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| # nipreps-book | ||
| # NiPreps Book | ||
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| NiPreps Book is a [Jupyter Book](https://jupyterbook.org) that accompanies the NiPreps | ||
| community workshops. The material walks readers through implementing a | ||
| head-motion–correction workflow for diffusion MRI (dMRI) data using tools from | ||
| [DIPY](https://dipy.org), [NiTransforms](https://nipy.org/nitransforms), and the | ||
| broader NiPreps ecosystem. Besides explaining the motivation behind the | ||
| "analysis-grade" data philosophy, the book provides hands-on notebooks that show | ||
| how to assemble reproducible preprocessing components. | ||
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| ## Get started | ||
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| ### Run it in your browser | ||
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| If you prefer not to install anything locally, launch the notebooks in an | ||
| ephemeral Binder session: | ||
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| [](https://mybinder.org/v2/gh/nipreps/nipreps-book/main?urlpath=lab/tree/docs/notebook) | ||
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| Binder sessions can take a few minutes to start and reset after inactivity. | ||
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| ### Build the book locally | ||
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| This repository is configured with [pixi](https://prefix.dev/pixi) for | ||
| reproducible environments: | ||
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| 1. [Install pixi](https://prefix.dev/docs/pixi/installation). | ||
| 2. Create the environment and install the dependencies: | ||
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| ```bash | ||
| pixi install | ||
| ``` | ||
| 3. Build the static HTML version of the book: | ||
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| ```bash | ||
| pixi run build-book | ||
| ``` | ||
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| The rendered site will be available under `docs/_build/html`. To explore the | ||
| notebooks interactively, launch JupyterLab with `pixi run serve` and open the | ||
| files inside `docs/notebook/`. | ||
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| ### Working with the tutorial dataset | ||
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| Several chapters rely on a small diffusion MRI dataset. The helper module | ||
| `tutorial_data.py` automatically downloads the dataset to `data/` the first time | ||
| it is requested. If you already have a copy of the file, set the | ||
| `NIPREPS_TUTORIAL_DATA` environment variable to point to it before running the | ||
| notebooks. | ||
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| ## Repository layout | ||
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| - `docs/` – Markdown content, notebook sources, and static assets for the book. | ||
| - `data/` – Cached example diffusion MRI dataset used throughout the tutorial. | ||
| - `binder/` – Configuration used to build the Binder environment. | ||
| - `pixi.toml` – Environment definition and common development tasks. | ||
| - `tutorial_data.py` – Utility functions for fetching the tutorial dataset. | ||
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| ## Contributing | ||
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| Issues, feature requests, and pull requests are welcome! Please review the | ||
| open issues on GitHub and let us know how the material can be improved. When | ||
| submitting changes, follow the standard GitHub workflow and ensure the book | ||
| builds locally (`pixi run build-book`) before opening a pull request. | ||
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| ## License and citation | ||
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| NiPreps Book is distributed under the terms of the [3-Clause BSD | ||
| License](LICENSE). If you use the material in your own work, please cite the | ||
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| project as described in [CITATION.cff](CITATION.cff). | ||
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