I have supplementary motor area (SMA) defined in standard MNI volume space and I would like to extract cortical thickness for this area. I have 80% of SMA in left hemisphere and 20% on right hemisphere. So I am stuck at the command mri_vol2surf before proceeding to mri_segstats.

In mri_vol2surf, I am not sure what should I specify for --hemi i.e. whether its left or right hemisphere (lh or rh). If I specify e.g. lh, then would not it convert left hemisphere SMA voxels to surface and later on extract the measure from left hemisphere only and vice-versa for right hemisphere.

I am not sure how would that work if portion of ROI is on both hemispheres and how can I run mri_vol2surf command? 

Thanks,

Sahil