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Try setting DYLD_LIBRARY_PATH to point to the subdirectories containing the Matlab libraries.

You could just delete what's there,

$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2

$ cd $FREESURFER_HOME

$ sudo rm MCRv97

- and re-run fs_Install_mcr,

$ cd  bin

$ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b

.... the script should output the paths to the subdirectories with the libraries to add to DYLD_LIBRARY_PATH at the end of it output. 

On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable:

/var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64

If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable.

The paths listed for your machine will be different compared to the above, but just copy and paste what is listed for the entire series of paths into the command,

$ export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/yy/abc/install-target/v97/runtime/maci64:/var/folders/yy/abc//install-target/v97/sys/os/maci64:/var/folders/yy/abc/install-target/v97/bin/maci64:/var/folders/abc/install-target/v97/extern/bin/maci64

- R.

On 10/3/23 21:35, Iglesias Gonzalez, Juan E. (JIGLESIASGONZALEZ@mgh.harvard..edu) wrote:

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Dera Lauren, I am a bit confused: is /Applications/freesurfer/7.3.2/MCRv97 pointing to  /Applications/MATLAB/MATLAB_Runtime/R2019b/MCRv97? Cheers, /Eugenio  

-- Juan Eugenio Iglesias

http://secure-web.cisco.com/1bqVymEumCTwxGQGbfGgRiZlYNLDyBIOW6zSN5FfiWaLUE4a...  

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lauren Stephens <laurenss@stanford.edu>

Date: Tuesday, October 3, 2023 at 1:23 PM

To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>

Subject: [Freesurfer] segmentThalamicNuclei.sh and Matlab Runtime

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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://secure-web.cisco.com/1ECsrk1Jpk7yzuD5ZaV9DNMKMMh3AzKfgXjXeiMKyBiQtU_... 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  

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