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Change to a for loop, where you use meanStdDev(C.col(i), mn, stdev) and store the results in an array of appropriate size.

meanStdDev only works up to 4 channels. Any more and the results wrap (I believe). With six channels you'd get (0+4, 1+5, 2, 3) (Again, I think). Either way, the documentation tells you that it only works up to 4.