External Email - Use Caution        

Hi Eugenio,

Thanks! I am able to run it now.

Best,
Emily
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, 
Eugenio [e.igles...@ucl.ac.uk]
Sent: Thursday, April 11, 2019 1:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfield version


        External Email - Use Caution
Hi Emily,
I suspect that you’re mixing versions. Please make sure that you source the dev 
version.
Cheers,
/E

--
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com


From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Emily Schwartz 
<emily.schwa...@einstein.yu.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 11 April 2019 at 13:02
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal subfield version


        External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, 
Eugenio [e.igles...@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-boun...@nmr.mgh.harvard.edu> on behalf of Emily Schwartz 
<emily.schwa...@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


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