Decomposition of voxel constituents into meaningful parameters may lead to informative measures that reflect changes in tissue microstructure. Magn Reson Med 77:1946-1958, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

§ indicates equal first authors, # indicates equal last authors. Highlights:Mouse barrel cortex can be visualised in high definition using stTDI stTDI produced superior barrel visualisation compared to conventional MRI and FA maps stTDI is a novel imaging technique for 3D characterization of barrel cortex stTDI can detect barrel changes resulting from infraorbital nerve cut Keywords: mouse brain, barrel cortex, magnetic resonance, diffusion weighted imaging, trackdensity imaging, infraorbital nerve cut. We describe the visualization of the barrel cortex of the primary somatosensory area (S1) of ex vivo adult mouse brain with short-tracks Track Density Imaging (stTDI). stTDI produced much higher definition of barrel structures than conventional fractional anisotropy (FA), directionally-encoded color FA maps, spin-echo T1-, T2-and gradient echo T1/T2*-weighted imaging. 3D high angular resolution diffusion imaging (HARDI) data were acquired at 48 micron isotropic resolution for a (3 mm) 3 block of cortex containing the barrel field and reconstructed using stTDI at 10 micron isotropic resolution. HARDI data were also acquired at 100 micron isotropic resolution to image the whole brain and reconstructed using stTDI at 20 micron isotropic resolution. The 10 micron resolution stTDI maps showed exceptionally clear delineation of barrel structures. Individual barrels could also be distinguished in the 20 micron stTDI maps but the septa separating the individual barrels appeared thicker compared to the 10 micron maps, indicating that the ability of stTDI to produce high quality structural delineation is dependent upon acquisition resolution. Close homology was observed between the barrel structure delineated using stTDI and reconstructed histological data from the same samples. stTDI also detects barrel deletions in the posterior medial barrel sub-field in mice with infraorbital nerve cuts. The results demonstrate that stTDI is a novel imaging technique that enables three-dimensional characterization of complex structures such as the barrels in S1, and provides an important complementary non-invasive imaging tool for studying synaptic connectivity, development and plasticity of the sensory system. Abbreviations: CSD

Ultra-high field magnetic resonance imaging data obtained using a multi-echo gradient echo sequence has been shown to contain information on tissue microstructure. Quantitative assessment of water fraction, relaxation time and frequency shift using multi-compartment signal modelling may help improve our understanding of diseases and disorders affecting the human brain. In this study, we explored tissue microstructure information by analysing voxel compartment water fraction and frequency shifts derived from 7T multi-echo gradient recalled echo MRI data. We aimed to test whether the parameters of a three compartment model could distinguish the normal cortex from the cortex affected by focal cortical dysplasia. We compartmentalised normal and dysplastic cortical regions in patients diagnosed with focal cortical dysplasia. We found the frequency shift parameter of the shortest T 2 * signal compartment to be sensitive to regions of dysplastic tissue. We conclude that mathematical modelling of echo time dependent gradient recalled echo MRI signals in patients with focal cortical dysplasia can potentially delineate cortical areas that have undergone microstructural changes in comparison to normal tissue.