EBME 461 Image Transformations and Atlas Based Segmentation Due: March 15, 2011 David Wilson, Ph.

D. Department of Biomedical Engineering Here is a group homework assignment. Please read the description carefully. The write-up should include a short discussion, processed images, and Matlab code. You should write your code so that someone versed in Matlab can use it easily! Images will be provided by the TA in the usual way. Please read the description carefully. We try to give you sufficient information to get you successfully started on this simple, but interesting, project. Images will be provided by the TA in the usual way. They are listed below. Brain.mat Atlas.mat Brain.tif Atlas.tif

In this laboratory assignment, you will use the Talairach Atlas. This atlas has many uses in neurosurgery and neuroscience. Often, 3D medical image data sets are transformed and registered to this atlas. Once this is done, one can relate normal anatomical structure to the medical image data. For example, one might register 25 human PET image data sets to the atlas in order to determine the average anatomical location of brain activation data. Note that if one properly aligns image data to an atlas, the atlas provides a segmentation of the image data. To learn more about how to use the atlas, please go to websites given later. To simplify the problem, you will work with 2D data rather than 3D image data. You will transform a 2D MRI image and align it with a slice from the Talairach Atlas. Steps are: 1. Develop an 8-paramter warp transformation that allows rigid body (rotation, translation), isotropic scaling, and skew using homogeneous matrix equations. 2. Match control points in the atlas image with corresponding points in the MRI image. Determine the transformation parameters using a least-squares approach. (You can use a pseudo-inverse on an over determined system of equations.) 3. Transform the atlas image to best align it with the MRI image. The MRI image will be the reference. 4. To measure the quality of the match, measure the distances between corresponding points following transformation. What is the average Euclidean distance in pixels between the corresponding control points following the transformation? 5. Use fewer control points. What happens? Mathematically, what is the minimum number of control points you can use? 6. Extra credit. Determine a method for image fusion of results.