arXiv subjects

Ilkay Oksuz

Publications and source records attributed to Ilkay Oksuz.

27 records · Page 2Linked to original sources

arXiv2020

Deep Learning Based Detection and Correction of Cardiac MR Motion Artefacts During Reconstruction for High-Quality Segmentation

Segmenting anatomical structures in medical images has been successfully addressed with deep learning methods for a range of applications. However, this success is heavily dependent on the quality of the image that is being segmented. A commonly neglected point in the medical image analysis community is the vast amount of clinical images that have severe image artefacts due to organ motion, movement of the patient and/or image acquisition related issues. In this paper, we discuss the implications of image motion artefacts on cardiac MR segmentation and compare a variety of approaches for jointly correcting for artefacts and segmenting the cardiac cavity. The method is based on our recently developed joint artefact detection and reconstruction method, which reconstructs high quality MR images from k-space using a joint loss function and essentially converts the artefact correction task to an under-sampled image reconstruction task by enforcing a data consistency term. In this paper, we propose to use a segmentation network coupled with this in an end-to-end framework. Our training optimises three different tasks: 1) image artefact detection, 2) artefact correction and 3) image segmentation. We train the reconstruction network to automatically correct for motion-related artefacts using synthetically corrupted cardiac MR k-space data and uncorrected reconstructed images. Using a test set of 500 2D+time cine MR acquisitions from the UK Biobank data set, we achieve demonstrably good image quality and high segmentation accuracy in the presence of synthetic motion artefacts. We showcase better performance compared to various image correction architectures.

eess.IV↗

arXiv2019

dAUTOMAP: decomposing AUTOMAP to achieve scalability and enhance performance

AUTOMAP is a promising generalized reconstruction approach, however, it is not scalable and hence the practicality is limited. We present dAUTOMAP, a novel way for decomposing the domain transformation of AUTOMAP, making the model scale linearly. We show dAUTOMAP outperforms AUTOMAP with significantly fewer parameters.

cs.LG↗

arXiv2019

Assessing the Impact of Blood Pressure on Cardiac Function Using Interpretable Biomarkers and Variational Autoencoders

Maintaining good cardiac function for as long as possible is a major concern for healthcare systems worldwide and there is much interest in learning more about the impact of different risk factors on cardiac health. The aim of this study is to analyze the impact of systolic blood pressure (SBP) on cardiac function while preserving the interpretability of the model using known clinical biomarkers in a large cohort of the UK Biobank population. We propose a novel framework that combines deep learning based estimation of interpretable clinical biomarkers from cardiac cine MR data with a variational autoencoder (VAE). The VAE architecture integrates a regression loss in the latent space, which enables the progression of cardiac health with SBP to be learnt. Results on 3,600 subjects from the UK Biobank show that the proposed model allows us to gain important insight into the deterioration of cardiac function with increasing SBP, identify key interpretable factors involved in this process, and lastly exploit the model to understand patterns of positive and adverse adaptation of cardiac function.

cs.LG↗

arXiv2019

Global and Local Interpretability for Cardiac MRI Classification

Deep learning methods for classifying medical images have demonstrated impressive accuracy in a wide range of tasks but often these models are hard to interpret, limiting their applicability in clinical practice. In this work we introduce a convolutional neural network model for identifying disease in temporal sequences of cardiac MR segmentations which is interpretable in terms of clinically familiar measurements. The model is based around a variational autoencoder, reducing the input into a low-dimensional latent space in which classification occurs. We then use the recently developed `concept activation vector' technique to associate concepts which are diagnostically meaningful (eg. clinical biomarkers such as `low left-ventricular ejection fraction') to certain vectors in the latent space. These concepts are then qualitatively inspected by observing the change in the image domain resulting from interpolations in the latent space in the direction of these vectors. As a result, when the model classifies images it is also capable of providing naturally interpretable concepts relevant to that classification and demonstrating the meaning of those concepts in the image domain. Our approach is demonstrated on the UK Biobank cardiac MRI dataset where we detect the presence of coronary artery disease.

eess.IV↗

arXiv2019

Mechanically Powered Motion Imaging Phantoms: Proof of Concept

Motion imaging phantoms are expensive, bulky and difficult to transport and set-up. The purpose of this paper is to demonstrate a simple approach to the design of multi-modality motion imaging phantoms that use mechanically stored energy to produce motion. We propose two phantom designs that use mainsprings and elastic bands to store energy. A rectangular piece was attached to an axle at the end of the transmission chain of each phantom, and underwent a rotary motion upon release of the mechanical motor. The phantoms were imaged with MRI and US, and the image sequences were embedded in a 1D non linear manifold (Laplacian Eigenmap) and the spectrogram of the embedding was used to derive the angular velocity over time. The derived velocities were consistent and reproducible within a small error. The proposed motion phantom concept showed great potential for the construction of simple and affordable motion phantoms

eess.IV↗

arXiv2019

Explicit topological priors for deep-learning based image segmentation using persistent homology

We present a novel method to explicitly incorporate topological prior knowledge into deep learning based segmentation, which is, to our knowledge, the first work to do so. Our method uses the concept of persistent homology, a tool from topological data analysis, to capture high-level topological characteristics of segmentation results in a way which is differentiable with respect to the pixelwise probability of being assigned to a given class. The topological prior knowledge consists of the sequence of desired Betti numbers of the segmentation. As a proof-of-concept we demonstrate our approach by applying it to the problem of left-ventricle segmentation of cardiac MR images of 500 subjects from the UK Biobank dataset, where we show that it improves segmentation performance in terms of topological correctness without sacrificing pixelwise accuracy.

cs.CV↗

arXiv2018

Magnetic Resonance Fingerprinting using Recurrent Neural Networks

Magnetic Resonance Fingerprinting (MRF) is a new approach to quantitative magnetic resonance imaging that allows simultaneous measurement of multiple tissue properties in a single, time-efficient acquisition. Standard MRF reconstructs parametric maps using dictionary matching and lacks scalability due to computational inefficiency. We propose to perform MRF map reconstruction using a recurrent neural network, which exploits the time-dependent information of the MRF signal evolution. We evaluate our method on multiparametric synthetic signals and compare it to existing MRF map reconstruction approaches, including those based on neural networks. Our method achieves state-of-the-art estimates of T1 and T2 values. In addition, the reconstruction time is significantly reduced compared to dictionary-matching based approaches.

cs.CV↗

arXiv2018

Automatic CNN-based detection of cardiac MR motion artefacts using k-space data augmentation and curriculum learning

Good quality of medical images is a prerequisite for the success of subsequent image analysis pipelines. Quality assessment of medical images is therefore an essential activity and for large population studies such as the UK Biobank (UKBB), manual identification of artefacts such as those caused by unanticipated motion is tedious and time-consuming. Therefore, there is an urgent need for automatic image quality assessment techniques. In this paper, we propose a method to automatically detect the presence of motion-related artefacts in cardiac magnetic resonance (CMR) cine images. We compare two deep learning architectures to classify poor quality CMR images: 1) 3D spatio-temporal Convolutional Neural Networks (3D-CNN), 2) Long-term Recurrent Convolutional Network (LRCN). Though in real clinical setup motion artefacts are common, high-quality imaging of UKBB, which comprises cross-sectional population data of volunteers who do not necessarily have health problems creates a highly imbalanced classification problem. Due to the high number of good quality images compared to the relatively low number of images with motion artefacts, we propose a novel data augmentation scheme based on synthetic artefact creation in k-space. We also investigate a learning approach using a predetermined curriculum based on synthetic artefact severity. We evaluate our pipeline on a subset of the UK Biobank data set consisting of 3510 CMR images. The LRCN architecture outperformed the 3D-CNN architecture and was able to detect 2D+time short axis images with motion artefacts in less than 1ms with high recall. We compare our approach to a range of state-of-the-art quality assessment methods. The novel data augmentation and curriculum learning approaches both improved classification performance achieving overall area under the ROC curve of 0.89.

cs.CV↗

arXiv2018

Deep Learning using K-space Based Data Augmentation for Automated Cardiac MR Motion Artefact Detection

Quality assessment of medical images is essential for complete automation of image processing pipelines. For large population studies such as the UK Biobank, artefacts such as those caused by heart motion are problematic and manual identification is tedious and time-consuming. Therefore, there is an urgent need for automatic image quality assessment techniques. In this paper, we propose a method to automatically detect the presence of motion-related artefacts in cardiac magnetic resonance (CMR) images. As this is a highly imbalanced classification problem (due to the high number of good quality images compared to the low number of images with motion artefacts), we propose a novel k-space based training data augmentation approach in order to address this problem. Our method is based on 3D spatio-temporal Convolutional Neural Networks, and is able to detect 2D+time short axis images with motion artefacts in less than 1ms. We test our algorithm on a subset of the UK Biobank dataset consisting of 3465 CMR images and achieve not only high accuracy in detection of motion artefacts, but also high precision and recall. We compare our approach to a range of state-of-the-art quality assessment methods.

cs.CV↗