\documentclass[monochrome]{../fithesis3}
\usepackage{ifxetex}
\ifxetex
  \usepackage{polyglossia}
  \setmainlanguage{slovak}
\else
  \usepackage[slovak]{babel}
\fi
\thesissetup{
  basepath=..,
  type=r,
  faculty=sci}
\begin{document}
  foo bar
\end{document}
