Dear FreeSurfer team,
My name is Diana Ortega, I am a Neuroscience PhD student at Universidad Politécnica of Madrid. I run a job to compute recon-all in parallel for 30 subjects remotely on a supercomputer at my research institution. This job finished due to timeout, and all subjects but one finished without errors. However, one of the subjects was not finished and it appears as if it was stuck on a loop. Its recon-all.log is constantly adding new lines (the file is 20GB in size), and from recon-all-status.log it appears to be stuck in the "Fix Topology" step. Have you ever encountered a similar situation? Would you know why this could have occurred?
Here are the details:
FreeSurfer version: 7.1.1-centos8_x86_64
Operative System: CentOS8
Line run for that subject:
recon-all -subjid NoUMA0233 -i filepath.nii -all -qcache -parallel -openmp 16
When opening recon-all.log, it keeps adding the following lines:
Remesher::removeTria( 240873 )
Remesher::removeTria( 240876 )
NEXTIDX : 88755
Remesher::removeCollapsedTrias( 88755 , 120326 )
v_to_t[vidx] :
Trias are identical : ... removing ...
When opening the error.log of the complete job, there are several lines of this error:
rm: No match.
Any advice will be of great help! Thanks a big lot!
Best,
Diana Ortega Cruz.
PhD Student
Laboratory for Clinical Neuroscience
Centro de Tecnología Biomédica - Universidad Politécnica de Madrid