The paper concentrates on obtaining hidden relationships among individual clauses of complex sentences from the Prague Dependency Treebank. The treebank contains only an information about mutual relationships among individual tokens (words, punctuation marks), not about more complex units (clauses). For the experiments with clauses and their parts (segments) it was therefore necessary to develop an automatic method transforming the original annotation into a scheme describing the syntactic relationships between clauses. The task was complicated by a certain degree of inconsistency in original annotation with regard to clauses and their structure. The paper describes the algorithm of deriving clause-related information from the existing annotation and its evaluation.