I'm using Freesurfer 6.0 dev version (Mac) to perform hippocampal subfields segmentation. I only need to measure total hippocampus volume, but measurements from basic `recon-all` were too volatile and I was hoping that using subfields with T2 modality would reduce variance. However, volume measured by hippocampal subfields is significantly different from volume in aseg.stats.

Here are volumes for right hippocampus from various methods:

aseg.stats - 3312.8

rh.hippoSfVolumes-T1.v10.txt (Mode A - only T1 used) - 2883.8

rh.hippoSfVolumes-T2.v10.txt (Mode B - using only additional scan) - 2503.97

rh.hippoSfVolumes-T1-T1T2.v10.txt (Mode B - Multispectral segmentation) - 2596.09

I checked labeling visually and there were no obvious problems. Is such a large difference common? Am I missing something? What number should be most trusted?