Hard to tell, Jenna!

Please do upload a sample subject using the instructions in the wiki, and I’ll take a look.

Cheers,

/E

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jenna Katherine Blujus <jkblujus@uwm.edu>
Reply to: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 14 July 2020 at 13:15
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment

        External Email - Use Caution        

Hi Eugenio, 

I might have fixed this particular issue. I ran AFNI's 3dUnifize on the T1 before submitting it to recon-all and this improved the segmentation (it now overlays on the hippocampus). However, I still have some other files that this solution did not work for (see attached picture). I have a few subjects where the segmentation is slightly superior to the hippocampus. Editing the aseg or running 3dUnifize did not fix this issue. Do you have any suggested solutions?

Thank you for your help!

Jenna