MRtrix3

Install

  • Before you install
  • Installing MRtrix3
  • Building MRtrix3 from source
  • Deploying MRtrix3
  • HPC clusters installation
  • Running MRtrix3 using containers

Getting started

  • Beginner DWI tutorial
  • Images and other data
  • Command-line usage
  • Configuration file

DWI Pre-processing

  • DWI denoising
  • DWI distortion correction using dwifslpreproc

Constrained Spherical Deconvolution

  • Response function estimation
  • Constrained spherical deconvolution
  • Multi-shell multi-tissue constrained spherical deconvolution

Fixel-Based Analysis

  • Fibre density and cross-section - Single-tissue CSD
  • Fibre density and cross-section - Multi-tissue CSD
  • Fixel image (directory) format
  • Mitigating the effects of brain cropping
  • Expressing the effect size relative to controls
  • Displaying results with streamlines

Quantitative Structural Connectivity

  • Anatomically-Constrained Tractography (ACT)
  • Spherical-deconvolution Informed Filtering of Tractograms (SIFT)
  • Structural connectome construction
  • Using the connectome visualisation tool
  • labelconvert: Explanation & demonstration
  • Global tractography
  • ISMRM tutorial - Structural connectome for Human Connectome Project (HCP)

Concepts

  • Diffusion gradient scheme handling
  • Phase encoding scheme handling
  • Global intensity normalisation
  • Spherical Harmonics
  • Maximum spherical harmonic degree lmax
  • “Fixels” (and “Dixels”)
  • Motivation for afdconnectivity
  • mrview’s “Lock To Image Axes”

Tips and Tricks

  • DICOM handling
  • Batch processing with for_each
  • External modules
  • Troubleshooting

Reference

  • List of MRtrix3 commands
  • List of MRtrix3 configuration file options
  • List of MRtrix3 environment variables
  • MRtrix 0.2 equivalent commands
  • References
MRtrix3
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