Frequently MRI data is characterised by a relatively low signal to noise ratio (SNR) or contrast to noise ratio (CNR). When developing automated Computer Assisted Diagnostic (CAD) techniques the errors introduced by the image noise are not acceptable. Thus, to limit these errors, a solution is to filter the data in order to increase the SNR. More importantly, the image filtering technique should be able to reduce the level of noise, but not at the expense of feature preservation. In this paper we detail the implementation of a number of 3D diffusion-based filtering techniques and we analyse their performance when they are applied to a large collection of MR datasets of varying type and quality.