
.. _list-of-mrtrix3-commands:

########################
List of MRtrix3 commands
########################




.. toctree::
    :hidden:

    commands/5tt2gmwmi
    commands/5tt2vis
    commands/5ttcheck
    commands/5ttedit
    commands/afdconnectivity
    commands/amp2response
    commands/amp2sh
    commands/connectome2tck
    commands/connectomestats
    commands/dcmedit
    commands/dcminfo
    commands/dirflip
    commands/dirgen
    commands/dirmerge
    commands/dirorder
    commands/dirsplit
    commands/dirstat
    commands/dwi2adc
    commands/dwi2fod
    commands/dwi2mask
    commands/dwi2tensor
    commands/dwidenoise
    commands/dwiextract
    commands/dwinormalise
    commands/fixel2sh
    commands/fixel2tsf
    commands/fixel2voxel
    commands/fixelcfestats
    commands/fixelconvert
    commands/fixelcorrespondence
    commands/fixelcrop
    commands/fixelreorient
    commands/fod2dec
    commands/fod2fixel
    commands/label2colour
    commands/label2mesh
    commands/labelconvert
    commands/maskdump
    commands/maskfilter
    commands/mesh2voxel
    commands/meshconvert
    commands/meshfilter
    commands/mraverageheader
    commands/mrcalc
    commands/mrcat
    commands/mrcheckerboardmask
    commands/mrclusterstats
    commands/mrconvert
    commands/mrcrop
    commands/mrdegibbs
    commands/mrdump
    commands/mredit
    commands/mrfilter
    commands/mrhistmatch
    commands/mrhistogram
    commands/mrinfo
    commands/mrmath
    commands/mrmetric
    commands/mrpad
    commands/mrregister
    commands/mrresize
    commands/mrstats
    commands/mrthreshold
    commands/mrtransform
    commands/mrview
    commands/mtnormalise
    commands/peaks2amp
    commands/sh2amp
    commands/sh2peaks
    commands/sh2power
    commands/sh2response
    commands/shbasis
    commands/shconv
    commands/shview
    commands/tck2connectome
    commands/tck2fixel
    commands/tckconvert
    commands/tckdfc
    commands/tckedit
    commands/tckgen
    commands/tckglobal
    commands/tckinfo
    commands/tckmap
    commands/tckresample
    commands/tcksample
    commands/tcksift2
    commands/tcksift
    commands/tckstats
    commands/tcktransform
    commands/tensor2metric
    commands/transformcalc
    commands/transformcompose
    commands/transformconvert
    commands/tsfdivide
    commands/tsfinfo
    commands/tsfmult
    commands/tsfsmooth
    commands/tsfthreshold
    commands/tsfvalidate
    commands/vectorstats
    commands/voxel2fixel
    commands/voxel2mesh
    commands/warp2metric
    commands/warpconvert
    commands/warpcorrect
    commands/warpinit
    commands/warpinvert


.. csv-table::
    :header: "Command", "Synopsis"

    :ref:`5tt2gmwmi`, "Generate a mask image appropriate for seeding streamlines on the grey matter-white matter interface"
    :ref:`5tt2vis`, "Generate an image for visualisation purposes from an ACT 5TT segmented anatomical image"
    :ref:`5ttcheck`, "Thoroughly check that one or more images conform to the expected ACT five-tissue-type (5TT) format"
    :ref:`5ttedit`, "Manually set the partial volume fractions in an ACT five-tissue-type (5TT) image using mask images"
    :ref:`afdconnectivity`, "Obtain an estimate of fibre connectivity between two regions using AFD and streamlines tractography"
    :ref:`amp2response`, "Estimate response function coefficients based on the DWI signal in single-fibre voxels"
    :ref:`amp2sh`, "Convert a set of amplitudes (defined along a set of corresponding directions) to their spherical harmonic representation"
    :ref:`connectome2tck`, "Extract streamlines from a tractogram based on their assignment to parcellated nodes"
    :ref:`connectomestats`, "Connectome group-wise statistics at the edge level using non-parametric permutation testing"
    :ref:`dcmedit`, "Edit DICOM file in-place"
    :ref:`dcminfo`, "Output DICOM fields in human-readable format"
    :ref:`dirflip`, "Optimise the polarity of the directions in a scheme with respect to a unipolar electrostatic repulsion model, by inversion of individual directions"
    :ref:`dirgen`, "Generate a set of uniformly distributed directions using a bipolar electrostatic repulsion model"
    :ref:`dirmerge`, "Splice or merge sets of directions over multiple shells into a single set, in such a way as to maintain near-optimality upon truncation"
    :ref:`dirorder`, "Reorder a set of directions to ensure near-uniformity upon truncation - i.e. if the scan is terminated early, the acquired directions are still close to optimal"
    :ref:`dirsplit`, "Split a set of evenly distributed directions (as generated by dirgen) into approximately uniformly distributed subsets"
    :ref:`dirstat`, "Report statistics on a direction set"
    :ref:`dwi2adc`, "Convert mean dwi (trace-weighted) images to mean ADC maps"
    :ref:`dwi2fod`, "Estimate fibre orientation distributions from diffusion data using spherical deconvolution"
    :ref:`dwi2mask`, "Generates a whole brain mask from a DWI image"
    :ref:`dwi2tensor`, "Diffusion (kurtosis) tensor estimation using iteratively reweighted linear least squares estimator"
    :ref:`dwidenoise`, "Denoise DWI data and estimate the noise level based on the optimal threshold for PCA"
    :ref:`dwiextract`, "Extract diffusion-weighted volumes, b=0 volumes, or certain shells from a DWI dataset"
    :ref:`dwinormalise`, "Intensity normalise the b=0 signal within a supplied white matter mask"
    :ref:`fixel2sh`, "Convert a fixel-based sparse-data image into an spherical harmonic image"
    :ref:`fixel2tsf`, "Map fixel values to a track scalar file based on an input tractogram"
    :ref:`fixel2voxel`, "Convert a fixel-based sparse-data image into some form of scalar image"
    :ref:`fixelcfestats`, "Fixel-based analysis using connectivity-based fixel enhancement and non-parametric permutation testing"
    :ref:`fixelconvert`, "Convert between the old format fixel image (.msf / .msh) and the new fixel directory format"
    :ref:`fixelcorrespondence`, "Obtain fixel-fixel correpondence between a subject fixel image and a template fixel mask"
    :ref:`fixelcrop`, "Crop/remove fixels from sparse fixel image using a binary fixel mask"
    :ref:`fixelreorient`, "Reorient fixel directions"
    :ref:`fod2dec`, "Generate FOD-based DEC maps, with optional panchromatic sharpening and/or luminance/perception correction"
    :ref:`fod2fixel`, "Perform segmentation of continuous Fibre Orientation Distributions (FODs) to produce discrete fixels"
    :ref:`label2colour`, "Convert a parcellated image (where values are node indices) into a colour image"
    :ref:`label2mesh`, "Generate meshes from a label image"
    :ref:`labelconvert`, "Convert a connectome node image from one lookup table to another"
    :ref:`maskdump`, "Print out the locations of all non-zero voxels in a mask image"
    :ref:`maskfilter`, "Perform filtering operations on 3D / 4D mask images"
    :ref:`mesh2voxel`, "Convert a mesh surface to a partial volume estimation image"
    :ref:`meshconvert`, "Convert meshes between different formats, and apply transformations"
    :ref:`meshfilter`, "Apply filter operations to meshes"
    :ref:`mraverageheader`, "Calculate the average (unbiased) coordinate space of all input images"
    :ref:`mrcalc`, "Apply generic voxel-wise mathematical operations to images"
    :ref:`mrcat`, "Concatenate several images into one"
    :ref:`mrcheckerboardmask`, "Create bitwise checkerboard image"
    :ref:`mrclusterstats`, "Voxel-based analysis using permutation testing and threshold-free cluster enhancement"
    :ref:`mrconvert`, "Perform conversion between different file types and optionally extract a subset of the input image"
    :ref:`mrcrop`, "Crop an image to a reduced field of view"
    :ref:`mrdegibbs`, "Remove Gibbs Ringing Artifacts"
    :ref:`mrdump`, "Print out the values within an image"
    :ref:`mredit`, "Directly edit the intensities within an image from the command-line"
    :ref:`mrfilter`, "Perform filtering operations on 3D / 4D MR images"
    :ref:`mrhistmatch`, "Modify the intensities of one image to match the histogram of another"
    :ref:`mrhistogram`, "Generate a histogram of image intensities"
    :ref:`mrinfo`, "Display image header information, or extract specific information from the header"
    :ref:`mrmath`, "Compute summary statistic on image intensities either across images, or along a specified axis of a single image"
    :ref:`mrmetric`, "Computes a dissimilarity metric between two images"
    :ref:`mrpad`, "Pad an image to increase the FOV"
    :ref:`mrregister`, "Register two images together using a symmetric rigid, affine or non-linear transformation model"
    :ref:`mrresize`, "Resize an image by defining the new image resolution, voxel size or a scale factor"
    :ref:`mrstats`, "Compute images statistics"
    :ref:`mrthreshold`, "Create bitwise image by thresholding image intensity"
    :ref:`mrtransform`, "Apply spatial transformations to an image"
    :ref:`mrview`, "The MRtrix image viewer."
    :ref:`mtnormalise`, "Multi-tissue informed log-domain intensity normalisation"
    :ref:`peaks2amp`, "Convert peak directions image to amplitudes"
    :ref:`sh2amp`, "Evaluate the amplitude of an image of spherical harmonic functions along specified directions"
    :ref:`sh2peaks`, "Extract the peaks of a spherical harmonic function at each voxel, by commencing a Newton search along a set of specified directions"
    :ref:`sh2power`, "Compute the total power of a spherical harmonics image"
    :ref:`sh2response`, "Generate an appropriate response function from the image data for spherical deconvolution"
    :ref:`shbasis`, "Examine the values in spherical harmonic images to estimate (and optionally change) the SH basis used"
    :ref:`shconv`, "Perform a spherical convolution"
    :ref:`shview`, "View spherical harmonics surface plots"
    :ref:`tck2connectome`, "Generate a connectome matrix from a streamlines file and a node parcellation image"
    :ref:`tck2fixel`, "Compute a fixel TDI map from a tractogram"
    :ref:`tckconvert`, "Convert between different track file formats"
    :ref:`tckdfc`, "Perform the Track-Weighted Dynamic Functional Connectivity (TW-dFC) method"
    :ref:`tckedit`, "Perform various editing operations on track files"
    :ref:`tckgen`, "Perform streamlines tractography"
    :ref:`tckglobal`, "Multi-Shell Multi-Tissue Global Tractography"
    :ref:`tckinfo`, "Print out information about a track file"
    :ref:`tckmap`, "Use track data as a form of contrast for producing a high-resolution image"
    :ref:`tckresample`, "Resample each streamline in a track file to a new set of vertices"
    :ref:`tcksample`, "Sample values of an associated image along tracks"
    :ref:`tcksift2`, "Successor to the SIFT method; instead of removing streamlines, use an EM framework to find an appropriate cross-section multiplier for each streamline"
    :ref:`tcksift`, "Filter a whole-brain fibre-tracking data set such that the streamline densities match the FOD lobe integrals"
    :ref:`tckstats`, "Calculate statistics on streamlines length"
    :ref:`tcktransform`, "Apply a spatial transformation to a tracks file"
    :ref:`tensor2metric`, "Generate maps of tensor-derived parameters"
    :ref:`transformcalc`, "Perform calculations on linear transformation matrices"
    :ref:`transformcompose`, "Compose any number of linear transformations and/or warps into a single transformation"
    :ref:`transformconvert`, "Convert linear transformation matrices"
    :ref:`tsfdivide`, "Divide corresponding values in track scalar files"
    :ref:`tsfinfo`, "Print out information about a track scalar file"
    :ref:`tsfmult`, "Multiply corresponding values in track scalar files"
    :ref:`tsfsmooth`, "Gaussian filter a track scalar file"
    :ref:`tsfthreshold`, "Threshold and invert track scalar files"
    :ref:`tsfvalidate`, "Validate a track scalar file against the corresponding track data"
    :ref:`vectorstats`, "Statistical testing of vector data using non-parametric permutation testing"
    :ref:`voxel2fixel`, "Map the scalar value in each voxel to all fixels within that voxel"
    :ref:`voxel2mesh`, "Generate a surface mesh representation from a voxel image"
    :ref:`warp2metric`, "Compute fixel-wise or voxel-wise metrics from a 4D deformation field"
    :ref:`warpconvert`, "Convert between different representations of a non-linear warp"
    :ref:`warpcorrect`, "Replaces voxels in a deformation field that point to 0,0,0 with nan,nan,nan"
    :ref:`warpinit`, "Create an initial warp image, representing an identity transformation"
    :ref:`warpinvert`, "Invert a non-linear warp field"
