| average | average an image along a specific axis. |
| cat_tracks | Concatenate two track files |
| 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. |
