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Your experiment with a performance of SURF vs FREAK would be more fair if you measured them for a one descriptor. To get more information about their performance I would split the measuring the descriptors computing and descriptors matching. From your message the possible reasons of slowdown of your experiment can be the following: 1) FAST gives you more keypoints than SURF. 2) If you used FlannBasedMatcher for the SURF you may use it for the FREAK too, but with LshIndexParams. How to do this and why it doesn't work now you can find here

I expect that FREAK has to be faster than SURF (for a one keypoint) because it's a binary descriptor.