RTDs are generally more accurate, more stable, and more expensive than thermocouples. RTDs usually have a smaller measurement range than thermocouples, however you've stated that both are sufficient in this respect. RTDs may be subject to problems with self heating, depending on the thermal conductivity of the media you are measuring. If the RTD is measuring a still gas, self heating can be a problem. If it's situated in a rapidly flowing liquid or mounted to couductive solid surface, this should not be an issue.
Regards,
Brent R.
Applications Engineer
National Instruments
