Skip to content

Commit 07ed1d7

Browse files
authored
Merge pull request #48 from nipreps/codex/create-readme.md-file
Update README with usage and contribution guidance
2 parents 897a376 + 5172652 commit 07ed1d7

File tree

1 file changed

+69
-1
lines changed

1 file changed

+69
-1
lines changed

README.md

Lines changed: 69 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1 +1,69 @@
1-
# nipreps-book
1+
# NiPreps Book
2+
3+
NiPreps Book is a [Jupyter Book](https://jupyterbook.org) that accompanies the NiPreps
4+
community workshops. The material walks readers through implementing a
5+
head-motion–correction workflow for diffusion MRI (dMRI) data using tools from
6+
[DIPY](https://dipy.org), [NiTransforms](https://nipy.org/nitransforms), and the
7+
broader NiPreps ecosystem. Besides explaining the motivation behind the
8+
"analysis-grade" data philosophy, the book provides hands-on notebooks that show
9+
how to assemble reproducible preprocessing components.
10+
11+
## Get started
12+
13+
### Run it in your browser
14+
15+
If you prefer not to install anything locally, launch the notebooks in an
16+
ephemeral Binder session:
17+
18+
[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/nipreps/nipreps-book/main?urlpath=lab/tree/docs/notebook)
19+
20+
Binder sessions can take a few minutes to start and reset after inactivity.
21+
22+
### Build the book locally
23+
24+
This repository is configured with [pixi](https://prefix.dev/pixi) for
25+
reproducible environments:
26+
27+
1. [Install pixi](https://prefix.dev/docs/pixi/installation).
28+
2. Create the environment and install the dependencies:
29+
30+
```bash
31+
pixi install
32+
```
33+
3. Build the static HTML version of the book:
34+
35+
```bash
36+
pixi run build-book
37+
```
38+
39+
The rendered site will be available under `docs/_build/html`. To explore the
40+
notebooks interactively, launch JupyterLab with `pixi run serve` and open the
41+
files inside `docs/notebook/`.
42+
43+
### Working with the tutorial dataset
44+
45+
Several chapters rely on a small diffusion MRI dataset. The helper module
46+
`tutorial_data.py` automatically downloads the dataset to `data/` the first time
47+
it is requested. If you already have a copy of the file, set the
48+
`NIPREPS_TUTORIAL_DATA` environment variable to point to it before running the
49+
notebooks.
50+
51+
## Repository layout
52+
53+
- `docs/` – Markdown content, notebook sources, and static assets for the book.
54+
- `data/` – Cached example diffusion MRI dataset used throughout the tutorial.
55+
- `binder/` – Configuration used to build the Binder environment.
56+
- `pixi.toml` – Environment definition and common development tasks.
57+
- `tutorial_data.py` – Utility functions for fetching the tutorial dataset.
58+
59+
## Contributing
60+
61+
Issues, feature requests, and pull requests are welcome! Please review the
62+
open issues on GitHub and let us know how the material can be improved. When
63+
submitting changes, follow the standard GitHub workflow and ensure the book
64+
builds locally (`pixi run build-book`) before opening a pull request.
65+
66+
## Citation
67+
68+
If you use the material in your own work, please cite the
69+
project as described in [CITATION.cff](CITATION.cff).

0 commit comments

Comments
 (0)