Summary of what happened:
the ‘Command terminated by signal 11’ error appeared when mris_fix_topology was applied during autorecon2.
I am running autorecon1 with pre-skullstripped t1w volumes
Command used (and if a helper script was used, a link to the helper script or the command generated):
recon-all -subjid "$d" -i "$d"_ses-1_T1wstripped.nii.gz -autorecon1 -noskullstrip
cd "$SUBJECTS_DIR"/"$d"/mri
ln -s T1.mgz brainmask.auto.mgz
ln -s brainmask.auto.mgz brainmask.mgz
recon-all -autorecon2 -subjid "$d"
Version: 7.4.1
Environment (Docker, Singularity / Apptainer, custom installation):
I am running this on a redhat linux (4.18.0-477.13.1.el8_8.x86_64) HPC without any dockers
Relevant log outputs (up to 20 lines):
mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 sub-010080 lh
reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nofix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
*************************************************************
Topology Correction Parameters
retessellation mode: genetic search
number of patches/generation : 10
number of generations : 10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient : 10.0
normal dot loglikelihood coefficient : 1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution : 2
eliminate vertices during search : 1
initial patch selection : 1
select all defect vertices : 0
ordering dependant retessellation: 0
use precomputed edge table : 0
smooth retessellated patch : 2
match retessellated patch : 1
verbose mode : 0
*************************************************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh'
7.4.1
7.4.1
before topology correction, eno=-146 (nv=136384, nf=273060, ne=409590, g=74)
using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology
Finding true center and radius of Spherical Surface...done
Surface centered at (0,0,0) with radius 100.0 in 8 iterations
marking ambiguous vertices...
28653 ambiguous faces found in tessellation
segmenting defects...
11 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
-merging segment 7 into 0
10 defects to be corrected
0 vertices coincident
reading input surface /home/junhong.yu/NC/output/sourcedata/freesurfer/sub-010080/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm segmentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.nofix
Computing Initial Surface Statistics
-face loglikelihood: -9.6305 (-4.8153)
-vertex loglikelihood: -6.8384 (-3.4192)
-normal dot loglikelihood: -3.4758 (-3.4758)
-quad curv loglikelihood: -6.0796 (-3.0398)
Total Loglikelihood : -26.0243
CORRECTING DEFECT 0 (vertices=14674, convex hull=2782, v0=20533)
Command terminated by signal 11
@#@FSTIME 2024:09:21:16:07:58 mris_fix_topology N 14 e 4725.15 S 4.36 U 4703.97 P 99% M 875500 F 0 R 647384 W 0 c 10759 w 199 I 9896 O 3216 L 24.70 28.79 33.39
@#@FSLOADPOST 2024:09:21:17:26:43 mris_fix_topology N 14 16.14 16.10 16.23
Linux hpc-wfly-r001 4.18.0-553.8.1.el8_10.x86_64 #1 SMP Tue Jul 2 17:10:26 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux