Fitting a Masked Image. How to skip zeros?

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Hi,
I've used the imtool to define a region of interest on a series of image files. I then use these image files to perform a pixel-wise fit. The masked images contain a large number of zero entries (outside the ROI), and only a few non-zero entries. Is there a way to identify and skip these zero entries in the fit loop to speed up the process?
Thanks,
Avi

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