External Email - Use Caution
Hi, thanks for the response
OS: Ubuntu 20.04 LTS (x86_64)
FreeSurfer version: 8.0.0-beta (build 20241102-b8aacdc)
I don't know if this is relevant to the current problem, but I did make an edit
at lines 3646-3647 of the recon-all binary:
Previous code at lines 3646-3647:
set cmd = ($cmd -no-save-sulc $xopts \
../surf/$hemi.smoothwm.nofix ../surf/$hemi.inflated.nofix)
Was leading to this error:
mris_inflate -no-save-sulc 100 ../surf/lh.smoothwm.nofix
../surf/lh.inflated.nofix
Not saving sulc
Reading 100
** failed to open GIFTI XML file '100.gii'
mrisReadGIFTIdanum: ERROR reading gifti 100.gii
[INFO] read, cannot find 100, trying 100.gii ...
error: No such file or directory
error: mris_inflate: could not read surface file 100
Command exited with non-zero status 255
So I changed lines 3646-3647 to:
set cmd = ($cmd -no-save-sulc \
../surf/$hemi.smoothwm.nofix ../surf/$hemi.inflated.nofix $xopts)
And this has run successfully on 30 subjects.
Regarding the current problem, here is the additional information from the log
files. There is no "backtrace" text. I can rerun with -debug flag if this would
help provide more info?
sub-06 recon-all.log ends: (full log attached to previous email)
CORRECTING DEFECT 0 (vertices=22492, convex hull=3826, v0=0)
*** stack smashing detected ***: terminated
Command terminated by signal 6
@#@FSTIME 2024:12:29:10:11:00 mris_fix_topology N 20 e 4449.03 S 0.72 U
4448.17 P 99% M 2083792 F 0 R 658337 W 0 c 17764 w 2 I 0 O 4104 L 10.70 4.98
3.69
@#@FSLOADPOST 2024:12:29:11:25:09 mris_fix_topology N 20 1.04 1.01 1.00
Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7
13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-06 exited with ERRORS at Sun 29 Dec 2024 11:25:09 AM GMT
sub-06 recon-all.error:
SUBJECT sub-06
DATE Sun 29 Dec 2024 11:25:09 AM GMT
USER me18
HOST bioeng427-pc
PROCESSOR x86_64
OS Linux
Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7
13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
8.0.0-beta (freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc)
/usr/local/freesurfer-8.0.0/bin/recon-all
PWD /data/DANCE-AE/work/sub-06/7t-struct/freesurfer8/sub-06/scripts
CMD mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated
inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1
-threads 1 sub-06 lh
sub-31 recon-all.log ends: (full log attached to previous email)
CORRECTING DEFECT 2 (vertices=14313, convex hull=1752, v0=4423)
*** stack smashing detected ***: terminated
Command terminated by signal 6
@#@FSTIME 2024:12:29:12:00:36 mris_fix_topology N 20 e 1163.34 S 0.43 U
1162.87 P 99% M 1187552 F 0 R 358352 W 0 c 4399 w 2 I 0 O 3072 L 3.25 4.20 3.46
@#@FSLOADPOST 2024:12:29:12:20:00 mris_fix_topology N 20 1.00 1.05 1.67
Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7
13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-31 exited with ERRORS at Sun 29 Dec 2024 12:20:00 PM GMT
sub-31 recon-all.error:
SUBJECT sub-31
DATE Sun 29 Dec 2024 12:20:00 PM GMT
USER me18
HOST bioeng427-pc
PROCESSOR x86_64
OS Linux
Linux bioeng427-pc 5.15.0-125-generic #135~20.04.1-Ubuntu SMP Mon Oct 7
13:56:22 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
8.0.0-beta (freesurfer-linux-ubuntu20_x86_64-8.0.0-beta-20241102-b8aacdc)
/usr/local/freesurfer-8.0.0/bin/recon-all
PWD /data/DANCE-AE/work/sub-31/7t-struct/freesurfer8/sub-31/scripts
CMD mris_fix_topology -threads 1 -mgz -sphere qsphere.nofix -inflated
inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 -threads 1
-threads 1 sub-31 rh
best wishes
Mike
________________________________
From: fsbuild <fsbu...@contbay.com>
Sent: 29 December 2024 23:22
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and
normalization failures with 7T MP2RAGE data
You don't often get email from fsbu...@contbay.com. Learn why this is
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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.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 ***: 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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