Abstract: Stroke is the second leading cause of death worldwide with about 50% of survivors being chronically disabled (Donkor, 2018). The behavioral improvement seen in stroke patients in the first weeks after a stroke is contributed by behavioral compensation, reorganization in somatotopic maps and activity in peri-infarct but also distant regions which are connected to the stroke area as supported by animal studies. Spontaneous recovery is related to region-specific changes in recovery-related genes (Ito et al., 2018), growth factor expression, axonal sprouting and dendritic spine turnover (Murphy and Corbett, 2009). These brain plasticity processes follow an intrinsic time-line with a limited period of heightened neuroplasticity for which the behavioral experience is a key modulator. However, experimental studies correlating structural and functional brain network changes during recovery are scarce and it remains controversial which mechanisms, regions and time points are most relevant and thus best suited for translational interventions. In that context, longitudinal in vivo imaging will be essential. MRI is particularly suited for repetitive, non-invasive imaging with high spatial resolution. Clinical stroke studies use routinely MRI in a standardized acquisition and post-processing regime for measuring the stroke size and location. In addition, structural connectivity analyses using diffusion MRI (dMRI) in the corticospinal and corticocortical fiber tracts effectively predict motor impairment and improvement, respectively (Koch et al., 2016). Stroke disrupts brain connectivity by primary mechanisms such as cell death and injury in white matter tracts, but also secondary mechanisms such as axonal degeneration which spreads to structurally connected cells (Cao et al., 2020). On the macroscopic level, dMRI, sensitive to tissue-specific water diffusion properties, offers the unique possibility to quantify microstructural changes, e.g. related to stroke-related processes of cell swelling, cell lysis and demyelination longitudinally on the whole brain level expressed in the dMRI measures of axial, radial, mean diffusivity, and fractional anisotropy. Furthermore, fiber tracking, a more complex post-processing and mathematical modeling of dMRI exploits the preferential diffusivity of protons along the myelin sheets to generate a quantitative measure of fiber tracts between brain regions. Experimental studies in rats and mice only recently evolved due to technical challenges such as the required signal-to-noise and susceptibility-induced image distortions (Hoehn and Aswendt, 2013). Based on pioneering work more than 20 years ago in a mouse model of reversible focal ischemia measuring the acute temporal dynamics of diffusion, so far, only ex vivo Diffusion Tensor Imaging (DTI) fiber tracking was applied in stroke mice to compare selected ipsi- vs. contralesional tracts (Granziera et al., 2007).