Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding
Dear FS gurus, I just want to give some feedback on an error message that has bedeviled some of us for the last few months even after running fs_update and turning off SIP.
I have been getting this error when I ran mri_coreg or mris_convert:
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
In my case there were multiple versions of libgomp.1.dylib. One in the current Freesurfer 6.0 install, one in the gcc-7.1 compiler library that I recently installed (after I ran into this error) and the third from an ANFI install from 2013. When I rearranged the order of the PATH as shown, the error went away.
This was my old path: /usr/local/bioimagesuite35:/usr/local/bioimagesuite35/sbin:/usr/local/bioimagesuite35/bin:/usr/local/bioimagesuite35/bin:/Users/fred/Dropbox/Research_Scripts/EpiSurg-iElvis/iELVis/iELVis_BASH:/Users/fred/Dropbox/Research_Scripts/Linux-Scripts:/Applications/MATLAB_R2015a.app/bin/:/usr/local/cuda/bin:/usr/local/AFNI:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/local/fsl/bin:/usr/local/afni
This is my new path: /Users/fred/Dropbox/Research_Scripts/EpiSurg-iElvis/iELVis/iELVis_BASH:/Users/fred/Dropbox/Research_Scripts/Linux-Scripts:/usr/local/gcc-7.1/bin:/Applications/MATLAB_R2015a.app/bin/:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/fsl/bin:/usr/local/AFNI:/usr/local/bioimagesuite35:/usr/local/bioimagesuite35/sbin:/usr/local/bioimagesuite35/bin:/usr/local/bioimagesuite35/bin:/usr/local/cuda/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/git/bin:/usr/local/fsl/bin:/usr/local/afni
Best, Fred
Fred Lado, MD PhD Director, Epilepsy - Central and Eastern Regions Northwell Health 917-608-1881 (mobile) 516-325-7000 (practice) 516-325-7001 (fax) flado@northwell.edu
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On Aug 24, 2017, at 12:00 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:
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Today's Topics:
- Re: recon-all error (Douglas N Greve)
- Re: Continuous co-variate by continuous co-variate interaction effects (Douglas N Greve)
- Re: Hard failure via XNAT pipeline (Freesurfer 6) (Rockers, Elijah D.)
- Using Total Cortical White Matter Volume as a "whole brain" covariate (Mehta, Chintan)
- Re: mri_coreg (Douglas N Greve)
- Functional Connectivity Motion Regression (Leathem, Logan Daniel)
- Qdec keyboard input error (???)
- Xlib: extension "GLX" missing on display "0.0" when running freeview (fengmei fan)
- cudadetect fails: wrong amount of memory and number of cores detected (Markus.Mertens@evkb.de)
- Re: mri_coreg (Joudy.carter)
- Re: QA tools for FS vs 6.0 (Antonietta Pepe)
- sub cortical analysis (John Anderson)
Message: 1 Date: Wed, 23 Aug 2017 14:54:29 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all error To: freesurfer@nmr.mgh.harvard.edu Message-ID: b83cfed1-8a92-fcc7-8ce5-96ec093e10fc@nmr.mgh.harvard.edu Content-Type: text/plain; charset=windows-1252; format=flowed
does this happen every time you run it? The message said that the job was killed, which suggests something outside of recon-all (eg, if you were running it on a cluster, sometimes a job will get killed if it runs out of memory or runs too long).
On 08/23/2017 02:30 PM, Cara Bohon wrote:
I have a couple of subjects "exited with ERRORS" after running almost 48 hours (when my others all took about 13-15 hours on the same server). Both exited during Fix Topology lh.
The only time "error" appears is in this line: IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = -0.0 tol 0.000010 - which prior messages to this list suggest is not meaningful or problematic.
I am brand new to Freesurfer, so I'm not quite sure where to start in troubleshooting. The orig.mgz file looks fine to me, but maybe I'm missing something. Any other tips for things to check? I'm attaching a recon-all.log file in case that is helpful. I am running Freesurfer 5.3.0 on Linux.
Thanks for any tips on addressing the error!
-Cara
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Message: 2 Date: Wed, 23 Aug 2017 14:57:53 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Continuous co-variate by continuous co-variate interaction effects To: freesurfer@nmr.mgh.harvard.edu Message-ID: e1a5bf46-9c3f-564b-fbe0-ce081f513ae8@nmr.mgh.harvard.edu Content-Type: text/plain; charset=utf-8; format=flowed
Is that your design matrix or the contrast matrix? To test for the interaction between two continuous variables, one usually creates a new variable by multiplying them together and then just testing for the regressor for that variable being different than zero
On 08/23/2017 12:34 PM, Timothy Hendrickson wrote:
Freesurfer experts,
I have created a design matrix in order to test for whether there is an interaction effect between two continuous co-variates controlling for a categorical variable.
So I have one categorical variable with two levels, and two continuous co-variates.
My design matrix is as follows:
0 0 1 1 0 0 0 0 0 0 1 1
Is this correct?
-Tim
Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay)
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Message: 3 Date: Wed, 23 Aug 2017 21:54:20 +0000 From: "Rockers, Elijah D." edrockers@houstonmethodist.org Subject: Re: [Freesurfer] Hard failure via XNAT pipeline (Freesurfer 6) To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: 1503525260.5299.80.camel@houstonmethodist.org Content-Type: text/plain; charset="utf-8"
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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