Installation Instruction¶

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 Multi-Scale Brain Parcellator is a BIDS App that relies on Docker. Make sure that you have Docker installed or follow the instructions found in Installation of Docker. Then, install the Multi-Scale Brain Parcellator by following the instructions found in Installation of the Multi-Scale Brain Parcellator.

Installation of Docker¶

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

Multi-Scale Brain Parcellator BIDSApp has been tested only on Ubuntu and MacOSX. For Windows users, it might be required to make few patches in the Dockerfile.

For Ubuntu, Docker could 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 the Multi-Scale Brain Parcellator¶

Installation and use of the Multi-Scale Brain Parcellator has been facilitated through the distribution of a Docker container image.

Open a terminal

Get the latest release of the BIDS App:

$ docker pull sebastientourbier/multiscalebrainparcellator:latest

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

You should see the docker image “multiscalebrainparcellator” with tag “latest” is now available.

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.