Welcome to the SCIL lab documentation!

Our lab works in diffusion MRI, from the acquisition sequences and local reconstruction to tractography and its usages in applied contexts, including tractometry.

Here, you will find a summary of the tools we develop, and some clues on how we do things in the lab, from using Linux to developing code.

Arriving in the lab

• Onboarding new students
• Useful links
• Our team

Intro to Computer Science

• Intro to Linux
• Intro to Python
• Intro to Git
• Intro to Software
• Intro to Virtual Machines
• Intro to Nextflow: users
• Intro to Nextflow: coding your own flow

Our tools

• SCILPY
• Flows
• Tractoflow
• RecobundlesX
• Checks and stats
• Machine Learning

Common tools

• DIPY
• CBRAIN

Coding standards in the lab

• General python coding tricks
• Scilpy coding standards
• Git

Dealing with heavy data

• Dealing with heavy data storage
• Dealing with heavy computing

Other

• Interesting conferences
• Interesting scholarships