Hauptseminar: Methods and Tools in Medical Imaging

by Tobias Lasser, Thomas Wendler and Prof. Dr. Nassir Navab

2 SWS, 4 ECTS

The seminar language is English.

Participation

If you are interested in taking part in the seminar please

• send an e-mail to .
• registration for the seminar is closed.

Please include last and first name, matriculation number, current semester, discipline (diploma, master, bachelor) including major, and a desired topic.

October 19th, 2007 will be the last withdrawal date to withdraw your registration. Not withdrawing before this date will result in a 5.0 grade for unacceptable or incomplete work.

Abstract

The use of computers in medicine had a rapid development over the last decade. More and more computer based technology is integrated in the surgery room and in the surgical workflow. Nowadays, medical images are available in digital form. Computers are used very extensively to preprocess, segment or register different imaging modalities such as computed tomography (CT), ultrasound (US), or magnetic resonance imaging (MRI). Furthermore, the fusion of these different imaging modalities often provide very valuable information for physicians and surgeons and can enable the intra-operative navigation.
In this seminar we present the various methods that are applicable in medical imaging. We will focus on specific and interesting algorithmic and mathematical topics in this field. After two introductory courses every student will prepare a talk on the basis of the selected topics (see table below). A short problem statement of the topic as well as the basic references is provided.

Proposed topics

• Mathematical Basics: 3D rotations and quaternions
• Fourier Transformation for Computed Tomography Reconstruction
• Algebraic Reconstruction Technique as applied to Optical Tomography
• Functional Imaging using Nuclear Probes
• Edge Detection
• Pose Estimation
• Feature-based Registration
• Intensity-based Registration
• Volume Segmentation
• Level-Set Methods
• 3D Tracking Techniques
• Compressed Sensing
• Surface Reconstruction
• Tracer Kinetic Modelling

Schedule

Date and time	Location	Topic	Student
Jan 9th 08, 16:00	MI 03.13.010	Feature extraction techniques	André Aichert
Jan 9th 08, 17:00	MI 03.13.010	Intensity-based registration	Ya Chen
Jan 16th 08, 14:00	MI 03.13.055	Optical tracking techniques	Stefan Holzer
Jan 16th 08, 15:00	MI 03.13.055	Feature-based registration	Agata Pernus
Jan 16th 08, 16:00	MI 03.13.055	Tomographic reconstruction for optical imaging	Coskun Özgür

Timeline

You are required to meet the following deadlines for discussing your work with your supervisor:

• 4-6 weeks before presentation: Outline
• 2 weeks before presentation: Handout
• 1 week before presentation: Presentation Slides

Some Related Research at our chair (CAMP)

Registration of Angiographic Data Angiographic images visualize vascular structure in different modalities like X-Ray, CT, or MR data sets. In many medical applications, a registration and proper visualization of the data sets, especially the vasculature is useful for a better navigation. The focus of this project lies on 2D/3D registration of angiographic data where intensity-based, feature-based, and hybrid approaches are evaluated, the latter two of them requiring an accurate 2D and 3D segmentation of the data. The main clinical partner is the radiology department of the Universitätsklinikum Großhadern (Ludwig-Maximilian Universität München) , industrial partner is Siemens Medical Solutions, Forchheim.

Navigated Beta Probes for Optimal Tumor Resection in collaboration with Nuclear Medicine Department at Klinikum rechts der Isar In minimally invasive tumor resection, the goal is to perform a minimal but complete removal of cancerous cells. In the last decades interventional beta probes supported the detection of remaining tumor cells. However, scanning the patient with an intraoperative probe and applying the treatment are not done simultaneously. The main contribution of this work is to extend the one dimensional signal of a nuclear probe to a four dimensional signal including the spatial information of the distal end of the probe. This signal can be then used to guide the surgeon in the resection of residual tissue and thus increase its spatial accuracy while allowing minimal impact on the patient.

CamC - Camera Augmented Mobile C-Arm in collaboration with the Trauma Surgery Department of Klinikum Innenstadt The problem of positioning mobile C-arms, e.g. for down the beam techniques, as well as repositioning during surgical procedures currently requires time, skill and additional radiation. The Camera-Augmented Mobile C-arm (CAMC) is able to speed up the procedure, simplify its execution and reduce the necessary radiation. The C-arm is extended by a CCD camera. The CCD camera is attached to the C-arm such that it is virtually at the same location than the x-ray source. This is done by a double mirror construction. A two step calibration routine has be done only once at the moment the camera is attached. Extensions for a lightwight, but complete navigation system for pedile screw placement or implant positioning is currently under investigation.

Navigated Gamma Probes for Tumor Localization in collaboration with Nuclear Medicine Department at Klinikum rechts der Isar Nuclear medicine imaging modalities assist commonly in surgical guidance given their functional nature. However, when used in the operating room they present limitations. Pre-operative tomographic 3D imaging can only serve as a vague guidance intra-operatively, due to movement, deformation and changes in anatomy since the time of imaging, while standard intra-operative nuclear measurements are limited to 1D or (in some cases) 2D images with no depth information. To resolve this problem we propose the synchronized acquisition of position, orientation and readings of gamma probes intra-operatively to reconstruct a 3D activity volume. In contrast to conventional emission tomography, here, in a first proof-of-concept, the reconstruction succeeds without requiring symmetry in the positions and angles of acquisition, which allows greater flexibility and thus opens doors towards 3D intra-operative nuclear imaging.

Registration of CT Fluoroscopy Slices in collaboration with Siemens Computed Tomography, Forchheim and Klinikum Grosshadern LMU Radiofrequency Ablation (RFA) of the liver is an interventional procedure applied to patients with unresectable primary liver tumors (HCC - hepatocellular carcinoma) and metastases. The percutaneous needle insertion is performed using different imaging guidance systems like CT, CT-Fluoroscopy, MRI or Ultrasound. We are investigating the registration of the CT-Fluoroscopy slices with the preinterventional CT volume. The aim is to display high resolution contrasted data in the operating room for aiding the needle insertion.

Hybrid Tracking In this project a complete real-time model-based tracking system for piecewise-planar objects which combines template-based and feature-based approaches is being developed. The main contributions are an extension to the ESM algorithm used for template-based tracking and the formulation of a feature-based tracking approach, which is specifically tailored for use in a real-time setting. In order to cope with highly dynamic scenarios, such as illumination changes, partial occlusions and fast object movement, the system adaptively switches between template-based tracking, feature-based tracking and a global initialization phase. The tracking system achieves real-time performance by applying a coarse-to-fine optimization approach and includes means to detect a loss of track.

Laparoscope Augmentation for Minimally Invasive Liver Resection in collaboration with Chirurgische Klinik und Poliklinik at Klinikum der LMU - Innenstadt and MITI Institute at Klinikum rechts der Isar In recent years, an increasing number of liver tumor indications were treated by minimally invasive laparoscopic resection. Besides the restricted view, a major issue in laparoscopic liver resection is the precise localization of the vessels to be divided. To navigate the surgeon to these vessels, pre-operative imaging data can hardly be used due to intra-operative organ deformations caused by appliance of carbon dioxide pneumoperitoneum and respiratory motion. Therefore, we propose to use an optically tracked mobile C-arm providing cone-beam computed tomography imaging capability intra-operatively. After patient positioning, port placement, and carbon dioxide insufflation, the liver vessels are contrasted and a 3D volume is reconstructed during patient exhalation. Without any further need for patient registration, the volume can be directly augmented on the live laparoscope video. This augmentation provides the surgeon with essential aid in the localization of veins, arteries, and bile ducts to be divided or sealed. Current research focuses on the intra-operative use and tracking of mobile C-arms as well as laparoscopic ultrasound, augmented visualization on the laparoscope's view, and methods to synchronize respiratory motion.

3D user interfaces for medical interventions in collaboration with Chirurgische Klinik und Poliklinik at Klinikum der LMU - Innenstadt This work group aims at practical user interfaces for 3D imaging data in surgery and medical interventions. The usual monitor based visualization and mouse based interaction with 3D data will not present acceptable solutions. Here we study the use of head mounted displays and advanced interaction techniques as alternative solutions. Different issues such as depth perception in augmented reality environment and optimal data representation for a smooth and efficient integration into the surgical workflow are the focus of our research activities. Furthermore appropriate ways of interaction within the surgical environment are investigated.

Navigated Bronchoscopy in collaboration with pneumology department Klinikum rechts der Isar A common task during broncoscopy procedures is to biopsy peripheral lung tumors. The video bronchoscope is not capable to reach the peripheral lung nodes, but only the biopsy needle. Thus there is no video feedback, but only feedback of the current location of the biopsy tool by fluoroscopy imaging during the intervention. This exposes patient and surgical staff to additional radiation. Another drawback is that tumors can not be visualized on the fluoroscope images and they are only a projection, thus do not report the three dimensional position of the biopsy tool. Electromagnetic tracking is capable of tracking the tip of flexible instrument. A field generator with three orthogonal coils introduces current and thus generates a magnetic field. A sensor composed also of three orthogonal coils is capable to estimate its position and orientation with respect to a coordinate system defined by the field generator. Currently we investigate the combination of all available information for navigation and solutions to represent it in one unified user interface. This includes the measurements of the electromagnetic tracking system, the c-arm, techniques of virtual bronchoscopy, and other data. Furthermore, clinical evaluation is conducted. We define the clinical endpoint and show through studies that the procedure will benefit from the usage of the navigation system.

NARVIS - navigated augmented reality visualization system Advanced visualization is getting increasingly important for the operation room of the future. The increasing number of available medical images must be presented to surgery team in new ways in order to support them rather than overloading with more information. In our project NARVIS we integrate an HMD-based (head mounted display) AR system into the operation room for 3D in situ visualization of computed tomography (CT) images. The final system aims at spinal surgery. The work is in close collaboration with our project partners “Klinikum für Unfallchirgie” at LMU, A.R.T. Weilheim, and Siemens Corporate Research in Princeton. The project is funded by Bayerische Forschungsstiftung.

Port Placement in Minimally Invasive Endoscopic Surgery in collaboration with Chirurgische Klinik und Poliklinik at Klinikum der LMU - Innenstadt and Deutsches Herzzentrum München Optimal port placement is a delicate issue in minimally invasive endoscopic surgery. A good choice of the instruments' and endoscope's ports can avoid time-consuming consecutive new port placement. We present a novel method to intuitively and precisely plan the port placement. The patient is registered to its pre-operative CT by just moving the endoscope around fiducials, which are attached to the patient's thorax and are visible in its CT. Their 3D positions are automatically reconstructed. Without prior time-consuming segmentation, the pre-operative CT volume is directly rendered with respect to the endoscope or instruments. This enables the simulation of a camera flight through the patient's interior along the instruments' axes to easily validate possible ports.

Patient Position Detection for SAR Optimization in Magnetic Resonance Imaging in collaboration with Siemens Medical Solutions (MR), Erlangen Although magnetic resonance imaging is considered to be non-invasive, there is at least one effect on the patient which has to be monitored: The heating which is generated by absorbed radio frequency (RF) power. It is described using the specific absorption rate (SAR). In order to obey legal limits for these SAR values, the scanner's duty cycle has to be adjusted. The limiting factor depends on the patient's position with respect to the scanner. Detection of this position allows a better adjustment of the RF power resulting in an improved scan performance and image quality. In this project, we use real-time methods for accurately detecting the patient's position with respect to the scanner. MR data of thirteen test persons acquired using a new "move during scan" protocol which provides low resolution MR data during the initial movement of the patient bed into the scanner, is used to validate the detection algorithm. When being integrated, our results would enable automatic SAR optimization within the usual acquisition workflow at no extra cost. Future developments seek an even more robust and accurate detection of more features of the patient than just head, neck, lung, and feet.

Multimodal Ultrasound Registration The fusion of ultrasound data with a tomographic modality like CT or MRT is beneficial for many applications, e.g. intra-operative navigation scenarios. In particular it can also support the treatment planning and delineation of the target volume for radiation therapy. We investigate methods for image-based registration and fusion of ultrasound images with CT/MRT scans. This includes techniques for tracking, calibration and compounding for 3D freehand ultrasound, registration algorithms, as well as visualization and navigation methods.

Literature for Seminar

For each topic references from current literature will be provided.

Schein requirements

As usual:

• attendance of the Hauptseminar meetings
• active class participation (discussions)
• handout (8 - 16 pages) in LaTeX
• presentation (approximately 60 minutes incl. discussion) in Powerpoint or PDF format

Templates

• Presentation template