# 📚 Reproducible Pipelines for <br>🧠 Neuroimaging Research
<span style="font-size:1.2em; font-weight:300; color:gray;">From Code to Visualization</span>

**Author/Presenter**:  
[*Sina Mansour L.*](https://sina-mansour.github.io/), Ph.D.  
National University of Singapore & The University of Melbourne

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16006869.svg)](https://doi.org/10.5281/zenodo.16006869)

```{note}
This Jupyter Book contains supporting material for the session titled *"From Code to Visualization: Reproducible Pipelines for Neuroimaging Research"* that was part of an educational course on ["Maximizing scientific efficiency through sustainability, reproducibility, and FAIRness"](https://ww6.aievolution.com/hbm2501/Events/viewEv?ev=2237), presented at the [2025 OHBM Annual Meeting in Brisbane](https://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=4229).

```

If you like to follow along the slides, you can find them [here](https://sina-mansour.github.io/ohbm2025-reproducible-research-slides/).

```{figure} /assets/slides.png
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The slides accompanying this book are [available online](https://sina-mansour.github.io/ohbm2025-reproducible-research-slides/):

🔗 [![Slides Badge](https://img.shields.io/badge/Slides%20-%20teal?style=for-the-badge&logo=codementor&logoColor=yellow&logoSize=auto&label=Online)](https://sina-mansour.github.io/ohbm2025-reproducible-research-slides/) 🔗

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## 💬 Synopsis

How can neuroimaging researchers ensure their findings are not only robust but also **transparent** and **reproducible**?

This book guides you through building research workflows with reproducible **code** and **visualizations**, designed to accompany your manuscript and support open science.

### 🧠 Why Reproducibility?
Reproducibility helps:
- ✅ Maximize trust in your work
- 🤝 Enable collaboration across teams
- 🔍 Improve transparency and accountability

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We provide examples and practical tips to boost reproducibility:

#### 💻 In your Code:

- 📝 Write clear, shareable scripts
- 🌟 Follow best practices for sharing code
- 🌐 Use open notebooks for full pipeline visibility

#### 🎨 In your Visualizations:

- 🖼️ Understand why reproducible figures matter
- 🔁 Learn how to make visualizations easy to recreate
- 🛠️ Build scriptable visualizations for:
  - 🧠 Cortical surface projections
  - 🧊 Volumetric plots
  - 〰️🧵 Tractography results
  - 🕸️ Brain network diagrams
  - ... & more!

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## 🗂️ Table of contents

Overview of the content of this book:

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