Seems, that you have achieved, what you wanted.
If you still want to use nauty, you would have to do the work to write functions to convert a sudoku to a graph and back (like Gordon said in his post), i.e. define a graph with 81 nodes (representing the cells in the sudoku), edges between all nodes, where the cells are in the same box/column/row, and 'colored' by the given numbers.
You can then use nauty's functions to canonicalize or color the whole graph (= solve the sudoku).
Unfortunately Mathimagics died in December, so he can't help you anymore.
See e.g. here, how it can be done.