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You could try running FS 5.1 on Ubuntu 12 using either a container or VM, but I’m not aware of a container with Freesurfer 5.1 already installed.

I would try the VirtualBox VM with Freesurfer 5.3 and see if that works.  That is a known to be good image of the OS with everything installed for at least FS 5.3 to run.   You could first make a snapshot of the VM and then try installing FS 5.1 in it and see if it works.  If you have IT staff, they should be able to help you with doing this if you are not familiar with VirtualBox.

- R.

On Oct 5, 2022, at 15:07, Leema_Murali@eisai.com wrote:

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Thank you so much for a detailed explanation. I have never tested FS 5.1 previously. This is my first time testing this version in a docker container. I’m not sure what older version of OS that should be used. Is there a docker base image available for FS 5.1 like it’s there for FS 7.2.
 
Regards,
Leema
 
From: fsbuild <fsbuild@contbay.com> 
Sent: Wednesday, October 5, 2022 2:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Leema Krishna Murali <Leema_Murali@eisai.com>
Subject: Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5.1
 
It looks like you are running into undefined symbols when running on Ubuntu 16.   You may need to use an older version of the OS.  I say that because we have an Ubuntu 12 VM with Freesurfer 5.3 that runs on VirtualBox available from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full..vdi.gz    And FS 5.1 predates FS 5.3.
 
We post a note you should be aware of about changing the operating system you run freesurfer on:
 
Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions).
 
I interpret that to mean you should try and run FS 5.1 on the version of the OS you previously ran it on.  Otherwise, you may not get the same floating point output from running your existing test subjects.
 
So as Paul mentioned, you can use a container, a virtual machine (VM) or any virtualization scheme to run FS 5.1 on am older version of the OS, and host the container, VM, etc. on Ubuntu 18.   Ubuntu Linux has its own built-in virtualization called QEMU.   I would at least start with whatever OS you previously ran FS 5.1 on as the reference..
 
- R.

 

On Oct 5, 2022, at 14:36, Leema_Murali@eisai.com wrote:
 
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Hi Paul,
 
Thank you for your response. I did try running FreeSurfer inside a docker derived from Ubuntu 16.04. Now there is no license invalid error. But I’m facing another error with regard to Segmentation. Please find the below screenshot.
 
<image002.png>
 
Thank you,
Leema
 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Wighton, Paul
Sent: Wednesday, October 5, 2022 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] Error while testing FS version 5.1
 
Hi Leema,
 
This is a known issue.  It has to do with the behaviour of the crypt() function provided by glibc, which has changed in more recent versions of ubuntu.  We don't have a solution for it at this time, unfortunately.
 
If you downgrade to ubuntu version 16.04 (glibc v2.23) the license mechanism should work, or you could upgrade your version of FreeSurfer.  If neither of those options are possible, you could run FreeSurfer inside a docker or singularity container derived from ubuntu 16.04.
 
-Paul
 
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Leema_Murali@eisai.com<Leema_Murali@eisai.com>
Sent: Wednesday, October 5, 2022 8:43 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FW: Error while testing FS version 5.1
 
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Hello FreeSurfer Developers,
 
I’m trying to use Freesurfer version 5.1 for my work. I get errors based on invalid license even though I have provided the right license within $FREESURFER_HOME/.license
 
Is there a specific way to define the license file for 5.1 version. I have been using the latest version before and I had just added the license..txt with $FREESURFER_HOME.
 
Please can anyone help me to troubleshoot this  issue..
 
Platform: Ubuntu 18.04
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
recon-all.log: see attached
 
<image003.png>
 
Looking forward for you reply.
 
Thank you,
Leema


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