Empirical Functional PCA for 3D Image Feature Extraction Through Fractal Sampling.

Medical image classification is currently a challenging task that can be used to aid the diagnosis of different brain diseases. Thus, exploratory and discriminative analysis techniques aiming to obtain representative features from the images play a decisive role in the design of effective Computer Aided Diagnosis (CAD) systems, which is especially important in the early diagnosis of dementia. In this work, we present a technique that allows using specific time series analysis techniques with 3D images. This is achieved by sampling the image using a fractal-based method which preserves the spatial relationship among voxels. In addition, a method called Empirical functional PCA (EfPCA) is presented, which combines Empirical Mode Decomposition (EMD) with functional PCA to express an image in the space spanned by a basis of empirical functions, instead of using components computed by a predefined basis as in Fourier or Wavelet analysis. The devised technique has been used to classify images from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the Parkinson Progression Markers Initiative (PPMI), achieving accuracies up to 93% and 92% differential diagnosis tasks (AD versus controls and PD versus Controls, respectively). The results obtained validate the method, proving that the information retrieved by our methodology is significantly linked to the diseases.This work was partly supported by the MINECO/ FEDER under TEC2015-64718-R and PSI2015- 65848-R projects and the Consejer´ıa de Innovaci´on, Ciencia y Empresa (Junta de Andaluc´ıa, Spain) under the Excellence Project P11-TIC-7103 as well as the Salvador deMadariaga Mobility Grants 2017. Data collection and sharing for this project was funded by the ADNI (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Depart ment of Defense award number W81XWH-12-2- 0012). ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contribu tions from the following: AbbVie, Alzheimer’s Asso ciation; Alzheimer’s Drug Discovery Foundation; Araclon Biotech; BioClinica, Inc.; Biogen; Bristol Myer Squibb Company; CereSpir, Inc.; Eisai Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; EuroImmun; F. Ho mann-La Roche Ltd and its ali ated company Genentech, Inc.; Fujirebio; GE Health care; IXICO Ltd.; Janssen Alzheimer Immunother apy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development LLC.; Lumosity; Lundbeck; Merck & Co., Inc.; Meso Scale Diagnostics, LLC.; NeuroRx Research; Neurotrack Technologies; Novartis Pharmaceuticals Corporation; P zer Inc.; Piramal Imaging; Servier; Takeda Pharmaceutical Company; and Transition Therapeutics. The Canadian Institutes of Health Research is providing funds to support ADNI clin ical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coor dinated by the Alzheimer’s Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of Southern Cali fornia. PPMI a public-private partnership is funded by the Michael J. Fox Foundation for Parkinson’s Research and funding partners, including [list the full names of all of the PPMI funding partners found at www.ppmi-info.org/fundingpartners]

Direct estimation of kinetic parametric images for dynamic PET.

Dynamic positron emission tomography (PET) can monitor spatiotemporal distribution of radiotracer in vivo. The spatiotemporal information can be used to estimate parametric images of radiotracer kinetics that are of physiological and biochemical interests. Direct estimation of parametric images from raw projection data allows accurate noise modeling and has been shown to offer better image quality than conventional indirect methods, which reconstruct a sequence of PET images first and then perform tracer kinetic modeling pixel-by-pixel. Direct reconstruction of parametric images has gained increasing interests with the advances in computing hardware. Many direct reconstruction algorithms have been developed for different kinetic models. In this paper we review the recent progress in the development of direct reconstruction algorithms for parametric image estimation. Algorithms for linear and nonlinear kinetic models are described and their properties are discussed

Parkinson’s Disease Detection Using Isosurfaces-Based Features and Convolutional Neural Networks

Computer aided diagnosis systems based on brain imaging are an important tool to assist in the diagnosis of Parkinson’s disease, whose ultimate goal is the detection by automatic recognizing of patterns that characterize the disease. In recent times Convolutional Neural Networks (CNN) have proved to be amazingly useful for that task. The drawback, however, is that 3D brain images contain a huge amount of information that leads to complex CNN architectures. When these architectures become too complex, classification performances often degrades because the limitations of the training algorithm and overfitting. Thus, this paper proposes the use of isosurfaces as a way to reduce such amount of data while keeping the most relevant information. These isosurfaces are then used to implement a classification system which uses two of the most well-known CNN architectures, LeNet and AlexNet, to classify DaTScan images with an average accuracy of 95.1% and AUC = 97%, obtaining comparable (slightly better) values to those obtained for most of the recently proposed systems. It can be concluded therefore that the computation of isosurfaces reduces the complexity of the inputs significantly, resulting in high classification accuracies with reduced computational burden.MINECO/FEDER under TEC2015-64718-R, PSI2015-65848-R, PGC2018-098813-B-C32, and RTI2018-098913-B-100 projects

PET image classification using HHT-based features through fractal sampling

Medical image classification is currently a challenging task that can be used to aid the diagnosis of different brain diseases. Thus, exploratory and discriminative analysis techniques aiming to obtain rep- resentative features from the images, play a decisive role in the design of effective Computer Aided Diagnosis (CAD) systems, which is spe- cially important in the early diagnosis of dementias. In this work we present a technique that allows extracting discriminative features from Positron Emission Tomography (PET) by means of an Empirical Mode Decomposition-based (EEMD) method. This requires to transform the 3D PET image into a time series which is addressed by sampling the image using a fractal-based method which allows to preserve the spa- tial relationship among voxels. The devised technique has been used to classify images from the Alzheimer's Disease Neuroimaging Initiat- ive (ADNI) achieving up to a 90.5% accuracy in a differential diagnosis task (AD vs. controls), which proves that the information retrieved by our methodology is significantly linked to the disease.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Label Aided Deep Ranking for the Automatic Diagnosis of Parkinsonian Syndromes.

Parkinsonism is the second most common neurodegenerative disease in the world. Its diagnosis usually relies on visual analysis of Emission Computed Tomography (SPECT) images acquired using 123I − io f lupane radiotracer. This aims to detect a deficit of dopamine transporters at the striatum. The use of Computer Aided tools for diagnosis based on statistical data processing and machine learning methods have significantly improved the diagnosis accuracy. In this paper we propose a classification method based on Deep Ranking which learns an embedding function that projects the source images into a new space in which samples belonging to the same class are closer to each other, while samples from different classes are moved apart. Moreover, the proposed approach introduces a new cost-sensitive loss function to avoid overfitting due to class imbalance (an usual issue in practical biomedical applications), along with label information to produce sparser embedding spaces. The experiments carried out in this work demonstrate the superiority of the proposed method, improving the diagnosis accuracy achieved by previous methodologies and validate our approach as an efficient way to construct linear classifiers.This work was partly supported by the MINECO/FEDER under TEC2015-64718- R and PSI2015-65848-R projects. We gratefully acknowledge the support of NVIDIA Corporation with the donation of one of the GPUs used for this research. PPMI - a pub435 lic - private partnership - is funded by The Michael J. Fox Foundation for Parkinson’s Research and funding partners, including Abbott, Biogen Idec, F. Hoffman-La Roche Ltd., GE Healthcare, Genentech and Pfizer Inc

Sparse Decomposition and Modeling of Anatomical Shape Variation

Recent advances in statistics have spawned powerful methods for regression and data decomposition that promote sparsity, a property that facilitates interpretation of the results. Sparse models use a small subset of the available variables and may perform as well or better than their full counterparts if constructed carefully. In most medical applications, models are required to have both good statistical performance and a relevant clinical interpretation to be of value. Morphometry of the corpus callosum is one illustrative example. This paper presents a method for relating spatial features to clinical outcome data. A set of parsimonious variables is extracted using sparse principal component analysis, producing simple yet characteristic features. The relation of these variables with clinical data is then established using a regression model. The result may be visualized as patterns of anatomical variation related to clinical outcome. In the present application, landmark-based shape data of the corpus callosum is analyzed in relation to age, gender, and clinical tests of walking speed and verbal fluency. To put the data-driven sparse principal component method into perspective, we consider two alternative techniques, one where features are derived using a model-based wavelet approach, and one where the original variables are regressed directly on the outcome

Statistical Neuroimage Modeling, Processing and Synthesis based on Texture and Component Analysis: Tackling the Small Sample Size Problem

The rise of neuroimaging in the last years has provided physicians and radiologist with the ability to study the brain with unprecedented ease. This led to a new biological perspective in the study of neurodegenerative diseases, allowing the characterization of different anatomical and functional patterns associated with them. CAD systems use statistical techniques for preparing, processing and extracting information from neuroimaging data pursuing a major goal: optimize the process of analysis and diagnosis of neurodegenerative diseases and mental conditions. With this thesis we focus on three different stages of the CAD pipeline: preprocessing, feature extraction and validation. For preprocessing, we have developed a method that target a relatively recent concern: the confounding effect of false positives due to differences in the acquisition at multiple sites. Our method can effectively merge datasets while reducing the acquisition site effects. Regarding feature extraction, we have studied decomposition algorithms (independent component analysis, factor analysis), texture features and a complete framework called Spherical Brain Mapping, that reduces the 3-dimensional brain images to two-dimensional statistical maps. This allowed us to improve the performance of automatic systems for detecting Alzheimer's and Parkinson's diseases. Finally, we developed a brain simulation technique that can be used to validate new functional datasets as well as for educational purposes