External Email - Use Caution
Dear Andrew,
Thank you for your reply. I shared with you the recon-all.cmd file via Drive, since I could not upload it directly to the mail. I also copy here (down) the last lines in this file.
I checked the resulting volumes and surfaces up to that point and the smoothwm.nofix surfaces look like they have a lot of holes, which I understand could cause the error. I also run again recon-all for that subject without parallelizing as you advised, but the process was again stuck at the same step.
Do you think it would be possible to change anything in the original file or the recon-all configuration to fix this issue?
Thanks a lot for your help!!! Best, Diana
#@# Fix Topology rh Tue May 18 04:37:48 UTC 2021 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 NoUMA0233 rh mris_euler_number ../surf/lh.orig.premesh cp ../surf/lh.orig.nofix ../surf/lh.orig.premesh mris_euler_number ../surf/rh.orig.premesh cp ../surf/rh.orig.nofix ../surf/rh.orig.premesh cp ../surf/lh.qsphere.nofix ../surf/lh.qsphere cp ../surf/lh.smoothwm.nofix ../surf/lh.smoothwm mris_topo_fixer -orig_name orig.nofix -out_name orig.premesh -mgz -warnings -seed 1234 NoUMA0233 lh cp ../surf/rh.qsphere.nofix ../surf/rh.qsphere cp ../surf/rh.smoothwm.nofix ../surf/rh.smoothwm mris_topo_fixer -orig_name orig.nofix -out_name orig.premesh -mgz -warnings -seed 1234 NoUMA0233 rh
mris_remesh --remesh --iters 3 --input /media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/lh.orig.premesh --output /media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/lh.orig
mris_remesh --remesh --iters 3 --input /media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/rh.orig.premesh --output /media/beegfs/home/t660/t660582/Cross-sectional-last-valid-scan/NoUMA0233/surf/rh.orig F
El mié, 26 may 2021 a las 1:59, Hoopes, Andrew (AHOOPES@mgh.harvard.edu) escribió:
Hi Diana,
Can you send the recon-all.cmd file? Have you tried running without parallel processing enabled?
Best,
Andrew
*From: *freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of DIANA ORTEGA CRUZ < 100315010@alumnos.uc3m.es> *Date: *Friday, May 21, 2021 at 11:00 AM *To: *freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Recon-all running on a loop
External Email - Use Caution *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
Hardware: Supercomputer - 68 nodes of Lenovo ThinkSystem SD530 https://secure-web.cisco.com/1Bch1AH1AvTKzQqcdunZ0FIqTIHtdhvL6XMYZuyZxpRjtV9TB6kEZn1nh48ZtbJGIw41ngjalVrelQDieE52ynIv7RkZ7f4BZtvzTIxvrOmGmA3JirLjPRIeUkGZzhBEi_NAarb-drp-U-IpLwb1OwHc9qiofX0w5uSIqj3r6yvgPVMj00Wrwio5IAMXe7yXue7tddIlb73tamNyfvbBKIuqQ_TSHGyNsCNyd4NSVZUxvMlbsarqYSxR1oVHqb0XP2bkT1mGLxlsjaijzsxSTjw/https%3A%2F%2Fwww.lenovo.com%2Fes%2Fes%2Fdata-center%2Fservers%2Fhigh-density%2FThinkSystem-SD530%2Fp%2F77XX7DSSD53
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
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