Well, the fat_proc_connec_vis program is designed to read in multiple data sets after "-in_rois ..", each assumed to be a mask/map of a single ROI. It then turns each of those into a separate surface file ("*.gii"), and then those can be viewed together with SUMA. (Supplementarily, it also makes+applies labels from each file name.)

You have a good idea to try to load in the GM ROIs and turn them into surfaces, the way in which those ROIs are stored is different and not really a good input for
fat_proc_connec_vis: all the ROIs are in a single file (identified by different integer values). At present, each ROI would have to be dumped out into a separate file and then input in a similar manner to the WM ones.

I am contemplating how best to view all the GM and WM, as well as possibly being able to input a file like the GM/GMI ROIs directly...

--pt