# 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 |

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 | Perform segmentation of continuous Fibre Orientation Distributions (FODs) to produce discrete fixels |

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 |

mesh2voxel | 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 |

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 |

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. |

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 |

tckdfc | Perform the Track-Weighted Dynamic Functional Connectivity (TW-dFC) method |

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 |

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 |

tcktransform | Apply a spatial transformation to a tracks file |

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 |

tsfvalidate | Validate a track scalar file against the corresponding track data |

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 |

voxel2mesh | Generate a surface mesh representation from a voxel image |

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 |

warpinvert | Invert a non-linear warp field |