core dumped while running recon-all

[dmd]

We're getting a core dump and not sure what to do about it.

We start with:

export SINGULARITYENV_TEMPLATEFLOW_HOME=/home/fmriprep/.cache/templateflow
/cm/shared/singularity/bin/singularity run \
    -B /data:/data -B /data1:/data1 -B /data2:/data2 -B /data3:/data3 -B /cm/shared:/cm/shared \
    -B /home/ajanes/.cache/fmriprep:/home/fmriprep/.cache/fmriprep \
    --cleanenv \
    /cm/shared/singularity/images/fmriprep-1.5.0.simg \
    /data1/ajanes/Axial \
    /data1/ajanes/Axial/derivatives \
    participant \
    --fs-license-file /cm/shared/freesurfer-6.0.1/license.txt \
    --participant_label 005 \
    --output-spaces "MNI152NLin2009cAsym:res-2 anat func fsaverage" \
    --n_cpus 4 \
    --mem-mb 8192 \
    --notrack \
    --use-aroma --ignore-aroma-denoising-errors \
    --use-syn-sdc \
    -w  /data1/ajanes/fmriprep-working

and it runs until:

CORRECTING DEFECT 37 (vertices=24, convex hull=24, v0=172721)
After retessellation of defect 37 (v0=172721), euler #=244 (46784,129300,82760) : difference with theory (0) = -244

CORRECTING DEFECT 38 (vertices=188655, convex hull=16433, v0=177560)
Segmentation fault (core dumped)
Linux node4 3.10.0-693.el7.x86_64 poldracklab/fmriprep#1 SMP Thu Jul 6 19:56:57 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-005 exited with ERRORS at Thu Oct 10 15:22:20 EDT 2019

For more details, see the log file /data1/ajanes/Axial/derivatives/freesurfer/sub-005/scripts/recon-all-rh.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

191010-15:22:24,104 nipype.workflow ERROR:
     could not run node: fmriprep_wf.single_subject_005_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs
191010-15:22:24,105 nipype.workflow ERROR:
     could not run node: fmriprep_wf.single_subject_005_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs

recon-all-rh.log

fmriprep.o433134.txt

[dmd]

This may be relevant too:

CORRECTING DEFECT 0 (vertices=146346, convex hull=18257, v0=0)
Excessive topologic defect encountered: could not allocate -659114128 edges for retessellation
Cannot allocate memory

[effigies]

Do you run into this while running FreeSurfer normally on that subject?

[dmd]

We can close this, this definitely was (a) a freesurfer issue and (b) a data issue.

[jelee2498]

How did you solve the error? I got same error as yours.

CORRECTING DEFECT 158 (vertices=200262, convex hull=34956, v0=308501) Excessive topologic defect encountered: could not allocate -993586868 edges for retessellation Cannot allocate memory