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Diffusion-weighted (DW) magnetic resonance imaging (MRI) can measure the orientation of the white matter structure of the brain, in vivo. From the voxel-wise tissue orientations, tractography algorithms can estimate white matter fascicles volume and position. Recent studies have shown that tractography algorithms can fail to recover some existing fascicles and in some cases, produce a large incidence of false positives, biasing the structural connectivity analysis. The false positive connections are largely due to complex tissue configurations of the white matter (e.g. crossing, kissing or merging). Moreover, the relationship between the tractography reconstruction and the underlying white matter microstructure characteristics remains poorly understood. Recent tractography methods have been proposed to reduce the rate of false positives by taking full advantage of the development DW-MRI microstructure acquisition, modeling and reconstruction techniques. Those methods, called microstructure informed tractography, uses prior information on the microstructure properties of neuronal tissue to reduce ambiguities and separate fascicle in area of complex tissue configurations. Simultaneously, microstructure informed tractography allows the characterization of the white matter tissue microstructure along fascicles. Those emerging techniques are paving the way quantitative brain structural connectivity analysis.