yes, but in the case of magnetoencephalography, do you say "em ee gee" or "Meg"?

Positron Emission Tomography is shortened to PET, which is an acronym.

Magnetic Resonance Imaging is shortened to MRI, which is an initilization or initilism.

Not a big deal, but it's nice to be aware of the difference.

(By the way, the New Yorker magazine typesets them differently in print, using small caps for acronyms, and regular caps for initilisms, but this distinction appears to be lost in their on-line version.)