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

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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:

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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.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.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

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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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