Installation

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
3. Alternatively (if using Anaconda/Miniconda), create a conda environment: conda create --name nipoppy_env python=3.9
4. Activate your env: source nipoppy_env/bin/activate
5. If using Anaconda/Miniconda: conda activate nipoppy_env
6. Clone this repo: git clone https://github.com/neurodatascience/nipoppy.git
7. Change directory to nipoppy
8. Install python dependencies: pip install -e .

Nipoppy dataset directory setup

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

python 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.