This error is related a new security feature implemented in OS X El Capitan:
https://support.apple.com/en-gb/HT204899
You should not be getting this error with version FS6.0, but if you are you can always get around it by disabling SIP:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-...
However, I am still curious how/why you are getting this error. Is there a trac-all .log file somewhere you can send me so I can see at what point exactly this error occurs?
-Zeke
On 03/28/2017 03:29 PM, VA Research wrote:
Hello,
i am on el capitan 10.11.6 , XQuartz 2.7.8
I named the old Applictions/freesurfer directory something else and installed freesurfer 6.0 and sourced through the script, i also changed the subject directory
but otherwise i think this is a clean install of FS 6.0
I am running trac-all -prep
and am getting the same error
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
dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
Trace/BPT trap ERROR: input file must be in NIfTI format Darwin 192.168.1.2 15.6.0 Darwin Kernel Version 15.6.0: Mon Jan 9 23:07:29 PST 2017; root:xnu-3248.60.11.2.1~1/RELEASE_X86_64 x86_64
i ran sudo -E fs_update as described on https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
but still get the same error
Were you guys able to resolve this issue?
Thanks so much
joseph
On Mon, Mar 6, 2017 at 9:26 AM, Fred Lado <ladofred@gmail.com mailto:ladofred@gmail.com> wrote:
yes, I have the /Applications/freesurfer/lib/gcc directory.(actually, ‘had’ as I reinstalled 5.3) I installed 6.0 on top of 5.3 without uninstalling 5.3 first, so it was not a clean install. I will try a clean re-install with the tar file with the steps you suggest. Thanks. Date: Sun, 5 Mar 2017 22:22:01 -0500 (EST) From: zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_vol2surf error in FS6 To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <62233.174.63.82.222.1488770521.squirrel@mail.nmr.mgh.harvard.edu <mailto:62233.174.63.82.222.1488770521.squirrel@mail.nmr.mgh.harvard.edu>> Content-Type: text/plain;charset=iso-8859-1 Hello Fred, Do you have the /Applications/freesurfer/lib/gcc directory? Also, out of curiosity, did freesurfer 5.3 exist on your system before installed 6.0? That error shouldnt happen if FS6 is cleanly installed and definitely shouldnt happen of SIPS is disabled. I suppose as a last resort could you just completely remove FS from your machine and just install it directly from the tar file (save the license.txt file): ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz> $> cp /Applications/freesurfer/license.txt ~ $> sudo rm -rf /Applications/freesurfer $> sudo tar -C /Applications -xzvf freesurfer-Darwin-OSX-stable-pub-v6.0.0.tar.gz $> sudo mv ~/license.txt /Applications/freesurfer/ > Dear FreeSurfer Experts, > I just installed FS6 and encountered the following error, which I can > replicate by just entering ???mri_vol2surf??? on the command line: > > /Users/fred 3> mri_vol2surf > 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 > > dyld: Symbol not found: ___emutls_get_address > Referenced from: > /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib > Expected in: /usr/lib/libSystem.B.dylib > > I am running Mac OS X El Capital 10.11.6, after searching the archives I > also tried turning off SIP, which did not help. Any other advice? > > Thanks, > Fred > > > Fred Lado, MD PhD > Director, Epilepsy - Central and Eastern Regions > Northwell Health > 917-608-1881 <tel:917-608-1881> (mobile) > 516-325-7000 <tel:516-325-7000> (practice) > 516-325-7001 <tel:516-325-7001> (fax) > flado@northwell.edu <mailto:flado@northwell.edu> > > > > > > Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 > PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any > attachments, is for the sole use of the intended recipient(s) and may > contain confidential and privileged information. Any unauthorized review, > use, disclosure or distribution is prohibited and may be unlawful. If you > are not the intended recipient, please delete this e-mail immediately. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline <http://www.partners.org/complianceline> . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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