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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1aIu0k7pAztgryDun7DPiNZhZjA6TAIwZb-MGH9rYcCM76b... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://secure-web.cisco.com/1UJcHFMvoYu36HvGYiXBWVTEC-BX8L7ePzyhbyarF-URbu2s... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.