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I have a similar problem with CV_TM_SQDIFF since using OpenCV 3.1. It worked fine for me in 2.4.5 as long, as I didn't specify the type (imread) when loading the grayscaled template and image to be searched in. If I specify the type when loading, I even get negative values for both versions on some test cases. After all, the locations seem to be correct...
Could you resolve the issue or may there be some bugs in OpenCV involved?
