I have run a vertex based gyrification index analysis. Now I want to create a mask/ROI from the cluster of vertices which are above the threshold of 3 in sig.mgh file (p<0.001). Which command should I use for this purpose? Is it mri_mask? or mri_vol2roi?

Next how do I extract the GI value (a numeric) from the above obtained ROI from individual scans? 

If anyone has done anything similar with thickness or volume (which I am sure many would have done), it would be helpful if you guided me. Eagerly waiting for your response.