Multiple Comparison Problem ROI to ROI analysis using anatomical atlas

Hi all,

I am conducting a resting state functional connectivity analysis and I am using a self defined seed region and want to look at the functional connectivity to the ROIs based on the Harvard Oxford Atlas. I was wondering how to deal with the multiple comparison problem. Is the functional connectivity between my seed region and each of the ROIs from the template computed sequentially or simultaneously? If I understand this process directly than this would have big implications for the multiple comparison problem.

Can someone help me with that?

Thank you very much,

Sebastian