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At the qualification round, each team plays one match against all other teams in its pool. Top four teams in each pool advance, the remaining two leave the competition.
At the second phase, usually called final round, teams play quarterfinals, semifinals and finals.
For the final round, matches are organized according to the results obtained in the qualification round. Let the top four teams in each pool be A1, A2, A3, A4; B1, B2, B3, B4. Quarterfinals would then be: A1xB4; A2xB3; A3xB2; A4xB1.
I don't think this is how teams are matched up at the knock-out stage in the Beijing Olympics. No problem with A1xB4 and A4xB1. But the other four teams (A2 B2 A3 B3) actaully drew a lot to decide who plays whom.