average | average an image along a specific axis.
bogus | this is used to test stuff.
csdeconv | perform non-negativity constrained spherical deconvolution.
dicom_filename | read a DICOM file and output a suitable filename for its storage.
dir2amp | convert directions image to amplitudes.
disp_profile | view spherical harmonics surface plots.
dwi2SH | convert base diffusion-weighted images to their spherical harmonic representation.
dwi2tensor | convert diffusion-weighted images to tensor images.
erode | erode (or dilate) mask (i.e. binary) image
estimate_response | estimate the fibre response function for use in spherical deconvolution.
find_SH_peaks | identify the orientations of the N largest peaks of a SH profile
gen_ROI | generate a mask ROI with the same dimensions as the input dataset, and all voxel values set to one in the regions specified
gen_WM_mask | generate a white matter probability mask from the DW images.
gen_unit_warp | generate a warp field corresponding to a no-warp operation. This is useful to obtain the warp fields from other normalisation applications, by applying the warp of interest to the the warp field generated by this program.
gendir | generate a set of directions evenly distributed over a hemisphere.
import_tracks | convert ascii track files into MRtrix format.
median3D | smooth images using a 3x3x3 median filter.
mrabs | take absolute value of image intensity
mradd | add or subtract images
mrcat | concatenate several images into one
mrconvert | perform conversion between different file types and optionally extract a subset of the input image.
mrinfo | display header information
mrmult | multiply images
mrstats | compute images statistics.
mrtransform | apply spatial transformations or reslice images.
mrview | the MRtrix image viewer.
normalise_tracks | apply a normalisation map to a tracks file.
read_dicom | output DICOM fields in human-readable format.
read_ximg | output XIMG fields in human-readable format.
resample_tracks | Resample tracks so they all have the same number of samples, spaced at constant intervals within the range specified.
sample_tracks | sample image intensity values along the tracks, producing one intensity value per point along each track.
sdeconv | perform linear spherical deconvolution.
streamtrack | perform streamlines tracking.
tensor2ADC | calculate map of mean apparent diffusion coefficient (ADC) from diffusion tensor image.
tensor2FA | calculate map of fractional anisotropy from diffusion tensor image.
tensor2vector | generate map of the major eigenvector.
tensor_metric | generate maps of tensor-derived parameters.
threshold | create bitwise image by thresholding image intensity.
track_info | print out information about track file
tracks2prob | convert a tracks file into a map of the fraction of tracks to enter each voxel.
truncate_tracks | truncate a tracks file by selecting only the first N tracks.