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ATLAS (ISLES 2022) Challenge - Getting Started

This repository provides detailed information for obtaining data associated with the ATLAS challenge at ISLES/MICCAI, 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)": image

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.

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Example usage of BIDSIO for input + output for use with the ISLES 2022 Challenge

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