On Tue, Mar 28, 2017 at 12:40 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

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-mac-os-x/

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>
> >
> >
> >
> >
> >
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