Date: Wed, 23 Aug 2017 11:54:06 -0400 From: Bruce Fischl <fischl@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6) To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <54B7B7A7-CDC3-46F1-8E1B-098142FD3DB2@nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" That defect is so big you probably ran out of memory. > On Aug 23, 2017, at 11:21 AM, Rockers, Elijah D. <edrockers@houstonmethodist.org> wrote: > > We encountered a hard failure, below is the tail of the log. We are currently running Freesurfer 6 again locally to see if it succeeds on a desktop machine (this is the first time encountering a hard failure on the XNAT server). Any suggestions? > > -merging segment 180 into 178 > 160 defects to be corrected > 0 vertices coincident > reading input surface /data/build/nnac/20170818_114535/alamode_MRI08162017/20170818114538/alamode_MRI08162017/surf/lh.qsphere.nofix... > reading brain volume from brain... > reading wm segmentation from wm... > Computing Initial Surface Statistics > -face loglikelihood: -8.7982 (-4.3991) > -vertex loglikelihood: -6.2982 (-3.1491) > -normal dot loglikelihood: -3.5611 (-3.5611) > -quad curv loglikelihood: -6.1931 (-3.0965) > Total Loglikelihood : -24.8505 > > CORRECTING DEFECT 0 (vertices=40706, convex hull=11265, v0=89) > XL defect detected... > Segmentation fault (core dumped) > Linux hhvrixnatp01 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10 22:19:54 EST 2013 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s alamode_MRI08162017 exited with ERRORS at Mon Aug 21 19:27:09 CDT 2017 > > To report a problem, see https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu_fswiki_BugReporting&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=UPo-wFt-ACmW_p7FRxtgmbsmsxyiC8zWu4xz_jMpwRM&e= > > Houston Methodist. Leading Medicine. > > Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_MethodistHosp&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=OO5cwh0TYxKrHk7C0DiMckR5_f7AfSahK9xF3CSe3Hw&e= and https://urldefense.proofpoint.com/v2/url?u=http-3A__facebook.com_HoustonMethodist&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=fT36tQ3TMuZagDYvb4HSxJ3fhMjgib0EdBJluu7uRAY&e= . > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=STACrwCfPSrQfmQMFLcII3rDEnp66bw5ZgRLLMyVSLs&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: https://urldefense.proofpoint.com/v2/url?u=http-3A__mail.nmr.mgh.harvard.edu_pipermail_freesurfer_attachments_20170823_25408482_attachment-2D0001.html&d=DwIBAg&c=QmPtDiFixEjkMvDKaP3E2Vb9C2z4M0PdarxyAHQ2iDQ&r=xbyrBxm81l6mG_XEX66jgCNTXfK3eVo30T9sVQVTz1Q&m=ZUxVIMrFX5hWNR4618Ng1NGK5pswnaS1K8_SrFxDwio&s=0_mTIdxw9CWUx4VItMCJF-bgRCkUw2l7BwLlpWLAvis&e= ------------------------------