Dynamic Volume Rendering of Functional Medical Data on Dissimilar Hardware Platforms

In the last 30 years, medical imaging has become one of the most used diagnostic tools in the medical profession. Computed Tomography (CT) and Magnetic Resonance Imaging (MRI) technologies have become widely adopted because of their ability to capture the human body in a non-invasive manner. A volumetric dataset is a series of orthogonal 2D slices captured at a regular interval, typically along the axis of the body from the head to the feet. Volume rendering is a computer graphics technique that allows volumetric data to be visualized and manipulated as a single 3D object. Iso-surface rendering, image splatting, shear warp, texture slicing, and raycasting are volume rendering methods, each with associated advantages and disadvantages. Raycasting is widely regarded as the highest quality renderer of these methods. Originally, CT and MRI hardware was limited to providing a single 3D scan of the human body. The technology has improved to allow a set of scans capable of capturing anatomical movements like a beating heart. The capturing of anatomical data over time is referred to as functional imaging. Functional MRI (fMRI) is used to capture changes in the human body over time. While fMRI’s can be used to capture any anatomical data over time, one of the more common uses of fMRI is to capture brain activity. The fMRI scanning process is typically broken up into a time consuming high resolution anatomical scan and a series of quick low resolution scans capturing activity. The low resolution activity data is mapped onto the high resolution anatomical data to show changes over time. Academic research has advanced volume rendering and specifically fMRI volume rendering. Unfortunately, academic research is typically a one-off solution to a singular medical case or set of data, causing any advances to be problem specific as opposed to a general capability. Additionally, academic volume renderers are often designed to work on a specific device and operating system under controlled conditions. This prevents volume rendering from being used across the ever expanding number of different computing devices, such as desktops, laptops, immersive virtual reality systems, and mobile computers like phones or tablets. This research will investigate the feasibility of creating a generic software capability to perform real-time 4D volume rendering, via raycasting, on desktop, mobile, and immersive virtual reality platforms. Implementing a GPU-based 4D volume raycasting method for mobile devices will harness the power of the increasing number of mobile computational devices being used by medical professionals. Developing support for immersive virtual reality can enhance medical professionals’ interpretation of 3D physiology with the additional depth information provided by stereoscopic 3D. The results of this research will help expand the use of 4D volume rendering beyond the traditional desktop computer in the medical field. Developing the same 4D volume rendering capabilities across dissimilar platforms has many challenges. Each platform relies on their own coding languages, libraries, and hardware support. There are tradeoffs between using languages and libraries native to each platform and using a generic cross-platform system, such as a game engine. Native libraries will generally be more efficient during application run-time, but they require different coding implementations for each platform. The decision was made to use platform native languages and libraries in this research, whenever practical, in an attempt to achieve the best possible frame rates. 4D volume raycasting provides unique challenges independent of the platform. Specifically, fMRI data loading, volume animation, and multiple volume rendering. Additionally, real-time raycasting has never been successfully performed on a mobile device. Previous research relied on less computationally expensive methods, such as orthogonal texture slicing, to achieve real-time frame rates. These challenges will be addressed as the contributions of this research. The first contribution was exploring the feasibility of generic functional data input across desktop, mobile, and immersive virtual reality. To visualize 4D fMRI data it was necessary to build in the capability to read Neuroimaging Informatics Technology Initiative (NIfTI) files. The NIfTI format was designed to overcome limitations of 3D file formats like DICOM and store functional imagery with a single high-resolution anatomical scan and a set of low-resolution anatomical scans. Allowing input of the NIfTI binary data required creating custom C++ routines, as no object oriented APIs freely available for use existed. The NIfTI input code was built using C++ and the C++ Standard Library to be both light weight and cross-platform. Multi-volume rendering is another challenge of fMRI data visualization and a contribution of this work. fMRI data is typically broken into a single high-resolution anatomical volume and a series of low-resolution volumes that capture anatomical changes. Visualizing two volumes at the same time is known as multi-volume visualization. Therefore, the ability to correctly align and scale the volumes relative to each other was necessary. It was also necessary to develop a compositing method to combine data from both volumes into a single cohesive representation. Three prototype applications were built for the different platforms to test the feasibility of 4D volume raycasting. One each for desktop, mobile, and virtual reality. Although the backend implementations were required to be different between the three platforms, the raycasting functionality and features were identical. Therefore, the same fMRI dataset resulted in the same 3D visualization independent of the platform itself. Each platform uses the same NIfTI data loader and provides support for dataset coloring and windowing (tissue density manipulation). The fMRI data can be viewed changing over time by either animation through the time steps, like a movie, or using an interface slider to “scrub” through the different time steps of the data. The prototype applications data load times and frame rates were tested to determine if they achieved the real-time interaction goal. Real-time interaction was defined by achieving 10 frames per second (fps) or better, based on the work of Miller [1]. The desktop version was evaluated on a 2013 MacBook Pro running OS X 10.12 with a 2.6 GHz Intel Core i7 processor, 16 GB of RAM, and a NVIDIA GeForce GT 750M graphics card. The immersive application was tested in the C6 CAVE™, a 96 graphics node computer cluster comprised of NVIDIA Quadro 6000 graphics cards running Red Hat Enterprise Linux. The mobile application was evaluated on a 2016 9.7” iPad Pro running iOS 9.3.4. The iPad had a 64-bit Apple A9X dual core processor with 2 GB of built in memory. Two different fMRI brain activity datasets with different voxel resolutions were used as test datasets. Datasets were tested using both the 3D structural data, the 4D functional data, and a combination of the two. Frame rates for the desktop implementation were consistently above 10 fps, indicating that real-time 4D volume raycasting is possible on desktop hardware. The mobile and virtual reality platforms were able to perform real-time 3D volume raycasting consistently. This is a marked improvement for 3D mobile volume raycasting that was previously only able to achieve under one frame per second [2]. Both VR and mobile platforms were able to raycast the 4D only data at real-time frame rates, but did not consistently meet 10 fps when rendering both the 3D structural and 4D functional data simultaneously. However, 7 frames per second was the lowest frame rate recorded, indicating that hardware advances will allow consistent real-time raycasting of 4D fMRI data in the near future

직접 볼륨 렌더링에서 점진적 렌즈 샘플링을 사용한 피사계 심도 렌더링

학위논문 (박사) -- 서울대학교 대학원 : 공과대학 전기·컴퓨터공학부, 2021. 2. 신영길.Direct volume rendering is a widely used technique for extracting information from 3D scalar fields acquired by measurement or numerical simulation. To visualize the structure inside the volume, the voxels scalar value is often represented by a translucent color. This translucency of direct volume rendering makes it difficult to perceive the depth between the nested structures. Various volume rendering techniques to improve depth perception are mainly based on illustrative rendering techniques, and physically based rendering techniques such as depth of field effects are difficult to apply due to long computation time. With the development of immersive systems such as virtual and augmented reality and the growing interest in perceptually motivated medical visualization, it is necessary to implement depth of field in direct volume rendering. This study proposes a novel method for applying depth of field effects to volume ray casting to improve the depth perception. By performing ray casting using multiple rays per pixel, objects at a distance in focus are sharply rendered and objects at an out-of-focus distance are blurred. To achieve these effects, a thin lens camera model is used to simulate rays passing through different parts of the lens. And an effective lens sampling method is used to generate an aliasing-free image with a minimum number of lens samples that directly affect performance. The proposed method is implemented without preprocessing based on the GPU-based volume ray casting pipeline. Therefore, all acceleration techniques of volume ray casting can be applied without restrictions. We also propose multi-pass rendering using progressive lens sampling as an acceleration technique. More lens samples are progressively used for ray generation over multiple render passes. Each pixel has a different final render pass depending on the predicted maximum blurring size based on the circle of confusion. This technique makes it possible to apply a different number of lens samples for each pixel, depending on the degree of blurring of the depth of field effects over distance. This acceleration method reduces unnecessary lens sampling and increases the cache hit rate of the GPU, allowing us to generate the depth of field effects at interactive frame rates in direct volume rendering. In the experiments using various data, the proposed method generated realistic depth of field effects in real time. These results demonstrate that our method produces depth of field effects with similar quality to the offline image synthesis method and is up to 12 times faster than the existing depth of field method in direct volume rendering.직접 볼륨 렌더링(direct volume rendering, DVR)은 측정 또는 수치 시뮬레이션으로 얻은 3차원 공간의 스칼라 필드(3D scalar fields) 데이터에서 정보를 추출하는데 널리 사용되는 기술이다. 볼륨 내부의 구조를 가시화하기 위해 복셀(voxel)의 스칼라 값은 종종 반투명의 색상으로 표현된다. 이러한 직접 볼륨 렌더링의 반투명성은 중첩된 구조 간 깊이 인식을 어렵게 한다. 깊이 인식을 향상시키기 위한 다양한 볼륨 렌더링 기법들은 주로 삽화풍 렌더링(illustrative rendering)을 기반으로 하며, 피사계 심도(depth of field, DoF) 효과와 같은 물리 기반 렌더링(physically based rendering) 기법들은 계산 시간이 오래 걸리기 때문에 적용이 어렵다. 가상 및 증강 현실과 같은 몰입형 시스템의 발전과 인간의 지각에 기반한 의료영상 시각화에 대한 관심이 증가함에 따라 직접 볼륨 렌더링에서 피사계 심도를 구현할 필요가 있다. 본 논문에서는 직접 볼륨 렌더링의 깊이 인식을 향상시키기 위해 볼륨 광선투사법에 피사계 심도 효과를 적용하는 새로운 방법을 제안한다. 픽셀 당 여러 개의 광선을 사용한 광선투사법(ray casting)을 수행하여 초점이 맞는 거리에 있는 물체는 선명하게 표현되고 초점이 맞지 않는 거리에 있는 물체는 흐리게 표현된다. 이러한 효과를 얻기 위하여 렌즈의 서로 다른 부분을 통과하는 광선들을 시뮬레이션 하는 얇은 렌즈 카메라 모델(thin lens camera model)이 사용되었다. 그리고 성능에 직접적으로 영향을 끼치는 렌즈 샘플은 최적의 렌즈 샘플링 방법을 사용하여 최소한의 개수를 가지고 앨리어싱(aliasing)이 없는 이미지를 생성하였다. 제안한 방법은 기존의 GPU 기반 볼륨 광선투사법 파이프라인 내에서 전처리 없이 구현된다. 따라서 볼륨 광선투사법의 모든 가속화 기법을 제한없이 적용할 수 있다. 또한 가속 기술로 누진 렌즈 샘플링(progressive lens sampling)을 사용하는 다중 패스 렌더링(multi-pass rendering)을 제안한다. 더 많은 렌즈 샘플들이 여러 렌더 패스들을 거치면서 점진적으로 사용된다. 각 픽셀은 착란원(circle of confusion)을 기반으로 예측된 최대 흐림 정도에 따라 다른 최종 렌더링 패스를 갖는다. 이 기법은 거리에 따른 피사계 심도 효과의 흐림 정도에 따라 각 픽셀에 다른 개수의 렌즈 샘플을 적용할 수 있게 한다. 이러한 가속화 방법은 불필요한 렌즈 샘플링을 줄이고 GPU의 캐시(cache) 적중률을 높여 직접 볼륨 렌더링에서 상호작용이 가능한 프레임 속도로 피사계 심도 효과를 렌더링 할 수 있게 한다. 다양한 데이터를 사용한 실험에서 제안한 방법은 실시간으로 사실적인 피사계 심도 효과를 생성했다. 이러한 결과는 우리의 방법이 오프라인 이미지 합성 방법과 유사한 품질의 피사계 심도 효과를 생성하면서 직접 볼륨 렌더링의 기존 피사계 심도 렌더링 방법보다 최대 12배까지 빠르다는 것을 보여준다.CHAPTER 1 INTRODUCTION 1 1.1 Motivation 1 1.2 Dissertation Goals 5 1.3 Main Contributions 6 1.4 Organization of Dissertation 8 CHAPTER 2 RELATED WORK 9 2.1 Depth of Field on Surface Rendering 10 2.1.1 Object-Space Approaches 11 2.1.2 Image-Space Approaches 15 2.2 Depth of Field on Volume Rendering 26 2.2.1 Blur Filtering on Slice-Based Volume Rendering 28 2.2.2 Stochastic Sampling on Volume Ray Casting 30 CHAPTER 3 DEPTH OF FIELD VOLUME RAY CASTING 33 3.1 Fundamentals 33 3.1.1 Depth of Field 34 3.1.2 Camera Models 36 3.1.3 Direct Volume Rendering 42 3.2 Geometry Setup 48 3.3 Lens Sampling Strategy 53 3.3.1 Sampling Techniques 53 3.3.2 Disk Mapping 57 3.4 CoC-Based Multi-Pass Rendering 60 3.4.1 Progressive Lens Sample Sequence 60 3.4.2 Final Render Pass Determination 62 CHAPTER 4 GPU IMPLEMENTATION 66 4.1 Overview 66 4.2 Rendering Pipeline 67 4.3 Focal Plane Transformation 74 4.4 Lens Sample Transformation 76 CHAPTER 5 EXPERIMENTAL RESULTS 78 5.1 Number of Lens Samples 79 5.2 Number of Render Passes 82 5.3 Render Pass Parameter 84 5.4 Comparison with Previous Methods 87 CHAPTER 6 CONCLUSION 97 Bibliography 101 Appendix 111Docto

Interactive deformation and visualization of level set surfaces using graphics hardware

Journal ArticleDeformable isosurfaces, implemented with level-set methods, have demonstrated a great potential in visualization for applications such as segmentation, surface processing, and surface reconstruction. Their usefulness has been limited, however, by their high computational cost and and reliance on significant parameter tuning. This paper presents a solution to these challenges by describing graphics processor (GPU) based algorithms for solving and visualizing levelset solutions at interactive rates. Our efficient GPU-based solution relies on packing the level-set isosurface data into a dynamic, sparse texture format. As the level set moves, this sparse data structure is updated via a novel GPU to CPU message passing scheme. When the level-set solver is integrated with a real-time volume renderer operating on the same packed format, a user can visualize and steer the deformable level-set surface as it evolves. In addition, the resulting isosurface can serve as a region-of-interest specifier for the volume renderer. This paper demonstrates the capabilities of this technology for interactive volume visualization and segmentation

Streaming narrow-band algorithm: interactive computation and visualization of level sets

Journal ArticleAbstract-Deformable isosurfaces, implemented with level-set methods, have demonstrated a great potential in visualization and computer graphics for applications such as segmentation, surface processing, and physically-based modeling. Their usefulness has been limited, however, by their high computational cost and reliance on significant parameter tuning. This paper presents a solution to these challenges by describing graphics processor (GPU) based algorithms for solving and visualizing level-set solutions at interactive rates. The proposed solution is based on a new, streaming implementation of the narrow-band algorithm. The new algorithm packs the level-set isosurface data into 2D texture memory via a multidimensional virtual memory system. As the level set moves, this texturebased representation is dynamically updated via a novel GPU-to-CPU message passing scheme. By integrating the level-set solver with a real-time volume renderer, a user can visualize and intuitively steer the level-set surface as it evolves. We demonstrate the capabilities of this technology for interactive volume segmentation and visualization

Towards Real-Time Novel View Synthesis Using Visual Hulls

This thesis discusses fast novel view synthesis from multiple images taken from different viewpoints. We propose several new algorithms that take advantage of modern graphics hardware to create novel views. Although different approaches are explored, one geometry representation, the visual hull, is employed throughout our work. First the visual hull plays an auxiliary role and assists in reconstruction of depth maps that are utilized for novel view synthesis. Then we treat the visual hull as the principal geometry representation of scene objects. A hardwareaccelerated approach is presented to reconstruct and render visual hulls directly from a set of silhouette images. The reconstruction is embedded in the rendering process and accomplished with an alpha map trimming technique. We go on by combining this technique with hardware-accelerated CSG reconstruction to improve the rendering quality of visual hulls. Finally, photometric information is exploited to overcome an inherent limitation of the visual hull. All algorithms are implemented on a distributed system. Novel views are generated at interactive or real-time frame rates.In dieser Dissertation werden mehrere Verfahren vorgestellt, mit deren Hilfe neue Ansichten einer Szene aus mehreren Bildströmen errechnet werden können. Die Bildströme werden hierzu aus unterschiedlichen Blickwinkeln auf die Szene aufgezeichnet. Wir schlagen mehrere Algorithmen vor, welche die Funktionen moderner Grafikhardware ausnutzen, um die neuen Ansichten zu errechnen. Obwohl die Verfahren sich methodisch unterscheiden, basieren sie auf der gleichen Geometriedarstellung, der Visual Hull. In der ersten Methode spielt die Visual Hull eine unterstützende Rolle bei der Rekonstruktion von Tiefenbildern, die zur Erzeugung neuer Ansichten verwendet werden. In den nachfolgend vorgestellten Verfahren dient die Visual Hull primär der Repräsentation von Objekten in einer Szene. Eine hardwarebeschleunigte Methode, um Visual Hulls direkt aus mehreren Silhouettenbildern zu rekonstruieren und zu rendern, wird vorgestellt. Das Rekonstruktionsverfahren ist hierbei Bestandteil der Renderingmethode und basiert auf einer Alpha Map Trimming Technik. Ein weiterer Algorithmus verbessert die Qualitaet der gerenderten Visual Hulls, indem das Alpha-Map-basierte Verfahren mit einer hardware-beschleunigten CSG Rekonstruktiontechnik kombiniert wird. Eine vierte Methode nutzt zusaetzlich photometrische Information aus, um eine grundlegende Beschraenkung des Visual-Hull-Ansatzes zu umgehen. Alle Verfahren ermoeglichen die interaktive oder Echtzeit- Erzeugung neuer Ansichten

Efficient data structures for piecewise-smooth video processing

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.Includes bibliographical references (p. 95-102).A number of useful image and video processing techniques, ranging from low level operations such as denoising and detail enhancement to higher level methods such as object manipulation and special effects, rely on piecewise-smooth functions computed from the input data. In this thesis, we present two computationally efficient data structures for representing piecewise-smooth visual information and demonstrate how they can dramatically simplify and accelerate a variety of video processing algorithms. We start by introducing the bilateral grid, an image representation that explicitly accounts for intensity edges. By interpreting brightness values as Euclidean coordinates, the bilateral grid enables simple expressions for edge-aware filters. Smooth functions defined on the bilateral grid are piecewise-smooth in image space. Within this framework, we derive efficient reinterpretations of a number of edge-aware filters commonly used in computational photography as operations on the bilateral grid, including the bilateral filter, edgeaware scattered data interpolation, and local histogram equalization. We also show how these techniques can be easily parallelized onto modern graphics hardware for real-time processing of high definition video. The second data structure we introduce is the video mesh, designed as a flexible central data structure for general-purpose video editing. It represents objects in a video sequence as 2.5D "paper cutouts" and allows interactive editing of moving objects and modeling of depth, which enables 3D effects and post-exposure camera control. In our representation, we assume that motion and depth are piecewise-smooth, and encode them sparsely as a set of points tracked over time. The video mesh is a triangulation over this point set and per-pixel information is obtained by interpolation. To handle occlusions and detailed object boundaries, we rely on the user to rotoscope the scene at a sparse set of frames using spline curves. We introduce an algorithm to robustly and automatically cut the mesh into local layers with proper occlusion topology, and propagate the splines to the remaining frames. Object boundaries are refined with per-pixel alpha mattes. At its core, the video mesh is a collection of texture-mapped triangles, which we can edit and render interactively using graphics hardware. We demonstrate the effectiveness of our representation with special effects such as 3D viewpoint changes, object insertion, depthof- field manipulation, and 2D to 3D video conversion.by Jiawen Chen.Ph.D

GPU-friendly marching cubes.

Xie, Yongming.Thesis (M.Phil.)--Chinese University of Hong Kong, 2008.Includes bibliographical references (leaves 77-85).Abstracts in English and Chinese.Abstract --- p.iAcknowledgement --- p.iiChapter 1 --- Introduction --- p.1Chapter 1.1 --- Isosurfaces --- p.1Chapter 1.2 --- Graphics Processing Unit --- p.2Chapter 1.3 --- Objective --- p.3Chapter 1.4 --- Contribution --- p.3Chapter 1.5 --- Thesis Organization --- p.4Chapter 2 --- Marching Cubes --- p.5Chapter 2.1 --- Introduction --- p.5Chapter 2.2 --- Marching Cubes Algorithm --- p.7Chapter 2.3 --- Triangulated Cube Configuration Table --- p.12Chapter 2.4 --- Summary --- p.16Chapter 3 --- Graphics Processing Unit --- p.18Chapter 3.1 --- Introduction --- p.18Chapter 3.2 --- History of Graphics Processing Unit --- p.19Chapter 3.2.1 --- First Generation GPU --- p.20Chapter 3.2.2 --- Second Generation GPU --- p.20Chapter 3.2.3 --- Third Generation GPU --- p.20Chapter 3.2.4 --- Fourth Generation GPU --- p.21Chapter 3.3 --- The Graphics Pipelining --- p.21Chapter 3.3.1 --- Standard Graphics Pipeline --- p.21Chapter 3.3.2 --- Programmable Graphics Pipeline --- p.23Chapter 3.3.3 --- Vertex Processors --- p.25Chapter 3.3.4 --- Fragment Processors --- p.26Chapter 3.3.5 --- Frame Buffer Operations --- p.28Chapter 3.4 --- GPU CPU Analogy --- p.31Chapter 3.4.1 --- Memory Architecture --- p.31Chapter 3.4.2 --- Processing Model --- p.32Chapter 3.4.3 --- Limitation of GPU --- p.33Chapter 3.4.4 --- Input and Output --- p.34Chapter 3.4.5 --- Data Readback --- p.34Chapter 3.4.6 --- FramebufFer --- p.34Chapter 3.5 --- Summary --- p.35Chapter 4 --- Volume Rendering --- p.37Chapter 4.1 --- Introduction --- p.37Chapter 4.2 --- History of Volume Rendering --- p.38Chapter 4.3 --- Hardware Accelerated Volume Rendering --- p.40Chapter 4.3.1 --- Hardware Acceleration Volume Rendering Methods --- p.41Chapter 4.3.2 --- Proxy Geometry --- p.42Chapter 4.3.3 --- Object-Aligned Slicing --- p.43Chapter 4.3.4 --- View-Aligned Slicing --- p.45Chapter 4.4 --- Summary --- p.48Chapter 5 --- GPU-Friendly Marching Cubes --- p.49Chapter 5.1 --- Introduction --- p.49Chapter 5.2 --- Previous Work --- p.50Chapter 5.3 --- Traditional Method --- p.52Chapter 5.3.1 --- Scalar Volume Data --- p.53Chapter 5.3.2 --- Isosurface Extraction --- p.53Chapter 5.3.3 --- Flow Chart --- p.54Chapter 5.3.4 --- Transparent Isosurfaces --- p.56Chapter 5.4 --- Our Method --- p.56Chapter 5.4.1 --- Cell Selection --- p.59Chapter 5.4.2 --- Vertex Labeling --- p.61Chapter 5.4.3 --- Cell Indexing --- p.62Chapter 5.4.4 --- Interpolation --- p.65Chapter 5.5 --- Rendering Translucent Isosurfaces --- p.67Chapter 5.6 --- Implementation and Results --- p.69Chapter 5.7 --- Summary --- p.74Chapter 6 --- Conclusion --- p.76Bibliography --- p.7