Can you send the recon-all.log file?
On 3/23/2021 3:31 PM, Taylor, Lisa Marie wrote:
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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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