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Welcome to the MRtrix user documentation!

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