New release
  CMP v2.1.0-beta

  •  •Preprocessing: Motion and eddy current correction
  •  •Custom atlases
  •  •New reconstuction schemes: CSD, ballstick, multitensor...
  •  •Probabilistic tractography: Camino, MRtrix, FSL probtrackx
  •  •Global tractography: Gibbs-tracker

Table Of Contents

Previous topic

Connectome Mapper

Next topic

Download Instruction

This Page

Installation Instruction


This software is for research purposes only and shall not be used for any clinical use. This software has not been reviewed or approved by the Food and Drug Administration or equivalent authority, and is for non-clinical, IRB-approved Research Use Only. In no event shall data or images generated through the use of the Software be used in the provision of patient care.

Installation instructions for the Connectome mapper are found in Manual installation (all distributions).

But before, make sure that you have installed the following prerequisites.


  • Installed version of Diffusion Toolkit:


    Diffusion toolkit executables (‘dtk’, ‘odf_recon’, ...) should be in the $PATH environmental variable, and $DSI_PATH needs to be set to the folder containing the diffusion matrices.

  • Installed and configured version of Freesurfer (


    $FREESURFER_HOME should have been declared and the Freesurfer setup script should have been sourced as described here:

  • Installed and configured version of FSL ( Installation can be done through the NeuroDebian repository:

    sudo apt-get install fsl fslview fslview-doc

    $FSLDIR should have been declared and the FSL setup script should have been sourced as described under “Installation” here:

  • Installed version of MRTrix:

  • Installed version of Camino:

  • Installed versions of Dipy and Camino-Trackvis converter:

    sudo apt-get install python-dipy
  • Installed version of the gibbs tracker:

  • At this point, make sure that you have setup the environment variables correctly for the external packages such as Freesurfer and Diffusion Toolkit (The FSL environment variables should be set automatically when installing FSL as described above). You should have the environment variables: FREESURFER_HOME, DTDIR, DSI_DIR and FSLDIR. You can check this if you enter in the bash shell (terminal), they should give you the correct path to your packages:

    echo $FSLDIR
    echo $DTDIR

    In case, you can update your bash configuration to automatically declare the variables:

    gedit /home/username/.bashrc

    It should contain something similar as (adapted to your installation paths):

    # FREESURFER configuration
    export FREESURFER_HOME="/usr/share/freesurfer"
    source "${FREESURFER_HOME}/"
    # DIFFUSION TOOLKIT configuration
    export DTDIR="/usr/share/dtk"
    export DSI_PATH="/usr/share/dtk/matrices"
    export PATH="${DTDIR}:${PATH}"
    # FSL configuration
    source /etc/fsl/4.1/
    # Camino to trackvis
    export CAMINO2TRK=/usr/share/camino-trackvis-
    # Update PATH
    export PATH="${DTDIR}:${CAMINO2TRK}:${PATH}"

Manual installation (all distributions)

Manual installation is divided between the Python libraries needed by the Connectome Mapper and the CMTKlib and the libraries needed by the DTB binaries. Files for manual installation is the zipped archive of the Connectome Mapper.

  • Download the zipped archive from here

  • As we will use easy_install in order to have access to the latest libraries even on older systems the python-setuptools package is needed. Ipython is strongly recommended for debugging purposes. Debian/Ubuntu command:

    sudo apt-get install python-setuptools ipython
  • Python libraries needed: traits, traitsui, pyface, nibabel, numpy, networkx, scipy. Easy_install command:

    sudo easy_install traits traitsui pyface nibabel numpy networkx scipy nose
  • Install our forked version of Nipype ( For now, we require a modified vesion Nipype interfaces that is available on our Github repository ( To install it clone to your machine the nipype fork by typing git clone git:// from your home folder, and run the install script with sudo python install. You will have to remove already installed versions of nipype if they were installed through apt-get (installation location: /usr/lib/pyshared) as it will take precedence over versions installed through the script.

  • Libraries needed by the DTB binaries: boost (module program-options), nifti, blitz: sudo apt-get install libboost-program-options-dev libnifti-dev libblitz0-dev

  • Extract the source code and install the Connectome Mapper from the Bash Shell using following commands:

    tar xzf <cmp-release>.tar.gz
    cd <cmp-release>/
    sudo python install


If you run into any problems or have any questions, you can post to the CMTK-users group. Code bugs can be reported by creating a “New Issue” on the github repository.