I have 2 time points on 60 subjects with most being in some form of AD.  There are considerable differences in hippocampal volume between time points.  I edited the raw images before making the template. I then had to edit the aseg template image and there were still problems on the -long images.  I tried to edit and rerun autorecon2-noaseg and autorecon3 and it does not appear to be keeping my edits.