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Hello FreeSurfer Developers,
I’m attempting to run FreeSurfer commands via Matlab [system(‘fscmd’)]. Some of the commands work but some don’t, though all the commands work well when run in Terminal.
Commands work in both Terminal and Matlab:
When I run “tksurfer” in Terminal or system(’tksurfer’) in Matlab, I will get the help information for ’tksurfer'.
Commands do not work in Matlab, but work in Terminal:
For example, when I run “mri_info" in terminal, I will get the help information for “mri_info”. However, when I run system(‘mri_info’) in Matlab, I got the following error (screeshot also attached):
=================================================================== dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer_6.0/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_6.0/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib
mri_info: Aborted
ans =
134 ===================================================================
I randomly tried some FreeSurfer commands and the commands do not work in Matlab (but work in Terminal) are: ‘mri_info’ ‘mri_coreg’ Commands work in both terminal and Matlab are: ’tksurfer’ ‘mri_convert’ ‘mri_head’
I did search for the error in FreeSurfer Archive and found the recommendation of disable System Integrity Protection. Before doing that, I wonder if there is any other solution to this.
Also, I tried to run these commands in both FreeSurfer 5.3-HCP and FreeSurfer 6.0 (on the same computer), and interestingly, the commands via Matlab work well in FS 5.3 (except that ‘mri_coreg’ cannot be found in FS 5.3) but the error will show in FS 6.0.
Additional information: 1) FreeSurfer version: error show for freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c, but not for freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0-HCP 2) Platform: macOS Mojave (version 10.14.5) iMac Pro (2017) 3) uname -a Darwin ADUAED07785WKMX.local 18.6.0 Darwin Kernel Version 18.6.0: Thu Apr 25 23:16:27 PDT 2019; root:xnu-4903.261.4~2/RELEASE_X86_64 x86_64
Please let me know if there is any other information will help.
Thanks in advance, Haiyang
