Your best bet I fear might be to try and build FreeSurfer yourself on your specific distro of Ubuntu.
https://surfer.nmr.mgh.harvard.edu/fswiki/ReadOnlyCVS
While not impossible (we have done this), it does require some detailed knowledge of Linux in general and Ubuntu in particular as you will have to resolve all the required dependencies and adapt the build commands accordingly. Still compiling your own FreeSurfer will mean that there will be no library version conflicts which is what most likely will happen in the case of running the CentOS version on Ubuntu. And once you compile your own version from source, it will run on all your cluster nodes w/o issues.
If you use a binary version (like the CentOS build), you would have to execute the instructions I presented (i.e. the synlinks) on *every* cluster node.
CentOS, like Ubuntu, is a distribution of Linux. That means that they are all Linux, but differ in the type and versions of various applications and libraries. CentOS is typically more conservative and generally has older versions of libraries than Ubuntu. Since the distributed FreeSurfer is dynamically compiled against the installation of CentOS at the NMR, it expects very specific version numbers on various system libraries. Usually these versions are no longer bundled on other more agile distributions like Ubuntu. Thankfully, it is usually sufficient to "trick" the various CentOS FreeSurfer apps on Ubuntu by simply making a symbolic from an existing system library to the name/version the FreeSurfer app expects. This is a "hack" and not guaranteed to always work. Having said that, the CentOS build of FreeSurfer works fine on Ubuntu 14.04+ using the link commands I listed earlier.
All you need to do is Just download the CentOS version and try those link command. Although, I'm not 100% sure about Ubuntu 12.04. As I said, those link instructions are valid for Ubuntu 14.04 and above, so your mileage might vary. Also, you will need to have root access on each machine that you want to run those commands on. In the case of a cluster, this would mean running those command (as sudo) on *all* cluster nodes. Unless you are the cluster administrator, this might be difficult (or impossible) to do.
It might be that the best option for you is to roll your own FreeSurfer by compiling it from source in your environment.
HTH -=R
On 10/02/2015 10:53 AM, Bruno LAD wrote:
Thanks for you reply, Rudolph.
We have a cluster environment in our university, and the best Ubuntu version to us for now is Ubuntu 12.04 (in a closest future we will update to a newer version, but not now...).
In the download page there is only FreeSurfer for CentOS, Mac and a Virtual Machine of Xubuntu, but not to Ubuntu. ( https://surfer.nmr.mgh.harvard.edu/fswiki/Download )
I couldn't find the binaries to compile, too. I've looked at ( http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ ).
To me the best choice is the binaries or the compiled source (not apt, yum, etc..) , because we put all applications in "/usr/local".
Could you help me to find one of these options to download?
Thanks again
-- Att, Bruno Bragança Mendes Laboratório de Alto Desempenho LAD/PUCRS Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120 +55 51 33538001 tel:%2B55%2051%2033538001
2015-10-01 18:40 GMT-03:00 Rudolph Pienaar <rudolph.nmr@gmail.com mailto:rudolph.nmr@gmail.com>:
Yes, FreeSurfer can be installed on Ubuntu without any issues. There is also no functional difference between Ubuntu server and Ubuntu Desktop. Do you have a compelling reason for wanting to use Ubuntu 12.04? It was released in 2012 and is rather ancient in Ubuntu terms. The current version of Ubuntu is 15.04 and in fact 15.10 is about to released in three weeks. I'd strongly recommend you update to a modern Ubuntu. Having said that, certainly on Ubuntu 14.04 and above, once installed you need to simply symlink some libraries since the versions FreeSurfer has been compiled against are depreciated on Ubuntu 14.04 and later. In a terminal, simply type (make sure that each command is on a single line -- the email formatting might have split it in two): For Trackvis and dtk sudo ln -s /usr/lib/x86_64-linux-gnu/libtiff.so.5 /usr/lib/x86_64-linux-gnu/libtiff.so.3 sudo ln -s /usr/lib/x86_64-linux-gnu/libmng.so.2.0.2 /usr/lib/x86_64-linux-gnu/libmng.so.1 For FreeSurfer: sudo ln -s /usr/lib/x86_64-linux-gnu/libvnl_algo.so /usr/lib/x86_64-linux-gnu/libvnl_algo.so.1.14 sudo ln -s /usr/lib/x86_64-linux-gnu/libvnl.so /usr/lib/x86_64-linux-gnu/libvnl.so.1.14 sudo ln -s /usr/lib/x86_64-linux-gnu/libv3p_netlib.so /usr/lib/x86_64-linux-gnu/libv3p_netlib.so.1.14 HTH -=R On 10/1/15 15:58 , Bruno LAD wrote: > Hi, could you help me please, because a couldn't find the answer for my > question in the wiki. > > Can FreeSurfer be installed on ubuntu server 12.04? How can I do it, if > it's possible? > > > Thank you. > > -- > Best Regards > Bruno Bragança Mendes > Laboratório de Alto Desempenho LAD/PUCRS > Av. Ipiranga, 6681 - Prédio 32 Térreo - Sala 120 > +55 51 33538001 <tel:%2B55%2051%2033538001> <tel:%2B55%2051%2033538001> > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph@nmr.mgh.harvard.edu <mailto:rudolph@nmr.mgh.harvard.edu> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer