Dear Isabella,
You need to download the development version to run segmentHA_T1.sh. However, you do not need to rerun your subjects through the development recon-all (in fact, you should *never* do that).
If/when you write a paper, you would state that you used FS 6.0 to recon the cases, and the development version of November 2019 to parcellate the hippocampus and amygdala.
Kind regards,
/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 Isabella Leung <isabella.leung@sydney.edu.au>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 12 November 2019 at 22:19
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Freesurfer6.0 hippocampal and amygdala segmentation-command not found error
External Email - Use Caution
To whom it may concern,
I am trying to run hippocampal and amygdala segmentation
I was able to run recon-all, however I am unable to run segmentHA_T1.sh and get the error message of "command
doesn't exist".
I'm not quite sure what the problem is. I have seen online that I should update the freesurfer to the development version? I'm not sure how to update my Freesurfer 6.0 to the development version.
Could you please let me know how I can update my freesurfer 6.0 so that I can run
segmentHA_T1.sh?
I have run recon-all on all my participants through Freesurfer 6.0. Will it mean that I will have to redo my recon-all in the freesurfer development version for all my participants before I try
to run the
segmentHA_T1.sh?
Thank you in advance for the help.
Best wishes,
Isabella
Isabella Hoi Kei Leung | PhD Candidate
Brain & Mind Centre | Central Clinical School | Faculty of Medicine
THE UNIVERSITY OF SYDNEY
Room 408, Level 4, Bldg M02K | 94 Mallett St, Camperdown NSW 2050 Australia
M +61 404 066 903
E isabella.leung@sydney.edu.au