External Email - Use Caution
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/1dSEOQ7tV8guTp0mVMuBTN-FnaRonB3-Do1A0IPLl4r-ZYZ...
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
External Email - Use Caution
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/1X-6jqhKciXd6EPCb1LpoJ_D-PycfnYplnrld0ymBSFrnC97...
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
External Email - Use Caution 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/1DPNspRGzh75krxD5Gs5bdv5mA3Fj4EDxDAbwNNfs-aZyRE... 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
freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Juan E. -
Lauren Stephens