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Nope, unless you rerun your subjects, which you totally shouldn’t (just run segmentHA_T1.sh) And of course, install on a different directory than 6.0 😉 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 "Chen, Christine" ChenC@kennedykrieger.org Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 26 July 2019 at 12:04 To: 'Freesurfer support list' freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found
External Email - Use Caution Hello,
Thank you for the response! I just want to double check before I install the development version, will installing the development version amend, delete, or override any of the previous FreeSurfer files or scripts we have with the non-development version? Thank you in advance.
Best, CC
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Friday, July 26, 2019 11:10 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found
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External Email - Use Caution Dear CC, You need the development version of FreeSurfer, since the amygdala was added to the atlas after the 6.0 release. Kind regards, /Eugenio
-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.comhttps://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com&data=02%7C01%7C%7Ca308e94491bc48d78eed08d711e2e037%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C1%7C636997538438104312&sdata=RdJA5s7mvqmGFKznklunjbfduLw35DZEq3FIRSU51gs%3D&reserved=0
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Chen, Christine" <ChenC@kennedykrieger.orgmailto:ChenC@kennedykrieger.org> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 26 July 2019 at 09:47 To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found
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I am trying to run hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmy...https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala&data=02%7C01%7C%7Ca308e94491bc48d78eed08d711e2e037%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C1%7C636997538438114306&sdata=nqRWqZOXt5TrF6IFPP8Nt6vambpplaQ7WLn2h8jBcak%3D&reserved=0) on FreeSurfer v6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c). I was able to run recon-all, however I am unable to run segmentHA_T1.sh because the command doesn't exist in $FREESURFER_HOME/bin. Instead, there is segmentSF_T1.sh. I've tried searching the email listings for information comparing the two scripts, but haven't been able to find much.
In order to run the hippocampal and amygdala segmentation, am I able to use segmentSF_T1.sh instead of segmentHA_T1.sh? Is there a more recent version of Freesurfer I have to install that includes segmentHA_T1.sh?
Thank you in advance for the help.
Best, CC
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