ISLES 2022 - Getting Started

This repository provides detailed information for obtaining data associated with ISLES 2022, along with examples of how to use BIDSIO to load batches and write out data in the format expected by the automatic evaluator.

Installation

The examples are provided in a Jupyter Notebook in this repo, called ISLES_Example.ipynb. If you've used Jupyter Notebooks before, you can install the packages in requirements.txt and start the notebook. Otherwise, this section will walk you through first-time setup of the notebook.

1. Linux Installation
2. MacOS Installation

Linux

We recommend that you use a Python virtual environment, for which you'll need the python3.x-venv package.

sudo apt-get install python3.9-venv

Next, create a virtual environment and source it:

python3.9 -m venv isles_venv
source isles_venv/bin/activate

We'll now install the required packages via pip:

pip install --upgrade pip
pip install -r requirements.txt

We can now install the kernel to make it available to our Jupyter notebook:

python3.9 -m ipykernel install --user --name isles_venv --display-name "Python 3.9 (isles_venv)"

Start the notebook:

jupyter-notebook ISLES_Example.ipynb

In the menu bar near the top of the window, you'll see an option named Kernel. Under it, you can use Change Kernel to select "Python 3.9 (isles_venv)":

You should now be able to run the notebook. You can execute individual cells using Shift + Enter.

MacOS

First ensure that Python3 is installed on your system. See the Python.org release page for the installer. Open the terminal (Finder -> Applications -> Terminal). The following instructions are commands to be run through the terminal.

Create a directory to store files for the project:

mkdir atlas2
cd atlas2

Create a virtual environment for the event, then source it.

python3 -m venv isles_venv
source isles_venv/bin/activate

Download this repository:

git clone https://github.com/npnl/isles_2022

We can now install the Python packages required by the notebook:

pip install --upgrade pip
pip install -r isles_2022/requirements.txt

Next, make the kernel available to the Jupyter notebook:

python3 -m ipykernel install --user --name isles_venv --display-name "Python 3 (isles_venv)"

Finally, start the notebook:

jupyter-notebook isles_2022/ISLES_Example.ipynb

You should now be able to run the notebook. You can execute individual cells using Shift + Enter.