Hi Eugenio,

Thank you so much. I downloaded the development version, but when I run

"segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]," it says command not found.

After I download the runtime2014 version, I get the MCRv84 folder, but when I try to run a subject through the hippocampal subfield it gives me an error and tells me to download runtime2012b. Once I do that I also get the MCRv80 folder and am able to run the hippocampal segmentation, but I assume this is the 2017 version since I cannot run the amygdala segmentation. I am not sure what I am doing wrong when I download the 2018 dev version.

Best,

Emily

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk]
Sent: Thursday, April 04, 2019 5:23 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfield version

External Email - Use Caution

Hi Emily,

You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0.

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 Emily Schwartz <emily.schwartz@einstein.yu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, 3 April 2019 at 15:44
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal subfield version

External Email - Use Caution

Hello FS experts,

I was planning to use the hippocampal subfield segmentation module in FreeSurfer 6.0 on a Linux ubuntu computer. I also would like to use the nuclei of the amygdala segmentation, but realized I need to download the development version in order to do that. Is there any reason why I shouldn't use the development version over the 6.0 release?

Thank you in advance.

Best,

Emily