FOS is basically calculated based on the type of material applied for the component.
If you remember, in Strength of Material or Mechanics of Materials, there are Five theories of Failure. Out of 5 theories Shear strain energy theory or Von-mises theory is the most valuable one. Since brittle materials does not have yield point, you can use ultimate tensile stress as failure criterion.
Nowadays FEA based solvers are well integrated to use failure theories. User can specify kind of failure criterion in his solution method. Shear strain energy theory is the most commonly used method. These softwares can produce Von-mises stress along material,which is based on Shear strain energy theory. So user can check whether maximum Von-mises stress induced in the body crosses maximum allowable stress value. It is a common practice to introduce Factor of Safety(F.S) while designing, in order to take care of worst loading scenario. So the engineer can say his design is safe if following condition satisfies.
tell us about your material and what kind of failure of the material you are concerned with
that helps you decide what criterion you can use
NOTE, the software solves the problems all the same. your question is relative to evaluating the results that come out of the software.