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Installation Instructions for Users


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.

The Connectome Mapper 3 is composed of a Docker image, namely the Connectome Mapper 3 BIDS App, and a Python Graphical User Interface, namely the Connectome Mapper BIDS App Manager.

Make sure that you have installed the following prerequisites.

The Connectome Mapper 3 BIDSApp



Connectome Mapper 3 BIDSApp has been tested only on Ubuntu and MacOSX. In principles, it should also run on Windows but it might require a few patches to make it work.

  • Manage Docker as a non-root user

    • Open a terminal

    • Create the docker group:

      $ sudo groupadd docker
    • Add the current user to the docker group:

      $ sudo usermod -G docker -a $USER
    • Reboot

      After reboot, test if docker is managed as non-root:

      $ docker run hello-world


Installation of the Connectome Mapper 3 has been facilitated through the distribution of a BIDSApp relying on the Docker software container technology.

  • Open a terminal

  • Get the latest release (|release|) of the BIDS App:

    $ docker pull sebastientourbier/connectomemapper-bidsapp:|release|
  • To display all docker images available:

    $ docker images

You should see the docker image "connectomemapper-bidsapp" with tag "|release|" is now available.

  • You are ready to use the Connectome Mapper 3 BIDS App from the terminal. See its commandline usage.

The Connectome Mapper 3 BIDSApp Manager (GUI)


  • Install miniconda3 (Python 3) from

    Download the Python 3 installer corresponding to your 32/64bits MacOSX/Linux/Win system.


The installation of the Connectome Mapper 3 BIDS App Manager (CMPBIDSAPPManager) consists of a clone of the source code repository, the creation of conda environment with all python dependencies installed, and eventually the installation of the CMPBIDSAPPManager itself, as follows:

  • Open a terminal

  • Go to the folder in which you would like to clone the source code repository:

  • Clone the source code repository:

    $ git clone connectomemapper3
  • Create a branch and checkout the code corresponding to this version release:

    $ cd connectomemapper3
    $ git fetch
    $ git checkout tags/|release| -b |release|


If a few bugs related to the Graphical User Interface were fixed after releasing the version, you might want to use the code at its latest version on the master branch (i.e. git checkout master).

  • Create a miniconda3 environment where all python dependencies will be installed:

    $ cd connectomemapper3
    $ conda env create -f conda/environment.yml


It seems there is no conda package for git-annex available on Mac. For your convenience, we created an additional conda/environment_macosx.yml miniconda3 environment where the line - git-annex=XXXXXXX has been removed. Git-annex should be installed on MacOSX using brew i.e. brew install git-annex. See for more details.

Note that git-annex is only necessary if you wish to use BIDS datasets managed by Datalad (

  • Activate the conda environment:

    $ source activate py37cmp-gui


    $ conda activate py37cmp-gui
  • Install the Connectome Mapper BIDS App Manager from the Bash Shell using pip:

    (py37cmp-gui)$ cd connectomemapper3/
    (py37cmp-gui)$ pip install .
  • You are ready to use the Connectome Mapper 3 (1) via its Graphical User Interface (GUI) aka CMP BIDS App Manager (See :ref:`guiusage` for the user guide), (2) via its python connectomemapper3_docker and connectomemapper3_singularity wrappers (See :ref:`wrapperusage` for commandline usage), or (3) by interacting directly with the Docker / Singularity Engine (See :ref:`<containerusage` for commandline usage).

In the future

If you wish to update Connectome Mapper 3 and the Connectome Mapper 3 BIDS App Manager, this could be easily done by (1) updating the git repository to a new tag with git fetch and git checkout tags/|release| -b |release| and (2) running pip 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 source code repository.