Hi Melissa,

If the command runs fine in the terminal but not from python, it’s most likely because python is messing with aspects of your env before running commands in a subshell. The easiest solution is to upgrade to FS v7, where this problem no longer exists, but if you’re stuck at v6, you should verify that the DYLD_LIBRARY_PATH env var in the python subshell is the same as in the terminal environment.

Best

Andrew

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Melissa Marie Rundle <mrundle@wakehealth.edu>
Date: Friday, May 7, 2021 at 2:59 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] mri_label2vol error

        External Email - Use Caution        

Hi,

I get the following error message when I run mri_label2vol (freesurfer v 6.0) in a jupyter notebook(6.1.4) with python (v3.8.5):

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
 
However, when I run mri_label2vol directly in a terminal window, the command runs just fine.  Nor do I have trouble
running similar commands such as mri_vol2vol or mri_convert using the jupyter notebook.  
 
I tried running "sudo -E fs_update" as suggested in MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
but that didn't solve the problem.
 
Any suggestions would be greatly appreciated.
 
Sincerely,
Melissa Rundle