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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 a screenshot of a participant who has all the expected files vs. a participant who is missing important files. I will also 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
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