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

Single-image super-resolution using sparsity constraints and non-local similarities at multiple resolution scales

Traditional super-resolution methods produce a clean high-resolution image from several observed degraded low-resolution images following an acquisition or degradation model. Such a model describes how each output pixel is related to one or more input pixels and it is called data fidelity term in the regularization framework. Additionally, prior knowledge such as piecewise smoothness can be incorporated to improve the image restoration result. The impact of an observed pixel on the restored pixels is thus local according to the degradation model and the prior knowledge. Therefore, the traditional methods only exploit the spatial redundancy in a local neighborhood and are therefore referred to as local methods. Recently, non-local methods, which make use of similarities between image patches across the whole image, have gained popularity in image restoration in general. In super-resolution literature they are often referred to as exemplar-based methods. In this paper, we exploit the similarity of patches within the same scale (which is related to the class of non-local methods) and across different resolution scales of the same image (which is also related to the fractal-based methods). For patch fusion, we employ a kernel regression algorithm, which yields a blurry and noisy version of the desired high-resolution image. For the final reconstruction step, we develop a novel restoration algorithm. The joint deconvolution/denoising algorithm is based on the split Bregman iterations and, as prior knowledge, the algorithm exploits the sparsity of the image in the shearlet-transformed domain. Initial results indicate an improvement over both classical local and state-of-the art non-local super-resolution methods

Comparative Analysis and Fusion of MRI and PET Images based on Wavelets for Clinical Diagnosis

Nowadays, Medical imaging modalities like Magnetic Resonance Imaging (MRI), Positron Emission Tomography (PET), Single Photon Emission Tomography (SPECT), and Computed Tomography (CT) play a crucial role in clinical diagnosis and treatment planning. The images obtained from each of these modalities contain complementary information of the organ imaged. Image fusion algorithms are employed to bring all of this disparate information together into a single image, allowing doctors to diagnose disorders quickly. This paper proposes a novel technique for the fusion of MRI and PET images based on YUV color space and wavelet transform. Quality assessment based on entropy showed that the method can achieve promising results for medical image fusion. The paper has done a comparative analysis of the fusion of MRI and PET images using different wavelet families at various decomposition levels for the detection of brain tumors as well as Alzheimer’s disease. The quality assessment and visual analysis showed that the Dmey wavelet at decomposition level 3 is optimum for the fusion of MRI and PET images. This paper also compared the results of several fusion rules such as average, maximum, and minimum, finding that the maximum fusion rule outperformed the other two