In this paper, a global approach based on 3D freehand ultrasound imaging is proposed to (a) correct the error of the neuronavigation system in image-patient registration and (b) compensate for the deformations of the cerebral structures occurring during a neurosurgical procedure. The rigid and non rigid multimodal registrations are achieved by matching the hyperechogenic structures of brain. The quantitative evaluation of the non rigid registration was performed within a framework based on synthetic deformation. Finally, experiments were carried out on real data sets of 4 patients with lesions such as cavernoma and low-grade glioma. Qualitative and quantitative results on the estimated error performed by neuronavigation system and the estimated brain deformations are given.