Update readme Fix #10

README.md

@@ -1,19 +1,4 @@
-[![DOI](https://zenodo.org/badge/657341621.svg)](https://zenodo.org/doi/10.5281/zenodo.10383685)
-
-# CMI-DAIR Template Python Repository
-
-Welcome to the CMI-DAIR Template Python Repository! This template is designed to streamline your project setup and ensure a consistent structure. To get started, follow these steps:
-
-- [x] Run `setup_template.py` to initialize the repository.
-- [ ] Replace the content of this `README.md` with details specific to your project.
-- [ ] Install the `pre-commit` hooks to ensure code quality on each commit.
-- [ ] Revise SECURITY.md to reflect supported versions or remove it if not applicable.
-- [ ] Remove the placeholder src and test files, these are there merely to show how the CI works.
-- [ ] If it hasn't already been done for your organization/acccount, grant third-party app permissions for CodeCov.
-- [ ] To set up an API documentation website, go to the `Settings` tab of your repository, scroll down to the `GitHub Pages` section, and select `GitHub Actions` as the source. This will generate a link to your API docs.
-- [ ] Update stability badge in `README.md` to reflect the current state of the project. A list of stability badges to copy can be found [here](https://github.com/orangemug/stability-badges). The [node documentation](https://nodejs.org/docs/latest-v20.x/api/documentation.html#documentation_stability_index) can be used as a reference for the stability levels.
-
-# Project name
+# RBC Pipeline
 
 [![Build](https://github.com/childmindresearch/rbc/actions/workflows/test.yaml/badge.svg?branch=main)](https://github.com/childmindresearch/rbc/actions/workflows/test.yaml?query=branch%3Amain)
 [![codecov](https://codecov.io/gh/childmindresearch/rbc/branch/main/graph/badge.svg?token=22HWWFWPW5)](https://codecov.io/gh/childmindresearch/rbc)
@@ -22,38 +7,110 @@ Welcome to the CMI-DAIR Template Python Repository! This template is designed to
 [![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/childmindresearch/rbc/blob/main/LICENSE)
 [![pages](https://img.shields.io/badge/api-docs-blue)](https://childmindresearch.github.io/rbc)
 
-What problem does this tool solve?
+Reference implementation of the Reproducible Brain Charts (RBC) preprocessing protocol for anatomical, functional, derivatives, and longitudinal neuroimaging data.
+
+## Overview
+
+This package provides a standalone implementation of the RBC preprocessing pipeline, originally developed in [C-PAC](https://fcp-indi.github.io/). This repository serves as the maintained reference implementation using [NiWrap](https://github.com/styx-api/niwrap) for neuroimaging tool integration.
+
+**Reference:** Shafiei et al. (2024). "Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health." *Neuron*, 113(22):3758-3779.
 
 ## Features
 
-- A few
-- Cool
-- Things
+- **Anatomical preprocessing**: Brain extraction (ANTs), tissue segmentation (FSL FAST), registration to MNI152
+- **Functional preprocessing**: Motion correction, slice timing, coregistration, single-step resampling to template space
+- **Nuisance regression**: 36-parameter and aCompCor methods with bandpass filtering
+- **Quantitative metrics**: ALFF/fALFF, ReHo, network centrality, atlas-based timeseries extraction
+- **Quality control**: XCP-style QC metrics with RBC-recommended thresholds
+- **BIDS-compatible**: Follows BIDS conventions for inputs and outputs
 
 ## Installation
 
-Install this package via :
+```bash
+pip install git+https://github.com/childmindresearch/rbc.git
+```
+
+### Dependencies
+
+The pipeline requires the following neuroimaging tools:
+- **AFNI**: Motion correction, despiking, nuisance regression
+- **FSL**: Tissue segmentation, registration, brain masking
+- **ANTs**: Brain extraction, registration
+
+## Usage
+
+```python
+from rbc.workflows import anatomical, functional
+
+# Anatomical preprocessing
+anatomical.single_session(
+    in_t1w="sub-01_T1w.nii.gz",
+    output_dir="derivatives/rbc"
+)
 
-```sh
-pip install APP_NAME
+# Functional preprocessing (in development)
+functional.single_session(
+    in_bold="sub-01_task-rest_bold.nii.gz",
+    in_t1w="sub-01_T1w.nii.gz",
+    output_dir="derivatives/rbc"
+)
 ```
 
-Or get the newest development version via:
+## Documentation
 
-```sh
-pip install git+https://github.com/childmindresearch/rbc
+- **[API Documentation](https://childmindresearch.github.io/rbc)**: Full API reference
+
+## Contributing
+
+Contributions are welcome! See [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines.
+
+## Testing
+
+```bash
+# Fast tests only (for development)
+pytest -m "not slow"
+
+# All tests including integration tests
+pytest
+
+# Full pipeline tests (slow, ~30+ min)
+pytest -m "full_pipeline"
 ```
 
-## Quick start
+See [tests/README.md](tests/README.md) for testing strategy and instructions.
 
-Short tutorial, maybe with a
+## License
 
-```Python
-import APP_NAME
+[MIT License](LICENSE)
 
-APP_NAME.short_example()
+## Citation
+
+If you use this pipeline, please cite:
+
+```bibtex
+@article{shafiei2024reproducible,
+  title={Reproducible Brain Charts: An open data resource for mapping brain development and its associations with mental health},
+  author={Shafiei, Golia and Esper, Natasha B and Hoffmann, Madeleine S and Ai, Lei and Chen, Andrew A and Cluce, Julia and Covitz, Sydney and Giavasis, Steven and Lane, Connor and Mehta, Kahini and Moore, Tyler M and Salo, Taylor and Tapera, Tinashe M and Calkins, Monica E and Colcombe, Stanley and Davatzikos, Christos and Gur, Raquel E and Gur, Ruben C and Pan, Pedro M and Jackowski, Andrea P and Rokem, Ariel and Rohde, Luis A and Shinohara, Russell T and Tottenham, Nim and Zuo, Xi-Nian and Cieslak, Matthew and Franco, Alexandre R and Kiar, Gregory and Salum, Giovanni A and Milham, Michael P and Satterthwaite, Theodore D},
+  journal={Neuron},
+  volume={113},
+  number={22},
+  pages={3758--3779},
+  year={2024},
+  publisher={Elsevier},
+  doi={10.1016/j.neuron.2024.08.026}
+}
 ```
 
-## Links or References
+## About RBC
+
+Reproducible Brain Charts (RBC) is an open resource integrating data from 5 large studies of brain development in youth from three continents (N = 6,346). The resource provides:
+
+- Harmonized psychiatric phenotypes using bifactor models
+- Quality-assured neuroimaging data processed with consistent pipelines
+- All data openly shared via the International Neuroimaging Data-sharing Initiative (INDI)
+
+RBC facilitates large-scale, reproducible, and generalizable research in developmental and psychiatric neuroscience.
+
+## Acknowledgments
 
-- [https://www.wikipedia.de](https://www.wikipedia.de)
+This implementation is based on the RBC protocol described in Shafiei et al. (2024) and originally implemented in C-PAC. Development is supported by the Child Mind Institute.