28 Mar
2017
28 Mar
'17
5:50 p.m.
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>>> > > > > > > > > > > > > > > > > > > Confidentiality Notice: This document is protected by EDUCATIONAL > > LAW 6527 > > > PUBLIC HEALTH LAW 2085, J, K, L, M. 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