EXAMPLE README

(see for more >> https://www.freecodecamp.org/news/how-to-write-a-good-readme-file)

Project Name

Brief description of what your project does and its main features.

Table of Contents

• Onboarding Documentation
• Prerequisites
• Installation
• Data Access
• Project Structure
• Contributing
• License

Onborading Documentation

Tip: Grab this from your existing project issue!!

• MRI Basics: https://radiopaedia.org/articles/MRI
• Awesome visualization: https://github.com/alpers/awesome-data-visualization
• Get a hugging face account https://huggingface.co/
• Downloading a model from hugging face: https://huggingface.co/docs/hub/models-downloading

Prerequisites

List all system requirements and dependencies needed before installing the project:

• Python 3.8+
• FSL 6.0+ (https://fsl.fmrib.ox.ac.uk/fsldownloads_registration/)
• FreeSurfer 7.0+ (https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall)
• Nipype (https://nipype.readthedocs.io/en/0.12.0/users/install.html) etc.

Installation

Step-by-step installation instructions:

# Clone the repository
git clone https://github.com/username/project-name.git

# Navigate to project directory
cd project-name

# Create and activate virtual environment (Python)
python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

# Install dependencies
pip install -r requirements.txt

Data Access

Explain how to access and set up the data required for the project:

Data Sources

• List all data sources and their purposes
• Include URLs or endpoints for API access
• Specify any authentication requirements

Example 1: Download from public dataset using dipy:

# Example using dipy's data fetcher
from dipy.data import fetch_stanford_t1
t1_fname = fetch_stanford_t1()
print(t1_fname)  # Location of downloaded data

Example 2: Download from our Box folder:

URL: https://vanderbilt.box.com/xxxx
Download these example subjects to /data folder to get started:

sub-001
sub-002
sub-003

Example 3: Download from AWS S3:

# Configure AWS credentials
aws configure
AWS Access Key ID [None]: YOUR_ACCESS_KEY
AWS Secret Access Key [None]: YOUR_SECRET_KEY
Default region name [None]: us-east-1
Default output format [None]: json

# Download example data
aws s3 cp s3://openneuro-test/ds000228/sub-01/anat/sub-01_T1w.nii.gz ./data

Project Structure

Explain the organization of your project. See the example below:

project/
├── src/              # Source code (if any)
├── data/             # Data files (if any
└── scripts/          # Utility scripts

Contributing

Instructions for potential contributors:

1. Fork the repository
2. Create a feature branch
3. Submit a pull request
4. Follow coding standards

License

This project is licensed under [license type]. The data used in this project is covered under the original data sharing agreement of [repository name].