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 ***: 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
For sub-04, can you look at the nu.mgz volume to see if that looks ok? Can you also see if the talairach registration looks ok? You should be able to run something like
tkregisterfv --s subject --fstal
It does not have to be perfect, but it is a problem if it is wildly off.
On 12/29/2024 10:54 AM, Michael Eyre 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 ***: 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
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Michael Eyre