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