Hello FreeSurfer experts,
We have some old clinical structural data we processed using version 5.0 and had extensively edited manually. We’re now hoping to re-process the data in version 5 to regenerate copies of the subjects that are free of manual edits. So far (because of the below core dump error), I’ve tried doing this two ways, first by running recon-all -autorecon-all -clean -s <subject> on copies of our manually edited data and, secondly, by using from the original, unaltered MPRAGE files and running recon-all -i ./path/to/MEMPRAGE.nii -s <subject> (which fails before we would then run recon-all -autorecon-all -s <subject>). In both cases I’ve run into an error I never encountered when last working with this data 2 years ago in version 5. Specifically I get a “Segmentation fault (core dumped)” when mri_convert is invoked. I’ve enclosed a copy of the recon-all.log and recon-all.error files as attachments and provided the specific commands that seem to trigger the core dump below (from recon-all.error file). I looked on the mail archive but I wasn’t able to find any answers.
I’m running version 5.0 (as that is the version our manually edited data was processed in): setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env
build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 I’m running Red Hat Enterprise Linux Release 6.7 (Santiago)
The specific commands that appear to be causing the (Segmentation fault) core dump in each of the two different cases are below (taken from recon error log):
When running: recon-all -i ./path/to/MEMPRAGE.nii -s <subject> the error occurs with.. mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii /autofs/cluster/roffman2/users/RPDR_FromRaw_No_Edits/00033/mri/orig/001.mgz
When running: recon-all -autorecon-all -clean -s <subject> the error occurs with.. mri_convert /autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/rawavg.mgz /autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/orig.mgz --conform
Notably, when I tried running the same commands (bolded above) in version 5.3 (source/usr/local/freesurfer/nmr-stable53-env) they both exit without errors, leading me to wonder if this is a software-version interaction issue. (In case it has any bearing, I’m running all of this while ssh’d into the Martinos servers.)
I suspect I may have missed something very simple, but I would be very grateful for any suggestions for how I might try to overcome this issue. I’m happy to provide clarification or any additional information that may be helpful.
Thank you, Kevin
Kevin F. Dowling Per-Diem Clinical Research Coordinator Brain Genomics Laboratory Department of Psychiatry Massachusetts General Hospital MD/PhD Candidate University of Pittsburgh & Carnegie Mellon University MSTP
For some reason, it is not capturing the terminal output in the log files. Can you just run mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii deleteme.mgz and send me the terminal output?
On 1/2/2021 2:23 PM, Dowling, Kevin Francis wrote: Hello FreeSurfer experts,
We have some old clinical structural data we processed using version 5.0 and had extensively edited manually. We’re now hoping to re-process the data in version 5 to regenerate copies of the subjects that are free of manual edits. So far (because of the below core dump error), I’ve tried doing this two ways, first by running recon-all -autorecon-all -clean -s <subject> on copies of our manually edited data and, secondly, by using from the original, unaltered MPRAGE files and running recon-all -i ./path/to/MEMPRAGE.nii -s <subject> (which fails before we would then run recon-all -autorecon-all -s <subject>). In both cases I’ve run into an error I never encountered when last working with this data 2 years ago in version 5. Specifically I get a “Segmentation fault (core dumped)” when mri_convert is invoked. I’ve enclosed a copy of the recon-all.log and recon-all.error files as attachments and provided the specific commands that seem to trigger the core dump below (from recon-all.error file). I looked on the mail archive but I wasn’t able to find any answers.
I’m running version 5.0 (as that is the version our manually edited data was processed in): setenv USE_STABLE_5_0_0 source /usr/local/freesurfer/nmr-stable50-env
build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319 I’m running Red Hat Enterprise Linux Release 6.7 (Santiago)
The specific commands that appear to be causing the (Segmentation fault) core dump in each of the two different cases are below (taken from recon error log):
When running: recon-all -i ./path/to/MEMPRAGE.nii -s <subject> the error occurs with.. mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii /autofs/cluster/roffman2/users/RPDR_FromRaw_No_Edits/00033/mri/orig/001.mgz
When running: recon-all -autorecon-all -clean -s <subject> the error occurs with.. mri_convert /autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/rawavg.mgz /autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/orig.mgz --conform
Notably, when I tried running the same commands (bolded above) in version 5.3 (source/usr/local/freesurfer/nmr-stable53-env) they both exit without errors, leading me to wonder if this is a software-version interaction issue. (In case it has any bearing, I’m running all of this while ssh’d into the Martinos servers.)
I suspect I may have missed something very simple, but I would be very grateful for any suggestions for how I might try to overcome this issue. I’m happy to provide clarification or any additional information that may be helpful.
Thank you, Kevin
Kevin F. Dowling Per-Diem Clinical Research Coordinator Brain Genomics Laboratory Department of Psychiatry Massachusetts General Hospital MD/PhD Candidate University of Pittsburgh & Carnegie Mellon University MSTP
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