If memory serves, :- Not sure about perimeters but in Slic3r you can partition the model and apply different infill's. I think you can use different z heights for the layers as well
You will have to search the web to find some info.
You have to be in slic3r, import the model, draw a box/volume over the area you want different and specify the appropriate parameters. Then slice and save the code.
It can't be done from a host program.