External Email - Use Caution
Signal 6 run time error indicates some kind of buffer overflow is
expected to happen like the stack is going to be corrupted, and so the process
is killed. Please let us know the OS name and version you are running
8.0.0-beta on that produced the error, e.g., what installer you used. If
what you listed is not the full text of the error output in the log, then
please include that as well. A more detailed message could look something
like,
**** stack smashing detected ***: foo.out terminated**======= Backtrace:
=========**<path>/libc.so.6(<symbol+offset>)Aborted*
- R.
On Dec 29, 2024, at 10:54, Michael Eyre <michael.e...@kcl.ac.uk>
wrote: External Email - Use
Caution Hello
I'm processing 7T MP2RAGE data (0.65mm isotropic) with FreeSurfer 8.0.0-beta. I
have processed 30 subjects successfully but am encountering two distinct issues
for 3 subjects:
1. Stack smashing errors during topology correction for subjects with large
defects (sub-06, sub-31):Copy*** stack smashing detected ***: terminatedCommand
terminated by signal 6
This occurs in mris_fix_topology when processing defects with many vertices:
sub-06: Left hemisphere, defect 0 with 22,492 verticessub-31: Right hemisphere,
defect 2 with 14,313 vertices
sub-06 does not have any obvious brain abnormalities. sub-31 has some white
matter abnormalities at the terminal zones of myelination (deep posterior white
matter).
2. Normalization failure for another subject (sub-04):Copyerror:
MRInormFindControlPoints: could not find enough control pointserror:
MRInormFindControlPoints failed
This subject has some very minor scattered white matter abnormalities
(perivascular spaces).
My recon-all command:export FS_ALLOW_DEEP=1recon-all -all -subject ${SUBJECT}
-sd ${WORK_PATH}/freesurfer8 -hires -i
${WORK_PATH}/${SUBJECT}_uni_masked.nii.gz -T2
${WORK_PATH}/${SUBJECT}_t2w_registered.nii.gz -T2pial -expert ${EXPERT_FILE}
-openmp 20
My EXPERT_FILE contains two lines:mris_inflate -n 100mris_fix_topology -threads
1
Preprocessing: Data are processed with 3D Gibbs deringing, ANTS DenoiseImage,
bias field correction and brain extraction prior to freesurfer.
Approaches tried: I have tried running without the EXPERT_FILE, and also
tried with additional recon-all flags -3T -gcut -norm1-n 4 -norm2-n 6, without
success.
Previous successful processing: The same subjects processed successfully
with FreeSurfer 7.4.1.
System info: Ubuntu 20.04, 64GB RAM, 20 CPUs. Subjects are running in
serial not in parallel, and no other processes with significant memory or CPU
use are running on the system at the same time.
Any suggestions would be greatly appreciated. I have attached the recon-all.log
files. Let me know if you need any additional information.
Best wishes
Mike Eyre
Dr Michael Eyre
Locum Consultant Paediatric Neurologist, Evelina London Children's
HospitalVisiting Research Fellow, School of Biomedical Engineering &
Imaging Sciences, King's College LondonSt Thomas' Hospital London SE1
7EH<sub-04_recon-all.log><sub-06_recon-all.log><sub-31_recon-all.log>_______________________________________________Freesurfer
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