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Hi Andrew,

No, I don't think we have seen something like that before.

I'm a bit doubtful about the "enhanced T1 images", though - for sure there is more information for samseg to work on when you feed it both T1 and FLAIR, compared to some fused image. If this issue persists even when you feed in T1 and FLAIR separately, it would be good for us to have a look at the images ourselves.

Koen
  


On Wed, Jun 9, 2021 at 4:16 PM Russo, Andrew William <AWRUSSO@mgh.harvard.edu> wrote:
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

Andrew Russo
Clinical Research Coordinator 
Multiple Sclerosis Imaging Lab 
Massachusetts General Hospital 
149 13th Street | Boston, MA 02129 
617-726-7531
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