I am trying to understand the cost function values that are coming out flirt. I am using the following command

flirt -in inimg.nii -ref refimg.nii -schedule $FSLDIR/etc/flirtsch/measurecost1.sch -cost somecostfunction

The cost function values are not what I would expect and in many cases are out side of the possible range of many of the cost functions. For instance, for some reason I am getting negative numbers for mutual information. In one of my tests I set the reference and input image as the same image. I get the following values for different cost functions

mutualinfo = -0.972365

corratio = 0.0138204

normcorr = 0.00646079

normmi = -1.39582

Is this what I would expect?

Aaron Tanenbaum

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