I recently obtained a set of infant templates. Out of curiousity, I decided to view one of the input brains with the provided segmented volume file. It appears that there is some misalignment. I wouldn't expect the alignment to be perfect, since I am basically overlaying an average of multiple brains onto one. However, it looks like this misalignment may be caused by either: 1.) the segmentation volume file being shifted down or 2.) the slices not lining up properly (i.e. one file starts before the other).

   Any ideas what could cause a problem like this? Could it be that the segmented files are simply not compatible with FreeSurfer? 

Thanks for the help,

Mark