NicolasGensollen / nilearn-tutorial-EUGLOH-2021

Materials for Nilearn tutorial for the EUGLOH Summer School focused on Neuroscience.

nilearn tutorial EUGLOH 2021

This repository holds the materials for the Nilearn tutorial for the EUGLOH Summer School focused on Neuroscience.

The notebooks are based from previous nilearn tutorials:

• Resting State and Brain Connectivity 2018 satellite workshop given by Gaël Varoquaux and Jacob Vogel.
• NHA 2020 tutorial given by Elizabeth Dupre.

Install

To be able to run the tutorial materials we need a few things:

• Python 3: Most recent systems come with Python pre-installed. However, depending on your system, you might still have python 2 as your default Python.

Danger: Nilearn does not support Python 2 anymore, so make sure to have Python 3 installed.

• pip: pip is the standard package manager for Python. It is a very powerful tool to manage your python packages. You can learn more on pip here.

Tip: If you want to check whether you have pip installed:

Linux:

$ python -m pip --version
pip X.Y.Z from .../site-packages/pip (python X.Y)

Windows:

C:\> py -m pip --version
pip X.Y.Z from ...\site-packages\pip (python X.Y)

• git: git is the most popular VCS (version controlled software). Although we recommand having git installed to download these notebooks, you can also use the download button on GitHub. You can learn more on git here.

The easy case

If you have these tools installed, you can download the repository with the notebooks:

$ git clone [e-mail]:NicolasGensollen/nilearn-tutorial-EUGLOH-2021.git
$ cd nilearn-tutorial-EUGLOH-2021

Install the requirements (this will install nilearn and its dependencies, as well as Jupyter-notebooks):

$ pip install -r requirements.txt

Launch the notebooks:

$ cd Notebooks
$ jupyter-notebook

The harder case

If you don't have these tools installed already, we recommand to rely on anaconda. Anaconda is a distribution of the Python programming languages for scientific computing which aims at simplifying package management and deployment. The distribution includes data-science packages suitable for Windows, Linux, and macOS.

Once you have downloaded and installed anaconda, you can create a new virtual environment dedicated to nilearn:

$ conda create -n nilearn python=3.9
$ conda activate nilearn

You can then go back to the "The easy case" section and follow the instructions.

Running the turorial notebooks online

Alternatively, you can run the notebooks online via Binder by clicking this link: https://mybinder.org/v2/gh/NicolasGensollen/nilearn-tutorial-EUGLOH-2021/HEAD or clicking the Binder badge at the top of the README file.