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 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 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.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
$> 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) flado@northwell.edu
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