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Intra-operative brain deformation (brain shift) limits the accuracy of image-guided neuro-surgery systems. Ultrasound imaging as a simple, fast and being real time has become an alternative to MR imaging which is an expensive system for brain shift calculation. The main challenges due to speckle noise and artifacts in US images, is to perform an accurate and fast registration of Us images with pre-operative MR images. In this paper an efficient point based registration method based on the alignment of probability density functions called Coherent Point Drift (CPD) is implemented and compared to the conventional ICP method. To perform this, a brain phantom that allows simulating the brain deformation is made. As the results of our phantom study confirm the CPD method clearly outperforms the ICP algorithm for brain shift calculation. Also the result proves that using intra-operative US has led to recover almost 80% of displacement in the region of interest.