MRtrix
0.3.16

Install

  • Before you install
  • Linux installation
  • MacOS X installation
  • Windows installation
  • HPC clusters installation

Getting started

  • Key features
  • Configuration file
  • Images and other data
  • Command-line usage
  • Troubleshooting

Tutorials

  • Basic DWI processing
  • DWI denoising
  • Structural connectome for Human Connectome Project (HCP)
  • Using the connectome visualisation tool
  • Structural connectome construction: Using labelconvert
  • Advanced debugging
  • Warping images using warps generated from other packages
  • Frequently Asked Questions (FAQ)

Workflows

  • DWI Pre-processing for Quantitative Analysis
  • Fixel-Based Analysis (FBA)
  • Anatomically-Constrained Tractography (ACT)
  • Spherical-deconvolution Informed Filtering of Tractograms (SIFT)
  • Structural connectome construction
  • Global tractography
  • Multi-tissue constrained spherical deconvolution

Concepts

  • Diffusion gradient scheme handling
  • Orthonormal Spherical Harmonic basis
  • Dixels and Fixels
  • Motivation for afdconnectivity
  • Response function estimation

Reference

  • List of MRtrix3 commands
  • Python scripts provided with MRtrix3
    • 5ttgen freesurfer
    • 5ttgen fsl
    • 5ttgen
    • dwi2response dhollander
    • dwi2response fa
    • dwi2response manual
    • dwi2response msmt_5tt
    • dwi2response tax
    • dwi2response tournier
    • dwi2response
    • dwibiascorrect
    • dwiintensitynorm
    • dwipreproc
    • labelsgmfix
    • population_template
  • List of MRtrix3 configuration file options
  • MRtrix 0.2 equivalent commands
MRtrix
  • Docs »
  • Python scripts provided with MRtrix3
  • Edit on GitHub

Python scripts provided with MRtrix3ΒΆ

  • 5ttgen freesurfer
  • 5ttgen fsl
  • 5ttgen
  • dwi2response dhollander
  • dwi2response fa
  • dwi2response manual
  • dwi2response msmt_5tt
  • dwi2response tax
  • dwi2response tournier
  • dwi2response
  • dwibiascorrect
  • dwiintensitynorm
  • dwipreproc
  • labelsgmfix
  • population_template
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