SIP disabled, fs_update run, still getting "dyld: lazy symbol binding failed" from within MATLAB
External Email - Use Caution
Greetings freesurfer folk,
Following previous posts here, as well as the freesurfer v6.0 release notes, I have disabled SIP (I'm in Mac High Sierra 10.13.4), updated my installation ($> sudo -E fs_update), and rebooted my computer, but I still get this problem. I am trying to run mri_vol2surf using the 'unix' command from within MATLAB (2017b), and upon doing so, I receive the dreaded "dyld: lazy symbol binding failed" error.
I can run mri_vol2surf just fine on the command line (outside of MATLAB), and I've made sure the unix path accessible within MATLAB matches the unix path on the command line, and that freesurfer environment variables are all accessible within MATLAB. Does anyone have any ideas on how I might fix this problem? Thank you very much for your time.
Best,
Fred
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Frederick Barrett, Ph.D
Assistant Professor of Psychiatry and Behavioral Sciences
Behavioral Pharmacology Research Unit
Johns Hopkins School of Medicine
5510 Nathan Shock Dr / Rm 3048
Baltimore, MD 21224
Voice/mail: (410) 550-9777
Email: fbarret2@jhmi.edumailto:fbarret2@jhmi.edu | frederick.barrett@gmail.commailto:frederick.barrett@gmail.com
Google Scholar: http://goo.gl/vjrrslhttp://scholar.google.com/citations?user=KCtXPmAAAAAJ
Hi Fred, you mention that the fs environment variables are accessible within MATLAB, but is freesurfer fully sourced in your MATLAB environment? I’m guessing this is an issue with your DYLD_LIBRARY_PATH not being set correctly. You should check to see if the DYLD_LIBRARY_PATH env variable in your MATLAB shell matches what you see in the terminal after sourcing freesurfer. You could also try to download the dev binary of mri_vol2surf (from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev_binaries/OSX-ElCa...) and use this instead.
Best, Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Frederick Barrett fbarret2@jhmi.edu Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Thursday, May 31, 2018 at 4:07 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SIP disabled, fs_update run, still getting "dyld: lazy symbol binding failed" from within MATLAB
External Email - Use Caution
Greetings freesurfer folk,
Following previous posts here, as well as the freesurfer v6.0 release notes, I have disabled SIP (I'm in Mac High Sierra 10.13.4), updated my installation ($> sudo -E fs_update), and rebooted my computer, but I still get this problem. I am trying to run mri_vol2surf using the 'unix' command from within MATLAB (2017b), and upon doing so, I receive the dreaded "dyld: lazy symbol binding failed" error.
I can run mri_vol2surf just fine on the command line (outside of MATLAB), and I've made sure the unix path accessible within MATLAB matches the unix path on the command line, and that freesurfer environment variables are all accessible within MATLAB. Does anyone have any ideas on how I might fix this problem? Thank you very much for your time.
Best,
Fred
----------------------------------------------------------
Frederick Barrett, Ph.D
Assistant Professor of Psychiatry and Behavioral Sciences
Behavioral Pharmacology Research Unit
Johns Hopkins School of Medicine
5510 Nathan Shock Dr / Rm 3048
Baltimore, MD 21224
Voice/mail: (410) 550-9777
Email: fbarret2@jhmi.edumailto:fbarret2@jhmi.edu | frederick.barrett@gmail.commailto:frederick.barrett@gmail.com
Google Scholar: http://goo.gl/vjrrslhttp://scholar.google.com/citations?user=KCtXPmAAAAAJ
freesurfer@nmr.mgh.harvard.edu
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Frederick Barrett -
Hoopes, Andrew