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: http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-... http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/
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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