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.
The Connectome Mapper 3 BIDSApp¶
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
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
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 (v3.0.0-RC2) of the BIDS App:
$ docker pull sebastientourbier/connectomemapper-bidsapp:v3.0.0-RC2
To display all docker images available:
$ docker images
You should see the docker image “connectomemapper-bidsapp” with tag “v3.0.0-RC2” 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)¶
Installed miniconda3 (Python 3) from the web page:
$ firefox https://conda.io/miniconda.html
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:
$ cd <INSTALLATION DIRECTORY>
Clone the source code repository:
$ git clone https://github.com/connectomicslab/connectomemapper3.git connectomemapper3
Create a branch and checkout the code corresponding to this version release:
$ git fetch $ git checkout tags/v3.0.0-RC2 -b v3.0.0-RC2
Create a miniconda3 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
It seems there is no conda package for
git-annex available on Mac.
Git-annex should be installed on MacOSX using brew (https://brew.sh/index_fr) i.e.
brew install git-annex.
git-annex is only necessary if you wish to use BIDS datasets managed by Datalad (https://www.datalad.org/), a very experimental feature. For the moment, I would not recommend to use right now as it has been a long time it has not been tested.
So, you can without any problem delete or comment the line
- git-annex=7.20190219 and all other lines related to datalad packages in the
environment.yml and it should then work!
Activate the conda environment:
$ source activate py37cmp-gui
$ conda activate py37cmp-gui
Install the Connectome Mapper BIDS App Manager from the Bash Shell using following commands:
(py37cmp-gui)$ cd connectomemapper3/ (py37cmp-gui)$ python setup_gui.py install
You are ready to use the Connectome Mapper 3 BIDS App Manager. See the dedicated user guide.