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By default FlannBasedMatcher works as KDTreeIndex with L2 norm. This is the reason why it works well with SURF descriptors and throws an exception for binary descriptors (that are matched by HAMMING distance) in your experiments. For the binary descriptors you should use flann::LshIndexParams. But there is some bug with it now, see my answer here http://answers.opencv.org/question/503/how-to-use-the-lshindexparams/
