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
    • 5tt2gmwmi
    • 5tt2vis
    • 5ttedit
    • afdconnectivity
    • amp2sh
    • connectome2tck
    • dcmedit
    • dcminfo
    • dirflip
    • dirgen
    • dirmerge
    • dirorder
    • dirsplit
    • dirstat
    • dwi2adc
    • dwi2fod
    • dwi2mask
    • dwi2noise
    • dwi2tensor
    • dwidenoise
    • dwiextract
    • dwinormalise
    • fixel2sh
    • fixel2tsf
    • fixel2voxel
    • fixelcalc
    • fixelcfestats
    • fixelcorrespondence
    • fixellog
    • fixelreorient
    • fixelstats
    • fixelthreshold
    • fod2dec
    • fod2fixel
    • label2colour
    • label2mesh
    • labelconvert
    • maskfilter
    • mesh2pve
    • meshconvert
    • meshfilter
    • mraverageheader
    • mrcalc
    • mrcat
    • mrcheckerboardmask
    • mrclusterstats
    • mrconvert
    • mrcrop
    • mrfilter
    • mrinfo
    • mrmath
    • mrmesh
    • mrmetric
    • mrpad
    • mrregister
    • mrresize
    • mrstats
    • mrthreshold
    • mrtransform
    • mrview
    • peaks2amp
    • sh2amp
    • sh2peaks
    • sh2power
    • sh2response
    • shbasis
    • shconv
    • shview
    • tck2connectome
    • tckconvert
    • tckedit
    • tckgen
    • tckglobal
    • tckinfo
    • tckmap
    • tcknormalise
    • tckresample
    • tcksample
    • tcksift
    • tcksift2
    • tckstats
    • tensor2metric
    • transformcalc
    • transformconvert
    • tsfdivide
    • tsfinfo
    • tsfmult
    • tsfsmooth
    • tsfthreshold
    • voxel2fixel
    • warp2metric
    • warpconvert
    • warpcorrect
    • warpinit
  • Python scripts provided with MRtrix3
  • List of MRtrix3 configuration file options
  • MRtrix 0.2 equivalent commands
MRtrix
  • Docs »
  • List of MRtrix3 commands
  • Edit on GitHub

List of MRtrix3 commandsΒΆ

  • 5tt2gmwmi
  • 5tt2vis
  • 5ttedit
  • afdconnectivity
  • amp2sh
  • connectome2tck
  • dcmedit
  • dcminfo
  • dirflip
  • dirgen
  • dirmerge
  • dirorder
  • dirsplit
  • dirstat
  • dwi2adc
  • dwi2fod
  • dwi2mask
  • dwi2noise
  • dwi2tensor
  • dwidenoise
  • dwiextract
  • dwinormalise
  • fixel2sh
  • fixel2tsf
  • fixel2voxel
  • fixelcalc
  • fixelcfestats
  • fixelcorrespondence
  • fixellog
  • fixelreorient
  • fixelstats
  • fixelthreshold
  • fod2dec
  • fod2fixel
  • label2colour
  • label2mesh
  • labelconvert
  • maskfilter
  • mesh2pve
  • meshconvert
  • meshfilter
  • mraverageheader
  • mrcalc
  • mrcat
  • mrcheckerboardmask
  • mrclusterstats
  • mrconvert
  • mrcrop
  • mrfilter
  • mrinfo
  • mrmath
  • mrmesh
  • mrmetric
  • mrpad
  • mrregister
  • mrresize
  • mrstats
  • mrthreshold
  • mrtransform
  • mrview
  • peaks2amp
  • sh2amp
  • sh2peaks
  • sh2power
  • sh2response
  • shbasis
  • shconv
  • shview
  • tck2connectome
  • tckconvert
  • tckedit
  • tckgen
  • tckglobal
  • tckinfo
  • tckmap
  • tcknormalise
  • tckresample
  • tcksample
  • tcksift
  • tcksift2
  • tckstats
  • tensor2metric
  • transformcalc
  • transformconvert
  • tsfdivide
  • tsfinfo
  • tsfmult
  • tsfsmooth
  • tsfthreshold
  • voxel2fixel
  • warp2metric
  • warpconvert
  • warpcorrect
  • warpinit
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