I think I've found how to do it:

* Do your CONN processing as usual, you need CONN >= 17f.
* At 2nd-level analysis, you should see a QA_GCOR_[session] variable. You can select it and regress it out, just like any other.
* I also added a "multicentric" 2nd-level covariate to model which subject belonged to which center.

I tried to regress both QA_GCOR and multicentric covariates, and I did a sanity check on controls from 2 different centers (with 2 different but close TR: 2.0 and 2.46). There were major differences, like more than between the patients vs controls!

Is there anything else that can be done to adjust for multicentric analysis in CONN? Thanks a lot in advance!