[Neurodebian-users] Many questions regarding FSL

[Benjamin Kay]

A few points:

1. There is no reason to compile FSL or download binaries from the FSL 
website. The Debian package for FSL has a history of being up-to-date, and the 
FSL package isn't crippled like the AFNI package is.

2. You don't necessarily need the Neurodebian repository. FSL has an official 
debian package.

3. Do 'apt-cache search ^fsl'. Note that there are separate packages for 
fslview, the atlases, etc.

4. Do 'dpkg -L fsl-4.1'. Note that, by default, binaries are installed to 
/usr/lib/fsl/4.1/ and symlinked to /usr/bin/fsl4.1-*. So, by default, to run 
'Glm' you would actually have to run 'fsl4.1-Glm'.

5. You can "fix" #4 each time you log in by running '. /etc/fsl/fsl.sh', as 
described in the README. You can "fix" this for all users by running:
sudo ln -s /etc/fsl/fsl.sh /etc/profile.d/fsl.sh
sudo sh -c "echo /usr/lib/fsl/4.1 > /etc/ld.so.conf.d/fsl.conf"

On Friday, March 16, 2012 08:12:53 Jonathan Berrebi wrote:
> Hi,
> 
> 
> I really enjoy using the neurodebian repositories on different versions of
> ubuntu.
> 
> 
> We would like to use FSL with most efficiency and I am still half a newbie
> in linux so I have some questions regarding FSL.
> 
> 
> * There are three ways of installing FSL. The first is installing the
> binaries from the website of FSL which is easy. The second is to compile
> the source from FSL website and that would be ok if it was possible to
> first compile  GCC 4.1 or 4.2 (harder to compile on debians because of the
> way libraries are placed in debian/ubuntu) to run on newer distributions
> of ubuntu (typically oneiric)...I am still blocked. The third would be to
> use the neurdebian repository, and "sudo apt-get install fsl" but then
> several questions come to me:
> 
> 
> 1 - where is fsl then installed? I have looked at previous threads and it
> looked like FSL should be installed under /usr/lib/fsl
> 
> 
> I got many links in return of the command, they were all pointing to
> /usr/lib/
> 
> Now I have deleted them and it is impossible to get them back.
> 
> ls -l /usr/bin/fsl4.1-fsl
> 
> but nothing under
> /usr/lib/
> 
> also nothing under
> 
> /usr/local/
> 
> /usr/local/share/
> 
> /usr/share/
> 
> The only thing "sudo apt-get install fsl" does is to create
> /etc/fsl/fsl.sh.
> 
> So I did sudo apt-get remove fsl
> and sudo apt-get --purge remove fsl
> 
> is still impossible to install fsl.
> 
> This is what I get from sudo apt-get install fsl:
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> The following NEW packages will be installed:
>   fsl
> 0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
> Need to get 18.4 kB of archives.
> After this operation, 41.0 kB of additional disk space will be used.
> Get:1 http://neuro.debian.net/debian/ oneiric/non-free fsl all
> 4.1.9-2~nd11.10+1 [18.4 kB] Fetched 18.4 kB in 0s (34.0 kB/s)
> Selecting previously deselected package fsl.
> (Reading database ... 341949 files and directories currently installed.)
> Unpacking fsl (from .../fsl_4.1.9-2~nd11.10+1_all.deb) ...
> Processing triggers for man-db ...
> Setting up fsl (4.1.9-2~nd11.10+1) ...
> 
> 2 - Are my problems due to an incorrect uninstall of fsl? In that case what
> should I do?
> 
> 3 -  I have more questions about if it would be better to do "sudo apt-get
> build-dep fsl" first and then "sudo apt-get -b source fsl" or if "install"
> is as good.
> 
> 4 - If I get all that then I could use your new package "condor"  for
> parallelising the jobs. But could I use "condor" for parallelising jobs
> run by manual installation (binaries, compiling) of FSL or should I modify
> anything?
> 
> I am sorry for all these questions but I hope this would help many
> neuro-debianer not always linux experts! :)
> 
> Thank you,
> 
> Jonathan Berrebi
> Karolinska Institute
> Stockholm Brain Institute
> Sweden