Ellen Brunenberg Curriculum Vitae

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1 Ellen Brunenberg Curriculum Vitae Personal Data Name Birth Ellen Johanna Leonarda Brunenberg November 4, Weert, The Netherlands Work Experience Address Hart van Brabantlaan LG Tilburg The Netherlands Phone e.j.l.brunenberg@tue.nl, ellenbrunenberg@gmail.com Website Present May 2007 Ph.D. candidate at Eindhoven University of Technology Biomedical Image Analysis group, department of Biomedical Engineering Description: image acquisition and analysis for deep brain stimulation (see also Research Record ). August2006 Student assistant at Eindhoven University of Technology (part-time) December 2002 Description: find and implement content management system for group website (March August 2006); assist in theinstruction of first- and second-year courses (December 2003 June2005);assist in tissue engineering lab (prepare bone plugs, stain tissue, manage protocols) (December 2002 November2003). Education March 2007 September 2004 August2004 September 2001 July 2001 September1995 Master of Science in Biomedical Engineering (with great appreciation) - including certificate Physics in theclinic Eindhoven University of Technology Bachelor of Science in Biomedical Engineering (cum laude) Eindhoven University of Technology Secondary school, preparatory scientific education - science and health profiles Bisschoppelijk College, Weert, The Netherlands

2 Graduate Courses Presentation using performance skills, masterclass at Eindhoven University of Technology 2009 Fundamentals of Biostatistics, course at Eindhoven University of Technology Presenting in English, course at Eindhoven University of Technology 2008 Writing Articles and Abstracts, course at Eindhoven University of Technology Supervising MSc Students, workshop at Eindhoven University of Technology Mathematics in Brain Imaging, summerschool at IPAM, University of California, LosAngeles Advanced Pattern Recognition, ASCIGraduate School course at Delft University of Technology fmri, 3rd M-Bic fmri workshop at Maastricht University 2007 Knowledge Driven Image Segmentation, ASCIGraduate School course at Leiden University Research Record Present May 2007 Ph.D. candidate at Eindhoven University of Technology Biomedical Image Analysis group, department of Biomedical Engineering Description: improving image acquisition and analysis for deep brain stimulation in Parkinson s disease. Funding: this project has been financed by an NWO Toptalent grant (see Awards & Stipends ). Supervisors: prof. Bart terhaar Romeny, prof. Veerle Visser-Vandewalle (promoters); dr. Bram Platel (co-promotor). Contribution: acquisition of rat and volunteer data, HARDI and fmri preprocessing, clustering of HARDI data, development of new distance measure for HARDI clustering, functional and structural connectivity calculation. Publications: 1 MICCAIpaper and 2 ISMRM abstracts (1 journal paper has been submitted; see Publications ). April March March 2007 March 2006 December 2005 September 2005 May 2005 December 2004 Externship at thesignal Processing Lab 5 (LTS5) of Jean-Philippe Thiran École polytechnique fédérale de Lausanne (EPFL) Description: visit to research group with expertise on functional and structural brain connectivity analysis. Contribution: preprocessing of resting state fmri data, calculation of functional connectivity, validation of anatomical segmentations togetherwith neurosurgeon. Publications: a joint journal paper is in preparation (see Publications ). Master s project in thebiomedical Image Analysis group, together with neurosurgery at Maastricht University Medical Center Description: automatic electrode trajectory planning for deep brain stimulation. Contribution: segmentation and visualization of important brain structures, optimal path calculation, development of an application with a graphical user interface in MeVisLab. Publications: this project has led to 1 MICCAIpaper (poster) (see Publications ). Externship at thecomputervision Center (group of prof. Petia Radeva) Universitat Autonoma de Barcelona Description: automatic IVUS segmentation of soft and fibrous plaque using feature extraction and snakes. Contribution: preprocessing of new data, creation of training and test sets,validation of feature extraction and classification, application of new Stop & Go snake. Publications: this project has led to 1 MICCAIpaper (poster) (see Publications ). Internship at thedepartment of Biophysics (group of Marc van Zandvoort) Maastricht University Description: motion correction by temporal matching on a time series of fluorescence microscopy. Contribution: exploration of thefield, extraction of templates, comparison of similarity measures, warping of theimages. Publications: this project has led to an authorship of a journal paper (see Publications ).

3 Awards and Stipends September Student travelgrantfor the13th MICCAIconference (September ) in Beijing, China. February February 2009 October 2007 April 2007 Student stipend for the18th ISMRM conference (May )in Stockholm, Sweden. Student stipend for the17th ISMRM conference (April 2009) in Honolulu, Hawai i. Poster award (best M.Sc. poster) at theresearch day of thedepartment of Biomedical Engineering. NWO Toptalent grant: a prestigious program for graduating talents with creative ideas for Ph.D. research. In 2007, the Dutch Organization for Scientific Research has given 42 talents a grant of EUR180,000 each. Extracurricular Activities November 2008 Memberof theorganizing committee of thenvphbv Fall Meeting 2008 Biomedical Image Analysis group, Eindhoven University of Technology Description: call for abstracts, organize review procedure, monitor budget. May 2003 November 2002 May 2002 November 2001 President of theorganizing committee of thesymposium Molecular Imaging BMEstudent association Protagoras, Eindhoven University of Technology Description: stimulate progress, maintain contact with speakers, find sponsoring, design printed matter. Treasurer of theorganizing committee of theparent visit BMEstudent association Protagoras, Eindhoven University of Technology Description: estimate and monitor budget, find sponsoring. Computer Skills Languages C++, JAVA, HTML (all basic knowledge) Environments Mathematica, Matlab, FSL, SPM,MeVisLab Other Windows, Mac OS X, LATEX, Adobe Photoshop, Microsoft Office Languages Dutch Mother tongue English Fluent Spanish Basic knowledge French Basic knowledge German Basic knowledge Interests Medical imaging and image analysis, popular science Music: playing thepiano, visiting concerts and festivals Traveling and travel photography Cooking Reading

4 Key Publications E.J.L. Brunenberg, R. Duits, B.M. terhaar Romeny, B. Platel. A Sobolev norm based distance measure for HARDI clustering - A feasibility study on phantom and real data, in proceedings of Medical Image Computation and Computer-Assisted Intervention (MICCAI), Lecture Notes in Computer Science 6361, pp E.J.L. Brunenberg, E. Pelgrim, B.M. ter Haar Romeny, B. Platel. k-means and graph cuts clustering of diffusion MRI in rat STN, in proceedings of Eighteenth Annual Meeting of theinternational Society for Magnetic Resonance in Medicine (ISMRM), pp E.J.L. Brunenberg, V. Prčkovska, B. Platel, G.J. Strijkers, B.M. ter Haar Romeny. Untangling a fiber bundle knot - Preliminary results on STNconnectivity using DTI and HARDI on rat brains, in proceedings of SeventeenthAnnual Meeting of theinternational Society for Magnetic Resonance in Medicine (ISMRM) 2009, pp E.J.L. Brunenberg, A. Vilanova, V. Visser-Vandewalle, Y. Temel, L. Ackermans, B. Platel, B.M. ter Haar Romeny. Automatic trajectory planning for Deep Brain Stimulation: A feasibility study, in proceedings of Medical Image Computation and Computer-Assisted Intervention (MICCAI) 2007,Lecture Notes in ComputerScience 4791,pp E.J.L. Brunenberg, O. Pujol, B.M. ter Haar Romeny, P. Radeva. Automatic IVUS segmentation of atherosclerotic plaque with Stop & Go snake, in proceedings of Medical Image Computation and Computer-Assisted Intervention (MICCAI) 2006, Lecture Notes in Computer Science 4191, pp Submitted / In Preparation E.J.L. Brunenberg, B. Platel, P.A.M. Hofman, B.M. ter Haar Romeny, V. Visser-Vandewalle. Magnetic resonance imaging techniques for visualization of thesubthalamic nucleus: a systematic review, submitted to Journal of Neurosurgery. E.J.L. Brunenberg, L. Cammoun, C. Pollo, W.H. Backes, V. Visser-Vandewalle, B.M. terhaar Romeny, J.-Ph. Thiran, B. Platel. Resting state functional connectivity of thehuman subthalamic nucleus, in preparation. E.J.L. Brunenberg, P. Moeskops, W.H. Backes, V. Visser-Vandewalle, B.M. terhaar Romeny, B. Platel. Structural connectivity of the human subthalamic nucleus, in preparation. Other Publications 2011 E.J.L. Brunenberg, R. Duits, B.M. ter Haar Romeny, B. Platel. Taking extrema into account: a new distance measure for HARDI clustering, in proceedings of Third Dutch Biomedical Engineering Conference E.J.L. Brunenberg, R. Duits, B.M. terhaar Romeny, B. Platel. A Sobolev norm based distance measure for HARDI clustering - A feasibility study on phantom and real data, in proceedings of Advanced School for Computing and Imaging (ASCI). L.Florack, E.Balmashnova, L.Astola, E. Brunenberg. A New Tensorial Framework for Single-Shell High Angular Resolution Diffusion Imaging, in Journal of Mathematical Imaging and Vision, 38(3),pp R.T.A. Megens, S. Reitsma, L. Prinzen, M.G. Oude Egbrink, W. Engels, P. Leenders, E.J.L. Brunenberg, K.D Reesink, B.J.A. Janssen, B.M. ter Haar Romeny, D.W. Slaaf, M.A.M.J. van Zandvoort. In vivo high-resolution structural imaging of large arteries in small rodents using two-photonlaser scanning microscopy, in Journal of Biomedical Optics, 15(1),pp E.J.L. Brunenberg, E. Pelgrim, B.M. ter Haar Romeny, B. Platel. k-means and graph cuts clustering of diffusion MRI in rat STN, in proceedings of Second ISMRM Benelux Meeting, pp. 118.

5 E.J.L. Brunenberg, V. Prčkovska, B. Platel, G.J. Strijkers, B.M. ter Haar Romeny. A comparison of DTI and HARDI in rat subthalamic nucleus, in proceedings of Advanced School for Computing and Imaging (ASCI) E.J.L. Brunenberg, B. Platel, B.M. ter Haar Romeny. Finding the subthalamic nucleus for deep brain stimulation using diffusionweighted MRI, in proceedings of Second Dutch Biomedical Engineering Conference E.J.L. Brunenberg, V. Prčkovska, B. Platel, G.J. Strijkers, B.M. ter Haar Romeny. Untangling a fiber bundle knot - Preliminary results on STN connectivity using DTI and HARDI on rat brains, in proceedings of First ISMRM Benelux Meeting 2008, pp. 45. E.J.L. Brunenberg, O. Pujol, B.M. ter Haar Romeny, P. Radeva. Automatic IVUS segmentation of atherosclerotic plaque with Stop & Go snake, in proceedings of Advanced School for Computing and Imaging (ASCI)