Assessing Topographic Structural Connectivity of the Human Basal Ganglia and Thalamus

Irtiza A. Gilani; Kader K. Oguz; Huseyin Boyaci; Katja Doerschner

Diffusion weighted imaging (DWI) is a structural magnetic resonance imaging (MRI) technique that enables white matter integrity analysis in vivo [Pierpaoli and Basser, 1996] , and by combining it with probabilistic tractography the trajectory and microstructural integrity of white matter pathways can be estimated. Researchers have used this approach [e.g. Behrens et al., 2003; Johansen-Berg et al., 2005; Leh et al., 2007] to perform thalamic-, and striatal connectivity-based parcellation to segment brain regions that were not directly detectable by conventional MRI techniques [Klein et al., 2007] . This connectivity-based segmentation of brain structures has also been used for segmenting the basal ganglia and thalamus [Draganski et al., 2008] , however, their automated segmentation failed to capture some of the connections, e.g. those to hippocampus, fusiform gyrus or substantia nigra. Here we use manual segmentation, in combination with highresolution and improved diffusion contrast to perform connection-based segmentation of basal ganglia and thalamus. Specifically, we propose to employ a rapid DWI acquisition method, with short TR and TE, since this strategy is beneficial for reduction in SNR loss due to T 2 decay inherent to the diffusion encoding and acquisition processes in MRI [Ugurbil et al. 2013 , Sotiropoulos et al. 2013 ]. Thus, this approach generates minimal SNR per unit time penalty, at 3T.