Hi Alfonso,
I have done a lot of reading and can't seem to find the answer, so thought I would post here in this forum.
We are conducting a rs-fmri study of cerebellum connectivity in two groups. There are 2 sites (melb1, melb2) and both patient and control data were collected at both sites. 
I have done all the preprocessing and denoising in CONN, treating the two sites as independent studies (i.e., I've generated a conn.mat file for melb1 and a separate conn.mat file for the melb2 site). This is partly due to the 2 sites having slightly different acquisition protocols (different TR's, number of slices). We are at the point of 2nd level analyses. Does CONN have the ability to 'merge' 2 conn.mat files such that the data can be analysed together, in 1 grouop-level analysis, with site added as a regressor at the 2nd level? I can't seem to find how to do this. The alternative is to run a 2 x 2 ANOVA in SPM which allows for the manual uploading of scans from different file locations/sites.

Thank you,
Rebecca