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Hello,

Can you please send the full terminal output from the 'segmentHA_T1.sh subj01' command?

Best, Jackson ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Mirsol Choi mirsol@ualberta.ca Sent: Monday, October 9, 2023 8:21 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash

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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 subj01

But 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.

Finished

R2014b installed successfully in /Applications/freesurfer/7.1.1/MCRv84

And 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/maci64

I 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.