Installation Instruction for Users

Warning

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

Make sure that you have installed the following prerequisites.

The Connectome Mapper 3 BIDSApp

Prerequisites

  • Installed Docker Engine corresponding to your system:

    • For Ubuntu 14.04/16.04/18.04, follow the instructions from the web page:

      $ firefox https://docs.docker.com/install/linux/docker-ce/ubuntu/
      
    • For Mac OSX (>=10.10.3), get the .dmg installer from the web page:

      $ firefox https://store.docker.com/editions/community/docker-ce-desktop-mac
      
    • For Windows (>=10), get the installer from the web page:

      $ firefox https://store.docker.com/editions/community/docker-ce-desktop-windows
      

Note

Connectome Mapper 3 BIDSApp has been tested only on Ubuntu and MacOSX. For Windows users, it might be required to make few patches in the Dockerfile.

  • Docker managed 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
      

Manual installation

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 of the BIDS App:

    $ docker pull sebastientourbier/connectomemapper-bidsapp:3.0.0-beta
    
  • To display all docker images available:

    $ docker images
    

You should see the docker image “connectomemapper-bidsapp” with tag “3.0.0-beta” is now available.

The Connectome Mapper 3 BIDSApp Manager (GUI)

Prerequisites

  • Installed miniconda2 (Python 2.7) from the web page:

    $ firefox https://conda.io/miniconda.html
    

    Download the Python 2.7 installer corresponding to your 32/64bits MacOSX/Linux/Win system.

Manual installation

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:

    $ cd <INSTALLATION DIRECTORY>
    
  • Clone the source code repository:

    $ git clone git@bitbucket.org:sinergiaconsortium/connectomemapper3.git connectomemapper3
    
  • Create a miniconda2 environment where all python dependencies will be installed, this by using the spec list “conda_packages_list.txt” provided by the repository:

    $ conda env create -f connectomemapper3/environment.yml
    
  • Activate the conda environment:

    $ source activate py27cmp
    

    or

    $ conda activate py27cmp

  • Install the Connectome Mapper BIDS App Manager from the Bash Shell using following commands:

    (py27cmp)$ cd connectomemapper3/
    (py27cmp)$ python setup_gui.py install
    
  • You are ready to use the Connectome Mapper 3 BIDS App Manager

Help/Questions

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.