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Thank you for your reply. 
This is the image you requested. The green line is the thalamus (from aseg.mgz) and the light purple area is the hp tail. Hope that now is better. 
Best, 
Alice 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@MGH.HARVARD.EDU>
Sent: Tuesday, August 27, 2024 3:13 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Question on hippocampus segmentation algorithm
 

Dear Alice:

  1. Can you please send another capture without the mask, or with the option “show label boundaries only” activated? It’s hard to tell, without seeing what’s behind 😊
  2. You can read the paper for free here: https://www.sciencedirect.com/science/article/pii/S1053811915003420

Cheers,

/Eugenio

 

--

Juan Eugenio Iglesias

http://www.jeiglesias.com

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Savoia, Alice (Stud. FPN) <a.savoia@student.maastrichtuniversity.nl>
Date: Tuesday, August 27, 2024 at 7:00 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Question on hippocampus segmentation algorithm

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Hi everyone!

I have segmented the hippocampus subfields using the segmentation tool provided by the latest version of FreeSurfer. I am now looking at the pictures and I have a few questions: 

  • In some cases, the hp tail takes a bit of the thalamus, does the size of the tail or its borders affect the subfields. This to know if we should exclude the participant or if we can just exclude the tail from t he analysis 
  • How the algorithm works?

I also have provided a picture as an example. 

Thank you for the help.