The best way that I know of is to measure the CC volume of the area between the top of the engine deck and the piston. Add the volume of the head gasket and the volume of the head chamber that you wish to buy and plug it all into the CR calculator formula. I do this when I mock up an engine to check static CR.
I find the TDC and then drop the piston into the hole one inch. I add grease between the piston and the cylinder to keep the measuring fluid from oozing out then use a piece of plexi glass with grease on it. I then pour light oil into the the volume with a burette thru a hole in the plexi glass so it can be measured by CC. Don't forget to calculate the volume of your cylinder 1" tall and subtract it from the total CC you just poured in. This if done accurately will give you the cylinder CC taking into account and piston dish and position of the top of piston as it relates to the top of deck.
Hope this makes sense.....