The issue only exists in v6 Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fsbuild fsbuild@contbay.com Date: Monday, February 8, 2021 at 9:01 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: costanza.bianca.parodi@gmail.com costanza.bianca.parodi@gmail.com Subject: Re: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release
External Email - Use Caution I have another library change you can try for freesurfer 6. I will send it to your private email shortly.
- R.
On Feb 8, 2021, at 06:14, Costanza Parodi <costanza.bianca.parodi@gmail..com> wrote:
External Email - Use Caution
no difference has been detected in the files but the same error comes up.
Error opening file dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib
I would like to avoid disabling the SIP. Any other suggestions? Does the v7 have the same bug?
On 6 Feb 2021, at 00:15, fsbuild <fsbuild@contbay.commailto:fsbuild@contbay.com> wrote:
If you followed the directions for the 6.0.0 patch, then you replaced the copy of libgomp.1.dylib inside the freesurfer application bundle with the updated version from the patch archive under,
./Freeview.app/Contents/Frameworks/libgomp.1.dylib
But there is another copy of libgomp under,
./lib/gcc/lib/libgomp.1.dylib
In the original 6.0.0 download, those 2 copies of libgomp are identical (or unpatched).
So you could try using the patched version of libgomp.1.dylib to replace the copy under ./lib/gcc/lib as well.
You could move it aside and replace it with something like,
$ sudo cd <base path>/freesurfer/lib/gcc/lib $ sudo mv libgomp.1.dylib OLD_libgomp.1.dylib $ sudo cp -p -f ../.../../Freeview.app/Contents/Frameworks/libgomp.1.dylib . $ sudo diff libgomp.1.dylib ../../../Freeview.app/Contents/Frameworks/libgomp.1.dylib … no diff results should be reported ...
Then try running your command again.
- R.
On Feb 5, 2021, at 12:37, Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote:
Yes, this probably has to do with SIP being enabled, which blocks libraries stored in /usr. This was a pretty common issue that people had with v6. You can try disabling SIP via MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-...http://secure-web.cisco.com/1tMo1B0Wev-AXmkf1seEjPbNhnfyxVDZnKjJOUZYe6-x5PHuinA4gCSlCb0JH0ey7YeEOp-964nB7hgiDIipWL3vfhYsC-oGkftqJW9NOit7OaiJ9Go-L6QrBZ3Q8PpRfpnIC8cVZWrbX4y4Efb3KKIyTHM60JP7QvcyM4UGuidKdOQaDNbbrGMb5bV0_f2IFFBaML5hrm8o26BZX515Cghx-xo9JudVGKYRaoB138MClzfpP8-WHM0Ljn9JEzvOG6NEz87ctVVVfCwdf8NP8aA/http%3A%2F%2Fosxdaily.com%2F2015%2F10%2F05%2Fdisable-rootless-system-integrity-protection-mac-os-x
best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr..mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Costanza Parodi <costanza.bianca.parodi@gmail.commailto:costanza.bianca.parodi@gmail.com> Date: Friday, February 5, 2021 at 9:30 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Lazy_symbol_error libstdc++.6.dylib: stable Version 6 Release External Email - Use Caution Hello Freesurfer Developers,
I was attempting to use the mri_cvs_register command ( mri_cvs_register -- mov subjid -- mni) and I received this error:
asegfname aseg Using m3z type morph files. 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
Abort
I resolved the issue by downloading the Freeview_6.0.0_MacOS patch, but a new error came up :
Error opening file dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib
dyld: Symbol not found: ___emutls_get_address Referenced from: /Volumes/NAME/Applications/freesurfer/bin/../lib/gcc/lib/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib
I did not find similar errors in the archive. Should I disable SIP? Could you help me trouble-shoot this error? My freesurfer is installed on an external hard disk and I am processing my subjects on my Mac desktop.
1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) MacOs High Sierra version 10.13.6 3)Darwin MacBook-Air.local 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 18 21:21:34 PDT 2020; root:xnu-4570.71.82.5~1/RELEASE_X86_64 x86_64 4)Xquartz 2.7..11
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