This repository is intented to show a typical pipeline when working with images in a clinical context and how Clinica can be simplify this task.
Create a conda environment and use poetry to install dependencies inside:
conda env create --file environment.yml -p ./env
conda activate ./env
poetry install
In order to share developments and to facilitate the review task, the contributions must be done in the form of Python script.
Then use jupytext to convert the pythos scripts into Jupyter notebooks
jupytext --to notebook file.py --output file.ipynb
- Connect to a XNAT DB and download images
- Convert images to nifty
- Use a pydra pipeline