Hello FreeSurfer Developers,

I ran longitudinal samseg on a group of subjects with MS (each with 5 MRI timepoints over 2 years) and found that the average volume of the pallidum increased over time, while other subcortical volumes (caudate, putamen, thalamus) decreased. I also tried longitudinal samseg using the --pallidum-separate flag and had similar results. As the putamen gets smaller it looks like the pallidum volume grows to fill in the space. Have you encountered this issue before? 

I am using enhanced T1 images (made from T1, FLAIR, and FA data) as the input for run_samseg_long (FreeSurfer v7).

Thank you,

Andrew