External Email - Use Caution Please try using the Matlab runtime environment which can be installed directly into the freesurfer tree via a script we provide. The runtime environment is free and requires no paid for Matlab license (since it does not include the Matlab compiler). For your existing install of freesurfer 7..1.1, the tested version of the Matlab runtime environment to install is R2014b (listed below as the version to use in the bash/zsh commands). However, if you were to update to the current freesurfer 7.4.1 release, https://secure-web.cisco.com/1EbuUGpusH65Vnhqyq32iw8lhOzpyphGTkomb1eGIHw58FD4ikSbt9f7VFH4X8deyqrzjKVzFMgqki-n63sKgin2kguxnvVJ0g1kgDFvZDwcE9MYyz4PxA482Uoppvj_xzoJ7FZfWzjxTRMYqj7SGcDj6ClpBf7YSyiSYJPwYvPDbNKVzBl_68uYwiEBaf4tA7hhc2wAcVv-dTmneINRGW4ayp1zoonJKmUYUsD5NNzRTiy0JBh5uS3MTuHXb8gq_Vb9DwI2znfq2inPePbqtqJtHEU4X372cxYJRMx9L8Q6tGQsl51lXryVbRgi7Mq5L7zTZ2UN8gInW9BnhIgczuQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg, then you could use the more recent R2019b Matlab runtime. $ export FREESURFER_HOME=<your install path>
$ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2014b <— change to R2019b if you end up using freesurfer 7.4.1 … answer y to any installer questions … The output from running that script will list what DYLD_LIBRARY_PATH should be set to. Please make sure you have otherwise removed any references to your previous matlab environment from DYLD_LIBRARY_PATH, PATH, etc. It might also work to add $FREESURFER_HOME/MCRv97/bin/glnxa64 to DYLD_LIBRARY_PATH but I would first try what the script prints out as the local paths on your machine. - R. On Oct 9, 2023, at 20:21, Mirsol Choi <mir...@ualberta.ca> wrote: External Email - Use Caution Hi there,I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am trying to utilize the segmentation function with this command:segmentHA_T1.sh subj01But I am met with this error saying that Matlab has crashed. The crash log is attached to this email. I have freesurfer version 7.1.1, running on MacOs 11.7.10.I have followed your website instructions to download Matlab R2014b.Following the installation process of Matlab, I was met with this message: Installing Product: MATLAB Compiler Runtime - Core 8.4(Oct 08, 2023 11:29:15) Installing Product: MATLAB Compiler Runtime - GPU 8.4(Oct 08, 2023 11:29:21) Notes: On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64:(Oct 08, 2023 11:29:21) Exiting with status 0(Oct 08, 2023 11:29:21) End - Successful.FinishedR2014b installed successfully in /Applications/freesurfer/7.1.1/MCRv84And so I have appended the path using this code into my bashrc profile: export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.aMmBemHB/install-target/v84/bin/maci64I am wondering if I can get some help with running the hippocampus segmentation protocol .Thank you so much for your time, I greatly appreciate your support. <matlab_crash_dump.28607-2>_______________________________________________Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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