Yes, you should be following the instructions here:

https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala

rather than the wiki page for 6.0 here:

https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

Cheers,

/Eugenio

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 Steve Petersen <marfneuro@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 11 December 2019 at 10:28
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal subfields: exporting results

        External Email - Use Caution        

Dear Eugenio, 

I noticed what was the problem. I used freesurfer dev version with the following command:

segmentHA_T2.sh 

I tried to export the hippocampal and amygdala results of several subjects with these commands and now everything works fine. 

quantifyHAsubregions.sh hippoSf HIPO-AMY hippocampal_results.txt

quantifyHAsubregions.sh amygNuc HIPO-AMY amygdala_results.txt

Is there some difference between the segmentHA_T2.sh  that I used and the command of the website? In that case I would like to use the most appropriated. 

recon-all -s <subject_name> -hippocampal-subfields-T2 <file name of additional scan> <analysisID>

 Thanks in advance. 

Best regards,