Yes, you're right. But in that case, these changes would be quite similar for right-hippocampus too.
Based on my analysis and literature, Freesurfer has more accurate measures than FSL. The doctors are quite conservative about boundaries so that measures are the smallest between Freesurfer and FSL. In other words, the measures obtained by Freesurfer are in the middle, they are bigger than manual and smaller than FSL. However, for left-hippocampus the volumes measured by Freesurfer are always bigger than FSL and Manual segmentation. The only reason I can find, once the softwares use the same criteria for left and right-hippocampus, is related with the doctor responsible for the manual segmentation.
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