Guides and Workflows

Use these guides to walk through the pipeline end-to-end. The left sidebar shows the section navigation for each topic; notebooks are linked where they match the workflow.

Core pipeline

Core pipeline

• Reconstruction
  • Inputs
  • Processing Blocks
  • Regridding
  • Cartesian and Non-Cartesian Sketches
  • Variational Solver
  • Model-Based Reconstruction
  • Common Checks
• Preprocessing Toolbox
  • Filtering
  • Regularized Denoising
  • BM3D and BM4D (optional, non-commercial license)
  • Drift Correction
  • SimpleITK Registration
  • Notebook
• Studies and Observables
  • Dimension handling
  • Multi-axis editing example
  • Joint experiments and partial fits
  • Defining a Study
  • Inserting observables from prior fits
  • Sanity checks
  • Planning and Execution
  • Visualization
• Batch Runs
  • Quickstart example
  • Selective execution
  • Custom analysis hooks
• Storage and ISMRMRD Export
  • Saving Results
  • Loading and Reuse
  • Folder Layout
• Post-fit Analysis
  • ROI statistics
  • Timecourse extraction
  • Group summaries and comparisons
  • Plotting summaries

Import Workflows

Import

• Importer Development
  • Validation status
  • What “Reconstruction-Ready K-Space” Means
  • Three Separate Problems
  • MRax Import Pipeline
  • Bruker Case Study
  • Implementing a New Vendor or Sequence
• Bruker Import
  • Validation scope
  • Quick Usage
  • Shared Import Schema
  • Intensity Scaling
  • Raw Cartesian K-Space
  • EPI K-Space
  • Non-Cartesian Raw Data
  • Frame Geometry
  • TimeStamps TR
  • Diffusion and Saturation Transfer
  • Storage
• Pulseq Import
  • Validation scope
  • Quick usage
  • Notebook walkthrough
  • K-space conventions
  • Non-Cartesian matching
  • Shared definitions

• Bruker import has been tested on ParaVision 360 3.6 data.

• Pulseq walkthrough notebook: Pulseq Import Demo

• Pulseq notebook download: pulseq_import_demo.ipynb

Quantitative mapping

Quantitative mapping

• Quantitative Mapping Recipes
  • T1 mapping (inversion recovery)
  • T2 mapping (multi-echo spin echo)
  • FAIR perfusion (selective + non-selective)
  • Saturation transfer (WASABI + AB-MT)
  • DTI (tensor model)
  • DKI (kurtosis model)
  • Notes on observables

Interactive Notebooks

• Rendered notebook: Getting Started

• Notebook (download): getting_started.ipynb