External Email - Use Caution
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 https://secure-web.cisco.com/1OwyjJ1rTGJ_2TzRiqQk1sQK1uz8hOtzOw5oFxzSzAGWIbR...; 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: External Email - Use Caution 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, PaulSent: Wednesday, October 5, 2022 11:30 AMTo: freesurfer@nmr.mgh.harvard.eduSubject: [EXTERNAL] Re: [Freesurfer] Error while testing FS version 5.1 Security First: External email, use caution clicking links or opening attachments.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 AMTo: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] FW: Error while testing FS version 5.1 External Email - Use Caution 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 18.04Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0recon-all.log: see attached <image003.png> Looking forward for you reply. Thank you,Leema[This e-mail message may contain privileged, confidential and/or proprietary information of Eisai. If you believe that it has been sent to you in error, please contact the sender immediately and delete the message including any attachments, without copying, using, or distributing any of the information contained therein. This e-mail message should not be interpreted to include a digital or electronic signature that can be used to authenticate an agreement, contract or other legal document, nor to reflect an intention to be bound to any legally-binding agreement or contract.] _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer