🎯 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!
This README is primarily for students, and will help you navigate the course materials and get started with the practical workshops.
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).
The MRICN course during Spring Term 2024-25 will have the following dates (subject to change):
| Week | Date | Workshop |
|---|---|---|
| Week 1 | TBD | No workshop |
| Week 2 | TBD | Introduction to BlueBEAR and Linux |
| Week 3 | TBD | No workshop |
| Week 4 | TBD | Basic MRI Skills |
| Week 5 | TBD | Basic diffusion MRI analyses |
| Week 6 | TBD | MRI demo at the CHBH (optional) |
| Week 7 | TBD | Advanced diffusion MRI analyses |
| Week 8 | TBD | First-level fMRI analysis |
| Week 9 | TBD | No workshop (Reading Week) |
| Week 10 | TBD | Bash scripting, submitting jobs, and containers |
| Week 11 | TBD | Higher-level fMRI analysis |
| Week 12 | TBD | Functional connectivity (optional) |
Workshops will be held at Computer Room G19, Gisbert Kapp, at the School of Psychology.
⚠️ 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).
If you encounter any issues or have questions please contact the following:
- Dr Magda Chechlacz (Module Lead)
- Charnjit Sidhu (Lead Computing Officer, CHBH)
- Aamir Sohail (Module Teaching Assistant)
⏰ Please contact us during working hours (9am-5pm)!
If you teach on the course, or are staff member at the CHBH and could like to contribute to the website, please follow the instructions below.
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:
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.txtThis assumes that you have push access. 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.
To build the documentation, simply use:
mkdocs buildTo test whether the documentation is building correctly, and whether all (internal) links are correct, use:
mkdocs build --strictThis command will exit with a non-zero exit code if mkdocs produces any errors or warnings.
To see a local preview of the rendered documentation in your browser, use
mkdocs serveor in the off chance that you are already running a localhost, use:
mkdocs serve -a localhost:XXXXand click the link that is provided, for example:
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!
After you have made your changes, you can then push them to the main branch.
If you have direct push access:
git status # check your changes here
git add .
git commit -m "brief description of your changes"
git push origin mainIf you do not have direct push access:
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-nameYou will then need to create a pull Request:
- Go to the original repository at https://github.com/chbh-opensource/mri-on-bear
- Click "Pull Requests" > "New Pull Request"
- Click "compare across forks"
- Select your fork and branch
- Click "Create Pull Request"
- Fill in the description of your changes
- Submit the pull request
We will then review your changes and merge them if we deem them worthy! 👀 ✨
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!
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.