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.

When I run “tksurfer” in Terminal or system(’tksurfer’) in Matlab, I will get the help information for ’tksurfer'.

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):

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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 

Please let me know if there is any other information will help.

Thanks in advance,

Haiyang