External Email - Use Caution        

This fixed the issue:

sudo rm -f /Applications/freesurfer/lib/gcc/lib/libgomp.1.dylib
sudo ln -s /usr/local/Cellar/gcc/8.2.0/lib/gcc/8/libgomp.1.dylib /Applications/freesurfer/lib/gcc/lib/libgomp.1.dylib





On Mar 11, 2019, at 6:14 PM, Shana Adise <Shana.Adise@uvm.edu> wrote:

Of note, I forgot to add that disabling SIP does not fix the problem: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/



On Mar 11, 2019, at 5:29 PM, Shana Adise <Shana.Adise@uvm.edu> wrote:

        External Email - Use Caution        


Hello,

I originally ran into some hiccups with AFNI’s @SUMA_make_spec_FS, which stems from a freesurfer error:

1. Error one: 

Abort
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

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
c_ras: Subscript out of range.
c_ras: Subscript out of range.


2. It appears that you are already aware of this issue: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes

3. However, I have a new issue when trying to run  sudo -E fs_update


rsync -zbrlv --progress --suffix=.1552339020_bakrsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurfer
receiving file list ... 
rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2)
0 files to consider

sent 4 bytes  received 9 bytes  26.00 bytes/sec
total size is 0  speedup is 0.00
rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-52.200.1/rsync/main.c(1404) [receiver=2.6.9]



Any suggestions?

Thanks,
Shana
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