Ditto. We developed a nice set of high-res hippocampal atlases[1] and multi-atlas segmentation method to use them[2] and compared it with FSL, and freesurfer and found FSL and freesurfer would often over-estimate segmentations. Good for a first pass because they are both dead-easy to run though.

[1] http://cobralab.ca/atlases/

[2] https://www.ncbi.nlm.nih.gov/pubmed/24784800

code here: http://cobralab.ca/software/MAGeTbrain/