<p>MR phase images contain essential information about local magnetic susceptibility sources in the brain, creating a new type of contrast in magnetic resonance imaging (MRI). The goal of this thesis is to demonstrate with a model of the brain how accurately the transformation of phase to susceptibility takes place.</p> <p>A 3D brain model uses the Forward process to calculate magnetic field perturbations caused by susceptibility properties of the tissues in the model. Homodyne High Pass (HP) filter and SHARP algorithm are used to process the simulated phase images. Similarly, MR magnitude data are simulated using tissue properties such as T₁, T₂^* relaxation times and spin density.</p> <p>The halo ring around red nucleus in the real phase data is believed to be an indicator of a capsule around red nucleus. Similar effect is seen in the simulated phase images without including the capsule of red nucleus in the model, this comparison explains that the halo effect may just be entirely or a part of the phase behavior around red nucleus. A negative susceptibility in the internal capsule region, seen in both simulated and real susceptibility maps, is discussed as a possible artifact caused by the processing techniques after comparing the simulated susceptibility maps produced from unprocessed and processed phase data. The brain model is used to determine the optimum echo time of the initial gradient echo sequence in order to produce a high quality susceptibility map with reasonably low error and better time efficiency.</p> / Master of Applied Science (MASc)