[Freesurfer] aseg.mgz looks worse after longitudinal processing on 5.1

Hi Surfers,

I have done some Longitudinal Processing on a bunch of subjects and although the pial and white surfaces are looking good after the Longitudinal Processing, the aseg segmentation for each subject is often looking much worse.

I have attached a sample screen grab to show you what I mean. The images on top show the Longitudinal Processed views. The images on bottom are of the same subject before the Longitudinal Processing  has occurred.

It is possible I am doing something wrong. I just thought I would throw it out to the experts to see if they are having similar experiences or if there are suggestions on things that I should do.

Thanks very much,

B.A.