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

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I am trying to run hippocampal and amygdala segmentation

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

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