niwrap-workshop

Welcome to the repository for the interactive niwrap workshop!

This workshop showcases how to use niwrap through a series of hands-on examples provided as Jupyter notebooks. All necessary data for running the examples is included in the repository.

To run the examples, some neuroimaging tools must be available - see Required neuroimaging tools for more details. These can be accessed via local installations, Docker, or Singularity.

• If the necessary tools are already installed on your local machine or Docker is available, you're all set - no further setup is needed.
• If you plan to use Singularity, a few additional setup steps are required - don't worry, detailed instructions are provided below!

Getting started

To run examples, the only prerequisite is to be able to run a Jupyter notebook. It is recommended to clone this repository, create a virtual environment and install Jupyter.

# Clone and navigate to directory
git clone https://github.com/styx-api/niwrap-workshop niwrap-workshop
cd niwrap-workshop

# Create and activate virtual environment
python -m venv .venv
source .venv/bin/activate

# Install Jupyter
pip install jupyter

Required neuroimaging tools

• ANTs
• FSL