Diffusivity of water molecules estimated from diffusion weighted MRI (DW-MRI) is an important biomarker to pinpoint regions with restricted diffusion such as inflamed bowel regions in patients with Crohn's Disease (CD). There is a need to fuse the information extracted from DW-MRI with other image modalities, e.g. structural T1w images, for more accurate and efficient diagnosis. However, due to low signal-to-noise ratio, distortion and lower resolution of DW-MR images compared to T1w images, fusion of these image modalities is challenging, especially in turns and folds of the bowel. This paper presents a novel method to register structural T1w and diffusion weighted images, which facilitates the image fusion. Based on the block-matching algorithm, the proposed method first determines multiple candidate matches in a neighborhood, and then iteratively finds the most probable match using additional geometric information. We examined the performance of the proposed method on five patients with confirmed CD. Our method outperformed other state-of-the-art registration methods, i.e. ANTS and Demons. This method has the potential for being a useful tool in structural and DW-MRI data fusion for more accurate CD diagnosis and severity assessment.