Hi Jay,

Try calling "source $FREESURFER_HOME/SetUpFreeSurfer.csh” (without the quotes) at the beginning of @SUMA_Make_Spec_FS (it’s a script that should be wherever AFNI is installed, like $HOME/abin).

Cheers,
Ruy
On Mar 26, 2018, at 12:54 PM, Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

Hi Jay, as a temporary fix for 6.0, I would suggest disabling SIP and rerunning:
 
best
Andrew
 
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Jay Edelman <jedelman@ccny.cuny.edu>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, March 22, 2018 at 10:02 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Problem running mri_convert
 
Dear Freesurfers,
 
I am running the program "mri_convert" within the AFNI script, @SUMA_Make_Spec_FS, and am receiving the error below. I just installed freesurfer from your website and am running this on a Mac running Yosemite. I've looked at the online forums and see this addressed in other contexts, but unfortunately I can't find any fix.
 
Thanks So Much!
Jay Edelman
Dept. of Biology, The City College of New York
 
mri_convert.bin -ot nii mri/wm.seg.mgz /Users/jedelman/Dropbox/freesurfer/asim/./SUMA/wm.seg.nii 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from mri/wm.seg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
writing to /Users/jedelman/Dropbox/freesurfer/asim/./SUMA/wm.seg.nii...
-- running 'mris_convert lh.smoothwm lh.smoothwm.asc'
Trace/BPT trap
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
​
 
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