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Hi  Eugenio and Bruce, 

We used freesurfer-6.0.0 to segment the brain-stem into different different structures. 

I see we get two mgz files after this process:
aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz

Do you have any recommendations to combine these two masks into a single mask ? 

I see pons in brainstemSsLabels.v10.FSvoxelSpace.mgz overlaps with the brain-stem in aparc+aseg.mgz but the midbrain in brainstemSsLabels.v10.FSvoxelSpace.mgz overlaps with brain-stem and the ventral-dc in aparc+aseg.mgz. 

Any recommendations are appreciated. 
Thanks
Mehul