External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu> on behalf of "Chen, Christine" <ch...@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-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@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 KKI SECURITY ALERT: This email is from an external source. Do not click on any links or open attachments unless you recognize the sender and know the content is safe. ________________________________ 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.com<https://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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Chen, Christine" <ch...@kennedykrieger.org<mailto:ch...@kennedykrieger.org>> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, 26 July 2019 at 09:47 To: "'freesurfer@nmr.mgh.harvard.edu'" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found External Email - Use Caution To whom it may concern, I am trying to run hippocampal and amygdala segmentation (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala<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 ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
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