This paper looks at RTT and how they affect TCP flows. Because of limited data they look at how to derive RTTs from analysis of tcpdump data (unidirectional).
Methods of getting estimates of RTT are:
SYNSYN-ACKACK – the time stamp between SYN and ACK in triple handshake.
Flight method – look at packets with near identical inter-packet times. Calculate time between start of flights (attempt to ignore rate-limited flows).