Hi Dr. Greve, Thanks so much for your reply. I ran the command as instructed (bolded) in 5.0 (and again in 5.3 for comparison, since that ran fine in my earlier troubleshooting efforts) and have placed the terminal outputs below.
In 5.0 the output I received in the terminal: (nmr-stable5.0-env) mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii deleteme.mgz mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii deleteme.mgz $Id: mri_convert.c,v 1.166.2.6 2010/11/24 15:19:30 nicks Exp $ reading from /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii... Segmentation fault (core dumped) And in 5.3 this was the result, which seemed to run normally: (nmr-stable53-env) mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii deleteme.mgz mri_convert /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii deleteme.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.101076, -0.994877, 0.0017413) j_ras = (-0.0677184, 0.0051337, -0.997691) k_ras = (-0.992571, 0.10096, 0.0678903) writing to deleteme.mgz... Thank you very much for your help, and for any thoughts you might have. Kind regards, Kevin Date: Tue, 12 Jan 2021 15:45:37 +0000 From: "Greve, Douglas N.,Ph.D." <dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0 To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <63bb4542-e9df-d7cc-926b-0731b6009...@mgh.harvard.edu<mailto:63bb4542-e9df-d7cc-926b-0731b6009...@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" 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 f ile). 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu><mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20210112/1a426098/attachment.html 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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