I was processing a particularly noisy participant which bombed out with the following error. Looking at the data, it shouldn't make it through the pipeline, but the error message seems more of a memory management issue. I've pasted it below, any thoughts?
Freesurfer 5.1 (new build), Mac Pro Workstation with 40GB RAM, Mac OS X 10.6.7
Error Message: CORRECTING DEFECT 48 (vertices=60474, convex hull=11331) mris_fix_topology(23279) malloc: *** mmap(size=3887681536) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Excessive topologic defect encountered: could not allocate 242979990 edges for retessellation Cannot allocate memory Darwin ella.haskins.yale.edu 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:16:10 PST 2011; root:xnu-1504.9.37~1/RELEASE_X86_64 x86_64
recon-all -s sn3086 exited with ERRORS at Thu May 26 22:47:37 EDT 2011
For more details, see the log file /zappa/freesurfer/PID/sn3086/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Hi Peter,
that error means that it found a gigantic topological defect - bigger than it could hold in memory - so it's a direct consequence of the noisy data.
cheers Bruce On Fri, 27 May 2011 peter.molfese@yale.edu wrote:
I was processing a particularly noisy participant which bombed out with the following error. Looking at the data, it shouldn't make it through the pipeline, but the error message seems more of a memory management issue. I've pasted it below, any thoughts?
Freesurfer 5.1 (new build), Mac Pro Workstation with 40GB RAM, Mac OS X 10.6.7
Error Message: CORRECTING DEFECT 48 (vertices=60474, convex hull=11331) mris_fix_topology(23279) malloc: *** mmap(size=3887681536) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug Excessive topologic defect encountered: could not allocate 242979990 edges for retessellation Cannot allocate memory Darwin ella.haskins.yale.edu 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:16:10 PST 2011; root:xnu-1504.9.37~1/RELEASE_X86_64 x86_64
recon-all -s sn3086 exited with ERRORS at Thu May 26 22:47:37 EDT 2011
For more details, see the log file /zappa/freesurfer/PID/sn3086/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-
Bruce Fischl -
peter.molfese＠yale.edu