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Hi FreeSurfers, 

I have been attempting to run segmentThalamicNuclei.sh and continue getting the error: 

ERROR: cannot find Matlab 2019b runtime in location:

     

/Applications/freesurfer/7.3.2/MCRv97

     

It is looking for either: 

  bin/glnxa64/libmwlaunchermain.so    (Linux 64b) or

  bin/maci64/libmwlaunchermain.dylib (Mac 64b)

 

The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.

To do so, please run the following command (you might need root permissions):

 

fs_install_mcr R2019b

 

For further details, please visit https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

Current path setup on our Mac: /Applications/freesurfer/7.3.2/MCRv97

Symbolic link setup on our Mac named MCRv97: /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97/bin/maci64/libmwlaunchermain.dylib 

However, I have already installed the runtime and have alternatively created a symbolic link with Matlab we already have installed on our Mac.  
I have also confirmed the runtime file exists on the machine 

ln: MCRv91/MATLAB_R2016b.app: File exists


We are using FreeSurfer version 7.3.2 on an iMac Pro with Ventura 13.6.  


Any suggestions for how to get the matlab runtime issue resolved in order to reun the segmentThalamicNuclei.sh code.  


Thank you, 


Lauren Stephens


Lauren Stephens, MS 

Assistant Clinical Research Coordinator 

Department of Psychiatry and Behavioral Science 

Stanford University School of Medicine  

E: laurenss@stanford.edu 

P: (650)-725-1716