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Dear Freesurfer Experts,

I ran the following command in FS:

recon-all -i /Users/benine/Desktop/PVS_validation_cohort/MultipleMS_MRI_export/SW1-1875_M12/Brain/DICOM/0000D7EA/AACF54F0/AAA4DDA4/000037CC/EE021428 -subject 000037CC -qcache -hippocampal-subfields-T1 -brainstem-structures -cw256 -3T -all

The command exited with error. Attached the log file.

Additionally, this message shows up in the terminal output:

ERROR: cannot find Matlab 2012b runtime in location:

/Applications/freesurfer/MCRv80

It is looking for either:

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

bin/maci64/libdctprocess.jnilib (Mac 64b)

You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2012b.

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

LINUX:

cd /Applications/freesurfer

curl " http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&..." -o "runtime2012b.tar.gz"

tar xvf runtime2012b.tar.gz

MAC:

cd /Applications/freesurfer

curl " http://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&..." -o "runtime2012b.tar.gz"

tar xvf runtime2012b.tar.gz

I did now download the runtime2012b according to the suggestion. The untaring created a folder called MCRv80. I moved this folder to the Freesurfer_Home.

Before I run everything again: 1.) Is the correct procedure to download the Matlab runtime? 2.) Did the recon-all run everything just without hippocampal subfields and brainstem? If yes, can I just re-run these two commands or do I need to re-run everything?

Many thanks for the support!

/Ben

____________________________________ Benjamin Victor Ineichen, MD PhD Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01

Dr. med. et Dr. rer. nat. ETH Benjamin Victor Ineichen Karolinska Institutet Center for Molecular Medicine Stockholm, Sweden ineichen@protonmail.ch +41 76 391 04 01