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¶
Install Docker Engine depending of your system:
For Ubuntu 14.04/16.04/18.04, follow the instructions at https://docs.docker.com/install/linux/docker-ce/ubuntu/
For Mac OSX (>=10.10.3), get the .dmg installer at https://store.docker.com/editions/community/docker-ce-desktop-mac
For Windows (>=10), get the installer at https://store.docker.com/editions/community/docker-ce-desktop-windows
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
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-RC4) of the BIDS App:
$ docker pull sebastientourbier/connectomemapper-bidsapp:v3.0.0-RC4
To display all docker images available:
$ docker images
You should see the docker image “connectomemapper-bidsapp” with tag “v3.0.0-RC4” 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 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:
$ cd connectomemapper3 $ git fetch $ git checkout tags/v3.0.0-RC4 -b v3.0.0-RC4
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 environment.yml
It seems there is no conda package for
git-annex available on Mac.
For your convenience, we created an additional
miniconda3 environment where the line
- git-annex=XXXXXXX has been removed.
Git-annex should be installed on MacOSX using brew
brew install git-annex. See https://git-annex.branchable.com/install/ for more details.
git-annex is only necessary if you wish to use BIDS datasets managed by Datalad (https://www.datalad.org/).
Activate the conda environment:
$ source activate py37cmp-gui
$ conda activate py37cmp-gui
Install the Connectome Mapper BIDS App Manager from the Bash Shell using
(py37cmp-gui)$ cd connectomemapper3/ (py37cmp-gui)$ pip install .
You are ready to use the Connectome Mapper 3 BIDS App Manager. See the dedicated user guide.