "after" sessions). But my problem is that I did not find any effect of treatment - this does not make sense to me. So I want to confirm with the FSL experts to see if I am wrong on anything. 

Here I attach some details in 2 slides - see the attachment. Could any experts advise me, if I am incorrect on anything?

Thank you very much,