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 <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6) To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <54B7B7A7-CDC3-46F1-8E1B-098142FD3DB2@nmr.mgh.harvard.edumailto: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.orgmailto: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 178160 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
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