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.

Installation of the MIALSRTK processing tools and pipelines has been facilitated through the distribution of a BIDSApp relying on the Docker and Singularity software container technologies, so in order to run MIALSRTK, Docker or Singularity must be installed (see instructions in Prerequisites).

Once Docker or Singularity is installed, the recommended way to run MIALSRTK is to use the corresponding mialsuperresolutiontoolkit wrapper. Installation instructions for the wrappers can be found in Wrappers Installation, which requires as prerequisites having Python3 (see Prerequisites) installed and an Internet connection.

If you need a finer control over the Docker/Singularity container execution, or you feel comfortable with the Docker/Singularity Engine, download instructions for the MIALSRTK BIDS App can be found in MIALSRTK Container Image Download.

Prerequisites

To run MIALSRTK you will need to have either Docker or Singularity containerization engine installed.

While Docker enables MIALSRTK to be run on all major operating systems where you have root privileges, Singularity allows you to run MIALSRTK on Linux systems where you might not have root privileges such as a High Performance Computing cluster.

Please check https://docs.docker.com/get-started/overview/ and https://sylabs.io/guides/3.7/user-guide/introduction.html If you want to learn more about Docker and Singularity.

Installation of Docker Engine

Install Docker Engine corresponding to your system:
- For Ubuntu 14.04/16.04/18.04, follow the instructions from https://docs.docker.com/install/linux/docker-ce/ubuntu/
- For Mac OSX (>=10.10.3), get the .dmg installer from https://store.docker.com/editions/community/docker-ce-desktop-mac
- For Windows (>=10), get the installer from https://store.docker.com/editions/community/docker-ce-desktop-windows

Note

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

Set Docker to be 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
```

Installation of Singularity Engine

Install singularity following instructions from the official documentation webpage at https://sylabs.io/guides/3.7/user-guide/quick_start.html#quick-installation-steps

Note

If you need to make the request to install Singularity on your HPC, Singularity provides a nice template at https://singularity.lbl.gov/install-request#installation-request to facilitate it.

MIALSRTK Container Image Download

Running Docker?

Open a terminal

Get the latest release (v2.1.0) of the BIDS App:

$ docker pull sebastientourbier/mialsuperresolutiontoolkit:v2.1.0

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

You should see the docker image “mialsuperresolutiontoolkit” with tag “v2.1.0” is now available.

You are ready to use the Docker image of MIALSRTK from the terminal. See its commandline usage.

Running Singularity?

Open a terminal

Get the latest release (v2.1.0) of the BIDS App:

$ singularity pull library://tourbier/default/mialsuperresolutiontoolkit:v2.1.0

You are ready to use the Singularity image of MIALSRTK. See its commandline usage.

The lightweight MIALSRTK wrappers

Prerequisites

The wrappers requires a Python3 environment. We recommend you tu use miniconda3 for which the installer corresponding to your 32/64bits MacOSX/Linux/Win system can be downloaded from https://conda.io/miniconda.html.

Wrappers Installation

Once Python3 is installed, the mialsuperresolutiontoolkit_docker and mialsuperresolutiontoolkit_singularity wrappers can be installed via pip as follows:

Open a terminal
Installation with pip:
```
$ pip install pymialsrtk==2.1.0
```
You are ready to use the mialsuperresolutiontoolkit_docker and mialsuperresolutiontoolkit_singularity wrappers. See their commandline usages.

Important

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 the Intel Power Gadget tool available here.

Help/Questions

Code bugs can be reported by creating a new GitHub Issue.