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Hi everyone,

I could really use some help with figuring out an issue I've been struggling with the last few months. It seems that when I run recon-all on over 20 of my participants, not all freesurfer files are created. But I am not understanding why, and my technical capabilities are limited. Particularly, it seems there's an issue reading the lh.BA1_exvivo.label.  I will attach the recon-all log file for any other information that it can provide. 

Also, I run a script for recon-all and these are the arguments: srun ${FREESURFER_HOME}/bin/recon-all -s imagedir/subid -no-isrunning -all -hippocampal-subfields-T1 -brainstem-structures -qcache

Not sure if this is pertinent, but our HPC has been updated, but I am unaware if that can impact how freesurfer is run. 

Thank you for any insight you can provide!

Lisa
(I previously sent an email with screen shots, but the email was waiting to be approved due to size)


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