New subject: mri_vol2surf error in FS6

6 Mar 2017

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>
Subject: Re: [Freesurfer] mri_vol2surf error in FS6
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: 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>>
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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>

 $> 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> (mobile)
> 516-325-7000 <tel:516-325-7000> (practice)
> 516-325-7001 <tel:516-325-7001> (fax)
> flado@northwell.edu <mailto:flado@northwell.edu>
>
>
>
>
>
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