MRI is, in essence, the imaging of water. The strong magnetic field aligns hydrogen atoms, which are most frequently within water molecules. RF pulses are used to change aligned atoms from a low energy stable state to a high energy unstable state. The atoms give up their energy and relax to the more stable low energy state and the energy emitted produces a signal that can be detected by coils placed around the patient. The signal received is then used to produce images. 



Different methods are used to evaluate different characteristics of the water within the area of interest. This is why multiple sequences are required. Because water is most plentiful in soft tissues, MRI provides superior soft tissue detail to other imaging modalities, however in order to gain enough signal for diagnostic images, the resolution used is typically less than in CT. Osseous structures can be evaluated to a certain degree, but imaging of osseous structures is preferentially performed with CT. The use of gadolinium, a paramagnetic material, helps better characterize alterations in soft tissues.



The physics of MRI means that in addition to multiple sequneces being acquired, multiple planes for certain sequences must also be acquired separately. This means that scan times are much longer than for CT. The patient must not move during series acquisition, and anesthesia needs to be employed in most situations (with the possible exception of cetaceans). Closed and open systems exist but gantry dimensions and table weight limitations may limit the use of MRI in some species. Discussion with the imaging facility prior to scanning that includes the animal size and weight, and the goals of the study to ensure that the most appropriate sequences are acquired is needed prior to scan day. 



Metal and, to a lesser degree, air can cause artifacts that distort the images, occasionally rendering them non-diagnostic.