Extended Data Figure 9. Topography of cortico-striatal and cortico-thalamic projections.

Average inter-group distance was used to quantify the degree of which inter-group spatial relationship within the cortex is preserved in target domains. a, Inter-group injection distances were obtained by computing the 3D Euclidean distances between injection site voxels of two experiments, one from each group, and then averaging over all injection pairs. For visualization, the distances are embedded into a 2D plane using multidimensional scaling to create a group-level injection flat-map. b, Inter-group projection distances were obtained by computing the 3D Euclidean distance between a pair of voxels in a target domain weighted by the product of voxel density of two injections, one from each group. The distances are then averaged over all voxel pairs in the target domain and injection pairs between groups. c, Inter-group projection distance matrices for each target domain visualized as false-coloured heatmaps. The black columns and rows in contralateral caudoputamen and thalamus are due to four missing structures. d, Inter-group projection distances are embedded into a 2D plane using multidimensional scaling to visualize the spatial relationship between groups. e, 3D tractography paths from decimated (every other indices in each dimension) voxels in both cortical hemispheres. Voxels belonging to the medial cortical groups have been omitted to reveal a reconstructed corpus callosum showing parallel crossings with a conserved spatial configuration. f, A top-down view of 3D tractography paths into the ipsilateral thalamus for all voxels excluding the RSP/VIS groups showing axonal projections passing through fibre tracts in the striatum, narrowing through the globus pallidus, before spreading throughout the thalamus.