For estimating where tetrodes will go from your surgery coordinates and for choosing good coordinates from a 3D version of the Rat Brain Atlas. Useful for drive design and for tetrode/electrode adjusting.
See example .pngs for examples of visulizations.
% change base to wherever you put the folder addpath(genpath('D:/BrainModel/scripts')) cd('D:/BrainModel/')
% try it out with my pre-defined areas and an example tetrode arrangement load('CoordinateInfo.mat') % edit the paths included in CoordinateInfo to go from your base path imagefile = 'NAc64TT.png'; areas_to_plot = [1 3 2 4 5 6];
% run the GUI run_brainmodel(CoordinateInfo,areas_to_plot,imagefile)
email me at abernerslee (either berkeley or gmail) with any questions