I can help you with this.
There is matlab script to use a different list of ROIs to compute the statistical measures. (item 6). You can specify the list of ROIs, names of surface and volume label files to this script and the script will output all the cortical and volumetric measures.
Also you can create their own atlas with you own ROIs (item 7) and then compute statistics on those.
Please give it a try and let me know if it works.