We present a system which allows for use of magnetic resonance (MR) images as primary RT workflow modality alone
and no longer limits the user to computed tomography data for radiation therapy (RT) planning, simulation and patient
localization. The single steps for achieving this goal are explained in detail.
For planning two MR data sets, MR1 and MR2 are acquired sequentially. For MR1 a standardized Ultrashort TE (UTE)
sequence is used enhancing bony anatomy. The sequence for MR2 is chosen to get optimal contrast for the target and the
organs at risk for each individual patient. Both images are naturally in registration, neglecting elastic soft tissue
deformations. The planning software first automatically extracts skin and bony anatomy from MR1. The user can semi-automatically
delineate target structures and organs at risk based on MR1 or MR2, associate all segmentations with MR1
and create a plan in the coordinate system of MR1. Projections similar to digitally reconstructed radiographs (DRR)
enhancing bony anatomy are calculated from the MR1 directly and can be used for iso-center definition and setup
verification. Furthermore we present a method for creating a Pseudo-CT data set which assigns electron densities to the
voxels of MR1 based on the skin and bone segmentations. The Pseudo-CT is then used for dose calculation.
Results from first tests under clinical conditions show the feasibility of the completely MR based workflow in RT for
necessary clinical cases. It needs to be investigated in how far geometrical distortions influence accuracy of MR-based
RT planning.
Image registration is always a trade-off between accuracy and speed. Looking towards clinical scenarios the
time for bringing two or more images into registration should be around a few seconds only. We present a new
scheme for subsampling 3D-image data to allow for efficient computation of cost functions in intensity-based
image registration. Starting from an arbitrary center point voxels are sampled along scan lines which do radially
extend from the center point. We analyzed the characteristics of different cost functions computed on the sub-sampled
data and compared them to known cost functions with respect to local optima. Results show the cost
functions are smooth and give high peaks at the expected optima. Furthermore we investigated capture range of
cost functions computed under the new subsampling scheme. Capture range was remarkably better for the new
scheme compared to metrics using all voxels or different subsampling schemes and high registration accuracy
was achieved as well. The most important result is the improvement in terms of speed making this scheme
very interesting for clinical scenarios. We conclude using the new subsampling scheme intensity-based 3D image
registration can be performed much faster than using other approaches while maintaining high accuracy. A
variety of different extensions of the new approach is conceivable, e.g. non-regular distribution of the scan lines
or not to let the scan lines start from a center point only, but from the surface of an organ model for example.
KEYWORDS: Image segmentation, Heart, Data modeling, 3D modeling, Rapid manufacturing, Binary data, Medical imaging, Imaging systems, 3D image processing, Surgery
Precise knowledge of the individual cardiac anatomy is essential for diagnosis and treatment of congenital heart disease. Complex malformations of the heart can best be comprehended not from images but from anatomic specimens. Physical models can be created from data using rapid prototyping techniques, e.g., lasersintering or 3D-printing. We have developed a system for obtaining data that show the relevant cardiac anatomy from high-resolution CT/MR images and are suitable for rapid prototyping. The challenge is to preserve all relevant details unaltered in the produced models. The main anatomical structures of interest are the four heart cavities (atria, ventricles), the valves and the septum separating the cavities, and the great vessels. These can be shown either by reproducing the morphology itself or by producing a model of the blood-pool, thus creating a negative of the morphology. Algorithmically the key issue is segmentation. Practically, possibilities allowing the cardiologist or cardiac surgeon to interactively check and correct the segmentation are even more important due to the complex, irregular anatomy and imaging artefacts. The paper presents the algorithmic and interactive processing steps implemented in the system, which is based on the open-source Medical Imaging Interaction Toolkit (MITK, www.mitk.org). It is shown how the principles used in MITK enable to assemble the system from modules (functionalities) developed independently from each other. The system allows to produce models of the heart (and other anatomic structures) of individual patients as well as to reproduce unique specimens from pathology collections for teaching purposes.
KEYWORDS: Image segmentation, 3D modeling, Lung, Magnetic resonance imaging, Data modeling, Medical imaging, 3D image processing, Heart, Process modeling, Image processing
Medical image segmentation is still a very time consuming task and therefore not often integrated into clinical routine. Various 3D segmentation approaches promise to facilitate the work. But they are rarely used in clinical setups due to complex intialization and parametrization of such models. Clinical users need interactive tools, intuitive and easy to handle. They do not want to play around with a set of parameters which will differ from dataset to dataset and often have a non-intuitive meaning. In this work new interactive constraints for deformable three-dimensional 2-simplex meshes are presented. The user can define attracting points in the original image data. These attractors are considered during model deformation and the new forces guarantee that the surface model will pass through these interactively set points. By using the constraints the model parameterization is simplified. Segmentation is started with a spherical surface model which is placed inside the structure of interest and then adapts to the boundaries. The user can directly influence the evolution of the deformable model and gets direct feedback during the segmentation process. The model deformation algorithm was implemented and integrated in ITK (Insight Segmentation and Registration Toolkit). The newly developed segmentation tool was tested on cardiac image data and MRI lung images, but is suitable for any kind of 3D and 3D+t medical image data. It has been shown that the model is less sensitive to preprocessing of the input data as well as model initialization.
Computer-assisted surgery aims at a decreased surgical risk and a reduced recovery time of patients. However, its use is still limited to complex cases because of the high effort. It is often caused by the extensive medical image analysis. Especially, image segmentation requires a lot of manual work. Surgeons and radiologists are suffering from usability problems of many workstations.
In this work, we present a dedicated workplace for interactive segmentation integratd within the CHILI (tele-)radiology system. The software comes with a lot of improvements with respect to its graphical user interface, the segmentation process and the segmentatin methods. We point out important software requirements and give insight into the concepts which were implemented. Further examples and applications illustrate the software system.
KEYWORDS: Visualization, Medical imaging, Image segmentation, Surgery, 3D vision, Data acquisition, 3D image processing, Image processing, Image processing algorithms and systems, Data processing
The aim of the Medical Imaging Interaction Toolkit (MITK) is to facilitate the creation of clinically usable
image-based software. Clinically usable software for image-guided procedures and image analysis require a high
degree of interaction to verify and, if necessary, correct results from (semi-)automatic algorithms. MITK is
a class library basing on and extending the Insight Toolkit (ITK) and the Visualization Toolkit (VTK). ITK
provides leading-edge registration and segmentation algorithms and forms the algorithmic basis. VTK has
powerful visualization capabilities, but only low-level support for interaction (like picking methods, rotation,
movement and scaling of objects). MITK adds support for high level interactions with data like, for example, the
interactive construction and modification of data objects. This includes concepts for interactions with multiple
states as well as undo-capabilities. Furthermore, VTK is designed to create one kind of view on the data
(either one 2D visualization or a 3D visualization). MITK facilitates the realization of multiple, different views
on the same data (like multiple, multiplanar reconstructions and a 3D rendering). Hierarchically structured
combinations of any number and type of data objects (image, surface, vessels, etc.) are possible. MITK can
handle 3D+t data, which are required for several important medical applications, whereas VTK alone supports
only 2D and 3D data. The benefit of MITK is that it supplements those features to ITK and VTK that are
required for convenient to use, interactive and by that clinically usable image-based software, and that are
outside the scope of both. MITK will be made open-source (http://www.mitk.org).
Spatial-spectral holography using spectral hole burning materials is a powerful technique for performing real-time, wide-bandwidth information storage and signal processing. For operation in the important 1.5 μm communication band, the material Er3+:Y2SiO5 enables applications such as laser frequency stabilization, all-optical correlators, analog signal processing, and data storage. Site-selective absorption and emission spectroscopy identified spectral hole burning transitions and excited state T1 lifetimes in the 1.5 μm spectral region. The effects of crystal temperature, Er3+-dopant concentration, magnetic field strength, and crystal orientation on spectral diffusion were explored using stimulated photon echo spectroscopy, which is the "prototype" interaction mechanism for device applications. The performance of Er3+:Y2SiO5 and related Er3+ materials has been dramatically enhanced by reducing the effect of spectral diffusion on the coherence lifetime T2 through fundamental material design coupled with the application of an external magnetic field oriented along specific directions. A preferred magnetic field orientation that maximized T2 by minimizing the effects of spectral diffusion was determined using the results of angle-dependent Zeeman spectroscopy. The observed linewidth broadening due to spectral diffusion was successfully modeled by considering the effect of one-phonon (direct) processes on Er3+ - Er3+ interactions. The reported studies improved our understanding of Er3+ materials, explored the range of conditions and material parameters required to optimize performance for specific applications, and enabled measurement of the narrowest optical resonance ever observed in a solid-with a homogeneous linewidth of 73 Hz. With the optimized materials and operating conditions, photon echoes were observed up to temperatures of 5 K, enabling 0.5 GHz bandwidth optical signal processing at 4.2 K and providing the possibility for operation with a closed-cycle cryocooler.
Single-frequency diode lasers have been frequency stabilized to 200 Hz at 1.5 microns and to 20 Hz at 793 nm with 10-100 ms integration times using narrow spectral holes in the absorption lines of Er3+ and Tm3+ doped cryogenic crystals. The narrow spectral holes are used as frequency references, and this laser performance was obtained without requiring vibrational isolation of either the laser or frequency reference. Kilohertz frequency stability for 100 s integration times is provided by these techniques, and that performance should be improved to the Hertz level and should be extended to longer integration times with further development. Miniaturized external cavity diode lasers and 5 mm-sized reference crystals will provide compact portable packages with a closed cycle cryocooler. The achieved frequency stabilization provides lasers that are ideal for interferometry, high-resolution spectroscopy such as photon echoes, real time optical signal processing based on spectral holography, and other applications requiring ultranarrow-band light sources or coherent detection.
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