Bayes on the brain

[garner-code]

Title

Bayes on the brain

Short description and the goals for the OHBM BrainHack

To write a tutorial notebook for Bayesian approaches to analysing fMRI data.

We aim to implement the equations from Friston & Penny (2007) Empirical Bayes and hierarchal models (SPM textbook). We also aim to simulate data and implement a basic analysis.

Link to the Project

https://github.com/crnolan/bayesonthebrain

Image for the OHBM brainhack website

https://upload.wikimedia.org/wikipedia/commons/d/d4/Thomas_Bayes.gif

Project lead

Kelly Garner [Github: kel-github Discord: kellygarner#2353]
Christopher Nolan [Github: crnolan Discord: ChrisN#3806]

Main Hub

Glasgow

Other Hub covered by the leaders

• Glasgow
• Asia / Pacific
• Europe / Middle East / Africa
• Americas

Skills

skills include going through text resources (SPM textbook), implementing equations/data simulation in python, writing plain language explanations of the equations, going through matlab/SPM functions for implementations, and reading/using the tutorial and providing feedback

Recommended tutorials for new contributors

• Set up a brainhack friendly computing environment
• A introduction to Bash
• Python: Writing a script
• Python: Data analysis with Python
• Python: Visualisation
• Machine learning basics
• BIDS
• Machine learning for neuroimaging
• VCS: Using Git and Github
• VCS: Data management with Datalad
• Virtualization
• High Performance Computing: Oracle cloud resource

Good first issues

reading Friston & Penny (2007) Empirical Bayes and hierarchical models

Twitter summary

Let's demystify what is behind the Bayes button on the SPM GUI. Join us to implement Bayesian fMRI analyses and provide a tutorial for all.

Short name for the Discord chat channel (~15 chars)

Bayesonthebrain

Please read and follow the OHBM Code of Conduct

• I agree to follow the OHBM Code of Conduct during the hackathon

[github-actions]

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[effigies]

Would suggest using this image instead: https://upload.wikimedia.org/wikipedia/commons/d/d4/Thomas_Bayes.gif

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[garner-code]

Thanks for finding the new image!

[likeajumprope]

Hey @kel-github, maybe you want to run your notebook on our brand new brainhack cloud?
https://brainhack.org/brainhack_cloud/

[djarecka]

Thank you for submitting the project! We have 35 projects right now, woohoo! But that means the projects pitches will have to be short. We will give you tomorrow 2 minutes to pitch your project, you can have one slide or no slides!
If you decide to use a slide, please include the link to the slide here.

And don't worry, you will still have more time to talk about your project during the BrainHack :-)

[garner-code]

Thanks Johanna! We'll apply for resources shortly.

…

On Wed, 15 Jun 2022 at 09:10, Johanna Bayer ***@***.***> wrote: Hey @kel-github <https://github.com/kel-github>, maybe you want to run your notebook on our brand new brainhack cloud? https://brainhack.org/brainhack_cloud/ — Reply to this email directly, view it on GitHub <#79 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABXC34ZA2MW47KTFUGZ34RTVPGFXRANCNFSM5YXIMWLA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Kelly Garner, PhD, she/her Postdoctoral Research Fellow Google Scholar <https://scholar.google.co.uk/citations?user=nmeSlZkAAAAJ&hl=en> ResearchGate <https://www.researchgate.net/profile/Kelly_Garner> *U**Q* *A**L**L**Y* :: *Supporting the diversity of sexuality, sex and gender at UQ.*

--I acknowledge the Traditional Owners of the land upon which I live and work. I pay my respects to Elders past, present and emerging.--

--I seek to maintain a good work-life balance. If you receive this email outside office hours then don’t feel you have to respond. Please expect the like from me.--

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