More info will be needed to tell you how you wish to get the R value. Are you setting up convection on all other sides? Are you wanting total resistance or are you interested in the thermal property of the material. Simulation will be able to provide you with the stress and tempature distribution.
another thread here has a post that I'm quoting
"We can define the thermal resitance as R = x/k*A, where x is the thickness of the part, k is the thermal conductivity, and A is the cross sectional area. "
which suggests: why do an fea for the resistance if all the things in that formula are known? I suppose if you know the steady state temperature and the boundary conditions like power and ambient conditions but not the thermal conductivity, you could calibrate it applying a power and convection on surfaces and converging on the temperature.
Thermal resisitance comes into play when two bodies are in contact, it's value depends on the type of the bond between surfaces, e.g we use thermal paste between an IC and Heat Sink...it reduces the thermal resistance between the surface and hence increases conductivity.
In SW Simulation, there are certain inputs & boundary conditions which has to be provided, these are then prcocessed and output is given in the form of temperature distribution, flux distribution and temperature gradient distribution only.
Thermal resistance being an input quantity can't be calculated...rather if i understood your problem well....if you know any of the result output mentioned above...you can vary input(thermal resistance) to get desired output and optimize it further.
Hope it may help you.