Integrating Clinica into Nipoppy

[mathdugre]

Title

Integrating Clinica into Nipoppy

Short description and the goals for the OHBM BrainHack

The goal of this hackathon is to strengthen the integration between Clinica converters and pipelines with Nipoppy.

During this project, you can learn how to:

• Containerize pipelines with Docker or Apptainer.
• Create Boutiques descriptors to enhance reproducibility of pipeline execution.
• Organize and process your data in a standard way with Nipoppy.
• Track your processing outputs with Nipoppy.

Or just talk to us to learn more about Clinica and Nipoppy

Link to the Project

https://nipoppy.readthedocs.io/en/latest

Image/Logo for the OHBM brainhack website

No response

Project lead

Mathieu Dugré, mathdugre, na_math
Alice Joubert, AliceJoubert, alice_8272
Michelle Wang, michellewang, michelle__wang
Matthieu Joulot, MatthieuJoulot, matt_jo
Adam Ismaili, Adam-Ismaili-92, adamismaili.

Main Hub

Bordeaux

Link to the Project pitch

https://docs.google.com/presentation/d/1fNfXwSJSG3_XzNWjW88-d9p6X2QkM90y39Kshmy9980/edit?usp=sharing

Other hubs covered by the leaders

• Bordeaux
• Hybrid (Asia / Pacific)
• Hybrid (Europe / Middle East / Africa)
• Hybrid (Americas)

Skills

• Neuroimaging preprocessing pipelines
• Boutiques
• Docker
• Bash
• Python

Recommended tutorials for new contributors

• Boutiques descriptor:
  https://nbviewer.org/github/boutiques/tutorial/blob/master/notebooks/boutiques-tutorial.ipynb
• Nipoppy pipeline development:
  https://nipoppy.readthedocs.io/en/latest/how_to_guides/pipeline_create/index.html

Good first issues

No response

Twitter summary

No response

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

clinica-nipoppy

Please read and follow the OHBM Code of Conduct

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