Four-dimensional Cone Beam CT Reconstruction and Enhancement using a Temporal Non-Local Means Method

Four-dimensional Cone Beam Computed Tomography (4D-CBCT) has been developed to provide respiratory phase resolved volumetric imaging in image guided radiation therapy (IGRT). Inadequate number of projections in each phase bin results in low quality 4D-CBCT images with obvious streaking artifacts. In this work, we propose two novel 4D-CBCT algorithms: an iterative reconstruction algorithm and an enhancement algorithm, utilizing a temporal nonlocal means (TNLM) method. We define a TNLM energy term for a given set of 4D-CBCT images. Minimization of this term favors those 4D-CBCT images such that any anatomical features at one spatial point at one phase can be found in a nearby spatial point at neighboring phases. 4D-CBCT reconstruction is achieved by minimizing a total energy containing a data fidelity term and the TNLM energy term. As for the image enhancement, 4D-CBCT images generated by the FDK algorithm are enhanced by minimizing the TNLM function while keeping the enhanced images close to the FDK results. A forward-backward splitting algorithm and a Gauss-Jacobi iteration method are employed to solve the problems. The algorithms are implemented on GPU to achieve a high computational efficiency. The reconstruction algorithm and the enhancement algorithm generate visually similar 4D-CBCT images, both better than the FDK results. Quantitative evaluations indicate that, compared with the FDK results, our reconstruction method improves contrast-to-noise-ratio (CNR) by a factor of 2.56~3.13 and our enhancement method increases the CNR by 2.75~3.33 times. The enhancement method also removes over 80% of the streak artifacts from the FDK results. The total computation time is ~460 sec for the reconstruction algorithm and ~610 sec for the enhancement algorithm on an NVIDIA Tesla C1060 GPU card.Comment: 20 pages, 3 figures, 2 table

Extracting respiratory signals from thoracic cone beam CT projections

Patient respiratory signal associated with the cone beam CT (CBCT) projections is important for lung cancer radiotherapy. In contrast to monitoring an external surrogate of respiration, such signal can be extracted directly from the CBCT projections. In this paper, we propose a novel local principle component analysis (LPCA) method to extract the respiratory signal by distinguishing the respiration motion-induced content change from the gantry rotation-induced content change in the CBCT projections. The LPCA method is evaluated by comparing with three state-of-the-art projection-based methods, namely, the Amsterdam Shroud (AS) method, the intensity analysis (IA) method, and the Fourier-transform based phase analysis (FT-p) method. The clinical CBCT projection data of eight patients, acquired under various clinical scenarios, were used to investigate the performance of each method. We found that the proposed LPCA method has demonstrated the best overall performance for cases tested and thus is a promising technique for extracting respiratory signal. We also identified the applicability of each existing method.Comment: 21 pages, 11 figures, submitted to Phys. Med. Bio

Optimizing 4DCBCT Projection Allocation to Respiratory Bins

Four dimensional cone beam computed tomography (4DCBCT) is an emerging image guidance strategy used in radiotherapy where projections acquired during a scan are sorted into respiratory bins based on the respiratory phase or displacement. 4DCBCT reduces the motion blur caused by respiratory motion but increases streaking artefacts due to projection under-sampling as a result of the irregular nature of patient breathing and the binning algorithms used. For displacement binning the streak artefacts are so severe that displacement binning is rarely used clinically. The purpose of this study is to investigate if sharing projections between respiratory bins and adjusting the location of respiratory bins in an optimal manner can reduce or eliminate streak artefacts in 4DCBCT images. We introduce a mathematical optimization framework and a heuristic solution method, which we will call the optimized projection allocation algorithm, to determine where to position the respiratory bins and which projections to source from neighbouring respiratory bins. Five 4DCBCT datasets from three patients were used to reconstruct 4DCBCT images. Projections were sorted into respiratory bins using equispaced, equal density and optimized projection allocation. The standard deviation of the angular separation between projections was used to assess streaking and the consistency of the segmented volume of a ducial gold marker was used to assess motion blur. The standard deviation of the angular separation between projections using displacement binning and optimized projection allocation was 30%-50% smaller than conventional phase based binning and 59%-76% smaller than conventional displacement binning indicating more uniformly spaced projections and fewer streaking artefacts. The standard deviation in the marker volume was 20%-90% smaller when using optimized projection allocation than using conventional phase based binning suggesting more uniform marker segmentation and less motion blur. Images reconstructed using displacement binning and the optimized projection allocation algorithm were clearer, contained visibly fewer streak artefacts and produced more consistent marker segmentation than those reconstructed with either equispaced or equal-density binning. The optimized projection allocation algorithm signi cantly improves image quality in 4DCBCT images and provides, for the rst time, a method to consistently generate high quality displacement binned 4DCBCT images in clinical applications

Surrogate driven respiratory motion model derived from CBCT projection data

Cone Beam Computed Tomography (CBCT) is the most common imaging method for Image Guided Radiation Therapy (IGRT). However due to the slow rotating gantry, the image quality of CBCT can be adversely affected by respiratory motion, as it blurs the tumour and nearby organs at risk (OARs), which makes visualization of organ boundaries difficult, in particular for organs in the thoracic region. Currently one approach to tackle the problem of respiratory motion is the use of respiratory motion model to compensate for the motion during CBCT image reconstruction. The overall goal of this work is to estimate the 3D motion, including the breath-to-breath variability, on the day of treatment directly from the CBCT projection data, without requiring any external devices. The work presented here consist of two main parts: firstly, we introduce a novel data driven method based on Principal Component Analysis PCA, with the goal to extract a surrogate signal related to the internal anatomy from the CBCT projections. Secondly, using the extracted signals, we use surrogate-driven respiratory motion models to estimate the patient’s 3D respiratory motion. We utilized a recently developed generalized framework that unifies image registration and correspondence model fitting into a single optimization. This enables the model to be fitted directly to unsorted/unreconstructed data (CBCT projection data), thereby allowing an estimate of the patient’s respiratory motion on the day of treatment. To evaluate our methods, we have used an anthropomorphic software phantom combined with CBCT projection simulations. We have also tested the proposed method on clinical data with promising results obtained

Optimization strategies for respiratory motion management in stereotactic body radiation therapy

Various challenges arise during the treatment of lung tumors with stereotactic body radiation therapy (SBRT), which is a form of hypofractionated high precision conformal radiation therapy delivered to small targets. The dose is applied in only a few fractions and respiratory organ and tumor motion is a source of uncertainty additional to interfractional set-up errors. Respiratory organ and tumor motion is highly patient-specific and it affects the whole radiotherapy treatment chain. In this thesis, motion management techniques for SBRT are evaluated and improved in a clinical setting. A clinical need for improvement has been present at the LMU university hospital for each issue addressed in this thesis: Initially, the usage of respiratory correlated computed tomography (4DCT), which is vital for SBRT treatment, was seen as impractical and prone to uncertainties in the data reconstruction in its current form. Therefore, the 4DCT reconstruction workflow has been improved to minimize these potential error sources. Secondly, treatment planning for tumors affected by respiratory motion was evaluated and subsequently improved. Finally, the treatment technique of respiratory gating was implemented at the clinic, which led to the need of evaluating the respiratory gating characteristics of the novel system configuration. At first, the 4DCT reconstruction workflow used in clinical practice was investigated, as in the presence of respiratory motion the knowledge of tumor position over time is essential in SBRT treatments. Using 4DCT, the full motion range of the individual tumor can be determined. However, certain 4DCT reconstruction methods can under- or overestimate tumor motion due to limitations in the data acquisition scheme and due to the incorrect sorting of certain X-ray computed tomography (CT) image slices into different respiratory phases. As the regular clinical workflow of cycle-based sorting (CBS) without maximum inspiration detection (and therefore no clear starting point for the individual breathing cycles) seemed to be affected by these potential errors, the usage of CBS with correct maximum detection and another sorting algorithm of the respiration states, so-called local amplitude-based sorting (LAS), both have been implemented for a reduction of image artifacts and improved 4DCT quality. The three phase binning algorithms have been investigated in a phantom study (using 10 different breathing waveforms) and in a patient study (with 10 different patients). The mis-representation of the tumor volume was reduced in both implemented sorting algorithms compared to the previously used CBS approach (without correct maximum detection) in the phantom and the patient study. The clinical recommendation was the use of CBS with improved maximum detection, as too many manual interventions would be needed for the LAS workflow. Secondly, a combination of the actual patient breathing trace during treatment, the log files generated by the linear accelerator (LINAC), and Monte Carlo (MC) four-dimensional (4D) dose calculations for each individual fraction was implemented as a 4D dose evaluation tool. This workflow was tested in a clinical environment for SBRT treatment planning on multiple CT datasets featuring: a native free-breathing 3DCT, an average intensity projection (AIP) as well as a maximum intensity projection (MIP), both obtained from the patient's 4DCT, and density overrides (DOs) in a 3DCT. This study has been carried out for 5 SBRT patients for three-dimensional conformal radiation therapy (3D-CRT) and volumetric modulated arc therapy (VMAT) treatment plans. The dose has been recalculated on each 4DCT breathing phase according the the patient's breathing waveform and accumulated to the gross tumor volume (GTV) at the end-of-exhale (EOE) breathing phase using deformable image registration. Even though the least differences in planned and recalculated dose were found for AIP and MIP treatment planning, the results indicate a strong dependency on individual tumor motion due to the variability of breathing motion in general, and on tumor size. The combination of the patient's individual breathing trace during each SBRT fraction with 4D MC dose calculation based on the LINAC log file information leads to a good approximation of actual dose delivery. Finally, in order to ensure precise and accurate treatment for respiratory gating techniques, the technical characteristics of the LINAC in combination with a breathing motion monitoring system as s surrogate for tumor motion have to be identified. The dose delivery accuracy and the latency of a surface imaging system in connection with a modern medical LINAC were investigated using a dynamic breathing motion phantom. The dosimetric evaluation has been carried out using a static 2D-diode array. The measurement of the dose difference between gated and ungated radiation delivery was found to be below 1% (for clinical relevant gating levels of about 30%). The beam-on latency, or time delay, determined using radiographic films was found to be up to 851 ms±100 ms. With these known parameters, an adjustment of the pre-selected gating level or the internal target volume (ITV) margins could be made. With the highly patient-specific character of respiratory motion, lung SBRT faces many additional challenges besides the specific issues addressed in this thesis. However, the findings of this thesis have improved clinical workflows at the Department of Radiation Oncology of the LMU University hospital. In a future perspective, a workflow using evaluation of the actual 4D dose in combination with accurate 4DCT image acquisition and specialized treatment delivery (such as respiratory gating) has the potential for a safe further reduction of treatment margins and increased sparing of organs-at-risk (OARs) in SBRT without compromising tumor dose targeting accuracy

Truncation artifact correction for micro-CT scanners

The work included in this project is framed on one of the lines of research carried out at the Laboratorio de Imagen Médica de la Unidad de Medicina y Cirugía Experimental (UMCE) of Hospital General Universitario Gregorio Marañón and the Bioengineering and Aerospace Department of Universidad Carlos III de Madrid. Its goal is to design, develop and evaluate new data acquisition systems, processing and reconstruction of multimodal images for application in preclinical research. Inside this research line, an x-ray computed tomography (micro-CT add on) system of high resolution has been designed for small animal. Nowadays, computed tomography (CT) is one of the techniques most widely used to obtain anatomical information from living subjects. Different artifacts from different nature usually degrade the qualitative and quantitative analysis of these images. This creates the urgent need of developing algorithms to compensate and/or reduce these artifacts. The general objective of the present thesis is to implement a method for compensating truncation artifact in the micro-CT add-on scanner for small animal developed at Hospital Universitario Gregorio Marañón. This artifact appears due to the acquisition of incomplete x-ray projections when part of the sample, especially obese rats, lies outside the field of view. As a result of these data inconsistencies, bright shading artifacts and quantification errors in the images may appear after the reconstruction process. First of all, truncation artifact in the high resolution micro-CT add-on scanner was studied. Then, after a review of the proposed methods in the literature, the optimal approach for the micro-CT add-on was selected, based on a sinogram extrapolation technique developed by Ohnesorge et al [1]. This method consists on a symmetric mirroring extrapolation of the truncated projections that guarantees continuity at the truncation point. It includes a sine shaping effect that ensures a smooth attenuation signal drop. Truncation artifact correction method has been validated in simulated and real studies. Results show an overall significant reduction of truncation artifact. This algorithm has been adapted and implemented in the reconstruction interface of the preclinical high-resolution micro-CT scanner, which is manufactured by SEDECAL S.L. and commercialized worldwide.El trabajo de este proyecto se encuadra dentro de una línea de investigación que se desarrolla en el Laboratorio de Imagen Médica de la Unidad de Medicina y Cirugía Experimental (UMCE) del Hospital General Universitario Gregorio Marañón y el Departamento de Bioingeniería e Ingeniería Aeroespacial de la Universidad Carlos III de Madrid. Su objetivo es diseñar, desarrollar y evaluar nuevos sistemas de adquisición de datos, procesamiento y reconstrucción de imágenes multi-modales para aplicaciones en investigación preclínica. Dentro de esta línea de investigación se ha desarrollado un tomógrafo de rayos X de alta resolución para pequeños animales (micro-TAC add-on). Actualmente, la tomografía axial computarizada es una de las técnicas más ampliamente utilizadas para la obtención de información anatómica in vivo. Existe una serie de artefactos de distinta naturaleza en este tipo de imágenes que generalmente degradan y dificultan el análisis cualitativo y cuantitativo de las imágenes, dando lugar a una necesidad imperante de desarrollar algoritmos de corrección y/o reducción de estos artefactos. El objetivo general del presente proyecto es la implementación de un algoritmo para la corrección del artefacto de truncamiento en el escáner micro-TAC add-on desarrollado en el Hospital Universitario Gregorio Marañón. Este artefacto aparece debido a la adquisición de proyecciones incompletas cuando parte de la muestra, especialmente ratas obesas, se extiende fuera del campo de visión. Estas inconsistencias en los datos obtenidos pueden dar lugar a la aparición de bandas brillantes y errores en la cuantificación de las imágenes después del proceso de reconstrucción. En primer lugar, se ha estudiado el artefacto de truncamiento en el escáner micro-TAC add-on de alta resolución. Seguidamente, se ha llevado a cabo una revisión de los métodos propuestos en la bibliografía, seleccionando una estrategia óptima para el micro-TAC add-on bajo estudio: una técnica de extrapolación del sinograma publicado por Ohnesorge et al [1]. Este método consiste en una extrapolación de espejo simétrico de las proyecciones truncadas que garantiza la continuidad en el punto de truncamiento. Incluye el modelado de una sinusoide que asegura una caída de señal en los valores de atenuación suave. Este método ha sido validado en estudios simulados y reales. Los resultados muestran una clara reducción del artefacto de truncamiento. El resultado de este proyecto ha sido incorporado en la interfaz de reconstrucción del escáner pre-clínico micro-TAC add-on de alta resolución fabricado por SEDECAL S.A. y comercializado por todo el mundo.Ingeniería Biomédic