Dear all,
I have two groups (autism/control) that I had defined as 2nd level covariate in setup. Now in the 2nd level analysis, to see ROI-ROI connectivities of each group I simply select it from the Subjects Effects and click on Results Explorer, which gave me the ROI.mat file. Is this wrong? Because I wonder if I should manually include QA_invalid scans and QA_MaxMotion and set my contrast to something like [1 0 0] in order to exclude invalid scans and scans with large motion before running the analysis? But on the other hand I suppose these corrections has already been done during the preprocessing step, so maybe there is no need to manually include them in the design matrix of my 2nd level analysis, and QA_ covariates are just there as reports? 
Sorry for my confusion.
And thanks a lot!