Hello all,
I¹ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I¹m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I¹ve included the recon-all.log files for two subjects who have had the problem. Thanks,
Nathan
Nathan,
This is a known and long-standing problem with mris_volmask. The fault occurs deep within a library, VTK, of which we make use (null pointer in vtkDataArrayTemplate<T>::GetTuple). We're trying to find a fix or workaround to this really annoying problem.
The cheap workaround is to run the -cortribbon -autorecon3 stages, and likely mris_volmask will succeed.
Nick
On Mon, 2009-08-03 at 14:18 -0400, Nathan Dankner wrote:
Hello all,
I’ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I’m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I’ve included the recon-all.log files for two subjects who have had the problem. Thanks,
Nathan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi,
actually in the newer FS versions (don't know when it started), the cortribbon is part of autorecon3. In those cases all that is necessary is to rerun the final steps: -cortribbon -aparc2aseg -wmparc
Martin
On Mon, 2009-08-03 at 14:18 -0400, Nathan Dankner wrote:
Hello all,
I’ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I’m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I’ve included the recon-all.log files for two subjects who have had the problem. Thanks,
Nathan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
looks like it's failing in mris_volmask. How much RAM do you have on your machine? On Mon, 3 Aug 2009, Nathan Dankner wrote:
Hello all,
I¹ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I¹m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I¹ve included the recon-all.log files for two subjects who have had the problem. Thanks,
Nathan
I have 4 gigs of ram on here. This is the response that I got from Nick Schmansky:
This is a known and long-standing problem with mris_volmask. The fault occurs deep within a library, VTK, of which we make use (null pointer in vtkDataArrayTemplate<T>::GetTuple). We're trying to find a fix or workaround to this really annoying problem.
The cheap workaround is to run the -cortribbon -autorecon3 stages, and likely mris_volmask will succeed.
On 8/3/09 3:32 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
looks like it's failing in mris_volmask. How much RAM do you have on your machine? On Mon, 3 Aug 2009, Nathan Dankner wrote:
Hello all,
I¹ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I¹m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I¹ve included the recon-all.log files for two subjects who have had the problem. Thanks,
Nathan
yes, I just saw that. I thought it only happened when the machine ran out of memory. Are you running more than 1 recon at a time? On Mon, 3 Aug 2009, Nathan Dankner wrote:
I have 4 gigs of ram on here. This is the response that I got from Nick Schmansky:
This is a known and long-standing problem with mris_volmask. The fault occurs deep within a library, VTK, of which we make use (null pointer in vtkDataArrayTemplate<T>::GetTuple). We're trying to find a fix or workaround to this really annoying problem.
The cheap workaround is to run the -cortribbon -autorecon3 stages, and likely mris_volmask will succeed.
On 8/3/09 3:32 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
looks like it's failing in mris_volmask. How much RAM do you have on your machine? On Mon, 3 Aug 2009, Nathan Dankner wrote:
Hello all,
I¹ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I¹m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I¹ve included the recon-all.log files for two subjects who have had the problem. Thanks,
Nathan
Do you mean running multiple subjects simultaneously or more than one recon on an individual subject? In either case, the answer is yes. I could try running them individually to see if the problem persists.
On 8/3/09 3:42 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
yes, I just saw that. I thought it only happened when the machine ran out of memory. Are you running more than 1 recon at a time? On Mon, 3 Aug 2009, Nathan Dankner wrote:
I have 4 gigs of ram on here. This is the response that I got from Nick Schmansky:
This is a known and long-standing problem with mris_volmask. The fault occurs deep within a library, VTK, of which we make use (null pointer in vtkDataArrayTemplate<T>::GetTuple). We're trying to find a fix or workaround to this really annoying problem.
The cheap workaround is to run the -cortribbon -autorecon3 stages, and likely mris_volmask will succeed.
On 8/3/09 3:32 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
looks like it's failing in mris_volmask. How much RAM do you have on your machine? On Mon, 3 Aug 2009, Nathan Dankner wrote:
Hello all,
I¹ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I¹m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I¹ve included the recon-all.log files for two subjects who have had the problem. Thanks,
Nathan
I mean multiple subjects simultaneously on the same machine
On Mon, 3 Aug 2009, Nathan Dankner wrote:
Do you mean running multiple subjects simultaneously or more than one recon on an individual subject? In either case, the answer is yes. I could try running them individually to see if the problem persists.
On 8/3/09 3:42 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
yes, I just saw that. I thought it only happened when the machine ran out of memory. Are you running more than 1 recon at a time? On Mon, 3 Aug 2009, Nathan Dankner wrote:
I have 4 gigs of ram on here. This is the response that I got from Nick Schmansky:
This is a known and long-standing problem with mris_volmask. The fault occurs deep within a library, VTK, of which we make use (null pointer in vtkDataArrayTemplate<T>::GetTuple). We're trying to find a fix or workaround to this really annoying problem.
The cheap workaround is to run the -cortribbon -autorecon3 stages, and likely mris_volmask will succeed.
On 8/3/09 3:32 PM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
looks like it's failing in mris_volmask. How much RAM do you have on your machine? On Mon, 3 Aug 2009, Nathan Dankner wrote:
Hello all,
I¹ve recently been having issues with several scans exiting with errors after autorecon2, and they have exclusively been segmentation faults. I¹m running stable version 4.2 on a machine with plenty of memory. Any ideas what the problem might be? I¹ve included the recon-all.log files for two subjects who have had the problem. Thanks,
Nathan
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Martin Reuter -
Nathan Dankner -
Nick Schmansky