It does look like it makes the ewc1/ewc2/ewc3 files for the gray, white, csf ROIs only for the first subject during this import ROI section. Never makes those files for the subsequent ones, if that might indicate where it is getting stuck?

Edit: I went ahead and had it make the thresholded ROIs for gray/white/csf directly for all subjects (instead of just subject 1, where it seemed to have stopped). Import ROIs still appears to be hanging...