Installation

Nipoppy docs are moving

Nipoppy is undergoing a major refactor to move from scripts to a command-line interface (CLI) and Python API. The new documentation website (work in progress) can be found at https://nipoppy.readthedocs.io/.

If you are using the (soon-to-be legacy) scripts from Nipoppy 0.1.0, this is still the correct place to be. But we encourage you to check out the new website!

Code installation and dataset setup

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The Nipoppy workflow comprises a Nipoppy codebase that operates on a Nipoppy dataset with a specific directory structure (initialized with a tree.py script).

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Nipoppy code+env installation

1. Change directory to where you want to clone this repo, e.g.: cd /home/<user>/projects/<my_project>/code/
2. Create a new venv: python3 -m venv nipoppy_env
   • Alternatively (if using Anaconda/Miniconda), create a conda environment: conda create --name nipoppy_env python=3.9
3. Activate your env: source nipoppy_env/bin/activate
   • If using Anaconda/Miniconda: conda activate nipoppy_env
4. Clone this repo: git clone https://github.com/neurodatascience/nipoppy.git
5. Change directory to nipoppy
6. Install python dependencies: pip install -e .

Nipoppy dataset directory setup

Run nipoppy/tree.py to create the Nipoppy dataset directory tree:

python nipoppy/tree.py --nipoppy_root <DATASET_ROOT>

Where:

• DATASET_ROOT: root (starting point) of the Nipoppy structured dataset

Suggestion

We suggest naming DATASET_ROOT directory after a study or a cohort.