Advanced-MRI

This repository contains scripts, Flywheel gears, and viewer protocols that support the processing, quality control, and visualization of Advanced MRI data, including MEGRE, ASL, and vNAV sequences. It provides a centralized, version-controlled workspace for developing, testing, and deploying tools used across CLARiTI, SCAN, and related imaging workflows.

Contents

• Scripts
  • Utilities for data preparation, DICOM metadata extraction, automated classification, reprocessing, and workflow orchestration.
• Flywheel Gears
  • Containerized analysis tools ready for execution within the Flywheel platform, including:
    • Sequence-specific QC pipelines
    • MEGRE => QSM workflows
    • ASL quantification and derived metrics
    • Reprocessing utilities for updated analysis methods
• Viewer Protocols
  • Standardized configurations for image inspection and QC in popular viewers (e.g., Flywheel's built-in viewer, ITK-SNAP, 3D Slicer).

Purpose

Advanced MRI techniques evolve rapidly, and this repository provides a shared home for:

• Reproducible analysis workflows
• Standardized QC tools
• Rapid prototyping of new methods
• Seamless integration with Flywheel for multisite studies
• Reprocessing capabilities when new algorithms or updates become available

Usage

Each component includes its own documentation in subdirectories. Typical uses include:

• Running automated QC on new uploads
• Deploying or updating Flywheel gears
• Testing new analysis approaches prior to production release
• Organizing viewer presets for consistent manual review across sites