Ubuntu 12.04 for MR scientists

Most MR scientists need to use Linux software, but end up using Exchange or some kind of virtualization to run it. This guide will provide a step by step installation of the most common MR software (freesurfer, fsl) for the Ubuntu 12.04.1 LTS distribution.

lines written in bold represent commands to be written in the terminal (simply copy/paste to the terminal)
to open a terminal: press CTRL + ALT + T

This installation was done on 11 Jan 2013

sudo apt-get update

To install cinnamon (OPTIONAL, alternative to the hideous Unity):
sudo add-apt-repository ppa:gwendal-lebihan-dev/cinnamon-stable
sudo apt-get update
sudo apt-get install cinnamon

(version 1.6.7 installed)
need to logout and login again with the cinnamon desktop selected


To install GIMP
sudo apt-get install gimp
(2.6.12 installed)

To install g++ compiler:
sudo apt-get install g++
(4.6.3 installed)

To install dropbox:
https://www.dropbox.com/install?os=lnx
and select Ubuntu 64 bit
(1.4.0 installed)

To install virtual box:
sudo apt-get install virtualbox
(4.1.12. installed)

To install VLC, avidemux, ffmpeg:
sudo apt-get install vlc
(2.0.3 installed)
sudo apt-get install avidemux
(2.5.4 installed)
sudo apt-get install ffmpeg
(0.8.4 installed)


Intel Compiler (13.0.1)
Intel® Parallel Studio XE 2013 for Linux*

couldn’t recognize the ia32 libs... better dowload pure 64 bit and not install ia32-libs
these instructions might have to be changed for newer versions

prerequisites for the full installation:
sudo apt-get install build-essential gcc-multilib rpm ia32-libs openjdk-6-jre-headless

extract the tar.gz and execute with
sudo ./install.sh

add these lines to .bashrc
source /opt/intel/vtune_amplifier_xe_2013/amplxe-vars.sh
source /opt/intel/inspector_xe_2013/inspxe-vars.sh
source /opt/intel/advisor_xe_2013/advixe-vars.sh
source /opt/intel/bin/compilervars.sh intel64

- To start the graphical user interface: amplxe-gui
- To start the graphical user interface: inspxe-gui
- To start the graphical user interface: advixe-gui


Matlab (2012a)

to fix the error
lib64/libc.so.6: not found
sudo ln -s /lib/x86_64-linux-gnu/libc.so.6 /lib64/libc.so.6

to fix the error /usr/local/MATLAB/R2012a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
sudo rm /usr/local/MATLAB/R2012a/sys/os/glnxa64/libstdc++.so.6
sudo ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /usr/local/MATLAB/R2012a/sys/os/glnxa64/libstdc++.so.6


FSL (5.0.2)

download the CentOS5 64-bit version from (bottom of page)
http://www.fmrib.ox.ac.uk/fsldownloads/

extract the installer script in ./fsl/doc/fsl/fsl_installer.sh
copy it to the same folder as the compressed tar.gz and run it:
sh fsl_installer.sh

then, add the following lines to the beginning of the .bashrc file

FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
PATH=${FSLDIR}/bin:${PATH}
export FSLDIR PATH

possible error:
/usr/local/fsl/bin/fslview_bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory
to avoid this error:
sudo apt-get install libjpeg62



Freesurfer (5.1.0)

download the latest version from ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz
extract the tar.gz file to /usr/local
add the following lines to the .bashrc file

export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh


ITK-SNAP (2.4.0)

http://downloads.sourceforge.net/project/itk-snap/itk-snap/2.4.0/itksnap-2.4.0-20121121-Linux-x86_64.tar.gz
and extract to /opt



Paraview (3.98)

Paraview does not need to be compiled. To download it, get the Linux 64 version from
http://www.paraview.org/
extract the tar.gz and move the extracted folder to /opt