afni.nimh.nih.gov

Hi, Marina-

For an ROI-based analysis, I don't think I would smooth- it would only smear data across ROI boundaries.

Do you want an functional connectivity matrix output? Have you looked at 3dNetCorr, whose inputs are:
+ a map of ROIs
+ an EPI (or other 4D) dataset
and whose output would be a functional connectivity matrix?

--pt