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....@gmail.com
<mailto:rudolph....@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>
>
>
>
> _______________________________________________
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<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: rudo...@nmr.mgh.harvard.edu
<mailto:rudo...@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
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@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
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.
