| average | average an image along a specific axis. | 
| cleanup_ANTS_warp | clean up warp field generated by ANTS (or more specifically, WarpMultiImageTransform, replacing background voxels with NaN when they map to regions outside the original image. | 
| 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. | 
| filter_tracks | Use regions-of-interest to select a sub-set of tracks from a given track file. | 
| 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. | 
| select_tracks | select tracks from one or several track files. | 
| 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 (optionally 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. | 
| tracks2vtk | convert a track file to a vtk format, cave: coordinates are in XYZ coordinates not reference | 
| truncate_tracks | truncate a tracks file by selecting only the first N tracks. |