[Neurodebian-users] Many questions regarding FSL

[Jonathan Berrebi]

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
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