3D nonrigid medical image registration using a new information theoretic measure.

International audienceThis work presents a novel method for the nonrigid registration of medical images based on the Arimoto entropy, a generalization of the Shannon entropy. The proposed method employed the Jensen-Arimoto divergence measure as a similarity metric to measure the statistical dependence between medical images. Free-form deformations were adopted as the transformation model and the Parzen window estimation was applied to compute the probability distributions. A penalty term is incorporated into the objective function to smooth the nonrigid transformation. The goal of registration is to optimize an objective function consisting of a dissimilarity term and a penalty term, which would be minimal when two deformed images are perfectly aligned using the limited memory BFGS optimization method, and thus to get the optimal geometric transformation. To validate the performance of the proposed method, experiments on both simulated 3D brain MR images and real 3D thoracic CT data sets were designed and performed on the open source elastix package. For the simulated experiments, the registration errors of 3D brain MR images with various magnitudes of known deformations and different levels of noise were measured. For the real data tests, four data sets of 4D thoracic CT from four patients were selected to assess the registration performance of the method, including ten 3D CT images for each 4D CT data covering an entire respiration cycle. These results were compared with the normalized cross correlation and the mutual information methods and show a slight but true improvement in registration accuracy

Developing advanced mathematical models for detecting abnormalities in 2D/3D medical structures.

Detecting abnormalities in two-dimensional (2D) and three-dimensional (3D) medical structures is among the most interesting and challenging research areas in the medical imaging field. Obtaining the desired accurate automated quantification of abnormalities in medical structures is still very challenging. This is due to a large and constantly growing number of different objects of interest and associated abnormalities, large variations of their appearances and shapes in images, different medical imaging modalities, and associated changes of signal homogeneity and noise for each object. The main objective of this dissertation is to address these problems and to provide proper mathematical models and techniques that are capable of analyzing low and high resolution medical data and providing an accurate, automated analysis of the abnormalities in medical structures in terms of their area/volume, shape, and associated abnormal functionality. This dissertation presents different preliminary mathematical models and techniques that are applied in three case studies: (i) detecting abnormal tissue in the left ventricle (LV) wall of the heart from delayed contrast-enhanced cardiac magnetic resonance images (MRI), (ii) detecting local cardiac diseases based on estimating the functional strain metric from cardiac cine MRI, and (iii) identifying the abnormalities in the corpus callosum (CC) brain structure—the largest fiber bundle that connects the two hemispheres in the brain—for subjects that suffer from developmental brain disorders. For detecting the abnormal tissue in the heart, a graph-cut mathematical optimization model with a cost function that accounts for the object’s visual appearance and shape is used to segment the the inner cavity. The model is further integrated with a geometric model (i.e., a fast marching level set model) to segment the outer border of the myocardial wall (the LV). Then the abnormal tissue in the myocardium wall (also called dead tissue, pathological tissue, or infarct area) is identified based on a joint Markov-Gibbs random field (MGRF) model of the image and its region (segmentation) map that accounts for the pixel intensities and the spatial interactions between the pixels. Experiments with real in-vivo data and comparative results with ground truth (identified by a radiologist) and other approaches showed that the proposed framework can accurately detect the pathological tissue and can provide useful metrics for radiologists and clinicians. To estimate the strain from cardiac cine MRI, a novel method based on tracking the LV wall geometry is proposed. To achieve this goal, a partial differential equation (PDE) method is applied to track the LV wall points by solving the Laplace equation between the LV contours of each two successive image frames over the cardiac cycle. The main advantage of the proposed tracking method over traditional texture-based methods is its ability to track the movement and rotation of the LV wall based on tracking the geometric features of the inner, mid-, and outer walls of the LV. This overcomes noise sources that come from scanner and heart motion. To identify the abnormalities in the CC from brain MRI, the CCs are aligned using a rigid registration model and are segmented using a shape-appearance model. Then, they are mapped to a simple unified space for analysis. This work introduces a novel cylindrical mapping model, which is conformal (i.e., one to one transformation and bijective), that enables accurate 3D shape analysis of the CC in the cylindrical domain. The framework can detect abnormalities in all divisions of the CC (i.e., splenium, rostrum, genu and body). In addition, it offers a whole 3D analysis of the CC abnormalities instead of only area-based analysis as done by previous groups. The initial classification results based on the centerline length and CC thickness suggest that the proposed CC shape analysis is a promising supplement to the current techniques for diagnosing dyslexia. The proposed techniques in this dissertation have been successfully tested on complex synthetic and MR images and can be used to advantage in many of today’s clinical applications of computer-assisted medical diagnostics and intervention

Brain and Human Body Modeling

This open access book describes modern applications of computational human modeling with specific emphasis in the areas of neurology and neuroelectromagnetics, depression and cancer treatments, radio-frequency studies and wireless communications. Special consideration is also given to the use of human modeling to the computational assessment of relevant regulatory and safety requirements. Readers working on applications that may expose human subjects to electromagnetic radiation will benefit from this book’s coverage of the latest developments in computational modelling and human phantom development to assess a given technology’s safety and efficacy in a timely manner. Describes construction and application of computational human models including anatomically detailed and subject specific models; Explains new practices in computational human modeling for neuroelectromagnetics, electromagnetic safety, and exposure evaluations; Includes a survey of modern applications for which computational human models are critical; Describes cellular-level interactions between the human body and electromagnetic fields

Brain and Human Body Modeling

This open access book describes modern applications of computational human modeling with specific emphasis in the areas of neurology and neuroelectromagnetics, depression and cancer treatments, radio-frequency studies and wireless communications. Special consideration is also given to the use of human modeling to the computational assessment of relevant regulatory and safety requirements. Readers working on applications that may expose human subjects to electromagnetic radiation will benefit from this book’s coverage of the latest developments in computational modelling and human phantom development to assess a given technology’s safety and efficacy in a timely manner. Describes construction and application of computational human models including anatomically detailed and subject specific models; Explains new practices in computational human modeling for neuroelectromagnetics, electromagnetic safety, and exposure evaluations; Includes a survey of modern applications for which computational human models are critical; Describes cellular-level interactions between the human body and electromagnetic fields

An evaluation of a checklist in Musculoskeletal (MSK) radiographic image interpretation when using Artificial Intelligence (AI)

Background: AI is being used increasingly in image interpretation tasks. There are challenges for its optimal use in reporting environments. Human reliance on technology and bias can cause decision errors. Trust issues exist amongst radiologists and radiographers in both over-reliance (automation bias) and reluctance in AI use for decision support. A checklist, used with the AI to mitigate against such biases, may optimise the use of AI technologies and promote good decision hygiene. Method: A checklist, to be used in image interpretation with AI assistance, was developed. Participants interpreted 20 examinations with AI assistance and then re- interpreted the 20 examinations with AI and a checklist. The MSK images were presented to radiographers as patient examinations to replicate the image interpretation task in clinical practice. Image diagnosis and confidence levels on the diagnosis provided were collected following each interpretation. The participant perception of the use of the checklist was investigated via a questionnaire.Results: Data collection and analysis are underway and will be completed at the European Congress of Radiology in Vienna, March 2023. The impact of the use of a checklist in image interpretation with AI will be evaluated. Changes in accuracy and confidence will be investigated and results will be presented. Participant feedback will be analysed to determine perceptions and impact of the checklist also. Conclusion: A novel checklist has been developed to aid the interpretation of images when using AI. The checklist has been tested for its use in assisting radiographers in MSK image interpretation when using AI.<br/

Precision Monitoring for Disease Progression in Patients with Multiple Sclerosis: A Deep Learning Approach

Artificial intelligence has tremendous potential in a range of clinical applications. Leveraging recent advances in deep learning, the works in this thesis has generated a range of technologies for patients with Multiple Sclerosis (MS) that facilitate precision monitoring using routine MRI and clinical assessments; and contribute to realising the goal of personalised disease management. MS is a chronic inflammatory demyelinating disease of the central nervous system (CNS), characterised by focal demyelinating plaques in the brain and spinal cord; and progressive neurodegeneration. Despite success in cohort studies and clinical trials, the measurement of disease activity using conventional imaging biomarkers in real-world clinical practice is limited to qualitative assessment of lesion activity, which is time consuming and prone to human error. Quantitative measures, such as T2 lesion load, volumetric assessment of lesion activity and brain atrophy, are constrained by challenges associated with handling real-world data variances. In this thesis, DeepBVC was developed for robust brain atrophy assessment through imaging synthesis, while a lesion segmentation model was developed using a novel federated learning framework, Fed-CoT, to leverage large data collaborations. With existing quantitative brain structural analyses, this work has developed an effective deep learning analysis pipeline, which delivers a fully automated suite of MS-specific clinical imaging biomarkers to facilitate the precision monitoring of patients with MS and response to disease modifying therapy. The framework for individualised MRI-guided management in this thesis was complemented by a disease prognosis model, based on a Large Language Model, providing insights into the risks of clinical worsening over the subsequent 3 years. The value and performance of the MS biomarkers in this thesis are underpinned by extensive validation in real-world, multi-centre data from more than 1030 patients

Intelligent Analysis of Cerebral Magnetic Resonance Images: Extracting Relevant Information from Small Datasets

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Escuela Politécnica Superior, Departamento de Ingeniería Informática. Fecha de lectura : 21-09-2017Los metodos de machine learning aplicados a imagenes medicas se estan convirtiendo en potentes herramientas para el analisis y diagnostico de pacientes. La alta disponibilidad de repositorios de im agenes de diferentes modalidades ha favorecido el desarrollo de sistemas que aprenden a extraer caracteristicas relevantes y construyen modelos predictivos a partir de grandes cantidades de informacion, por ejemplo, los metodos de deep learning. Sin embargo, el analisis de conjuntos de imagenes provenientes de un menor numero de sujetos, como es el caso de las imagenes adquiridas en entornos de investigacion cl nica y pre-cl nica, ha recibido considerablemente menos atencion. El objetivo de esta tesis es implementar un conjunto de herramientas avanzadas para resolver este problema, permitiendo el analisis robusto de Im agenes de Resonancia Magn etica (MRI por sus siglas en ingl es) cuando se dispone de pocos sujetos de estudio. En este contexto, las herramientas propuestas se emplean para analizar de manera autom atica conjuntos de datos obtenidos de imagenes funcionales de MR del cerebro en estudios de regulacion del apetito en roedores y humanos, y de im agenes funcionales y estructurales de MR de desarrollos tumorales en modelos animales y humanos. Los metodos propuestos se derivan de la idea de considerar cada voxel del conjunto de im agenes como un patron, en lugar de la nocion convencional de considerar cada imagen como un patr on. El Cap tulo 1 describe la motivaci on de esta tesis, incluyendo los objetivos propuestos, la estructura general del documento y las contribuciones de esta investigaci on. El Capitulo 2 contiene una introduccion actualizada del estado del arte en MRI, los procedimientos mas usados en el pre-procesamiento de imagenes, y los algoritmos de machine learning m as utiles y sus aplicaciones en MRI. El Cap tulo 3 presenta el dise~no experimental y los pasos de pre-procesamiento aplicados a los conjuntos de datos de regulaci on de apetito y desarrollo tumoral. El Capitulo 4 implementa nuevos metodos de aprendizaje supervisados para el analisis de conjuntos de datos de MRI obtenidos de un conjunto peque~no de sujetos. Se ilustra este enfoque presentando primero la metodolog a Fisher Maps, que permite la visualizaci on cuantitativa y no invasiva de la circuiter a cerebral del apetito, mediante el an alisis autom atico de Im agenes Ponderadas en Difusi on (DWI por sus siglas en ingl es). Esta metodolog a se extiende a la clasi caci on de im agenes completas combinando las predicciones obtenidas de cada p xel. El Cap tulo 5 propone un nuevo algoritmo de aprendizaje no supervisado, ilustrando su desempe~no sobre datos sint eticos y datos provenientes de estudios de tumores cerebrales y crecimiento tumoral. Por ultimo, en el Cap tulo 6 se resumen las principales conclusiones de este trabajo y se plantean amplias v as para su desarrollo futuro. En resumen, esta tesis presenta un nuevo enfoque capaz de trabajar en contextos con baja disponibilidad de sujetos de estudio, proponiendo algoritmos de aprendizaje supervisado y no supervisado. Estos metodos pueden ser facilmente generalizados a otros paradigmas o patologias, e incluso, a distintas modalidades de imagenes