How to convert infrared image matrices to binary?

I have background corrected BW infrared images of fuel injections. What is the best way to take into account pixel value increases from temperature as the cycles progress and convert the matrices to binary? Right now I have for loops to load each matrix one by one in for loops. To convert I'm using a basic '> 'value' ' command to convert it to binary, but using either the range or mean for example, what is the best way to obtain the needed value?