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 |