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-bounces@nmr.mgh.harvard.edu> on behalf of "Taylor, Lisa Marie" <ltaylor2@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

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Hi,

Thank you for getting back to me. Is one of these the correct log file?

Lisa

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@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

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Taylor, Lisa Marie" <ltaylor2@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

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