List of MRtrix3 commands

Command Synopsis
5tt2gmwmi Generate a mask image appropriate for seeding streamlines on the grey matter-white matter interface
5tt2vis Generate an image for visualisation purposes from an ACT 5TT segmented anatomical image
5ttcheck Thoroughly check that one or more images conform to the expected ACT five-tissue-type (5TT) format
5ttedit Manually set the partial volume fractions in an ACT five-tissue-type (5TT) image using mask images
afdconnectivity Obtain an estimate of fibre connectivity between two regions using AFD and streamlines tractography
amp2response Estimate response function coefficients based on the DWI signal in single-fibre voxels
amp2sh Convert a set of amplitudes (defined along a set of corresponding directions) to their spherical harmonic representation
connectome2tck Extract streamlines from a tractogram based on their assignment to parcellated nodes
connectomestats Connectome group-wise statistics at the edge level using non-parametric permutation testing
dcmedit Edit DICOM file in-place
dcminfo Output DICOM fields in human-readable format
dirflip Optimise the polarity of the directions in a scheme with respect to a unipolar electrostatic repulsion model, by inversion of individual directions
dirgen Generate a set of uniformly distributed directions using a bipolar electrostatic repulsion model
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
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
dirsplit Split a set of evenly distributed directions (as generated by dirgen) into approximately uniformly distributed subsets
dirstat Report statistics on a direction set
dwi2adc Convert mean dwi (trace-weighted) images to mean ADC maps
dwi2fod Estimate fibre orientation distributions from diffusion data using spherical deconvolution
dwi2mask Generates a whole brain mask from a DWI image
dwi2noise Estimate noise level voxel-wise using residuals from a truncated SH fit
dwi2tensor Diffusion (kurtosis) tensor estimation using iteratively reweighted linear least squares estimator
dwidenoise Denoise DWI data and estimate the noise level based on the optimal threshold for PCA
dwiextract Extract diffusion-weighted volumes, b=0 volumes, or certain shells from a DWI dataset
dwinormalise Intensity normalise the b=0 signal within a supplied white matter mask
fixel2sh Convert a fixel-based sparse-data image into an spherical harmonic image
fixel2tsf Map fixel values to a track scalar file based on an input tractogram
fixel2voxel Convert a fixel-based sparse-data image into some form of scalar image
fixelcfestats Fixel-based analysis using connectivity-based fixel enhancement and non-parametric permutation testing
fixelconvert Convert between the old format fixel image (.msf / .msh) and the new fixel directory format
fixelcorrespondence Obtain fixel-fixel correpondence between a subject fixel image and a template fixel mask
fixelcrop Crop/remove fixels from sparse fixel image using a binary fixel mask
fixelreorient Reorient fixel directions
fod2dec Generate FOD-based DEC maps, with optional panchromatic sharpening and/or luminance/perception correction
fod2fixel Use a fast-marching level-set method to segment fibre orientation distributions, and save parameters of interest as fixel images
label2colour Convert a parcellated image (where values are node indices) into a colour image
label2mesh Generate meshes from a label image
labelconvert Convert a connectome node image from one lookup table to another
maskdump Print out the locations of all non-zero voxels in a mask image
maskfilter Perform filtering operations on 3D / 4D mask images
mesh2pve Convert a mesh surface to a partial volume estimation image
meshconvert Convert meshes between different formats, and apply transformations
meshfilter Apply filter operations to meshes
mraverageheader Calculate the average (unbiased) coordinate space of all input images
mrcalc Apply generic voxel-wise mathematical operations to images
mrcat Concatenate several images into one
mrcheckerboardmask Create bitwise checkerboard image
mrclusterstats Voxel-based analysis using permutation testing and threshold-free cluster enhancement
mrconvert Perform conversion between different file types and optionally extract a subset of the input image
mrcrop Crop an image to a reduced field of view
mrdegibbs Remove Gibbs Ringing Artifacts
mrdump Print out the values within an image
mredit Directly edit the intensities within an image from the command-line
mrfilter Perform filtering operations on 3D / 4D MR images
mrhistmatch Modify the intensities of one image to match the histogram of another via a non-linear transform
mrhistogram Generate a histogram of image intensities
mrinfo Display image header information, or extract specific information from the header
mrmath Compute summary statistic on image intensities either across images, or along a specified axis of a single image
mrmesh Generate a mesh file from an image
mrmetric Computes a dissimilarity metric between two images
mrpad Pad an image to increase the FOV
mrregister Register two images together using a symmetric rigid, affine or non-linear transformation model
mrresize Resize an image by defining the new image resolution, voxel size or a scale factor
mrstats Compute images statistics
mrthreshold Create bitwise image by thresholding image intensity
mrtransform Apply spatial transformations to an image
mrview The MRtrix image viewer.
mtbin Multi-Tissue Bias field correction and Intensity Normalisation (WARNING: deprecated).
mtnormalise Multi-tissue informed log-domain intensity normalisation
peaks2amp Convert peak directions image to amplitudes
sh2amp Evaluate the amplitude of an image of spherical harmonic functions along specified directions
sh2peaks Extract the peaks of a spherical harmonic function at each voxel, by commencing a Newton search along a set of specified directions
sh2power Compute the total power of a spherical harmonics image
sh2response Generate an appropriate response function from the image data for spherical deconvolution
shbasis Examine the values in spherical harmonic images to estimate (and optionally change) the SH basis used
shconv Perform a spherical convolution
shview View spherical harmonics surface plots
tck2connectome Generate a connectome matrix from a streamlines file and a node parcellation image
tck2fixel Compute a fixel TDI map from a tractogram
tckconvert Convert between different track file formats
tckedit Perform various editing operations on track files
tckgen Perform streamlines tractography
tckglobal Multi-Shell Multi-Tissue Global Tractography
tckinfo Print out information about a track file
tckmap Use track data as a form of contrast for producing a high-resolution image
tcknormalise Apply a normalisation map to a tracks file
tckresample Resample each streamline in a track file to a new set of vertices
tcksample Sample values of an associated image along tracks
tcksift2 Successor to the SIFT method; instead of removing streamlines, use an EM framework to find an appropriate cross-section multiplier for each streamline
tcksift Filter a whole-brain fibre-tracking data set such that the streamline densities match the FOD lobe integrals
tckstats Calculate statistics on streamlines length
tensor2metric Generate maps of tensor-derived parameters
transformcalc Perform calculations on linear transformation matrices
transformcompose Compose any number of linear transformations and/or warps into a single transformation
transformconvert Convert linear transformation matrices
tsfdivide Divide corresponding values in track scalar files
tsfinfo Print out information about a track scalar file
tsfmult Multiply corresponding values in track scalar files
tsfsmooth Gaussian filter a track scalar file
tsfthreshold Threshold and invert track scalar files
vectorstats Statistical testing of vector data using non-parametric permutation testing
voxel2fixel Map the scalar value in each voxel to all fixels within that voxel
warp2metric Compute fixel-wise or voxel-wise metrics from a 4D deformation field
warpconvert Convert between different representations of a non-linear warp
warpcorrect Replaces voxels in a deformation field that point to 0,0,0 with nan,nan,nan
warpinit Create an initial warp image, representing an identity transformation