Towards reliable reconstruction of the mouse brain thalamocortical connectivity using diffusion MRI

Diffusion magnetic resonance imaging (dMRI) tractography has yielded intriguing insights into brain circuits and their relationship to behavior in response to gene mutations or neurological diseases across a number of species. Still, existing tractography approaches suffer from limited sensitivity and specificity, leading to uncertain interpretation of the reconstructed connections. Hence, in this study, we aimed to optimize the imaging and computational pipeline for reliable reconstruction of the mouse brain thalamocortical network. We developed a dMRI-based atlas of the mouse forebrain with structural labels imported from the Allen Mouse Brain Atlas (AMBA). Using the atlas and tracer data from the Allen Mouse Brain Connectivity Atlas (AMBCA) as ground truth, we investigated the accuracy of reconstructed node-to-node thalamocortical structural connectivity and effects of imaging and tractography parameters. Our results suggest that these parameters significantly affect tractography outcomes and our atlas can be used to investigate macroscopic structural connectivity in the mouse brain. Furthermore, tractography in mouse brain gray matter still face challenges and need improved imaging and tractography methods.