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Thank you for your time and the information.

I appreciate it.

Unfortunately, we are running longitudinal data across a good bit of time and therefore do not wish to alter to a newer version of freesurfer.

I will work with what I can. Thank you for the tips!

However, is there a reason this file was removed?

https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar

Thank you,

Jeanette

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From: fsbuild <fsbuild@contbay.com>
Sent: Wednesday, June 25, 2025 3:33 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Re: FS 6 matlab runtime and libcurses in docker

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Hello Jeanette,

Freesurfer 6 was released back in 2017 for CentOS6,

https://surfer.nmr.mgh.harvard.edu/fswiki/rel6downloads

We don’t expect the freesurfer 6 distribution (FS6) to entirely work on Rocky8 linux, e.g., you will probably get run time library errors, because the Linux system libraries have been updated to newer (incompatible) versions some 8 years later for more recent versions of Linux such as Rocky8. The fs_install_mcr script is part of more recent FS7 and FS8 distributions, but is not part of (or supported in) FS6.

If you must use FS6, then your best bet is to make a CentOS6 or CentOS7 docker container and run FS6 in that instead, e.g., download and unarchive the tar images from the above link into your CentOS6/CentOS7 docker container. Or put whatever version of FS6 you have already been running into that (new) container.

Then you could subsequently download and install a version of Matlab that supports the version of CentOS6/CentOS7 running in the container. I’m not sure there is a Matlab run time environment matching those older OS's, but there should be a full version of Matlab.

Unless there is work already done with Freesurfer 6 that you need to continue to work on or support with that same version for continuity, then on Rocky 8 linux, e.g., for new work, we recommend you download and run the FS8 rocky8 linux installer from,

https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads

- R.

On Jun 25, 2025, at 12:55, Kenley, Jeanette <jkkenley@wustl.edu> wrote:

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Hello installation experts.

I am creating a docker which runs OS Rocky 8.

I am placing FS6 in said docker.

I would like to run recon-all with the -hippocampal-subfields-T1(T2) flag, which requires the libcurses libraries.

I cannot download and execute this file in the docker successfully because it throws a VM library error when executed. (I apologize the exact error is no longer available to me)
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr

Thus I was attempting to load this file into the docker:
https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2012bLinux.tar

Which I planned to subsequently untar and add the libcurses to the MCRv80 output folder, but unlike on 18 June 2025, the file is no longer available.

Is there a reason this file was removed?
Or do you have a recommendation on how to make the above script run, which then I can add the libcurse libraries to?


Thank you for your time.
Jeanette
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