MRtrix
3.0_RC3

Install

  • Before you install
  • Linux installation
  • macOS installation
  • Windows installation
  • Deploying MRtrix3
  • HPC clusters installation

Getting started

  • Key features
  • Commands and scripts
  • Beginner DWI tutorial
  • Images and other data
  • Command-line usage
  • Configuration file

DWI Pre-processing

  • DWI denoising
  • DWI distortion correction using dwipreproc

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
  • 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)

Spatial Normalisation

  • Warping images using warps generated from other packages

Concepts

  • Diffusion gradient scheme handling
  • Phase encoding scheme handling
  • Global intensity normalisation
  • Orthonormal Spherical Harmonic basis
  • Maximum spherical harmonic degree lmax
  • “Fixels” (and “Dixels”)
  • Motivation for afdconnectivity

Tips and Tricks

  • DICOM handling
  • Batch processing with foreach

Troubleshooting

  • Crashes, errors and performance issues
  • Display issues
  • Frequently Asked Questions (FAQ)
  • Advanced debugging

Reference

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