In the newer releases of FreeSurfer (development versions more recent than June 2015, and the upcoming 6.0 stable version) you can find an implementation of our  brainstem structure segmentation. The method combines a statistical atlas of the brainstem - built upon data from our collaborators at UCSF - with a Bayesian inference method to computed automated segmentations of the medulla, pons, SCP and brainstem from an input MRI scan.

Instructions on how to download and use the software