NiPreps generalizations for diffusion MRI (MRIQC+dMRIPrep)

[arokem]

Title

dmri-nipreps

Short description and the goals for the OHBM BrainHack

We plan to continue expanding the support for different modalities of NiPreps. Continuing on that line, we recently released MRIQC with beta support for dMRI data. dMRIPrep has long been in the works, and we expect to make progress on this front too. Finally, we may delve into the eddymotion project with the implementation of a Gaussian Process model for eddymotion, thereby enhancing the dMRIPrep preprocessing pipeline's capability to handle motion-related artifacts.
Therefore, we are planning to act on the following lines, depending on the appetite and preferences of brain hackers

• MRIQC
  • improving the reportlets of the visual reports, including color FA, anisotropic power map, and/or carpetplot.
• eddymotion
  • developing new models for diffusion and PET data:
  • Gaussian Process model to allow comparison vs. FSL topup (this line is most likely to directly contribute to DIPY).
  • PET model (continuing with the work initiated in the 2022 hackathon at OHBM Glasgow)
• dMRIPrep
  • pipeline, package and containers makeover

https://github.com/nipreps/mriqc
https://github.com/nipreps/eddymotion
https://github.com/nipreps/dmriprep

Link to the Project

https://github.com/nipreps

Image for the OHBM brainhack website

No response

Project lead

Ariel rokem (GitHub: @arokem, Discord: @arokem) and Teresa Gomez (Github: @teresamg)

Main Hub

Montreal

Other Hub covered by the leaders

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

Skills

While we encourage participants of all skill levels to join, a good understanding of Python is recommended to contribute to this project. Some knowledge of diffusion MRI would also be helpful.

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

No response

Twitter summary

No response

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

nipreps-dmri

Please read and follow the OHBM Code of Conduct

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