Image registration is an important step in the radiotherapy treatment planning process. It provides a method of fusing different types of diagnostic imaging information. One such application is to combine magnetic resonance spectroscopic images (MRSI) of the prostate with anatomical MRI and/or computed tomography images that are routinely used in the radiation treatment planning of prostate cancer. MRSI provides in vivo information related to the underlying metabolic activity of tissues, and can be related to the presence of cancer. However, the inflated endorectal coil required during MRS imaging poses a potential problem by deforming the prostate when it is filled with ~100 cm³ of air during image acquisition. This pushes the prostate superiorly/anteriorly, deforming the prostate and consequently the spectroscopic imaging data in a nonlinear manner. In this application, the coil-deformed MRS images are warped back to a non-deformed state, using a single data set. A nonlinear warping algorithm is presented to achieve this. Results indicate that the algorithm attains an accuracy of 97% (4 cm³ difference) when reproducing the total prostate volume compared to a Radiation Oncologist defined prostate volume. This difference is slightly smaller than the measured intra-operator variance of ±1.5 cm³ (deflated coil) and the measured algorithm variance of ±1.0 cm³. Additionally, intraprostatic nodules were used to assess the accuracy of the warping algorithm in regions inside the prostate. While choosing anatomical tie points along the external prostate surface, analysis of the nodules revealed the algorithm accuracy reduced to 63–93%.