Which has less side effects on body especially brain, ct scan or mri?

Both very safe: However, MRI is likely safer because it does not use ionizing radiation like ct. Mri is essentially a very fancy radio, and ct is a very fancy x-ray machine, taking images from multiple directions to make a picture. Contrast agents, usually injected into a vein as part of both MRI and ct, have risks as well, however they are very low, well known and easily avoided or managed.