MRI-on-BEAR

Purpose: A freely available resource for the 'Magnetic Resonance Imaging in Cognitive Neuroscience' course at the Centre for Human Brain Health

Welcome to the MRI-on-BEAR website, a freely available resource created by researchers at the Centre for Human Brain Health, University of Birmingham. The website is made for students on the 'Magnetic Resonance Imaging in Cognitive Neuroscience' course, but may also be useful to external students and researchers. However, please BEAR in mind that the course materials were designed to run on computing resources at the University of Birmingham!

Table of contents

• Course Overview
• Getting Started
• Support and Contact
  • Course-related Issues
  • IT Support
  • Website Support
• Contributing
  • Development Setup
  • Building
  • Testing
  • Previewing
  • Pushing the changes using git
  • Issues
• License
• Citation

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Course Overview

The series of workshops collectively provide a comprehensive introduction to Magnetic Resonance Imaging (MRI) techniques in cognitive neuroscience, including the analysis of diffusion and functional magnetic resonance imaging (fMRI) data. In doing so, you will also learn how to access the BEAR Portal, BlueBEAR and basic programming skills required for working with neuroimaging data (e.g., Linux commands and bash scripting).

Getting Started

⚠️ Important: Before the first workshop, it is important that you have access to the BlueBEAR system. Instructions on how do do so can be found on the website (see the 'Getting Started' page).

Whilst not mandatory, additional resources related to the course can also be found on the website (see the 'Resources' page).

Support and contact

If you encounter any issues or have questions please contact the following:

Course-related Issues

• Dr Magda Chechlacz (Module Lead)
  • m.chechlacz@bham.ac.uk

IT/Computing Support

• Charnjit Sidhu (Lead Computing Officer, CHBH)
  • c.sidhu@bham.ac.uk

Website/GitHub enquiries

• Aamir Sohail (Module Teaching Assistant)
  • axs2210@bham.ac.uk

Contributing (for CHBH staff)

If you teach on the course, or are a staff member at the CHBH and could like to contribute to the website, please follow the instructions below.

Development Setup

You will firstly need to re-create the website locally. The website is built using MkDocs, which is nice and easy to work with. After cloning the repository, to install all the required mkdocs Python packages, use the provided requirements.txt file within the root of this repository. The recommendation for development is to do this inside a dedicated virtual environment.

All of these steps can be done using the commands below (if you have push access):

shell git clone https://github.com/chbh-opensource/mri-on-bear cd mri-on-bear python -m venv ./.venv source ./.venv/bin/activate pip install -r requirements.txt

If you do not, you will need to git clone from your own GitHub account:

git clone https://github.com/YOUR-USERNAME/mri-on-bear

The subsequent steps remain the same.

Building

To build the documentation, simply use:

shell mkdocs build

Testing

To test whether the documentation is building correctly, and whether all (internal) links are correct, use:

shell mkdocs build --strict

This command will exit with a non-zero exit code if mkdocs produces any errors or warnings.

Previewing

To see a local preview of the rendered documentation in your browser, use

shell mkdocs serve

or in the off chance that you are already running a localhost, use:

shell mkdocs serve -a localhost:XXXX

and click the link that is provided, for example:

shell INFO - Documentation built in 0.24 seconds INFO - [17:52:07] Watching paths for changes: 'docs', 'mkdocs.yml' INFO - [17:52:07] Serving on http://127.0.0.1:8000/

This preview of the rendered documentation will automatically refresh when the documentation sources are updated!

Pushing the changes using git

After you have made your changes, you can then push them to the main branch.

If you have direct push access:

shell git status # check your changes here git add . git commit -m "brief description of your changes" git push origin main

If you do not have direct push access:

shell git checkout -b feature/your-feature-name git status git add . git commit -m "brief description of your changes" git push origin feature/your-feature-name

You will then need to create a pull Request:

1) Go to the original repository at https://github.com/chbh-opensource/mri-on-bear 2) Click "Pull Requests" > "New Pull Request" 3) Click "compare across forks" 4) Select your fork and branch 5) Click "Create Pull Request" 6) Fill in the description of your changes 7) Submit the pull request

We will then review your changes and merge them if we deem them worthy! 👀 ✨

Issues

If you (e.g., students, externals) have an idea for the website, or have highlighted a bug, but would prefer that we did the work, feel free to open an issue!

LICENSE

All content in this repository is licensed under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) license. See the LICENSE for more details.

Citation

If you use these materials in your own work, please use the citation below:

Sohail, A., Quinn, A. J., Carpenter, J. J., Hansen, P. C., & Chechlacz, M. (2025). MRI on BEAR (Birmingham Environment for Academic Research): Magnetic Resonance Imaging in Cognitive Neuroscience at the Centre for Human Brain Health. Zenodo. https://doi.org/10.5281/zenodo.15804715