Thanks for your response Daniel. I, too, am confused. I am using an atlas of visual cortical regions (Wang et al 2015, Cerebral Cortex) where each regions is assigned one integer value. I am hoping to obtain the center mass for each visual cortical ROI. I had to use CONN toolbox, which required me to import an *.annot file to use the atlas. CONN toolbox then output a *.nii file. Since I'm more familiar with AFNI (volume data) I thought I could use this to obtain the ROI centers. But from your response it seems like I should start earlier in the process and work from a *.gii file.

Which AFNI/SUMA program would this *.gii atlas file be fed to so that I could extract the ROI center coordinates?

Andrew