We'll try to process it on a blade server tongiht... if it succeeds we can edit any incorrect results as needed.
The image is from a separate site, it has OK resolution (1x1x1.5) but has an enormous amount of gibbs ringing compared to our on-site images, which is probably causing the issue... Thanks, Eli Date: Wed, 23 Aug 2017 11:54:06 -0400 From: Bruce Fischl <fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6) To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <54b7b7a7-cdc3-46f1-8e1b-098142fd3...@nmr.mgh.harvard.edu<mailto:54b7b7a7-cdc3-46f1-8e1b-098142fd3...@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. > <edrock...@houstonmethodist.org<mailto:edrock...@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<mailto: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= ------------------------------
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