The index used when you set ds.sites_to_use is the index that the data is stored in the binned_data cell array. This should be the same order as that the raster files are loaded (based on the create_binned_data_from_raster_data function). You do not need to add a filed in raster_site_info to get this working – although having meta information in raster_site_info might help to make the correspondence between the index of each neuron and other information about the neuron when looking at the binned_data.