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 <zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@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 <zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu> > > <mailto:zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@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 > <ladof...@gmail.com <mailto:ladof...@gmail.com> > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com>> > > > <mailto:ladof...@gmail.com <mailto:ladof...@gmail.com> > <mailto:ladof...@gmail.com <mailto:ladof...@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: zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu> > > <mailto:zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu>> > > <mailto:zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu> > > <mailto:zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@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.squir...@mail.nmr.mgh.harvard.edu > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu> > > > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu>> > > > > > > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu> > > > <mailto:62233.174.63.82.222.1488770521.squir...@mail.nmr.mgh.harvard.edu > > <mailto:62233.174.63.82.222.1488770521.squir...@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) > > > > fl...@northwell.edu <mailto:fl...@northwell.edu> > <mailto:fl...@northwell.edu <mailto:fl...@northwell.edu>> > > <mailto:fl...@northwell.edu <mailto:fl...@northwell.edu> > <mailto:fl...@northwell.edu <mailto:fl...@northwell.edu>>> > > > > > > > > > > > > > > > > > > > > > > > > Confidentiality Notice: This document is protected by > EDUCATIONAL > > > LAW 6527 > > > > PUBLIC HEALTH LAW 2085, J, K, L, M. 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