@article{preim-2009-sve, title = "Survey of the Visual Exploration and Analysis of Perfusion Data", author = "Bernhard Preim and Steffen Oeltze and Matej Mlejnek and Eduard Gr\"{o}ller and Anja Hennemuth", year = "2009", issn = "1077-2626", journal = "IEEE Transaction on Visualization and Computer Graphics", number = "2", volume = "15", pages = "205--220", URL = "https://www.cg.tuwien.ac.at/research/publications/2009/preim-2009-sve/", } @phdthesis{Mlejnek_2006_MVOA, title = "Medical Visualization for Orthopedic Applications", author = "Matej Mlejnek", year = "2006", abstract = "This dissertation discusses visualization techniques of articular cartilage for both quantitative and qualitative assessment. Articular cartilage is a very thin structure covering the endings of human bones. Thus, even slight changes in its thickness and inner structure may indicate an occurrence or progress of degeneration. The early detection of these factors is crucial for diagnosis and treatment of cartilage degeneration. Research to find treatments to stop or even reverse these degenerative changes is well in progress. Magnetic resonance imaging is currently the best and most used non-invasive technique for acquisition of soft tissue structures like articular cartilage. In this work we use two types of data: a high-resolution anatomical scan of the cartilage and a T2 map, which is computed from a set of sequences with varying parameters. While the thickness of the data can be precisely assessed fromthe anatomical scan, the T2 map offers information on the inner structures of the cartilage. Since the femoral cartilage is a curved thin-wall structure with a relatively small extent in one direction, it is very difficult to estimate its thickness from a stack of slices or even from a three-dimensional reconstruction of its surface. We discuss inspection of the tissue by unfolding and, thus, representing the tissue as a two-dimensional height field. Such a transformation of the object enables the application of 2D geometrical operations in order to observe subtle details in the thickness of the tissue. Nowadays scanners allow a quality assessment checking disruptions in the pattern of the T2 map of the patellar cartilage. The T2 map illustrates the quality of the cartilage and changes in the pattern of T2 map indicate defects before changes in the thickness itself occur. We propose the Profile Flags - an intuitive interface for probing of the T2 maps by browsing the reconstructed surface of the cartilage. The Profile Flag is positioned on the reconstructed surface of the tissue, and can be moved along it. The Profile Flags can be applied to annotate local as well as global characteristics of the underlying data in a single still image. Furthermore, we present a set of extensions to Profile Flags for selection, classification and automatic positioning. Profile Flags can also be used to measure time-varying dynamic contrast enhanced magnetic resonance imaging data.", address = "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria", school = "Institute of Computer Graphics and Algorithms, Vienna University of Technology ", keywords = "applications of visualization, visualization in medicine", URL = "https://www.cg.tuwien.ac.at/research/publications/2006/Mlejnek_2006_MVOA/", } @inproceedings{Mlejnek_2005_AOEPF, title = "Application-Oriented Extensions of Profile Flags", author = "Matej Mlejnek and Pierre Ermes and Anna Vilanova i Bartroli and Rob van der Rijt and Harrie van den Bosch and Eduard Gr\"{o}ller and Frans Gerritsen", year = "2006", abstract = "This paper discusses two applications of probing dense volumetric data for MR orthopedics and dynamic contrast enhanced MRI mammography. In order not to reduce the context information and to extract the essential part of the data, we apply Profile Flags. A Profile Flag is a 3D glyph for probing and annotating the volumetric data. The first application area deals with visualization of T2 profiles for interactive inspection of knee cartilage and detection of lesions. In the second application, we present the usability the Profile Flags for measuring of time-signal profiles for a set of time-dependent MR volumes. Several extensions of the basic Profile Flag concept are described in detail and discussed. These extensions include selection of a set of profiles based on spatial as well as curve differences, automatic positioning of the Profile Flags, and adaptation for probing of time-varying volumetric data. Additionally, we include the evaluation of the used methods by our medical partners.", publisher = "IEEE CS", booktitle = "Proceedings of Eurographics / IEEE VGTC Symposium on Visualization", pages = "339--346", keywords = "applications of visualization, visualization in medicine", URL = "https://www.cg.tuwien.ac.at/research/publications/2006/Mlejnek_2005_AOEPF/", } @inproceedings{Mlejnek_2004_PF, title = "Profile Flags: a Novel Metaphor for Probing of T2 Maps", author = "Matej Mlejnek and Pierre Ermes and Anna Vilanova i Bartroli and Rob van der Rijt and Harrie van den Bosch and Frans Gerritsen and Eduard Gr\"{o}ller", year = "2005", abstract = "This paper describes a tool for the visualization of T2 maps of knee cartilage. Given the anatomical scan and the T2 map of the cartilage, we combine the information on the shape and the quality of the cartilage in a single image. The Profile Flag is an intuitive 3D glyph for probing and annotating of the underlying data. It comprises a bulletin board pin-like shape with a small flag on top of it. While moving the glyph along the reconstructed surface of an object, the curve data measured along the pin's needle and in its neighborhood are shown on the flag. The application area of the Profile Flag is manifold, enabling the visualization of profile data of dense but inhomogeneous objects. Furthermore, it extracts the essential part of the data without removing or even reducing the context information. By sticking Profile Flags into the investigated structure, one or more significant locations can be annotated by showing the local characteristics of the data at that locations. In this paper we are demonstrating the properties of the tool by visualizing T2 maps of knee cartilage.", month = oct, isbn = "0780394623", publisher = "IEEE CS", location = "Minneapolis, USA", editor = "C. T. Silva, E. Gr\"{o}ller, H. Rushmeier", booktitle = "Proceedings of IEEE Visualization 2005", pages = "599--606", keywords = "applications of visualization, visualization in medicine", URL = "https://www.cg.tuwien.ac.at/research/publications/2005/Mlejnek_2004_PF/", } @inproceedings{Mlejnek-2004-ITVAC, title = "Interactive Thickness Visualization of Articular Cartilage", author = "Matej Mlejnek and Anna Vilanova i Bartroli and Eduard Gr\"{o}ller", year = "2004", abstract = "This paper describes a method to visualize the thickness of curved thin objects. Given the MRI volume data of articular cartilage, medical doctors investigate pathological changes of the thickness. Since the tissue is very thin, it is impossible to reliably map the thickness information by direct volume rendering. Our idea is based on unfolding of such structures preserving their thickness. This allows to perform anisotropic geometrical operations (e.g., scaling the thickness). However, flattening of a curved structure implies a distortion of its surface. The distortion problem is alleviated through a focus-and-context minimization approach. Distortion is smallest close to a focal point which can be interactively selected by the user.", month = oct, booktitle = "Proceedings of Visualization 2004", pages = "521--527", keywords = "visualization in medicine, applications of visualization", URL = "https://www.cg.tuwien.ac.at/research/publications/2004/Mlejnek-2004-ITVAC/", } @inproceedings{Neumann-2002-Fea, title = "Feature-Preserving Volume Filtering", author = "L\'{a}szl\'{o} Neumann and Bal\'{a}zs Cs\'{e}bfalvi and Ivan Viola and Matej Mlejnek and Eduard Gr\"{o}ller", year = "2002", abstract = "In this paper a feature-preserving volume filtering method is presented. The basic idea is to minimize a three-component global error function penalizing the density and gradient errors and the curvature of the unknown filtered function. The optimization problem leads to a large linear equation system defined by a sparse coefficient matrix. We will show that such an equation system can be efficiently solved in frequency domain using fast Fourier transformation (FFT). For the sake of clarity, first we illustrate our method on a 2D example which is a dedithering problem. Afterwards the 3D extension is discussed in detail since we propose our method mainly for volume filtering. We will show that the 3D version can be efficiently used for elimination of the typical staircase artifacts of direct volume rendering without losing fine details. Unlike local filtering techniques, our novel approach ensures a global smoothing effect. Previous global 3D methods are restricted to binary volumes or segmented iso-surfaces and they are based on area minimization of one single reconstructed surface. In contrast, our method is a general volume-filtering technique, implicitly smoothing all the iso-surfaces at the same time. Although the strength of the presented algorithm is demonstrated on a specific 2D and a specific 3D application, it is considered as a general mathematical tool for processing images and volumes.", month = may, publisher = "ACM", booktitle = "Data Visualization 2002", pages = "105--114", keywords = "antialiasing, noise filtering, derivative and gradient estimation, feature-preserving smoothing, direct volume rendering", URL = "https://www.cg.tuwien.ac.at/research/publications/2002/Neumann-2002-Fea/", }