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 (Tournier et al.. 2004; Tournier et al., 2007; Jeurissen et al., 2014), a probabilisitic streamlines algorithm for fibre tractography of white matter (Tournier et al., 2012), fixel-based analysis of apparent fibre density and fibre cross-section (Raffelt et al., 2012; Raffelt et al., 2015; Raffelt et al., 2016), quantitative structural connectivity analysis (Smith et al., 2012; Smith et al., 2013; Smith et al., 2015; Christiaens et al., 2015), and non-linear spatial registration of fibre orientation distribution images (Raffelt et al., 2011).
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.
installation/before_install installation/linux_install installation/mac_install installation/windows_install installation/hpc_clusters_install
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
dwi_preprocessing/denoising dwi_preprocessing/dwipreproc
constrained_spherical_deconvolution/response_function_estimation constrained_spherical_deconvolution/lmax constrained_spherical_deconvolution/multi_tissue_csd
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
fixel_based_analysis/ss_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
spatial_normalisation/warping_images_with_warps_from_other_packages
concepts/dw_scheme concepts/global_intensity_normalisation concepts/orthonormal_basis concepts/dixels_fixels concepts/afd_connectivity
tips_and_tricks/dicom_handling tips_and_tricks/batch_processing_with_foreach
troubleshooting/FAQ troubleshooting/display_issues troubleshooting/compiler_error_during_build troubleshooting/hanging_or_crashing troubleshooting/advanced_debugging
reference/commands_list reference/scripts_list reference/config_file_options reference/mrtrix2_equivalent_commands