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
