Hello! I am trying to do something very simple but not having much luck. I want to use the adult mouse brain atlas to get average depths / thicknesses of cortical layers to use in a modeling project. Is there a simple way to do this? And is this information available in the human atlas as well?
Sorry, our applications and services does not currently support cortical thickness calculations.
Hello @bmarsh , are you looking for depths/thicknesses as a proportion (percent) of total cortical thickness, or in terms of raw measurements? If the former, the solution to Laplace’s equation within the isocortex (http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/cortical_coordinates/ccf_2017/laplacian_10.nrrd) can be used in conjunction with the atlas labels. If you’re looking for depth in physical units, I have generated streamlines for a previous project over which thickness can be computed. Happy to share those resources + code if you want.