On Tue, Mar 28, 2017 at 2:50 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

freesurfer depends on certain environment variables to run properly, but
SIP prevents the passing of those environment variables at runtime,
namely LD_LIBRARY_PATH. This causes the error.

I have uploaded a fix to our server. If SIP was still enabled, running
'sudo -E fs_update' would update a script in your freesurfer
installation which should bypass the issue. But I guess your all set anyway.

On 03/28/2017 05:32 PM, VA Research wrote:
> disabled SIP got it working
>
> briefly why would SIP (files system not accessible) halt the trac-all?
>
>
>
> On Tue, Mar 28, 2017 at 12:59 PM, Z K <zkaufman@nmr.mgh.harvard.edu
> <mailto: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>
> > <mailto: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>
> > <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/>
> >
> <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>
> > <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>>
> > > <mailto: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>>
> > <mailto: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>>
> > > <mailto: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>>
> > > <mailto: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>>
> > >
> >
> <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
> <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>>
> > >
> >
> <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>> <tel: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>> <tel: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>> <tel: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>>
> > <mailto:flado@northwell.edu <mailto:flado@northwell.edu>
> <mailto:flado@northwell.edu <mailto:flado@northwell.edu>>>
> > > >
> > > >
> > > >
> > > >
> > > >
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