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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