Re: [Freesurfer] Seg fault during autorecon2

2009-08-03 Thread Bruce Fischl
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 pr

Re: [Freesurfer] Seg fault during autorecon2

2009-08-03 Thread Nathan Dankner
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" wrote: > yes, I just saw that. I thought it only hap

Re: [Freesurfer] Seg fault during autorecon2

2009-08-03 Thread Bruce Fischl
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 pro

Re: [Freesurfer] Seg fault during autorecon2

2009-08-03 Thread Nathan Dankner
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::GetTuple). We're trying to find a fix or worka

Re: [Freesurfer] Seg fault during autorecon2

2009-08-03 Thread Bruce Fischl
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 sta

Re: [Freesurfer] Seg fault during autorecon2

2009-08-03 Thread Martin Reuter
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 recen

Re: [Freesurfer] Seg fault during autorecon2

2009-08-03 Thread Nick Schmansky
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::GetTuple). We're trying to find a fix or workaround to this really annoying problem. The cheap workaround is to run the -