Hi Lisa, It seems that the main recon-all died for some reason, so the brainstem and hippocampal modules never ran. You should probably figure out what the problem was with recon-all (hopefully Doug can help with this), and then run: recon-all -s /pub/ltaylor2/*PARTICIPANT* -brainstem-structures recon-all -s /pub/ltaylor2/*PARTICIPANT* -hippocampal-subfields-T1
You could also try running these 2 commands directly… since recon-all crashed towards the ends, they may actually work. But it’s probably a better idea / cleaner to fix the problem with recon-all first. 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 "Taylor, Lisa Marie" <ltayl...@hs.uci.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, March 24, 2021 at 10:17 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Missing 'brainstemSsLabels.v10.mgz' file External Email - Use Caution Hi, Thank you for getting back to me. Is one of these the correct log file? Lisa ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <jiglesiasgonza...@mgh.harvard.edu> Sent: Tuesday, March 23, 2021 12:56 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Missing 'brainstemSsLabels.v10.mgz' file Dear Lisa, Maybe the brainstem module failed for some reason? If you send us the log files, we can take a look. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com<https://secure-web.cisco.com/1cfggmCQWsW-CceYbirau8QCe9sLm6H7Y5QVnStgsK42DLWrc45zYmc2EH_Ty4NKgjwdDb8yoAnACZx4s_SFAiL9XiC8OQOU8cRyTH9OBAe1a3MxMeVGRafeq4GenT6zGeY3mud8fqXq4Dl7gb6IUmeeXN7fQ-7DdDR8Nax5WuoYZktbPZ8FWk54FbLMZ4hZayRIU4xTUFNBL-6VMorkO0ONFTxPierRF7jFNjV7J5MfCoZizB7xaEQJwMvR3Ntse/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fwww.jeiglesias.com__%3B%21%21OLgoXmg%21GHwecJCQkA52c1bQHBEwKOPXJuEpHJULzqDmv6FkVQqGkWlt22OZJbo7rP64LCKlIEo%24> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Taylor, Lisa Marie" <ltayl...@hs.uci.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, March 23, 2021 at 15:32 To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Missing 'brainstemSsLabels.v10.mgz' file External Email - Use Caution Hi, This is the first time I have encountered this problem. I have a participant that has been through recon all, but when trying to create PET masks, the error that comes up is that the 'brainstemSsLabels.v10.mgz' file is missing in the MRI directory. I am unsure of how to have this label created when it has been created in other participants from freesurfer. Here is the command and the arguments used when running this participant (every one of our participants has had the same command): ${FREESURFER_HOME}/bin/recon-all -s /pub/ltaylor2/*PARTICIPANT* -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache Any understanding as to why this particular participant is not having this file created? Any leads would be greatly appreciated! Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacomplia...@uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacomplia...@uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.
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