Master Thesis: Simultaneous Deformation of Medical Images

Student: Mehmet Yigitsoy Advisor: Nassir Navab Supervision by: Christian Wachinger Abstract The registration – spatial alignment – of images is of great interest for medical image processing and general computer vision tasks. Often, not just the registration of two images, but the registration of multiple images is needed. An example is the creation of a medical brain atlas, for which a number of brain volumes have to be aligned. Since the human brains vary significantly, a deformable registration or warping between the images is necessary to correctly align the images. In the scope of this thesis, we will implement an algorithm for simultaneous deformable registration. Description An example for 40 brain images before registration are shown on the right (courtesy of L. Zöllei). The registration of the images is necessary for the atlas construction, which basically corresponds to the calculation of the mean of a population of images. On the atlas image on the lower right, the mean before and after the alignment is shown. One can clearly see the improvement and clarity of structures after the alignment. In the scope of this master or diploma thesis we want to implement a simultaneous deformable registration algorithm. For this purpose, the open source registration toolkit (ITK) will be used, which already provides a huge set of functionalities. This project is matter of current research and of high interest for the research community. The student should have experience working with C++ and image processing. Moreover, basic mathematical skills are necessary for understanding the underlying theory. This thesis will jointly be supervised by Tom Vercauteren (Mauna Kea Technologies, Paris, France). Requirements Knowledge: C++, Matlab. Basic knowledge: Image registration Interest in medical imaging What you get out of it Experience in different fields of research in computer science: Medical Imaging, Computer Vision, Visualization, Software Engineering Knowledge about image registration Work on an exciting research topic within an interdisciplinary and international research team Finally a diploma thesis and your degree Literature C. Wachinger, N. Navab A Contextual Maximum Likelihood Framework for Modeling Image Registration IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Providence, Rhode Island (USA), June 2012. (bib) C. Wachinger, N. Navab Manifold Learning for Multi-Modal Image Registration 21st British Machine Vision Conference (BMVC), Aberystwyth, United Kingdom, August 31 - September 3 2010. (bib) C. Wachinger, N. Navab Structural Image Representation for Image Registration IEEE Computer Society Conference on Computer Vision and Pattern Recognition, San Francisco, California, June 2010. Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA). (bib) C. Wachinger, N. Navab Alignment of Viewing-Angle Dependent Ultrasound Images. Medical Image Computing and Computer-Assisted Intervention (MICCAI), London, UK, September 20-24 2009 (bib) O. Kutter, W. Wein, N. Navab Multi-modal registration based Ultrasound Mosaicing Medical Image Computing and Computer-Assisted Intervention (MICCAI), London, UK, September 20-24 2009 (bib) C. Wachinger, N. Navab Similarity Metrics and Efficient Optimization for Simultaneous Registration IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), Miami, Florida (USA), June 2009. (bib) C. Wachinger, B. Glocker, J. Zeltner, N. Paragios, N. Komodakis, M. S. Hansen, N. Navab Deformable Mosaicing for Whole-body MRI Medical Image Computing and Computer-Assisted Intervention (MICCAI), New York, USA, September 6-10 2008 (bib) C. Wachinger Insights Into Three-Dimensional Ultrasound Mosaicing: Strategies for the alignment of multiple ultrasound volumes VDM Verlag Dr. Müller, Stuttgart, ISBN: 3836488264, December 23 2008, Amazon (bib) C. Wachinger, W. Wein, N. Navab Registration Strategies and Similarity Measures for Three-dimensional Ultrasound Mosaicing Journal of the University Radiologists, Academic Radiology 15 (11), pp.1404-1415. Special issue of MICCAI 2007 (bib) S. Atasoy, D. Noonan, S. Benhimane, N. Navab, G. Z. Yang A Global Approach for Automatic Fibroscopic Video Mosaicing in Minimally Invasive Diagnosis Medical Image Computing and Computer-Assisted Intervention, MICCAI, 2008, New York, USA, September 6-10 2008 (bib) C. Wachinger, R. Shams, N. Navab Estimation of Acoustic Impedance from Multiple Ultrasound Images with Application to Spatial Compounding IEEE Computer Society Conference on Computer Vision and Pattern Recognition, Anchorage, Alaska (USA), June 2008. Workshop on Mathematical Methods in Biomedical Image Analysis (MMBIA). (bib) C. Wachinger, N. Navab Ultrasound Specific Similarity Measures for Three-Dimensional Mosaicing. SPIE Medical Imaging, San Diego, California, USA, 16-21 February 2008 (bib) C. Wachinger, W. Wein, N. Navab Three-Dimensional Ultrasound Mosaicing Medical Image Computing and Computer-Assisted Intervention, MICCAI, 2007, Brisbane, Australia, October 29 - November 2 2007 (bib) C. Wachinger, W. Wein, N. Navab Ultrasound Volume Stitching 6. Jahrestagung der Deutschen Gesellschaft für Computer-und Roboter-Assistierte Chirurgie (CURAC 2007), Karlsruhe, Germany, October 2007 (bib) Contact If you are interested in this project, please send an email to Christian Wachinger.

Before Registration (Image courtesy of L. Zöllei.) After Registration (Image courtesy of L. Zöllei.) Atlas before and after registration (Image courtesy of L. Zöllei.)