Hi Yuko

I think you can use multiple label tags when using mri_label2vol like below:

mri_label2vol --subject $subject_name --hemi $hemi --label $label1 --label $label2 --label $label3 --temp $template --o $output --fillthresh 0.3 --proj frac 0 1 0.1 --identity

The output volume would have non-zero voxels, marked with three different values. 

Best

Cheol