Deep learning assisted MRI guided attenuation correction in PET

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonPositron emission tomography (PET) is a unique imaging modality that provides physiological and functional details of the tissue at the molecular level. However, the acquired PET images have some limitations such as the attenuation. PET attenuation correction is an essential step to obtain the full potential of PET quantification. With the wide use of hybrid PET/MR scanners, magnetic resonance (MR) images are used to address the problem of PET attenuation correction. The MR images segmentation is one simple and robust approach to create pseudo computed tomography (CT) images, which are used to generate attenuation coefficient maps to correct the PET attenuation. Recently, deep learning has been proposed and used as a promising technique to efficiently perform MR and various medical images segmentation. In this research work, deep learning guided segmentation approaches have been proposed to enhance the bone class segmentation of MR brain images in order to generate accurate pseudo-CT images. The first approach has introduced the combination of handcrafted features with deep learning features to enrich the set of features. Multiresolution analysis techniques, which generate multiscale and multidirectional coefficients of an image such as contourlet and shearlet transforms, are applied and combined with deep convolutional neural network (CNN) features. Different experiments have been conducted to investigate the number of selected coefficients and the insertion location of the handcrafted features. The second approach aims at reducing the segmentation algorithm’s complexity while maintaining the segmentation performance. An attention based convolutional encode-decoder network has been proposed to adaptively recalibrate the deep network features. This attention based network consists of two different squeeze and excitation blocks that excite the features spatially and channel wise. The two blocks are combined sequentially to decrease the number of network’s parameters and reduces the model complexity. The third approach has been focuses on the application of transfer learning from different MR sequences such as T1 weighted (T1-w) and T2 weighted (T2-w) images. A pretrained model with T1-w MR sequences is fine tuned to perform the segmentation of T2-w images. Multiple fine tuning approaches and experiments have been conducted to study the best fine tuning mechanism that is able to build an efficient segmentation model for both T1-w and T2-w segmentation. Clinical datasets of fifty patients with different conditions and diagnosis have been used to carry an objective evaluation to measure the segmentation performance of the results obtained by the three proposed methods. The first and second approaches have been validated with other studies in the literature that applied deep network based segmentation technique to perform MR based attenuation correction for PET images. The proposed methods have shown an enhancement in the bone segmentation with an increase of dice similarity coefficient (DSC) from 0.6179 to 0.6567 using an ensemble of CNNs with an improvement percentage of 6.3%. The proposed excitation-based CNN has decreased the model complexity by decreasing the number of trainable parameters by more than 46% where less computing resources are required to train the model. The proposed hybrid transfer learning method has shown its superiority to build a multi-sequences (T1-w and T2-w) segmentation approach compared to other applied transfer learning methods especially with the bone class where the DSC is increased from 0.3841 to 0.5393. Moreover, the hybrid transfer learning approach requires less computing time than transfer learning using open and conservative fine tuning

EpilepsyNet: Novel automated detection of epilepsy using transformer model with EEG signals from 121 patient population

Background: Epilepsy is one of the most common neurological conditions globally, and the fourth most common in the United States. Recurrent non-provoked seizures characterize it and have huge impacts on the quality of life and financial impacts for affected individuals. A rapid and accurate diagnosis is essential in order to instigate and monitor optimal treatments. There is also a compelling need for the accurate interpretation of epilepsy due to the current scarcity in neurologist diagnosticians and a global inequity in access and outcomes. Furthermore, the existing clinical and traditional machine learning diagnostic methods exhibit limitations, warranting the need to create an automated system using deep learning model for epilepsy detection and monitoring using a huge database. Method: The EEG signals from 35 channels were used to train the deep learning-based transformer model named (EpilepsyNet). For each training iteration, 1-min-long data were randomly sampled from each participant. Thereafter, each 5-s epoch was mapped to a matrix using the Pearson Correlation Coefficient (PCC), such that the bottom part of the triangle was discarded and only the upper triangle of the matrix was vectorized as input data. PCC is a reliable method used to measure the statistical relationship between two variables. Based on the 5 s of data, single embedding was performed thereafter to generate a 1-dimensional array of signals. In the final stage, a positional encoding with learnable parameters was added to each correlation coefficient’s embedding before being fed to the developed EpilepsyNet as input data to epilepsy EEG signals. The ten-fold cross-validation technique was used to generate the model. Results: Our transformer-based model (EpilepsyNet) yielded high classification accuracy, sensitivity, specificity and positive predictive values of 85%, 82%, 87%, and 82%, respectively. Conclusion: The proposed method is both accurate and robust since ten-fold cross-validation was employed to evaluate the performance of the model. Compared to the deep models used in existing studies for epilepsy diagnosis, our proposed method is simple and less computationally intensive. This is the earliest study to have uniquely employed the positional encoding with learnable parameters to each correlation coefficient’s embedding together with the deep transformer model, using a huge database of 121 participants for epilepsy detection. With the training and validation of the model using a larger dataset, the same study approach can be extended for the detection of other neurological conditions, with a transformative impact on neurological diagnostics worldwide

A review on the rule-based filtering structure with applications on computational biomedical images

concepts in the filtering structure. It is crucial for understanding and discussing different principles associated with fuzzy filter design procedures. A number of typical fuzzy multichannel filtering approaches are provided in order to clarify the different fuzzy filter designs and compare different algorithms. In particular, in most practical applications (i.e., biomedical image analysis), the emphasis is placed primarily on fuzzy filtering algorithms, with the main advantages of restoration of corrupted medical images and the interpretation capability, along with the capability of edge preservation and relevant image information for accurate diagnosis of diseases

Development of a Real-Time Single-Lead Single-Beat Frequency-Independent Myocardial Infarction Detector

The central aim of this research is the development and deployment of a novel multilayer machine learning design with unique application for the diagnosis of myocardial infarctions (MIs) from individual heartbeats of single-lead electrocardiograms (EKGs) irrespective of their sampling frequencies over a given range. To the best of our knowledge, this design is the first to attempt inter-patient myocardial infarction detection from individual heartbeats of single-lead (lead II) electrocardiograms that achieves high accuracy and near real-time diagnosis. The processing time of 300 milliseconds to a diagnosis is just at the time range in between extremely fast heartbeats of around 300 milliseconds, or 200 beats per minute. The design achieves stable performance metrics over the frequency range of 202Hz to 2.8kHz with an accuracy of 77.12%, positive predictive value (PPV) of 75.85%, and a negative predictive value (NPV) of 83.02% over the entire PTB database; 85.07%, 81.54%, 87.31% over the PTB-XL (the largest EKG database available for research) validation set, and 84.17%, 78.37%, 87.55% over the PTB-XL test set. Major design contributions and findings of this work reveal (1) a method for the realtime detection of ventricular depolarization events in the PQRST complex from 12-lead electrocardiograms using Independent Component Analysis (ICA), with a slightly different use of ICA proposed for electrocardiogram analysis and R-peak detection/localization; (2) a multilayer Long-Short Term Memory (LSTM) neural network design that identifies infarcted patients from a single heartbeat of a single-lead (lead II) electrocardiogram; (3) and integrated LSTM neural network with an algorithm that detects the R-peaks in real time for instantaneous detection of myocardial infarctions and for effective monitoring of patients under cardiac stress and/or at risk of myocardial infarction; (4) a fully integrated 12-lead real-time classifier with even higher detection metrics and a deeper neural architecture, which could serve as a near real-time monitoring tool that could gauge disease progression and evaluate benefits gained from early intervention and treatment planning; (5) a real-time frequency-independent design based on a single-lead single-beat MI detector, which is of pivotal importance to deployment as there is no standard sampling frequency for EKGs, making them span a wider frequency spectrum. vi

Electroencephalogram signal classification based on shearlet and contourlet transforms

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Epilepsy is a disorder that affects approximately 50 million people of all ages, according to World Health Organization (2016), which makes it one of the most common neurological diseases worldwide. Electroencephalogram (EEG) signals have been widely used to detect epilepsy and other brain abnormalities. In this work, we propose and evaluate a novel methodology based on shearlet and contourlet transforms to decompose the EEG signals into frequency bands. A set of features are extracted from these time frequency coefficients and used as input to different classifiers. Experiments are conducted on a public data set to demonstrate the effectiveness of the proposed classification method. The developed system can help neurophysiologists identify EEG patterns in epilepsy diagnostic tasks. (C) 2016 Elsevier Ltd. All rights reserved.Epilepsy is a disorder that affects approximately 50 million people of all ages, according to World Health Organization (2016), which makes it one of the most common neurological diseases worldwide. Electroencephalogram (EEG) signals have been widely used67140147FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOCNPQ - CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICOFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)2011/22749-8307113/2012-