Publications
166 results found
Qin C, Bai W, Schlemper J, et al., 2018, Joint learning of motion estimation and segmentation for cardiac MR image sequences, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Publisher: Springer Verlag, Pages: 472-480
Cardiac motion estimation and segmentation play important roles in quantitatively assessing cardiac function and diagnosing cardiovascular diseases. In this paper, we propose a novel deep learning method for joint estimation of motion and segmentation from cardiac MR image sequences. The proposed network consists of two branches: a cardiac motion estimation branch which is built on a novel unsupervised Siamese style recurrent spatial transformer network, and a cardiac segmentation branch that is based on a fully convolutional network. In particular, a joint multi-scale feature encoder is learned by optimizing the segmentation branch and the motion estimation branch simultaneously. This enables the weakly-supervised segmentation by taking advantage of features that are unsupervisedly learned in the motion estimation branch from a large amount of unannotated data. Experimental results using cardiac MlRI images from 220 subjects show that the joint learning of both tasks is complementary and the proposed models outperform the competing methods significantly in terms of accuracy and speed.
Bai W, Suzuki H, Qin C, et al., 2018, Recurrent neural networks for aortic image sequence segmentation with sparse annotations, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), ISSN: 0302-9743
Segmentation of image sequences is an important task in medical image analysis, which enables clinicians to assess the anatomy and function of moving organs. However, direct application of a segmentation algorithm to each time frame of a sequence may ignore the temporal continuity inherent in the sequence. In this work, we propose an image sequence segmentation algorithm by combining a fully convolutional network with a recurrent neural network, which incorporates both spatial and temporal information into the segmentation task. A key challenge in training this network is that the available manual annotations are temporally sparse, which forbids end-to-end training. We address this challenge by performing non-rigid label propagation on the annotations and introducing an exponentially weighted loss function for training. Experiments on aortic MR image sequences demonstrate that the proposed method significantly improves both accuracy and temporal smoothness of segmentation, compared to a baseline method that utilises spatial information only. It achieves an average Dice metric of 0.960 for the ascending aorta and 0.953 for the descending aorta.
Qin C, Bai W, Schlemper J, et al., 2018, Joint motion estimation and segmentation from undersampled cardiac MR image, Machine Learning for Medical Image Reconstruction Workshop, Pages: 55-63, ISSN: 0302-9743
© 2018, Springer Nature Switzerland AG. Accelerating the acquisition of magnetic resonance imaging (MRI) is a challenging problem, and many works have been proposed to reconstruct images from undersampled k-space data. However, if the main purpose is to extract certain quantitative measures from the images, perfect reconstructions may not always be necessary as long as the images enable the means of extracting the clinically relevant measures. In this paper, we work on jointly predicting cardiac motion estimation and segmentation directly from undersampled data, which are two important steps in quantitatively assessing cardiac function and diagnosing cardiovascular diseases. In particular, a unified model consisting of both motion estimation branch and segmentation branch is learned by optimising the two tasks simultaneously. Additional corresponding fully-sampled images are incorporated into the network as a parallel sub-network to enhance and guide the learning during the training process. Experimental results using cardiac MR images from 220 subjects show that the proposed model is robust to undersampled data and is capable of predicting results that are close to that from fully-sampled ones, while bypassing the usual image reconstruction stage.
Schlemper J, Oktay O, Bai W, et al., 2018, Cardiac MR segmentation from undersampled k-space using deep latent representation learning, International Conference On Medical Image Computing & Computer Assisted Intervention, Publisher: Springer, Cham, Pages: 259-267, ISSN: 0302-9743
© Springer Nature Switzerland AG 2018. Reconstructing magnetic resonance imaging (MRI) from undersampled k-space enables the accelerated acquisition of MRI but is a challenging problem. However, in many diagnostic scenarios, perfect reconstructions are not necessary as long as the images allow clinical practitioners to extract clinically relevant parameters. In this work, we present a novel deep learning framework for reconstructing such clinical parameters directly from undersampled data, expanding on the idea of application-driven MRI. We propose two deep architectures, an end-to-end synthesis network and a latent feature interpolation network, to predict cardiac segmentation maps from extremely undersampled dynamic MRI data, bypassing the usual image reconstruction stage altogether. We perform a large-scale simulation study using UK Biobank data containing nearly 1000 test subjects and show that with the proposed approaches, an accurate estimate of clinical parameters such as ejection fraction can be obtained from fewer than 10 k-space lines per time-frame.
Schlemper J, Castro DC, Bai W, et al., 2018, Bayesian deep learning for accelerated MR image reconstruction, International Workshop on Machine Learning for Medical Image Reconstruction, Publisher: Springer, Cham, Pages: 64-71, ISSN: 0302-9743
Recently, many deep learning (DL) based MR image reconstruction methods have been proposed with promising results. However, only a handful of work has been focussing on characterising the behaviour of deep networks, such as investigating when the networks may fail to reconstruct. In this work, we explore the applicability of Bayesian DL techniques to model the uncertainty associated with DL-based reconstructions. In particular, we apply MC-dropout and heteroscedastic loss to the reconstruction networks to model epistemic and aleatoric uncertainty. We show that the proposed Bayesian methods achieve competitive performance when the test images are relatively far from the training data distribution and outperforms when the baseline method is over-parametrised. In addition, we qualitatively show that there seems to be a correlation between the magnitude of the produced uncertainty maps and the error maps, demonstrating the potential utility of the Bayesian DL methods for assessing the reliability of the reconstructed images.
Bai W, Sinclair M, Tarroni G, et al., 2018, Automated cardiovascular magnetic resonance image analysis with fully convolutional networks, Journal of Cardiovascular Magnetic Resonance, Vol: 20, Pages: 1-12, ISSN: 1097-6647
Background: Cardiovascular magnetic resonance (CMR) imaging is a standard imaging modality for assessing cardiovascular diseases (CVDs), the leading cause of death globally. CMR enables accurate quantification of the cardiac chamber volume, ejection fraction and myocardial mass, providing information for diagnosis and monitoring of CVDs. However, for years, clinicians have been relying on manual approaches for CMR imageanalysis, which is time consuming and prone to subjective errors. It is a major clinical challenge to automatically derive quantitative and clinically relevant information from CMR images.Methods: Deep neural networks have shown a great potential in image pattern recognition and segmentation for a variety of tasks. Here we demonstrate an automated analysis method for CMR images, which is based on a fully convolutional network (FCN). The network is trained and evaluated on a large-scale dataset from the UK Biobank, consisting of 4,875 subjects with 93,500 pixelwise annotated images. The performance of the method has been evaluated using a number of technical metrics, including the Dice metric, mean contour distance and Hausdorff distance, as well as clinically relevant measures, including left ventricle (LV)end-diastolic volume (LVEDV) and end-systolic volume (LVESV), LV mass (LVM); right ventricle (RV) end-diastolic volume (RVEDV) and end-systolic volume (RVESV).Results: By combining FCN with a large-scale annotated dataset, the proposed automated method achieves a high performance in segmenting the LV and RV on short-axis CMR images and the left atrium (LA) and right atrium (RA) on long-axis CMR images. On a short-axis image test set of 600 subjects, it achieves an average Dice metric of 0.94 for the LV cavity, 0.88 for the LV myocardium and 0.90 for the RV cavity. The meanabsolute difference between automated measurement and manual measurement was 6.1 mL for LVEDV, 5.3 mL for LVESV, 6.9 gram for LVM, 8.5 mL for RVEDV and 7.2 mL for RVESV. On long-ax
Robinson R, Oktay O, Bai W, et al., 2018, Real-time prediction of segmentation quality, International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Publisher: Springer Verlag, Pages: 578-585, ISSN: 0302-9743
Recent advances in deep learning based image segmentationmethods have enabled real-time performance with human-level accuracy.However, occasionally even the best method fails due to low image qual-ity, artifacts or unexpected behaviour of black box algorithms. Beingable to predict segmentation quality in the absence of ground truth is ofparamount importance in clinical practice, but also in large-scale studiesto avoid the inclusion of invalid data in subsequent analysis.In this work, we propose two approaches of real-time automated qualitycontrol for cardiovascular MR segmentations using deep learning. First,we train a neural network on 12,880 samples to predict Dice SimilarityCoefficients (DSC) on a per-case basis. We report a mean average error(MAE) of 0.03 on 1,610 test samples and 97% binary classification accu-racy for separating low and high quality segmentations. Secondly, in thescenario where no manually annotated data is available, we train a net-work to predict DSC scores from estimated quality obtained via a reversetesting strategy. We report an MAE = 0.14 and 91% binary classifica-tion accuracy for this case. Predictions are obtained in real-time which,when combined with real-time segmentation methods, enables instantfeedback on whether an acquired scan is analysable while the patient isstill in the scanner. This further enables new applications of optimisingimage acquisition towards best possible analysis results.
Duan J, Schlemper J, Bai W, et al., 2018, Deep Nested Level Sets: Fully Automated Segmentation of Cardiac MR Images in Patients with Pulmonary Hypertension, International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Pages: 595-603, ISSN: 0302-9743
Bhuva A, Treibel TA, De Marvao A, et al., 2018, Septal hypertrophy in aortic stenosis and its regression after valve replacement is more plastic in males than females: insights from 3D machine learning approach, European-Society-of-Cardiology Congress, Publisher: European Society of Cardiology, Pages: 1132-1132, ISSN: 0195-668X
Background: Evaluation of left ventricular non-compaction (LVNC) is an increasingly common indication for cardiac magnetic resonance imaging (MRI). Fractal dimension (FD) is a unitless measure of geometrical complexity which can be used to quantify LV trabeculation. FD is increased in LVNC, but there have been few studies on FD in normal subjects. The aim of the study was to establish reference ranges for FD in a healthy population, and identify covariates which are associated with FD.Methods: MRI was performed in 1,913 volunteers without hypertension, diabetes, or heart disease (1055 female, 858 male; median age 40, range 19-82). FD was derived from LV short-axis images, using a custom MATLAB box-counting algorithm. The maximal FD in the apical half of the LV was used for all analyses, as previously described.Results: Normal ranges (2.5-97.5th percentile) for female and male subjects were 1.154 - 1.367 and 1.179 - 1.392, respectively. FD was significantly correlated with age, gender, ethnicity, body surface area (BSA), activity score, and systolic blood pressure. In multivariable analysis, FD was independently correlated with increased age (β 0.11, p<0.001), male gender (β 0.09, p<0.001), African/Afro-Caribbean ethnicity (β 0.18, p<0.001), increased BSA (β 0.27, p<0.001), and increased activity score (β 0.07, p=0.002). Since ethnicity was found to significantly affect FD, normal ranges were calculated for each subgroup (see table).Conclusions: This is the largest study on FD in healthy subjects, and the first to present gender- and race-specific normal ranges. The association between FD and age suggests that LV trabeculation is a dynamic phenotype which may change with age.
Valindria VV, Lavdas I, Bai W, et al., 2018, Domain adaptation for MRI organ segmentation using reverse classification accuracy, International Conference on Medical Imaging with Deep Learning (MIDL)
The variations in multi-center data in medical imaging studies have broughtthe necessity of domain adaptation. Despite the advancement of machine learningin automatic segmentation, performance often degrades when algorithms areapplied on new data acquired from different scanners or sequences than thetraining data. Manual annotation is costly and time consuming if it has to becarried out for every new target domain. In this work, we investigate automaticselection of suitable subjects to be annotated for supervised domain adaptationusing the concept of reverse classification accuracy (RCA). RCA predicts theperformance of a trained model on data from the new domain and differentstrategies of selecting subjects to be included in the adaptation via transferlearning are evaluated. We perform experiments on a two-center MR database forthe task of organ segmentation. We show that subject selection via RCA canreduce the burden of annotation of new data for the target domain.
Dawes TJW, Serrani M, Bai W, et al., 2018, Myocardial trabeculae improve left ventricular function: a combined UK Biobank and computational analysis, GAT Annual Scientific Meeting 2018, Publisher: Association of Anaesthetists of Great Britain and Ireland
Koch LM, Rajchl M, Bai W, et al., 2018, Multi-atlas segmentation using partially annotated data: methods and annotation strategies, IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol: 40, Pages: 1683-1696, ISSN: 0162-8828
Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due to the time required for the labelling task. Segmentation methods requiring only a proportion of each atlas image to be labelled could therefore reduce the workload on expert raters tasked with annotating atlas images. To address this issue, we first re-examine the labelling problem common in many existing approaches and formulate its solution in terms of a Markov Random Field energy minimisation problem on a graph connecting atlases and the target image. This provides a unifying framework for multi-atlas segmentation. We then show how modifications in the graph configuration of the proposed framework enable the use of partially annotated atlas images and investigate different partial annotation strategies. The proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets for hippocampal and cardiac segmentation. Experiments were performed aimed at (1) recreating existing segmentation techniques with the proposed framework and (2) demonstrating the potential of employing sparsely annotated atlas data for multi-atlas segmentation.
Puyol-Anton E, Ruijsink B, Bai W, et al., 2018, Fully automated myocardial strain estimation from cine MRI using convolutional neural networks, International Symposium on Biomedical Imaging, Pages: 1139-1143, ISSN: 1945-7928
© 2018 IEEE. Cardiovascular magnetic resonance myocardial feature tracking (CMR-FT) is a promising method for quantification of cardiac function from standard steady-state free precession (SSFP) images. However, currently available techniques require operator dependent and time-consuming manual intervention, limiting reproducibility and clinical use. In this paper, we propose a fully automated pipeline to compute left ventricular (LV) longitudinal and radial strain from 2- and 4-chamber cine acquisitions, and LV circumferential and radial strain from the short-axis imaging. The method employs a convolutional neural network to automatically segment the myocardium, followed by feature tracking and strain estimation. Experiments are performed using 40 healthy volunteers and 40 ischemic patients from the UK Biobank dataset. Results show that our method obtained strain values that were in excellent agreement with the commercially available clinical CMR-FT software CVI42(Circle Cardiovascular Imaging, Calgary, Canada).
de Marvao A, Biffi C, Walsh R, et al., 2018, Defining The Effects Of Genetic Variation Using Machine Learning Analysis Of CMRs: A Study In Hypertrophic Cardiomyopathy And In A Healthy Population, Joint Meeting of the British-Society-of-Cardiovascular-Imaging/British-Society-of-Cardiovascular-CT, British-Society-of-Cardiovascular-Magnetic-Resonance and British-Nuclear-Cardiac-Society on British Cardiovascular Imaging, Publisher: BMJ PUBLISHING GROUP, Pages: A7-A8, ISSN: 1355-6037
Suinesiaputra A, Ablin P, Alba X, et al., 2018, Statistical Shape Modeling of the Left Ventricle: Myocardial Infarct Classification Challenge, IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS, Vol: 22, Pages: 503-515, ISSN: 2168-2194
Kamnitsas K, Bai W, Ferrante E, et al., 2018, Ensembles of Multiple Models and Architectures for Robust Brain Tumour Segmentation, MICCAI BrainLes Workshop
Oktay O, Ferrante E, Kamnitsas K, et al., 2018, Anatomically Constrained Neural Networks (ACNN): application to cardiac image enhancement and segmentation, IEEE Transactions on Medical Imaging, Vol: 37, Pages: 384-395, ISSN: 0278-0062
Incorporation of prior knowledge about organ shape and location is key to improve performance of image analysis approaches. In particular, priors can be useful in cases where images are corrupted and contain artefacts due to limitations in image acquisition. The highly constrained nature of anatomical objects can be well captured with learning based techniques. However, in most recent and promising techniques such as CNN based segmentation it is not obvious how to incorporate such prior knowledge. State-of-the-art methods operate as pixel-wise classifiers where the training objectives do not incorporate the structure and inter-dependencies of the output. To overcome this limitation, we propose a generic training strategy that incorporates anatomical prior knowledge into CNNs through a new regularisation model, which is trained end-to-end. The new framework encourages models to follow the global anatomical properties of the underlying anatomy (e.g. shape, label structure) via learnt non-linear representations of the shape. We show that the proposed approach can be easily adapted to different analysis tasks (e.g. image enhancement, segmentation) and improve the prediction accuracy of the state-of-the-art models. The applicability of our approach is shown on multi-modal cardiac datasets and public benchmarks. Additionally, we demonstrate how the learnt deep models of 3D shapes can be interpreted and used as biomarkers for classification of cardiac pathologies.
Sinclair M, Peressutti D, Puyol-Anton E, et al., 2018, Myocardial strain computed at multiple spatial scales from tagged magnetic resonance imaging: Estimating cardiac biomarkers for CRT patients, MEDICAL IMAGE ANALYSIS, Vol: 43, Pages: 169-185, ISSN: 1361-8415
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Balaban G, Halliday BP, Costa CM, et al., 2018, The Effects of Non-ischemic Fibrosis Texture and Density on Mechanisms of Reentry, 45th Computing in Cardiology Conference (CinC), Publisher: IEEE, ISSN: 2325-8861
Suzuki HS, Gao HG, Bai WB, et al., 2017, Abnormal brain white matter microstructure is associated withboth pre-hypertension and hypertension, PLoS ONE, Vol: 12, ISSN: 1932-6203
ObjectivesTo characterize effects of chronically elevated blood pressure on the brain, we tested for brain white matter microstructural differences associated with normotension, pre-hypertension and hypertension in recently available brain magnetic resonance imaging data from 4659 participants without known neurological or psychiatric disease (62.3±7.4 yrs, 47.0% male) in UK Biobank.MethodsFor assessment of white matter microstructure, we used measures derived from neurite orientation dispersion and density imaging (NODDI) including the intracellular volume fraction (an estimate of neurite density) and isotropic volume fraction (an index of the relative extra-cellular water diffusion). To estimate differences associated specifically with blood pressure, we applied propensity score matching based on age, sex, educational level, body mass index, and history of smoking, diabetes mellitus and cardiovascular disease to perform separate contrasts of non-hypertensive (normotensive or pre-hypertensive, N = 2332) and hypertensive (N = 2337) individuals and of normotensive (N = 741) and pre-hypertensive (N = 1581) individuals (p<0.05 after Bonferroni correction).ResultsThe brain white matter intracellular volume fraction was significantly lower, and isotropic volume fraction was higher in hypertensive relative to non-hypertensive individuals (N = 1559, each). The white matter isotropic volume fraction also was higher in pre-hypertensive than in normotensive individuals (N = 694, each) in the right superior longitudinal fasciculus and the right superior thalamic radiation, where the lower intracellular volume fraction was observed in the hypertensives relative to the non-hypertensive group.SignificancePathological processes associated with chronically elevated blood pressure are associated with imaging differences suggesting chronic alterations of white matter axonal structure that may affect cognitive functions even with pre-hypertension.
Sinclair M, Bai W, Puyol-Antón E, et al., 2017, Fully automated segmentation-based respiratory motion correction of multiplanar cardiac magnetic resonance images for large-scale datasets, International Conference On Medical Image Computing & Computer Assisted Intervention, Pages: 332-340, ISSN: 0302-9743
© Springer International Publishing AG 2017. Cardiac magnetic resonance (CMR) can be used for quantitative analysis of heart function. However, CMR imaging typically involves acquiring 2D image planes during separate breath-holds, often resulting in misalignment of the heart between image planes in 3D. Accurate quantitative analysis requires a robust 3D reconstruction of the heart from CMR images, which is adversely affected by such motion artifacts. Therefore, we propose a fully automated method for motion correction of CMR planes using segmentations produced by fully convolutional neural networks (FCNs). FCNs are trained on 100 UK Biobank subjects to produce short-axis and long-axis segmentations, which are subsequently used in an iterative registration algorithm for correcting breath-hold induced motion artifacts. We demonstrate significant improvements in motion-correction over image-based registration, with strong correspondence to results obtained using manual segmentations. We also deploy our automatic method on 9,353 subjects in the UK Biobank database, demonstrating significant improvements in 3D plane alignment.
Bai W, Oktay O, Sinclair M, et al., 2017, Semi-supervised learning for network-based cardiac MR image segmentation, International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), Publisher: Springer Verlag, Pages: 253-260, ISSN: 0302-9743
Training a fully convolutional network for pixel-wise (or voxel-wise) image segmentation normally requires a large number of training images with corresponding ground truth label maps. However, it is a challenge to obtain such a large training set in the medical imaging domain, where expert annotations are time-consuming and difficult to obtain. In this paper, we propose a semi-supervised learning approach, in which a segmentation network is trained from both labelled and unlabelled data. The network parameters and the segmentations for the unlabelled data are alternately updated. We evaluate the method for short-axis cardiac MR image segmentation and it has demonstrated a high performance, outperforming a baseline supervised method. The mean Dice overlap metric is 0.92 for the left ventricular cavity, 0.85 for the myocardium and 0.89 for the right ventricular cavity. It also outperforms a state-of-the-art multi-atlas segmentation method by a large margin and the speed is substantially faster.
Biffi C, Simoes Monteiro de Marvao A, Attard M, et al., 2017, Three-dimensional Cardiovascular Imaging-Genetics: A Mass Univariate Framework, Bioinformatics, ISSN: 1367-4803
Motivation: Left ventricular (LV) hypertrophy is a strong predictor of cardiovascular outcomes, but its genetic regulation remains largely unexplained. Conventional phenotyping relies on manual calculation of LV mass and wall thickness, but advanced cardiac image analysis presents an opportunity for highthroughput mapping of genotype-phenotype associations in three dimensions (3D).Results: High-resolution cardiac magnetic resonance images were automatically segmented in 1,124 healthy volunteers to create a 3D shape model of the heart. Mass univariate regression was used to plot a 3D effect-size map for the association between wall thickness and a set of predictors at each vertex in the mesh. The vertices where a significant effect exists were determined by applying threshold-free cluster enhancement to boost areas of signal with spatial contiguity. Experiments on simulated phenotypic signals and SNP replication show that this approach offers a substantial gain in statistical power for cardiac genotype-phenotype associations while providing good control of the false discovery rate. This framework models the effects of genetic variation throughout the heart and can be automatically applied to large population cohorts.Availability: The proposed approach has been coded in an R package freely available at https://doi.org/10.5281/zenodo.834610 together with the clinical data used in this work.
Robinson R, Valindria V, Bai W, et al., 2017, Automatic quality control of cardiac MRI segmentation in large-scale population imaging, Medical Image Computing and Computer Assisted Intervention - MICCAI 2017, Publisher: Springer, Pages: 720-727, ISSN: 0302-9743
The trend towards large-scale studies including population imaging poses new challenges in terms of quality control (QC). This is a particular issue when automatic processing tools such as image segmentation methods are employed to derive quantitative measures or biomarkers for further analyses. Manual inspection and visual QC of each segmentation result is not feasible at large scale. However, it is important to be able to detect when an automatic method fails to avoid inclusion of wrong measurements into subsequent analyses which could otherwise lead to incorrect conclusions. To overcome this challenge, we explore an approach for predicting segmentation quality based on reverse classification accuracy, which enables us to discriminate between successful and failed cases. We validate this approach on a large cohort of cardiac MRI for which manual QC scores were available. Our results on 7,425 cases demonstrate the potential for fully automatic QC in the context of large-scale population imaging such as the UK Biobank Imaging Study.
Suzuki H, Gao H, Bai W, et al., 2017, Hypertension and white matter microstructures in healthy participants in UK Biobank, Publisher: OXFORD UNIV PRESS, Pages: 248-249, ISSN: 0195-668X
Lorch B, Vaillant G, Baumgartner C, et al., 2017, Automated detection of motion artefacts in MR imaging using decision forests, Journal of Medical Entomology, Vol: 2017, ISSN: 0022-2585
The acquisition of a Magnetic Resonance (MR) scan usually takes longer than subjects can remain still. Movement of the subject such as bulk patient motion or respiratory motion degrades the image quality and its diagnostic value by producing image artefacts like ghosting, blurring, and smearing. This work focuses on the effect of motion on the reconstructed slices and the detection of motion artefacts in the reconstruction by using a supervised learning approach based on random decision forests. Both the effects of bulk patient motion occurring at various time points in the acquisition on head scans and the effects of respiratory motion on cardiac scans are studied. Evaluation is performed on synthetic images where motion artefacts have been introduced by altering the k-space data according to a motion trajectory, using the three common k-space sampling patterns: Cartesian, radial, and spiral. The results suggest that a machine learning approach is well capable of learning the characteristics of motion artefacts and subsequently detecting motion artefacts with a confidence that depends on the sampling pattern.
Tarroni G, Oktay O, Bai W, et al., 2017, Learning-based heart coverage estimation for short-axis cine cardiac MR images, Functional Imaging and Modelling of the Heart (FIMH), Publisher: Springer, Pages: 73-82
The correct acquisition of short axis (SA) cine cardiac MRimage stacks requires the imaging of the full cardiac anatomy betweenthe apex and the mitral valve plane via multiple 2D slices. While in theclinical practice the SA stacks are usually checked qualitatively to en-sure full heart coverage, visual inspection can become infeasible for largeamounts of imaging data that is routinely acquired, e.g. in populationstudies such as the UK Biobank (UKBB). Accordingly, we propose alearning-based technique for the fully-automated estimation of the heartcoverage for SA image stacks. The technique relies on the identificationof cardiac landmarks (i.e. the apex and the mitral valve sides) on twochamber view long axis images and on the comparison of the landmarks’positions to the volume covered by the SA stack. Landmark detection isperformed using a hybrid random forest approach integrating both re-gression and structured classification models. The technique was appliedon 3000 cases from the UKBB and compared to visual assessment. Theobtained results (error rate = 2.3%, sens. = 73%, spec. = 90%) indicatethat the proposed technique is able to correctly detect the vast majorityof the cases with insufficient coverage, suggesting that it could be usedas a fully-automated quality control step for CMR SA image stacks.
Valindria V, Lavdas I, Bai W, et al., 2017, Reverse classification accuracy: predicting segmentation performance in the absence of ground truth, IEEE Transactions on Medical Imaging, Vol: 36, Pages: 1597-1606, ISSN: 1558-254X
When integrating computational tools such as au-tomatic segmentation into clinical practice, it is of utmostimportance to be able to assess the level of accuracy on newdata, and in particular, to detect when an automatic methodfails. However, this is difficult to achieve due to absence of groundtruth. Segmentation accuracy on clinical data might be differentfrom what is found through cross-validation because validationdata is often used during incremental method development, whichcan lead to overfitting and unrealistic performance expectations.Before deployment, performance is quantified using differentmetrics, for which the predicted segmentation is compared toa reference segmentation, often obtained manually by an expert.But little is known about the real performance after deploymentwhen a reference is unavailable. In this paper, we introduce theconcept ofreverse classification accuracy(RCA) as a frameworkfor predicting the performance of a segmentation method onnew data. In RCA we take the predicted segmentation froma new image to train a reverse classifier which is evaluatedon a set of reference images with available ground truth. Thehypothesis is that if the predicted segmentation is of good quality,then the reverse classifier will perform well on at least some ofthe reference images. We validate our approach on multi-organsegmentation with different classifiers and segmentation methods.Our results indicate that it is indeed possible to predict the qualityof individual segmentations, in the absence of ground truth. Thus,RCA is ideal for integration into automatic processing pipelines inclinical routine and as part of large-scale image analysis studies.
Giannakidis A, Oktay O, Keegan J, et al., 2017, Super-resolution Reconstruction of Late Gadolinium Cardiovascular Magnetic Resonance Images using a Residual Convolutional Neural Network, The 25th Scientific Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM 2017)
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