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Register a new userDeep Learning using K-space Based Data Augmentation for Automated Cardiac MR Motion Artefact Detection
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Added by
Ilkay Oksuz
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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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.
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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.
In fully sampled cardiac MR (CMR) acquisitions, motion can lead to corruption of k-space lines, which can result in artefacts in the reconstructed images. In this paper, we propose a method to automatically detect and correct motion-related artefacts in CMR acquisitions during reconstruction from k-space data. Our correction method is inspired by work on undersampled CMR reconstruction, and uses deep learning to optimize a data-consistency term for under-sampled k-space reconstruction. Our main methodological contribution is the addition of a detection network to classify motion-corrupted k-space lines to convert the problem of artefact correction to a problem of reconstruction using the data consistency term. We train our network to automatically correct for motion-related artefacts using synthetically corrupted cine CMR k-space data as well as uncorrupted CMR images. Using a test set of 50 2D+time cine CMR datasets from the UK Biobank, we achieve good image quality in the presence of synthetic motion artefacts. We quantitatively compare our method with a variety of techniques for recovering good image quality and showcase better performance compared to state of the art denoising techniques with a PSNR of 37.1. Moreover, we show that our method preserves the quality of uncorrupted images and therefore can be also utilized as a general image reconstruction algorithm.
In the clinical routine, short axis (SA) cine cardiac MR (CMR) image stacks are acquired during multiple subsequent breath-holds. If the patient cannot consistently hold the breath at the same position, the acquired image stack will be affected by inter-slice respiratory motion and will not correctly represent the cardiac volume, introducing potential errors in the following analyses and visualisations. We propose an approach to automatically correct inter-slice respiratory motion in SA CMR image stacks. Our approach makes use of probabilistic segmentation maps (PSMs) of the left ventricular (LV) cavity generated with decision forests. PSMs are generated for each slice of the SA stack and rigidly registered in-plane to a target PSM. If long axis (LA) images are available, PSMs are generated for them and combined to create the target PSM; if not, the target PSM is produced from the same stack using a 3D model trained from motion-free stacks. The proposed approach was tested on a dataset of SA stacks acquired from 24 healthy subjects (for which anatomical 3D cardiac images were also available as reference) and compared to two techniques which use LA intensity images and LA segmentations as targets, respectively. The results show the accuracy and robustness of the proposed approach in motion compensation.
The effectiveness of a cardiovascular magnetic resonance (CMR) scan depends on the ability of the operator to correctly tune the acquisition parameters to the subject being scanned and on the potential occurrence of imaging artefacts such as cardiac and respiratory motion. In the clinical practice, a quality control step is performed by visual assessment of the acquired images: however, this procedure is strongly operator-dependent, cumbersome and sometimes incompatible with the time constraints in clinical settings and large-scale studies. We propose a fast, fully-automated, learning-based quality control pipeline for CMR images, specifically for short-axis image stacks. Our pipeline performs three important quality checks: 1) heart coverage estimation, 2) inter-slice motion detection, 3) image contrast estimation in the cardiac region. The pipeline uses a hybrid decision forest method - integrating both regression and structured classification models - to extract landmarks as well as probabilistic segmentation maps from both long- and short-axis images as a basis to perform the quality checks. The technique was tested on up to 3000 cases from the UK Biobank as well as on 100 cases from the UK Digital Heart Project, and validated against manual annotations and visual inspections performed by expert interpreters. The results show the capability of the proposed pipeline to correctly detect incomplete or corrupted scans (e.g. on UK Biobank, sensitivity and specificity respectively 88% and 99% for heart coverage estimation, 85% and 95% for motion detection), allowing their exclusion from the analysed dataset or the triggering of a new acquisition.
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.
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