Hi Sumit
Can you post some images? It looks like the topo fixer ran out of memory:
CORRECTING DEFECT 0 (vertices=2851, convex hull=1075, v0=1654)
An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from wm.mgz.
This may cause recon-all to run very slowly or crash.
if so, see
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview
normal vector of length zero at vertex 114560 with 3 faces
After retessellation of defect 0 (v0=1654), euler #=-20 (113675,336915,223220) : difference with theory (-37) = -17
CORRECTING DEFECT 1 (vertices=8265, convex hull=3246, v0=37850)
Command terminated by signal 11
@#@FSTIME 2021:12:02:05:30:32 mris_fix_topology N 14 e 2616.82 S 1.24 U 2616.83 P 100% M 1058736 F 0 R 1648336 W 0 c 6333 w 61 I 0 O 3264 L 3.04 2.97 2.96
@#@FSLOADPOST 2021:12:02:06:14:09 mris_fix_topology N 14 2.95 2.91 2.88
Linux neuralnet 3.13.0-95-generic #142-Ubuntu SMP Fri Aug 12 17:00:09 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
The first two defects it found were both quite large so it is likely something went seriously wrong
Cheers
Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Sumit Sharma
Sent: Thursday, December 9, 2021 3:54 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error: recon-all exited with ERRORS: failing without generating all surf files: How to modify wm.mgz to make it work?
External Email - Use Caution
Hello FreeSurfer Developers,
I'm attempting to generate the segmentation files by running the "the recon-all" command. The command is failing and I am getting the below error.
ERROR: recon-all -s out_24 exited with ERRORS at Thu
I searched and open the wm.mgz and other files using the below command following the tutorials:
MailScanner
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
Command:
freeview -v out_24/mri/brainmask.mgz \
out_24/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \
-f out_24/surf/lh.white:edgecolor=yellow \
out_24/surf/lh.pial:edgecolor=red \
out_24/surf/rh.white:edgecolor=yellow \
out_24/surf/rh.pial:edgecolor=red \
out_24/surf/lh.orig.nofix:visible=0
However, there are no surface files which are mentioned in the above command. The surface folder contains only the below files:
lh.defect_borders lh.defect_labels lh.orig.nofix lh.qsphere.nofix rh.defect_borders rh.defect_labels rh.orig.nofix rh.smoothwm.nofix
lh.defect_chull lh.inflated.nofix lh.orig.premesh lh.smoothwm.nofix rh.defect_chull rh.inflated.nofix rh.qsphere.nofix
Please suggest on how should I modify the wm.mgz file in such case: Below are my doubts:
What I understood so far that wm.mgz contains information of white and non-white matter (whether gray matter or CSF), however I could see yellow color pixels of intensity 255 near the corpus callosum cavity which is non-white matter region, however when I modify
the voxels in freeview using recon-edit option, I need to give 255 pixel value to the white matter region, I am a little bit confused on how to edit wm.mgz, whether to edit voxels in the white matter region with 255 value and erase in the non white region
or do the opposite, Please guide.
What is the best way to modify the wm.mgz if the surfaces are not generated? Please advise.
1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551
2) Platform: ubuntu
3) recon-all.log: (PFA).
Thanks and Regards
Sumit Sharma
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Sumit Sharma