It is common to have some pixels in the output from FLAASH with negative values. If your FLAASH parameters are appropriate for the input data, though, then the majority of the pixels should have non-negative values, and most of the pixels with negative values should have only slightly negative values. This indicates a slight over correction in some areas, which is very common.
If you have a lot of pixels in your FLAASH output that have very negative values, then that is probably telling you that something about your input parameters is not appropriate for the input data. For example, perhaps you have used an incorrect scale factor for the radiance units stored in the input image.
- Peg
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