On Tue, Mar 28, 2017 at 12:59 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

Thanks for the log file. I believe this is a real bug on OSX platforms.
I should have a fix by tomorrow.

-Zeke

On 03/28/2017 03:46 PM, VA Research wrote:
> I will try to disable SIP
>
> (although i dont want to restart the system because i am curious if this
> XL defect will ever be corrected running 80 plus hours now... lol)
>
> attached is the trac -all.log
>
> On Tue, Mar 28, 2017 at 12:40 PM, Z K <zkaufman@nmr.mgh.harvard.edu

> <mailto: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
> <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/
> <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
> <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>

> > <mailto: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>
> <mailto: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>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > Cc: freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto: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>
> >
> <mailto: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>
> >
> <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> <tel:917-608-1881
> <tel:917-608-1881>> (mobile)
> > > 516-325-7000 <tel:516-325-7000> <tel:516-325-7000
> <tel:516-325-7000>> (practice)
> > > 516-325-7001 <tel:516-325-7001> <tel:516-325-7001
> <tel:516-325-7001>> (fax)
> > > flado@northwell.edu <mailto:flado@northwell.edu>
> <mailto:flado@northwell.edu <mailto:flado@northwell.edu>>
> > >
> > >
> > >
> > >
> > >
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