Hi Diana,
If there are a lot of obvious holes in the surface topology, it might be worth
doing some manual fixing of the white-matter segmentation. The tutorial at
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEditsV6.0 walks
through that process.
Best
Andrew
From: DIANA ORTEGA CRUZ <100315...@alumnos.uc3m.es>
Date: Thursday, May 27, 2021 at 3:32 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>, Hoopes, Andrew
<ahoo...@mgh.harvard.edu>
Subject: Re: [Freesurfer] Recon-all running on a loop
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
(<ahoo...@mgh.harvard.edu<mailto:ahoo...@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-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of DIANA ORTEGA CRUZ
<100315...@alumnos.uc3m.es<mailto:100315...@alumnos.uc3m.es>>
Date: Friday, May 21, 2021 at 11:00 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto: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
Centro de Tecnología Biomédica - Universidad Politécnica de Madrid
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