Mevan Ekanayake

Mevan Ekanayake, Zhifeng Chen, Mehrtash Harandi et al.

In Magnetic Resonance Imaging (MRI), image acquisitions are often undersampled in the measurement domain to accelerate the scanning process, at the expense of image quality. However, image quality is a crucial factor that influences the accuracy of clinical diagnosis; hence, high-quality image reconstruction from undersampled measurements has been a key area of research. Recently, deep learning (DL) methods have emerged as the state-of-the-art for MRI reconstruction, typically involving deep neural networks to transform undersampled MRI images into high-quality MRI images through data-driven processes. Nevertheless, there is clear and significant room for improvement in undersampled DL MRI reconstruction to meet the high standards required for clinical diagnosis, in terms of eliminating aliasing artifacts and reducing image noise. In this paper, we introduce a self-supervised pretraining procedure using contrastive learning to improve the accuracy of undersampled DL MRI reconstruction. We use contrastive learning to transform the MRI image representations into a latent space that maximizes mutual information among different undersampled representations and optimizes the information content at the input of the downstream DL reconstruction models. Our experiments demonstrate improved reconstruction accuracy across a range of acceleration factors and datasets, both quantitatively and qualitatively. Furthermore, our extended experiments validate the proposed framework's robustness under adversarial conditions, such as measurement noise, different k-space sampling patterns, and pathological abnormalities, and also prove the transfer learning capabilities on MRI datasets with completely different anatomy. Additionally, we conducted experiments to visualize and analyze the properties of the proposed MRI contrastive learning latent space.

Mevan Ekanayake, Kamlesh Pawar, Mehrtash Harandi et al.

Global correlations are widely seen in human anatomical structures due to similarity across tissues and bones. These correlations are reflected in magnetic resonance imaging (MRI) scans as a result of close-range proton density and T1/T2 parameters. Furthermore, to achieve accelerated MRI, k-space data are undersampled which causes global aliasing artifacts. Convolutional neural network (CNN) models are widely utilized for accelerated MRI reconstruction, but those models are limited in capturing global correlations due to the intrinsic locality of the convolution operation. The self-attention-based transformer models are capable of capturing global correlations among image features, however, the current contributions of transformer models for MRI reconstruction are minute. The existing contributions mostly provide CNN-transformer hybrid solutions and rarely leverage the physics of MRI. In this paper, we propose a physics-based stand-alone (convolution free) transformer model titled, the Multi-head Cascaded Swin Transformers (McSTRA) for accelerated MRI reconstruction. McSTRA combines several interconnected MRI physics-related concepts with the transformer networks: it exploits global MR features via the shifted window self-attention mechanism; it extracts MR features belonging to different spectral components separately using a multi-head setup; it iterates between intermediate de-aliasing and k-space correction via a cascaded network with data consistency in k-space and intermediate loss computations; furthermore, we propose a novel positional embedding generation mechanism to guide self-attention utilizing the point spread function corresponding to the undersampling mask. Our model significantly outperforms state-of-the-art MRI reconstruction methods both visually and quantitatively while depicting improved resolution and removal of aliasing artifacts.

Mevan Ekanayake, Zhifeng Chen, Gary Egan et al.

Implicit Neural Representations (INRs) have recently advanced the field of deep learning due to their ability to learn continuous representations of signals without the need for large training datasets. Although INR methods have been studied for medical image super-resolution, their adaptability to localized priors in medical images has not been extensively explored. Medical images contain rich anatomical divisions that could provide valuable local prior information to enhance the accuracy and robustness of INRs. In this work, we propose a novel framework, referred to as the Semantically Conditioned INR (SeCo-INR), that conditions an INR using local priors from a medical image, enabling accurate model fitting and interpolation capabilities to achieve super-resolution. Our framework learns a continuous representation of the semantic segmentation features of a medical image and utilizes it to derive the optimal INR for each semantic region of the image. We tested our framework using several medical imaging modalities and achieved higher quantitative scores and more realistic super-resolution outputs compared to state-of-the-art methods.

Mevan Ekanayake, Kamlesh Pawar, Gary Egan et al.

Deep learning (DL) models are capable of successfully exploiting latent representations in MR data and have become state-of-the-art for accelerated MRI reconstruction. However, undersampling the measurements in k-space as well as the over- or under-parameterized and non-transparent nature of DL make these models exposed to uncertainty. Consequently, uncertainty estimation has become a major issue in DL MRI reconstruction. To estimate uncertainty, Monte Carlo (MC) inference techniques have become a common practice where multiple reconstructions are utilized to compute the variance in reconstruction as a measurement of uncertainty. However, these methods demand high computational costs as they require multiple inferences through the DL model. To this end, we introduce a method to estimate uncertainty during MRI reconstruction using a pixel classification framework. The proposed method, PixCUE (stands for Pixel Classification Uncertainty Estimation) produces the reconstructed image along with an uncertainty map during a single forward pass through the DL model. We demonstrate that this approach generates uncertainty maps that highly correlate with the reconstruction errors with respect to various MR imaging sequences and under numerous adversarial conditions. We also show that the estimated uncertainties are correlated to that of the conventional MC method. We further provide an empirical relationship between the uncertainty estimations using PixCUE and well-established reconstruction metrics such as NMSE, PSNR, and SSIM. We conclude that PixCUE is capable of reliably estimating the uncertainty in MRI reconstruction with a minimum additional computational cost.

Yasiru Ranasinghe, Sanjaya Herath, Kavinga Weerasooriya et al.

In the remote sensing context spectral unmixing is a technique to decompose a mixed pixel into two fundamental representatives: endmembers and abundances. In this paper, a novel architecture is proposed to perform blind unmixing on hyperspectral images. The proposed architecture consists of convolutional layers followed by an autoencoder. The encoder transforms the feature space produced through convolutional layers to a latent space representation. Then, from these latent characteristics the decoder reconstructs the roll-out image of the monochrome image which is at the input of the architecture; and each single-band image is fed sequentially. Experimental results on real hyperspectral data concludes that the proposed algorithm outperforms existing unmixing methods at abundance estimation and generates competitive results for endmember extraction with RMSE and SAD as the metrics, respectively.