It can be done in a research facility, where they will use a battery of tests to detemine fun stuff such as your respotroy echnage ratio, blah blah blah ...

A better way is to use an on-line calculator such as this one:

http://www.stevenscreek.com/goodies/jcalories.shtml

It's not an EXACT science, but neither is whatthey do in the labs. What they can measure (not metabolic rate) is kinda like looking at your gas guage and gas peddle to see how fast you are going .. not the best way to check your speed, but since the human body doesn't have a "speedometer", you just have to make the best of what you have.

The calculator I linked to is pretty good, and takes into account activity.

Give it a go.