I segmented the given example subject 'bert' by using the command (following the steps https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures)

Step-1: recon-all -all -s bert -brainstem-structures

Step-2: recon-all -s bert -brainstem-structures

Step-3_a: mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz --id 173 --l midbrain_vt.label

Step-3_b: mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpacemgz --id 173 --l midbrain_vx.label  

Now when i view the label file along with the respective segmented volumes, the results i get for both the vertex domain and voxel domain, does not cover the whole midbrain. as shown below. 

freeview -l midbrain_vt.label -v $SUBJECTS_DIR/bert/mri/nu.mgz -v $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz:colormap=lut

freeview -l midbrain_vx.label -v $SUBJECTS_DIR/bert/mri/nu.mgz -v $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz:colormap=lut

Question No.1. Please let me know, what is wrong with my steps? 

Question No.2. Please let me know is it possible to generate label files in voxal space but with better resolution? like vertex space.

Warm Regards, 

Safi