Subscribe via RSS Feed

Installation procedure

We will use the APT (Advanced Packaging Tool) which install packages and manage dependencies automatically and take care of their configuration files while upgrading [see here for apt commands.]

Matlab Installation
  • Go on
  • Search for Matlab
  • Download the Licence file for the UCL Licence Manager
  • Download Matlab 2014a linux:
  • Download the licence network.lic

Run the Matlab Installer:

  • cd ~/Applications/MATLAB_dir
  • sudo ./install
  • The MathWorks Installer box will pop up. Full path for installation Folder: /usr/local/MATLAB/R2014a

  • Use the provided Installation Key
  • Use the Typical Installation
  • Licence file location to be provided: ~/Applications/MATLAB/network.lic
  • Check box ‘create symbolic link to matlab in /usr/local/bin’

In case Matlab doesn’t launch from any directory:

  • gedit ~/.bashrc
  • Create your alias: alias matlab=”/opt/matlab/R2013a/bin/matlab”

  • source ~/.bashrc
  • [an other solution for substitute users: sudo ln -s /opt/matlab/R2013a/bin/matlab matlab]
Matlab Toolbox for Dimensionality Reduction

[web site: Matlab toolbox for dimensionality reduction]

  • Download the ToolBox
  • Extract the files: tar -xvf drtoolbox.tar.gz
  • Copy this toolbox in /usr/local/MATLAB/R2014a/toolbox/
  • Start matlab with sudo matlab
  • Select ‘Set path…’ from the File menu. Click the ‘Add with subfolders…’ button, select the folder /usr/local/MATLAB/R2014a/toolbox/drtoolbox in the file dialog, and press Open. Subsequently, press the Save button in order to save your changes to the Matlab search path. The toolbox is now installed.
Matlab GE Toolbox:pettoolbox and motiontoolbox
  • Download the GEToolBox
  • open matlab
  • Select ‘Set path…’ from the File menu. Click the ‘Add with subfolders…’ button, select the folder …/PTBREL2.0_UCL/pettoolbox and …/PTBREL2.0_UCL/motiontoolbox in the file dialog, and press Open. Subsequently, press the Save button in order to save your changes to the Matlab search path. The toolbox is now installed.
  • If you do not already have one, create a startup.m in your MATLAB directory with the following command lines
  • pettoolboxpath=’/home/…./PTBREL2.0_UCL/pettoolbox’; % adjust this to wherever you put the pettoolbox

  • Open Matlab and type: startup
AMIDE: Amide’s a Medical Imaging Data Examiner

First we need to install a few packages before installing Amide. These packages will allow us to open DICOM format data [see here for the list of packages that you might need.]

1) XMEDCON installation:

  • Download xmedcon-0.13.0.tar.gz in ~/Applications/XMEDCON/
  • cd ~/Applications/XMEDCON/xmedcon-0.13.0
  • ./configure
  • make
  • sudo make install
  • 2) GSL installation:

  • Download gsl-1.16.tar.gz in ~/Applications/GSL/
  • cd ~/Applications/GSL/gsl-1.16
  • ./configure –prefix=/usr –disable-static [see here
  • make
  • sudo make install
  • 3) add PATHS in your ~/.bashrc:

  • gedit ~/.bashrc &
  • export PATH=$PATH:/usr/local/bin:/usr/local/xmedcon/bin
  • source ~/.bashrc
  • 4) Install these packages:

    sudo apt-get install dcmtk
    sudo apt-get install intltool
    sudo apt-get install libgtk2.0-dev
    sudo apt-get install libxml2-dev
    sudo apt-get install libgnomecanvas2-dev
    sudo apt-get install libgconf2-dev
    sudo apt-get install libgnomevfs2-dev
    sudo apt-get install gnome-doc-utils
    sudo apt-get install libdcmtk-dev

    5) Install AMIDE now:
    Download the source code [here].

  • Download Amide amide-1.0.5.tgz in ~/Applications/AMIDE/
  • Extract all files in ~/Applications/AMIDE/:

  • You might get the following warning messages:
    Gtk-WARNING **: Attempting to store changes into `/root/.local/share/recently-used.xbel’, but failed: Failed to create file ‘/root/.local/share/recently-used.xbel.ZHBB8W’: No such file or directory
    Gtk-WARNING **: Attempting to set the permissions of `/root/.local/share/recently-used.xbel’, but failed: No such file or directory

    The error shows that Gtk attempting to get read/write access and try to save (temporary) files in the directory. This is not working because this folder is missing, see the last part of the first line of the error: No such file or directory. The solution is to manually create this folder: sudo mkdir -p /root/.local/share

  • cd ~/Applications/AMIDE/amide-1.0.5

  • configure:3629: checking whether the C compiler works
    configure:3651: gcc conftest.c >&5
    /usr/bin/ld: cannot find crt1.o: No such file or directory

    The compiler was not properly installed: sudo apt-get install g++

    Which gcc version:
    gcc -v

    Which GTK+ version:
    dpkg -l libgtk[0-9]* | grep ^i
    find /usr/lib -name *libgtk*

    sudo make install

    ITK (Insight Tool Kit) Installation
  • mkdir ~/Applications/InsightToolKit
  • cd ~/Applications/InsightToolKit
  • git clone
  • sudo apt-get install cmake-curses-gui
  • sudo apt-get install build-essential
  • mkdir ITK-build
  • cd ITK-build
  • ccmake ../ITK
  • [Press [c] to ‘Configure’]

  • Module_ITKReview should be ON!
  • [this is needed by the INMTools because the ITKGeometryImageFilter is in the ITKReview module]

  • make
  • sudo make install
  • INMTools

    The following packages are needed:

  • sudo apt-get install zenity
  • sudo apt-get install texlive-latex-base
  • sudo apt-get install pgf
  • sudo apt-get install texlive-pictures
  • sudo apt-get install texlive-extra-utils
  • cd ~/Applications
  • git clone -b vcuplov
  • cd ~/Applications/INMTools
  • mkdir build
  • mkdir install
  • cd build
  • ccmake ../src
    CMAKE_INSTALL_PREFIX /home/…/Applications/INMTools/install
    ITK_DIR /usr/local/lib/cmake/ITK-4.7

  • make -j
  • mkdir ~/Applications/GIF
  • cd ~/Applications/GIF
  • sudo apt-get install qt4-qmake qt-sdk (440MB!)
  • copy the latest tarball from Jorge and latest CMakeLists.txt in GIF/Source_INM
  • mkdir Build_INM
  • mkdir Install_INM
  • cd Build_INM
  • ccmake ../Source_INM
  • [Press [c] to ‘Configure’]

  • make -j
  • add PATHS in your ~/.bashrc:

  • gedit ~/.bashrc &
  • export PATH=$PATH:/home/…/GIF/Install_INM/bin
  • export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/…/GIF/Install_INM/lib
  • source ~/.bashrc
  • PVC
  • cd ~/Applications
  • git clone
  • cd ~/Applications/PETPVC
  • mkdir PETPVC-build
  • cd PETPVC-build
  • ccmake ../

  • /usr/local [or an other place that you would have created, for example: ~/Applications/PETPVC/PETPVC-install]

  • make -j
  • sudo make install
  • [sudo if you install in /usr/local]

    GATE Installation (and CLHEP, ROOT, GEANT4)

    * CLHEP, ROOT and GEANT4 are needed.
    * git clone
    * rename opengate-public as gate_v6.2
    * create gate.6.2-build and gate.6.2-install
    * in gate.6.2-build: ccmake ../gate_v6.2
    * the install directory should be /PATHTOGATE/gate.6.2-install
    * make -j8 and make install

    ROOT Installation

    cd root
    git tag -l
    git checkout -b v5-34-08 v5-34-08


    add the following in your bashrc:
    export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/home/uclh-vesna-mint/Applications/root/lib

    GEANT4 Installation
    * Create two directories to build and install GEANT4 (geant4.9.5.p02-build and geant4.9.5.p02-install)
    * In the build directory: ccmake ../geant4.9.5.p02
    * Configure
    * Add paths to CLHEP_LIBRARY to point to the
    * Needs the following packages (sudo apt-get install libxt-dev libibtk-dev freeglut3-dev libxmu-dev qt4-dev-tools)
    * make -jN (N is the number of processor(s) in your PC)
    * make install

    NiftySEG Installation

    Look at the latest code at

    Clicking on History shows that [r162] has been modified on 2014-04-15 16:20:17

    sudo apt-get install subversion
    svn checkout niftyseg-code
    >>>>> Checked out revision 162.

    * Create 2 directories: niftyseg-build and niftyseg-install at the same level as the actual source code niftyseg-code
    * cd niftyseg-build
    * ccmake ../niftyseg-code
    * Press [c] to ‘Configure’

    * Press [g] to ‘Generate and Exit’
    * make
    * make install

    Working on the UCL cluster Legion

    * ssh -Y

    How to load Matlab:
    * module avail
    * module load compilers/gnu/4.6.3
    * module load matlab/full/r2013a/default