Effect of partial volume modeling, use anatmical templates, and bias-field correction on the repeatability of MRI regional volume quantification

[Abstract] 11th Annual Meeting of the Organization for Human Brain Mapping, June 2005, Toronto, CanadaThe aim of this work is to measure the repeatability of different segmentation strategies on regional volume estimates. We choose to focus on three possible alternatives of the most widely used segmentation method, the EM algoritIun. Thus, we have obtained regional volumetric data using raw EM, EM with PVE modeling, and EM using anatomical templates. To account for the most common sources of error, tIlese methods have been evaluated under different conditions of patient positioning, MR scarmer, and bias field correctionSupported in part by: TIC (2001-3697-C03-03), FIS (02/1178,0213095), Red TeITk'ltica 1M3 G031185Publicad

An Accurate and Robust Numerical Scheme for Transport Equations

En esta tesis se presenta una nueva técnica de discretización para ecuaciones de transporte en problemas de convección-difusión para el rango completo de números de Péclet. La discretización emplea el flujo exacto de una ecuación de transporte unidimensional en estado estacionario para deducir una ecuación discreta de tres puntos en problemas unidimensionales y cinco puntos en problemas bidimensionales. Con "flujo exacto" se entiende que se puede obtener la solución exacta en función de integrales de algunos parámetros del fluido y flujo, incluso si estos parámetros son vari- ables en un volumen de control. Las cuadraturas de alto orden se utilizan para lograr resultados numéricos cercanos a la precisión de la máquina, incluso con mallas bastas.Como la discretización es esencialmente unidimensional, no está garantizada una solución con precisión de máquina para problemas multidimensionales, incluso en los casos en que las integrales a lo largo de cada coordenada cartesiana tienen una primitiva. En este sentido, la contribución principal de esta tesis consiste en una forma simple y elegante de obtener soluciones en problemas multidimensionales sin dejar de utilizar la formulación unidimensional. Además, si el problema es tal que la solución tiene precisión de máquina en el problema unidimensional a lo largo de las líneas coordenadas, también la tendrá para el dominio multidimensional.In this thesis, we present a novel discretization technique for transport equations in convection-diffusion problems across the whole range of Péclet numbers. The discretization employs the exact flux of a steady-state one-dimensional transport equation to derive a discrete equation with a three-point stencil in one-dimensional problems and a five-point stencil in two-dimensional ones. With "exact flux" it is meant that the exact solution can be obtained as a function of integrals of some fluid and flow parameters, even if these parameters are variable across a control volume. High-order quadratures are used to achieve numerical results close to machine- accuracy even with coarse grids. As the discretization is essentially one-dimensional, getting the machine- accurate solution of multidimensional problems is not guaranteed even in cases where the integrals along each Cartesian coordinate have a primitive. In this regard, the main contribution of this thesis consists in a simple and elegant way of getting solutions in multidimensional problems while still using the one-dimensional formulation. Moreover, if the problem is such that the solution is machine-accurate in the one-dimensional problem along coordinate lines, it will also be for the multidimensional domain.<br /

Integración de imágenes biomédicas : técnicas basadas en teoría de la información

Resumen Esta Tesis Doctoral profundiza en los métodos de registro de estudios multimodales (anatómicos y funcionales) de animales de laboratorio mediante técnicas basadas en teoría de la información. Se realiza un análisis de la influencia de los parámetros del algoritmo de registro, así como una validación sistemática de los resultados. Para poder evaluar el funcionamiento de los métodos de registro basados en teoría de la información, se presentan una serie de estudios patrón que se registran gracias a un conjunto de marcadores externos. En estos estudios se calcula la precisión del registro que se consigue por medio de los marcadores, validando el diseño y configuración de éstos. Se evalúa la convergencia y precisión de los algoritmos de registro, y su dependencia de diversos factores (desalineamiento inicial y parámetros del algoritmo), por medio de un diseño experimental que permite una validación sistemática. Los resultados permiten cuantificar la influencia de los factores en el resultado. Dado que los métodos descritos en esta Tesis Doctoral tienen como principal limitación el desalineamiento inicial máximo que son capaces de resolver, se propone un método basado en los ejes principales y los centros de masas de las imágenes, para prealinear los estudios. Utilizando este método se consigue mejorar el comportamiento de los algoritmos automáticos, consiguiendo un porcentaje de éxitos para las transformaciones evaluadas cercano al 100%. Finalmente, todos los algoritmos desarrollados y utilizados en esta Tesis Doctoral se encuentran integrados dentro de una interfaz de adquisición, reconstrucción, visualización y análisis denominada MMWKS, específicamente diseñada para estudios de animales de laboratorio. De esta forma los usuarios de este tipo de dispositivos pueden integrar la información proveniente de distintas modalidades con facilidad. Abstract The main topic of this PhD Thesis is multimodality (anatomical and functional) image registration of small animal studies, using information theory based techniques. The influence of algorithm parameters in the result and a systematic validation of these methods are also addressed. A set of reference studies are presented in order to evaluate the behavior of information theory based registration algorithms. These studies are registered using external references. The accuracy of the registration calculated from these markers is obtained, and allows validating their design and configuration. Since the methods described in this PhD Thesis have the initial misalignment they are able to solve as principal limitation, a method to pre-align the studies is proposed. This method is based in the principal axes transformation. By using this previous step, the results form automatic algorithms are improved, reaching a percentage of successful registrations near to 100%. Finally, algorithms developed and used in this PhD Thesis are part of a specific user interface named MMWKS. This software is designed to acquire, reconstruct, visualize and analyze small animal studies. By using the software developed, the users of small animal imaging devices can integrate information from different modalities easily

Simulación numérica de flujos magnetoreológicos

El presente proyecto consiste en la simulación numérica de fluidos cuyas propiedades, y en consecuencia su movimiento, se ven afectadas y modificadas mediante la aplicación externa de campos magnéticos. Dichas simulaciones se realizará sobre una geometría de placas planas, paralelas y fijas. Para llevar a cabo lo comentado anteriormente, se dispondrá de un software académico desarrollado por el profesorado del Área de Mecánica de Fluidos de la Universidad de Zaragoza denominado CRETINO (Código de Resolución de Ecuaciones de Transporte con Introducción Numérica de Opciones). Dicho software, que es utilizado por los alumnos del centro en prácticas, puede simular tanto flujos laminares como turbulentos, estacionarios y transitorios mediante el método de discretización de “Volúmenes Finitos”, método muy empleado en el ámbito de la mecánica de fluidos computacional (CFD). Para poder alcanzar la meta de nuestro proyecto es necesario modificar el código interno del programa. Al tener una nueva variable de cálculo, es necesario incorporar por un lado, un término adicional a la ecuación del movimiento lineal del fluido debido a la aparición de fuerzas de origen magnético. Y por otro lado, incorporar la ecuación de inducción magnética que nos permitiría resolver el campo magnético inducido que se generaría debido a que el propio movimiento del fluido modifica el campo magnético en el que está sumergido. Todos estos resultados se validarán con la literatura científica existente en revistas especializadas y libros técnicos, para así proveer de un código académico en el cálculo de flujos que se ven modificados mediante campos magnéticos externos

New Technologies to Improve Surgical Outcome during Open-Cranial Vault Remodeling

Current approaches for the surgical correction of craniosynostosis are highly dependent on surgeon experience. Therefore, outcomes are often inadequate, causing suboptimal esthetic results. Novel methods for cranial shape analysis based on statistical shape models enable accurate and objective diagnosis from preoperative 3D photographs or computed tomography scans. Moreover, advanced algorithms are now available to calculate a reference cranial shape for each patient from a multi-atlas of healthy cases, and to determine the most optimal approach to restore normal calvarial shape. During surgery, multiple technologies are available to ensure accurate translation of the preoperative virtual plan into the operating room. Patient-specific cutting guides and templates can be designed and manufactured to assist during osteotomy and remodeling. Then, intraoperative navigation and augmented reality visualization can provide real-time guidance during the placement and fixation of the remodeled bone. Finally, 3D photography enables intraoperative surgical outcome evaluation and postoperative patient follow-up. This chapter summarizes recent literature on all these technologies, showing how their integration into the surgical workflow could increase reproducibility and reduce inter-surgeon variability in open cranial vault remodeling procedures

ABANICCO: A New Color Space for Multi-Label Pixel Classification and Color Analysis

Classifying pixels according to color, and segmenting the respective areas, are necessary steps in any computer vision task that involves color images. The gap between human color perception, linguistic color terminology, and digital representation are the main challenges for developing methods that properly classify pixels based on color. To address these challenges, we propose a novel method combining geometric analysis, color theory, fuzzy color theory, and multi-label systems for the automatic classification of pixels into 12 conventional color categories, and the subsequent accurate description of each of the detected colors. This method presents a robust, unsupervised, and unbiased strategy for color naming, based on statistics and color theory. The proposed model, "ABANICCO" (AB ANgular Illustrative Classification of COlor), was evaluated through different experiments: its color detection, classification, and naming performance were assessed against the standardized ISCC-NBS color system; its usefulness for image segmentation was tested against state-of-the-art methods. This empirical evaluation provided evidence of ABANICCO's accuracy in color analysis, showing how our proposed model offers a standardized, reliable, and understandable alternative for color naming that is recognizable by both humans and machines. Hence, ABANICCO can serve as a foundation for successfully addressing a myriad of challenges in various areas of computer vision, such as region characterization, histopathology analysis, fire detection, product quality prediction, object description, and hyperspectral imaging.This research was funded by the Ministerio de Ciencia, Innovacción y Universidades, Agencia Estatal de Investigación, under grant PID2019-109820RB, MCIN/AEI/10.13039/501100011033 co-financed by the European Regional Development Fund (ERDF) "A way of making Europe" to A.M.-B. and L.N.-S.Publicad

Automatic pre-alignment of multimodality rat brain images using principal axes transformation

Abstract of: AMI Annual Conference 2006, March 25-29The use of small animal studies of different modalities isnowadays widespread, since functional studies like positron emission tomography (PET) or single photon emission computed tomography (SPECT) are better analyzed when mapped to the underlying anatomical structure coming from magnetic resonance imaging (MRI) or computed tomography (CT). The different positioning of the animals in the scanners results in the need for automated image registration methods. One important drawback of the existing algorithms is their limited capture range: if case of large initial misregistration (large translations and rotations) the optimization may not converge to the right solution, and the images do not become correctly coregistered. To avoid this problem we propose the use of a pre-alignment step based on the principal axes transformation.Publicad

Cuantificación del infarto de miocardio en imágenes PET mediante mapas polares

Actas de: XXVIII Congreso Anual de la Sociedad Española de Ingeniería Biomédica (CASEIB 2010). Madrid, 24-26 de noviembre de 2010.El análisis de la imagen de miocardio en cardiología nuclear es una herramienta muy importante para la valoración de la enfermedad coronaria, dado que permite la cuantificación objetiva de la extensión y de la intensidad del infarto de miocardio. En este trabajo se presenta una herramienta que permite realizar dicha cuantificación mediante el uso de mapas polares tanto estáticos como dinámicos, resultantes del análisis de la imagen PET que se viene realizando en los pacientes. Esta aproximación es una alternativa que permite la visualización integral del infarto en vez de requerir una segmentación (manual o asistida) de todas las rodajas tomográficas que componen el estudio.Este trabajo ha sido financiado por los proyectos del Ministerio de Ciencia e Innovación, TEC2007-64731, TEC 2008-06715-C02-1, la RETIC-RECAVA del Ministerio de Sanidad y Consumo, y el programa ARTEMIS S2009/DPI-1802 de la Comunidad de Madrid.Publicad

Evaluation of optical tracking and augmented reality for needle navigation in sacral nerve stimulation

Background and objective: Sacral nerve stimulation (SNS) is a minimally invasive procedure where an electrode lead is implanted through the sacral foramina to stimulate the nerve modulating colonic and urinary functions. One of the most crucial steps in SNS procedures is the placement of the tined lead close to the sacral nerve. However, needle insertion is very challenging for surgeons. Several x-ray projections are required to interpret the needle position correctly. In many cases, multiple punctures are needed, causing an increase in surgical time and patient's discomfort and pain. In this work we propose and evaluate two different navigation systems to guide electrode placement in SNS surgeries designed to reduce surgical time, minimize patient discomfort and improve surgical outcomes. Methods: We developed, for the first alternative, an open-source navigation software to guide electrode placement by real-time needle tracking with an optical tracking system (OTS). In the second method, we present a smartphone-based AR application that displays virtual guidance elements directly on the affected area, using a 3D printed reference marker placed on the patient. This guidance facilitates needle insertion with a predefined trajectory. Both techniques were evaluated to determine which one obtained better results than the current surgical procedure. To compare the proposals with the clinical method, we developed an x-ray software tool that calculates a digitally reconstructed radiograph, simulating the fluoroscopy acquisitions during the procedure. Twelve physicians (inexperienced and experienced users) performed needle insertions through several specific targets to evaluate the alternative SNS guidance methods on a realistic patient-based phantom. Results: With each navigation solution, we observed that users took less average time to complete each insertion (36.83 s and 44.43 s for the OTS and AR methods, respectively) and needed fewer average punctures to reach the target (1.23 and 1.96 for the OTS and AR methods respectively) than following the standard clinical method (189.28 s and 3.65 punctures). Conclusions: To conclude, we have shown two navigation alternatives that could improve surgical outcome by significantly reducing needle insertions, surgical time and patient's pain in SNS procedures. We believe that these solutions are feasible to train surgeons and even replace current SNS clinical procedures.Research supported by projects PI18/01625 and AC20/00102 (Ministerio de Ciencia, Innovación y Universidades, Instituto de Salud Carlos III, Asociación Española Contra el Cáncer and European Regional Development Fund "Una manera de hacer Europa"), IND2018/TIC-9753 (Comunidad de Madrid) and project PerPlanRT (ERA Permed). Funding for APC: Universidad Carlos III de Madrid (Read & Publish Agreement CRUE-CSIC 2022)

Quasi pseudo-inverse reconstruction for rotating PET scanners

Proceeding of: 2005 IEEE Nuclear Science Symposium Conference Record, Puerto Rico, 23-29 Oct. 2005A new reconstruction strategy is proposed for 3D images acquired with rotating PET scanners. This method is based on the decomposition of the System Response Matrix (SRM) into a projection and a rotation components that are inverted independently. We present the rationale of the new reconstruction procedure as well as some examples to compare with analytical 3D reconstruction (3DRP) and 3D statistical reconstruction (3D-OSEM)Part of this work is founded by the IM3 network (G03/185 Ministerio de Sanidad), with grants from the Ministerio de Educación y Ciencia, project TEC2004 07052 C02 01, and Ministerio de Industria, Turismo y Comercio project FIT 330101 2004