Hello, 

I made an atlas of 312 ROIs, each with a 4mm radius, in the MNI152NLin2009cSym space. But in this space, 18 of the ROIs overlap with each other. I don’t want to remove any of them since most of the overlaps are pretty minor. Is there a way I can still calculate the functional connectivity (FC) for all 312 ROIs?

I was thinking of creating a separate .nii.gz file for each ROI and importing all 312 files into CONN. But I’m not sure if I go this route, will I still be able to run network-level FC analysis without introducing any artifacts?

Thank you!