Nick,
I have 8 Gig of mem 2 quad cores, but I have been running 6 or more freesurfer jobs concurrently, ill run them by themselves and see if it persists and let you know.
thankx
G.
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Nick Schmansky Sent: Wed 5/13/2009 3:39 PM To: Kirk Gregory R. Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] segmentation fault
Greg,
How much memory does the system have available at the time mris_volmask is run? It will consume about 1GB within a minute or two of starting, and I know that the underlying code (VTK library) doesnt handle memory alloc failures very gracefully.
If running this stage (-cortribbon) fails consistently on a subject, perhaps i can supply you with a debug-built version of mris_volmask so that it generates a core file with info on exactly where this is segfaulting. We've never been able to replicate this problem locally.
Nick
On Wed, 2009-05-13 at 14:42 -0500, Kirk Gregory R. wrote:
Hi all,
I got in the recon-all log
#@# Cortical ribbon mask Tue May 12 17:56:52 CDT 2009 /home/gkirk/freesurfer/freesurfer/subjects/P21/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance P21 SUBJECTS_DIR is /home/gkirk/freesurfer/freesurfer/subjects Segmentation fault Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 GNU/Linux recon-all exited with ERRORS at Tue May 12 18:10:33 CDT 2009
running build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0 Linux debian01 2.6.26-1-amd64 #1 SMP Mon Dec 15 17:25:36 UTC 2008 x86_64 GNU/Linux
i have gotten 4 of these out of 21 ADNI data sets, I saw Nurunisa at Barry Kosofsky's site reported this also and Nick ask here to send the data set. 11 Nov 2008,
got any info on this one ?, i am guessing it is a data quality issue that is breaking something in an uncontrolled way.
thanks
Greg.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer