External Email - Use Caution        

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.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-mac-os-x
 
best
Andrew
 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Costanza Parodi <costanza.bianca.parodi@gmail.com>
Date: Friday, February 5, 2021 at 9:30 AM
To: freesurfer@nmr.mgh.harvard.edu <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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