MRtrix provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI. Features include the estimation of fibre orientation distributions using constrained spherical deconvolution ([Tournier2004]_; [Tournier2007]_; [Jeurissen2014]_), visualisation of these via directionally-encoded colour maps ([Dhollander2015a]_) and panchromatic sharpening ([Dhollander2015b]_), a probabilisitic streamlines algorithm for fibre tractography of white matter ([Tournier2012]_), fixel-based analysis of apparent fibre density and fibre cross-section ([Raffelt2012]_; [Raffelt2015]_; [Raffelt2017]_), quantitative structural connectivity analysis ([Smith2012]_; [Smith2013]_; [Smith2015]_; [Christiaens2015]_), and non-linear spatial registration of fibre orientation distribution images ([Raffelt2011]_).
These applications have been written from scratch in C++, using the functionality provided by Eigen, and Qt. The software is currently capable of handling DICOM, NIfTI and AnalyseAVW image formats, amongst others. The source code is distributed under the Mozilla Public License.
.. toctree:: :maxdepth: 1 :caption: Install installation/before_install installation/linux_install installation/mac_install installation/windows_install installation/deployment installation/hpc_clusters_install
.. toctree:: :maxdepth: 1 :caption: Getting started getting_started/key_features getting_started/commands_and_scripts getting_started/beginner_dwi_tutorial getting_started/image_data getting_started/command_line getting_started/config
.. toctree:: :maxdepth: 1 :caption: DWI Pre-processing dwi_preprocessing/denoising dwi_preprocessing/dwipreproc
.. toctree:: :maxdepth: 1 :caption: Constrained Spherical Deconvolution constrained_spherical_deconvolution/response_function_estimation constrained_spherical_deconvolution/constrained_spherical_deconvolution constrained_spherical_deconvolution/multi_shell_multi_tissue_csd
.. toctree:: :maxdepth: 1 :caption: Fixel-Based Analysis fixel_based_analysis/st_fibre_density_cross-section fixel_based_analysis/mt_fibre_density_cross-section fixel_based_analysis/computing_effect_size_wrt_controls fixel_based_analysis/displaying_results_with_streamlines
.. toctree:: :maxdepth: 1 :caption: Quantitative Structural Connectivity quantitative_structural_connectivity/act quantitative_structural_connectivity/sift quantitative_structural_connectivity/structural_connectome quantitative_structural_connectivity/connectome_tool quantitative_structural_connectivity/labelconvert_tutorial quantitative_structural_connectivity/global_tractography quantitative_structural_connectivity/ismrm_hcp_tutorial
.. toctree:: :maxdepth: 1 :caption: Spatial Normalisation spatial_normalisation/warping_images_with_warps_from_other_packages
.. toctree:: :maxdepth: 1 :caption: Concepts concepts/dw_scheme concepts/pe_scheme concepts/global_intensity_normalisation concepts/orthonormal_sh_basis concepts/sh_basis_lmax concepts/fixels_dixels concepts/afd_connectivity
.. toctree:: :maxdepth: 1 :caption: Tips and Tricks tips_and_tricks/dicom_handling tips_and_tricks/batch_processing_with_foreach
.. toctree:: :maxdepth: 1 :caption: Troubleshooting troubleshooting/performance_and_crashes troubleshooting/display_issues troubleshooting/FAQ troubleshooting/advanced_debugging
.. toctree:: :maxdepth: 1 :caption: Reference reference/commands_list reference/scripts_list reference/config_file_options reference/mrtrix2_equivalent_commands reference/references