mris_inflate -no-save-sulc 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix

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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.eyre@kcl.ac.uk> wrote:

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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 ***: terminated

Command 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 vertices

sub-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 points

error: MRInormFindControlPoints failed

This subject has some very minor scattered white matter abnormalities (perivascular spaces).

My recon-all command:

export FS_ALLOW_DEEP=1

recon-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 100

mris_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 Hospital

Visiting Research Fellow, School of Biomedical Engineering & Imaging Sciences, King's College London

St Thomas' Hospital

London SE1 7EH

<sub-04_recon-all.log><sub-06_recon-all.log><sub-31_recon-all.log>_______________________________________________
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