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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 <
awru...@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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