Installation Instructions 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 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

Prerequisites

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

Note

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

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) of the BIDS App:

$ docker pull sebastientourbier/connectomemapper-bidsapp:v3.0.0

To display all docker images available:
```
$ docker images
```

You should see the docker image “connectomemapper-bidsapp” with tag “v3.0.0” 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)

Prerequisites

Install miniconda3 (Python 3) from https://conda.io/miniconda.html

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

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 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 -b v3.0.0
```

Note

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
```

Important

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 https://git-annex.branchable.com/install/ for more details.

Note that 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

or:

$ 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 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 <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 ..

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.