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Hello

So my specific problem was that I ran AANsegment.sh and it produced errors including:

/usr/local/freesurfer/8.2.0//bin//mri_robust_register: /usr/local/freesurfer/8.2.0//MCRv97//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /usr/local/freesurfer/8.2.0//bin//mri_robust_register)
/usr/local/freesurfer/8.2.0//bin//mri_robust_register: /usr/local/freesurfer/8.2.0//MCRv97//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/local/freesurfer/8.2.0//bin//mri_robust_register)
/usr/local/freesurfer/8.2.0//bin//mri_robust_register: /usr/local/freesurfer/8.2.0//MCRv97//sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.32' not found (required by /lib/x86_64-linux-gnu/libitkvnl_algo-5.3.so.1)

Creating a soft link to the libraries solved the problem for me, but I'd be interested in any other solution which doesn't involve changing the contents of the matlab distribution.

Thanks

Michael


From: fsbuild <fsbuild@contbay.com>
Sent: Tuesday, October 20, 2026 13:43
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: Matlab runtime and freesurfer 8

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The Wiki Page you referenced shows the install of R2014b and R2012b for older Freesurfer releases.

The most recent install information is available from the main Freesurfer release page for 8.X (and 7.X) releases.
https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

Follow the link there under the 8.2.0 release for 8.X setup and patch updates, and you will load the page,
https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads/rel8notes

Then scroll down to the section for SETUP A MATLAB DISTRIBUTION and you will see the example install for the R2019b (MCRv97) runtime.

I’m not aware of issues with Fresurfer 8.2.0 binaries using R2019b, but even if that is the case, I  don’t think the Mathworks supports overriding the included libc with a different one.

- R.

On Oct 20, 2026, at 08:04, Michael Firbank <michael.firbank@newcastle.ac.uk> wrote:

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Below, an issue, and solution to matlab runtime libraries with freesurfer8 on Ubuntu 24.

I was trying to use the AANSegment tool: https://surfer.nmr.mgh.harvard.edu/fswiki/AANSegment

And came across some problems (now solved).

1) The utility uses the Matlab runtime. I have freesurfer 8 installed, but the instructions on that page (and also the
MatlabRuntime page) only refer to version 6 and 7. Could this be updated?

2) Having got the right matlab version, I ran into problems with missing libraries.
Discussing this with our IT team, they said:

"The problem is that the MCR runtime is supplying its own version of libstdc++ (the GLIBC C++ standard library) which is conflicting with other software/libraries which are loaded at the same time, namely /lib/x86_64-linux-gnu/libitkvnl_algo-5.3.so.1 (probably some other code/application which is part of freesurfer is wanting that library).

So the MCR runtime is adjusting the library path to load its own libstdc++ library (an older version), but other code which is running wants libitkvnl_algo-5.3.so.1 which in turn wants the (later) version of libstdc++ which is included as part of the Ubuntu 24 OS."

Their solution was to replace the library in the MCR directory with a symbolic link to the ubuntu system one.
ie that
/usr/local/freesurfer/8.2.0/MCRv97/sys/os/glnxa64/libstdc++.so.6
is now a symbolic link to
/lib/x86_64-linux-gnu/libstdc++.so.6

which seemed to solve the problem.

Best wishes

Michael

Michael Firbank       #mynameis   [my-kel fur-bank]                                                                 
Newcastle University
Health Innovation Neighbourhood (formerly Campus for Ageing and Vitality)
Newcastle upon Tyne, NE4 5PL                                                      

 

 

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