Hi Reza, 

I saw your question, I am new to CONN toolbox so I don't know the answer for your request. I am also trying to create groups as in control subjects and diagonised patients. May I know how did you do it?

Do we have to upload all the subjects as input first and then by giving values of 0s and 1s in 2nd level covariates tab, did you create the groups? or did you create the groups through scripting???

 Can you share your knowledge on this regard.

Thank you .