FSuB-Extractor

[smeisler]

Title

FSuB-Extractor

Short description and the goals for the OHBM BrainHack

• [ ] 1. Begin migration to Pydra or Nipype workflows
• [ ] 2. Reorganize / Rename / BIDS-ify outputs
• [ ] 3. Make a software container with dependencies
• [ ] 4. Set up testing / continuous integration workflows on repository
• [ ] 5. More beta testers!

Link to the Project

https://github.com/smeisler/fsub_extractor

Image for the OHBM brainhack website

No response

Project lead

Steven Meisler (Americas / Montreal) https://github.com/smeisler Discord Login: JazzyVibes#1404 smeisler@g.harvard.edu

Main Hub

Montreal

Other Hub covered by the leaders

• [x] Montreal
• [ ] Asia / Pacific
• [ ] Europe / Middle East / Africa
• [x] Americas

Skills

Familiarity with one or multiple of:

• Python
• MRtrix
• DIPY
• CIFTI processing
• FreeSurfer
• Pydra or Nipype
• CircleCI
• Docker/Apptainer/Singularity containerization

Recommended tutorials for new contributors

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

Good first issues

• Documentation
• Beta testing / error reporting

Twitter summary

Hi! The FSuB-Extractor is a tool that enables users to extract and analyze white matter bundles based on their intersection with gray matter functional ROIs. This approach has been used to study functional sub-components of bundles (FSuB) that support certain cognitive and perceptive tasks (e.g., Kubota et al., 2022, Cerebral Cortex).

Right now we have a functioning workflow, but we would like to formalize it more by migrating our workflow to something like Pydra or Nipype, and set up a software container and continuous integration workflow. We would also like to have outputs that follow BIDS as much as they can (keeping in mind the BIDS derivatives conventions -including connectivity derivatives- are still being codified). Even if you are unexperienced with contributing to code bases, we would still greatly appreciate feedback from beta testers!

Please contact me if you are interested or have questions!

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

fsub-extractor

Please read and follow the OHBM Code of Conduct

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

[anibalsolon]

hi @smeisler can you provide the content and/or figure for this project to be added to Brainhack Proceeding 2023 by 15th May? Also, please remember to fill out your team member's details using this form: https://forms.gle/Ku3AVHcXvpUqVVkV7 . Cheers

[smeisler]

Hi @anibalsolon, I ended up mostly working on other projects and didn't make much progress on this during the Brainhack. I also was the only team member.

[ufangYang]

@smeisler, Thank you for the update. Although we won't include this project in the Proceedings 2023, please feel free to reach out if you have any questions or comments. Cheers!