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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


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