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 <ladof...@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: zkauf...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_vol2surf error in FS6 > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Cc: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <62233.174.63.82.222.1488770521.squir...@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 > > $> 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 (mobile) > > 516-325-7000 (practice) > > 516-325-7001 (fax) > > fl...@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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > 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 . 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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