MRtrix

MRtrix is an open-source software package for diffusion magnetic resonance imaging (dMRI) analysis and white matter tractography. The project provides MRtrix3, a cross-platform, modular framework designed for high performance and reproducible pipelines. It combines a comprehensive set of command-line tools with scripting capabilities to support end-to-end workflows from raw diffusion-weighted data to fiber models, tractography outputs, and visualization, along with quality control utilities.

Key features include preprocessing utilities such as denoising with MP-PCA, Gibbs ringing removal, and correction for motion and susceptibility-induced distortions. It offers advanced diffusion reconstruction methods, notably constrained spherical deconvolution (CSD) for estimating fiber orientation distributions, and supports multi-shell data for multi-tissue modeling. Tractography capabilities encompass probabilistic approaches (such as iFOD2) and anatomically constrained tractography (ACT), enabling more biologically plausible streamline generation. Additional tools support tissue segmentation, response function estimation, streamline filtering, and integration with visualization platforms.

MRtrix uses a native image format (.mif) but can read common formats like NIfTI and DICOM via conversion utilities. It interoperates with other neuroimaging software such as FSL and ANTs and is designed to fit into reproducible research workflows. The project maintains comprehensive documentation, tutorials, and exemplar pipelines, with an active user community contributing extensions, workflows, and best practices. MRtrix is widely employed in neuroscience research to study white matter architecture, connectivity, and diffusion-model development, as well as in clinical investigations involving tractography-informed analyses.