MRIs are taken for various reasons. Braces don't always need to come off for and MRI. An MRI for the head may require braces removal where an MRI for the chest or back likely would not. I am certain that all of my colleges would want to do anything possible to ensure you accomplish the best image possible.
Sometimes it is helpful for the MD to speak to the orthodontist in making this decision to help minimize cost and going through having them removed and replaced.