What unit is used for region Surface brightness in DS9? The value of the surface brightness is in what unit? I hope it is in Rayleighs. Is that true?
ds9 is a common image analysis tool used in astronomy (http://ds9.si.edu/site/Home.html). 
The units of surface brightness are simply detector counts per square arcsecond as that is all that can easily be deduced from an image. If you want to turn that into more physical units, you will need to know the gain of the CCD (how many photons produce each count) and you will need to make some assumptions about the wavelength of light that is producing the surface brightness of the emission this Note on Rayleighs may help; if all of this emission is coming from Halpha, then this is a reasonable assumption.