Nipreps - Reporting FreeSurfer outcomes with NiReports

[esavary]

Title

Reporting FreeSurfer outcomes with NiReports

Short description and the goals for the OHBM BrainHack

This project aims to gather the output of FreeSurfer in comprehensive reports. Using the powerful NiReports tooling, reportlets will be created from FreeSurfer runs to visualize and assess the quality of neuroimaging processing steps.

The project will leverage the NiReports assembler, which utilizes PyBIDS, to collect the reportlets generated by FreeSurfer. The assembler follows a report specification in YAML format, specifying the query for specific reportlets, their associated metadata, and text annotations. Ultimately, the assembler combines the reportlets into a single HTML file, providing an informative and concise summary of the FreeSurfer analysis.

FreeSurfer is a widely used software package for structural and functional neuroimaging analysis, while NiReports, a part of the NiPreps' reporting and visualization tools, offers a powerful framework for organizing and presenting the results. This hackathon project aims to streamline the reporting process and enhance the visualization of FreeSurfer output, facilitating the interpretation and analysis of neuroimaging data.

Link to the Project

https://github.com/nipreps/nireports

Image for the OHBM brainhack website

No response

Project lead

Michael Dayan, GitHub: @neurorepro , discord:

Main Hub

Montreal

Other Hub covered by the leaders

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

Skills

To make the most of this hackathon project, having some Python knowledge is important. While prior experience with FreeSurfer and NiReports is appreciated, it's not a requirement. We encourage you to join us and contribute your skills, regardless of your level of expertise.

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)

nireports_freesurfer

Please read and follow the OHBM Code of Conduct

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