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Could I get the password for the Ubuntu virtual machine zip file? If you also have the license file to include as well, that would be great!

Thank you, Stacey

Stacey M. Schaefer, Ph.D. Center for Healthy Minds

University of Wisconsin-Madison

625 W Washington Ave

Madison WI 53703

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Tuesday, September 13, 2022 2:04 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 223, Issue 22

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Today's Topics:

1. Re: Follow Up License Freesurfer 5.3 Ubuntu (Wighton, Paul) 2. Re: Freesurfer: fs_install_mcr: Unzip command not found (Justina Lee) 3. Re: Follow Up License Freesurfer 5.3 Ubuntu (fsbuild) 4. Re: Freesurfer: fs_install_mcr: Unzip command not found (Wighton, Paul) 5. Re: Follow Up License Freesurfer 5.3 Ubuntu (Wighton, Paul) 6. Re: Freesurfer: fs_install_mcr: Unzip command not found (Justina Lee) 7. Re: Freesurfer: fs_install_mcr: Unzip command not found (Wighton, Paul) 8. Re: Freesurfer: fs_install_mcr: Unzip command not found (Justina Lee) 9. Re: Freesurfer: fs_install_mcr: Unzip command not found (Wighton, Paul) 10. Re: Freesurfer: fs_install_mcr: Unzip command not found (Justina Lee) 11. Re: Freesurfer: fs_install_mcr: Unzip command not found (Wighton, Paul)

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Message: 1 Date: Tue, 13 Sep 2022 17:28:39 +0000 From: "Wighton, Paul" PWIGHTON@mgh.harvard.edu Subject: Re: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: BN8PR04MB57952410B3C48F5F89851D4382479@BN8PR04MB5795.namprd04.prod.outlook.com

Content-Type: text/plain; charset="iso-8859-1"

Hi R?diger,

This is really interesting.. I'm able to reproduce this issue in a docker container. Anyone else who would like to reproduce or look into this issue can use the following containers

- The container `pwighton/freesurfer:5.3.0-HCP` is based off of ubuntu 16.04 (glibc v2.23) and everything works as expected in this container. - The container `pwighton/freesurfer:5.3.0-HCP-focal` is based off of ubuntu 20.04 (glib2 v2.31) and I am experiencing the same issue you describe. - The container `pwighton/freesurfer:7.3.2-focal` is based off of ubuntu 20.04 and has the latest version of FreeSurfer installed. Everything works as expected in this container.

So the issue seems to be some interaction between the v5.3 license checking code and the crypt() function provided by different versions of glibc, but that is just speculation at this point.

I'm sorry I don't have any solution for this at the moment. You mention you are using lmod, would it be possible to define LD_LIBRARY_PATH inside the FreeSurfer 5.3 module to point to an older version of glibc?

-Paul

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ludwig, R?diger r.ludwig@eni-g.de Sent: Tuesday, September 13, 2022 11:32 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Follow Up License Freesurfer 5.3 Ubuntu

Hello again,

I realized I might have missed some important information in my question about freesurfer 5.3 license files a few days ago:

We use Ubuntu 20 with lmod. FREESURFER_HOME is ''/opt/apps/freesurfer/5.3/'' for freesurfer 5.3

When we try ''mri_convert sample-001.mgz sample-001.nii.gz'' without a proper license file we get the Error: ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txt

After we copy the license file to the proper position we get: ERROR: Invalid FreeSurfer license key found in license file /opt/apps/freesurfer/5.3/license.txt

So the file is obviously read but rejected. We get the same result it with a brand new license file, and one that still works for freesurfer 5.3 on our CentOS 7 node. We do not have any problems reading the license file in freesurfer 7.2 or freesurfer 7.3

If you need any further information to help us, we am more than willing to provide that.

Thank you so much in advance

Ruediger

--- R?diger Ludwig (he/him) IT-Service European Neuroscience Institute A Joint Initiative of the University Medical Center G?ttingen and the Max Planck Society Grisebachstr. 5 37077 G?ttingen

Tel: +49 551-39 61308 Email: r.ludwig@eni-g.de Office: 0.051