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.

  • Installation instructions for the Connectome mapper 3 BIDS App are found in Installation.

  • Installation instructions for the Connectome mapper 3 BIDS App Manager are found in Installation.

Make sure that you have installed the following prerequisites.


On Mac and Windows, if you want to track the carbon emission incurred by the processing with the --track_carbon_footprint option flag, you will need to install in addition the Intel Power Gadget tool available here.

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

  • Download and extract the latest release (v3.1.0) of the BIDS App:

$ docker pull sebastientourbier/connectomemapper-bidsapp:v3.1.0


This can take some time depending on your connection speed and your machine. The docker image of the BIDSApp has a compressed size of 6.28 GB on DockerHub and should take 17.6 GB of space on your machine after download and extraction.

  • To display all docker images available:

    $ docker images

    You should see the docker image “connectomemapper-bidsapp” with tag “v3.1.0” 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)


  • Download the Python 3 installer of miniconda3 corresponding to your 32/64bits MacOSX/Linux/Win system and install it following the instructions at


The installation of the Connectome Mapper 3, including cmpbidsappmanager, consists of the creation of conda environment with all python dependencies installed, and the installation of connectomemapper via the Python Package Index (PyPI) as follows:

  • Download the appropriate environment.yml / environment_macosx.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 (

  • Open a terminal.

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

    $ conda env create -f /path/to/downloaded/conda/environment[_macosx].yml


    This can take some time depending on your connection speed and your machine. It should take around 2.8GB of space on your machine.

  • Activate the conda environment:

    $ source activate py39cmp-gui


$ conda activate py39cmp-gui
  • Install finally the latest released version of Connectome Mapper 3 with the Python Package Index (PyPI) using pip:

    (py39cmp-gui)$ pip install connectomemapper
  • You are ready to use the Connectome Mapper 3 (1) via its Graphical User Interface (GUI) aka CMP BIDS App Manager (See Graphical User Interface for the user guide), (2) via its python connectomemapper3_docker and connectomemapper3_singularity wrappers (See With the wrappers for commandline usage), or (3) by interacting directly with the Docker / Singularity Engine (See With the Docker / Singularity Engine 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 running pip install connectomemapper==v3.X.Y.


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.