Clinica's image processing pipeline QC

[MatthieuJoulot]

Title

Clinica's image processing pipeline QC

Short description and the goals for the OHBM BrainHack

The goal is to establish a QC protocol that includes both metric and visual-based assessment, for the various image processing pipelines available in Clinica.

The project would be planned would be as follows:

• First, a round table to discuss the different practices of the participants, on which pipelines participants will be working on, as well as the objectives for the end of the hackathon. Before the end of the round table, two work groups should be established: one working on image quality metrics (IQMs), and the second working on visual QC
• Next, we expect the two groups to work independently:
  • The IQM group will select some metrics that feel relevant, and evaluate them.
  • The visual QC group will set-up a few different visual QC proposal (i.e. views) for each pipeline they're studying, and attempt to evaluate their effectiveness

We expect the outcomes of this hackathon to be a set of IQM candidates and of graphical representation that could be included in the QC tools of Clinica

Link to the Project

https://github.com/aramis-lab/clinica

Image for the OHBM brainhack website

https://www.clinica.run/assets/images/clinica-icon-257x257.png

Project lead

Name: Matthieu Joulot
GitHub: MatthieuJoulot
Discord: Matthieu Joulot

Main Hub

Montreal

Other Hub covered by the leaders

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

Skills

The skills we are looking for are:

• expertise in visual QC of neuro-imaging (structural MRI, diffusion MRI, PET) processing (segmentation, registration, ...)
• expertise in the use of IQMs for quantitative QC of neuro-imaging (structural MRI, diffusion MRI, PET) processing (segmentation, registration, ...)

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)

processing-qc

Please read and follow the OHBM Code of Conduct

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