Imperial College London

ProfessorDanielRueckert

Faculty of EngineeringDepartment of Computing

Head of Department of Computing
 
 
 
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Contact

 

+44 (0)20 7594 8333d.rueckert Website

 
 
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Location

 

568Huxley BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
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726 results found

Bhuva AN, Treibel TA, De Marvao A, Biffi C, Dawes TJW, Doumou G, Bai W, Patel K, Boubertakh R, Rueckert D, O'Regan DP, Hughes AD, Moon JC, Manisty CHet al., 2020, Sex and regional differences in myocardial plasticity in aortic stenosis are revealed by 3D model machine learning., Eur Heart J Cardiovasc Imaging, Vol: 21, Pages: 417-427

AIMS: Left ventricular hypertrophy (LVH) in aortic stenosis (AS) varies widely before and after aortic valve replacement (AVR), and deeper phenotyping beyond traditional global measures may improve risk stratification. We hypothesized that machine learning derived 3D LV models may provide a more sensitive assessment of remodelling and sex-related differences in AS than conventional measurements. METHODS AND RESULTS: One hundred and sixteen patients with severe, symptomatic AS (54% male, 70 ± 10 years) underwent cardiovascular magnetic resonance pre-AVR and 1 year post-AVR. Computational analysis produced co-registered 3D models of wall thickness, which were compared with 40 propensity-matched healthy controls. Preoperative regional wall thickness and post-operative percentage wall thickness regression were analysed, stratified by sex. AS hypertrophy and regression post-AVR was non-uniform-greatest in the septum with more pronounced changes in males than females (wall thickness regression: -13 ± 3.6 vs. -6 ± 1.9%, respectively, P < 0.05). Even patients without LVH (16% with normal indexed LV mass, 79% female) had greater septal and inferior wall thickness compared with controls (8.8 ± 1.6 vs. 6.6 ± 1.2 mm, P < 0.05), which regressed post-AVR. These differences were not detectable by global measures of remodelling. Changes to clinical parameters post-AVR were also greater in males: N-terminal pro-brain natriuretic peptide (NT-proBNP) [-37 (interquartile range -88 to -2) vs. -1 (-24 to 11) ng/L, P = 0.008], and systolic blood pressure (12.9 ± 23 vs. 2.1 ± 17 mmHg, P = 0.009), with changes in NT-proBNP correlating with percentage LV mass regression in males only (ß 0.32, P = 0.02). CONCLUSION: In patients with severe AS, inc

Journal article

Onofrey JA, Staib LH, Huang X, Zhang F, Papademetris X, Metaxas D, Rueckert D, Duncan JSet al., 2020, Sparse data-driven learning for effective and efficient biomedical image segmentation., Annual Review of Biomedical Engineering, Vol: 22, Pages: 127-153, ISSN: 1523-9829

Sparsity is a powerful concept to exploit for high-dimensional machine learning and associated representational and computational efficiency. Sparsity is well suited for medical image segmentation. We present a selection of techniques that incorporate sparsity, including strategies based on dictionary learning and deep learning, that are aimed at medical image segmentation and related quantification. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 22 is June 4, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Journal article

Chen C, Qin C, Qiu H, Tarroni G, Duan J, Bai W, Rueckert Det al., 2020, Deep learning for cardiac image segmentation: A review, Frontiers in Cardiovascular Medicine, Vol: 7, Pages: 1-33, ISSN: 2297-055X

Deep learning has become the most widely used approach for cardiac imagesegmentation in recent years. In this paper, we provide a review of over 100cardiac image segmentation papers using deep learning, which covers commonimaging modalities including magnetic resonance imaging (MRI), computedtomography (CT), and ultrasound (US) and major anatomical structures ofinterest (ventricles, atria and vessels). In addition, a summary of publiclyavailable cardiac image datasets and code repositories are included to providea base for encouraging reproducible research. Finally, we discuss thechallenges and limitations with current deep learning-based approaches(scarcity of labels, model generalizability across different domains,interpretability) and suggest potential directions for future research.

Journal article

Jaubert O, Cruz G, Bustin A, Schneider T, Koken P, Doneva M, Rueckert D, Botnar RM, Prieto Cet al., 2020, Free-running cardiac magnetic resonance fingerprinting: Joint T1/T2 map and Cine imaging., Magn Reson Imaging, Vol: 68, Pages: 173-182

PURPOSE: To develop and evaluate a novel non-ECG triggered 2D magnetic resonance fingerprinting (MRF) sequence allowing for simultaneous myocardial T1 and T2 mapping and cardiac Cine imaging. METHODS: Cardiac MRF (cMRF) has been recently proposed to provide joint T1/T2 myocardial mapping by triggering the acquisition to mid-diastole and relying on a subject-dependent dictionary of MR signal evolutions to generate the maps. In this work, we propose a novel "free-running" (non-ECG triggered) cMRF framework for simultaneous myocardial T1 and T2 mapping and cardiac Cine imaging in a single scan. Free-running cMRF is based on a transient state bSSFP acquisition with tiny golden angle radial readouts, varying flip angle and multiple adiabatic inversion pulses. The acquired data is retrospectively gated into several cardiac phases, which are reconstructed with an approach that combines parallel imaging, low rank modelling and patch-based high-order tensor regularization. Free-running cMRF was evaluated in a standardized phantom and ten healthy subjects. Comparison with reference spin-echo, MOLLI, SASHA, T2-GRASE and Cine was performed. RESULTS: T1 and T2 values obtained with the proposed approach were in good agreement with reference phantom values (ICC(A,1) > 0.99). Reported values for myocardium septum T1 were 1043 ± 48 ms, 1150 ± 100 ms and 1160 ± 79 ms for MOLLI, SASHA and free-running cMRF respectively and for T2 of 51.7 ± 4.1 ms and 44.6 ± 4.1 ms for T2-GRASE and free-running cMRF respectively. Good agreement was observed between free-running cMRF and conventional Cine 2D ejection fraction (bias = -0.83%). CONCLUSION: The proposed free-running cardiac MRF approach allows for simultaneous assessment of myocardial T1 and T2 and Cine imaging in a single scan.

Journal article

Tarroni G, Bai W, Oktay O, Schuh A, Suzuki H, Glocker B, Matthews P, Rueckert Det al., 2020, Large-scale quality control of cardiac imaging in population studies: application to UK Biobank, Scientific Reports, ISSN: 2045-2322

In large population studies such as the UK Biobank (UKBB), quality control of the acquired images by visual assessment isunfeasible. In this paper, we apply a recently developed fully-automated quality control pipeline for cardiac MR (CMR) imagesto the first 19,265 short-axis (SA) cine stacks from the UKBB. We present the results for the three estimated quality metrics(heart coverage, inter-slice motion and image contrast in the cardiac region) as well as their potential associations with factorsincluding acquisition details and subject-related phenotypes. Up to 14.2% of the analysed SA stacks had sub-optimal coverage(i.e. missing basal and/or apical slices), however most of them were limited to the first year of acquisition. Up to 16% of thestacks were affected by noticeable inter-slice motion (i.e. average inter-slice misalignment greater than 3.4 mm). Inter-slicemotion was positively correlated with weight and body surface area. Only 2.1% of the stacks had an average end-diastoliccardiac image contrast below 30% of the dynamic range. These findings will be highly valuable for both the scientists involvedin UKBB CMR acquisition and for the ones who use the dataset for research purposes.

Journal article

Biffi C, Cerrolaza Martinez JJ, Tarroni G, Bai W, Simoes Monteiro de Marvao A, Oktay O, Ledig C, Le Folgoc L, Kamnitsas K, Doumou G, Duan J, Prasad S, Cook S, O'Regan D, Rueckert Det al., 2020, Explainable anatomical shape analysis through deep hierarchical generative models, IEEE Transactions on Medical Imaging, ISSN: 0278-0062

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer’s disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating highthroughput analysis of normal anatomy and pathology in largescale studies of volumetric imaging.

Journal article

Biffi C, Doumou G, Duan J, Prasad SK, Cook SA, O Regan DP, Rueckert D, Cerrolaza JJ, Tarroni G, Bai W, De Marvao A, Oktay O, Ledig C, Le Folgoc L, Kamnitsas Ket al., 2020, Explainable anatomical shape analysis through deep hierarchical generative models., Publisher: arXiv

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer's disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating highthroughput analysis of normal anatomy and pathology in largescale studies of volumetric imaging.

Working paper

Jokinen H, Koikkalainen J, Laakso HM, Melkas S, Nieminen T, Brander A, Korvenoja A, Rueckert D, Barkhof F, Scheltens P, Schmidt R, Fazekas F, Madureira S, Verdelho A, Wallin A, Wahlund L-O, Waldemar G, Chabriat H, Hennerici M, O'Brien J, Inzitari D, Lotjonen J, Pantoni L, Erkinjuntti Tet al., 2020, Global Burden of Small Vessel Disease-Related Brain Changes on MRI Predicts Cognitive and Functional Decline, STROKE, Vol: 51, Pages: 170-178, ISSN: 0039-2499

Journal article

Rachmadi MF, Valdes-Hernandez MDC, Li H, Guerrero R, Meijboom R, Wiseman S, Waldman A, Zhang J, Rueckert D, Wardlaw J, Komura Tet al., 2020, Limited One-time Sampling Irregularity Map (LOTS-IM) for Automatic Unsupervised Assessment of White Matter Hyperintensities and Multiple Sclerosis Lesions in Structural Brain Magnetic Resonance Images, COMPUTERIZED MEDICAL IMAGING AND GRAPHICS, Vol: 79, ISSN: 0895-6111

Journal article

Rueckert D, Schnabel JA, 2020, Model-Based and Data-Driven Strategies in Medical Image Computing, PROCEEDINGS OF THE IEEE, Vol: 108, Pages: 110-124, ISSN: 0018-9219

Journal article

Chen L, Lobotesis K, Rueckert D, Bentley P, Cuervas-Mons C, Hallett C, Fernandes C, Huntington D, Williams R, Patel R, Cohen Det al., 2019, Timing an ischaemic stroke with just plain CT (and a little deep learning), Publisher: SAGE PUBLICATIONS LTD, Pages: 29-29, ISSN: 1747-4930

Conference paper

Meng Q, Zimmer V, Hou B, Rajchl M, Toussaint N, Oktay O, Schlemper J, Gomez A, Housden J, Matthew J, Rueckert D, Schnabel JA, Kainz Bet al., 2019, Weakly supervised estimation of shadow confidence maps in fetal ultrasound imaging, IEEE Transactions on Medical Imaging, Vol: 38, Pages: 2755-2767, ISSN: 0278-0062

Detecting acoustic shadows in ultrasound images is important in many clinical and engineering applications. Real-time feedback of acoustic shadows can guide sonographers to a standardized diagnostic viewing plane with minimal artifacts and can provide additional information for other automatic image analysis algorithms. However, automatically detecting shadow regions using learning-based algorithms is challenging because pixel-wise ground truth annotation of acoustic shadows is subjective and time consuming. In this paper we propose a weakly supervised method for automatic confidence estimation of acoustic shadow regions. Our method is able to generate a dense shadow-focused confidence map. In our method, a shadow-seg module is built to learn general shadow features for shadow segmentation, based on global image-level annotations as well as a small number of coarse pixel-wise shadow annotations. A transfer function is introduced to extend the obtained binary shadow segmentation to a reference confidence map. Additionally, a confidence estimation network is proposed to learn the mapping between input images and the reference confidence maps. This network is able to predict shadow confidence maps directly from input images during inference. We use evaluation metrics such as DICE, inter-class correlation and etc. to verify the effectiveness of our method. Our method is more consistent than human annotation, and outperforms the state-of-the-art quantitatively in shadow segmentation and qualitatively in confidence estimation of shadow regions. We further demonstrate the applicability of our method by integrating shadow confidence maps into tasks such as ultrasound image classification, multi-view image fusion and automated biometric measurements.

Journal article

Chen L, Bentley P, Mori K, Misawa K, Fujiwara M, Rueckert Det al., 2019, Self-supervised learning for medical image analysis using image context restoration., Medical Image Analysis, Vol: 58, Pages: 1-12, ISSN: 1361-8415

Machine learning, particularly deep learning has boosted medical image analysis over the past years. Training a good model based on deep learning requires large amount of labelled data. However, it is often difficult to obtain a sufficient number of labelled images for training. In many scenarios the dataset in question consists of more unlabelled images than labelled ones. Therefore, boosting the performance of machine learning models by using unlabelled as well as labelled data is an important but challenging problem. Self-supervised learning presents one possible solution to this problem. However, existing self-supervised learning strategies applicable to medical images cannot result in significant performance improvement. Therefore, they often lead to only marginal improvements. In this paper, we propose a novel self-supervised learning strategy based on context restoration in order to better exploit unlabelled images. The context restoration strategy has three major features: 1) it learns semantic image features; 2) these image features are useful for different types of subsequent image analysis tasks; and 3) its implementation is simple. We validate the context restoration strategy in three common problems in medical imaging: classification, localization, and segmentation. For classification, we apply and test it to scan plane detection in fetal 2D ultrasound images; to localise abdominal organs in CT images; and to segment brain tumours in multi-modal MR images. In all three cases, self-supervised learning based on context restoration learns useful semantic features and lead to improved machine learning models for the above tasks.

Journal article

Jaubert O, Cruz G, Bustin A, Schneider T, Lavin B, Koken P, Hajhosseiny R, Doneva M, Rueckert D, Botnar RM, Prieto Cet al., 2019, Water-fat Dixon cardiac magnetic resonance fingerprinting, MAGNETIC RESONANCE IN MEDICINE, ISSN: 0740-3194

Journal article

Leiner T, Rueckert D, Suinesiaputra A, Baessler B, Nezafat R, Isgum I, Young AAet al., 2019, Machine learning in cardiovascular magnetic resonance: basic concepts and applications, JOURNAL OF CARDIOVASCULAR MAGNETIC RESONANCE, Vol: 21, ISSN: 1097-6647

Journal article

Bhuva AN, Bai W, Lau C, Davies RH, Ye Y, Bulluck H, McAlindon E, Culotta V, Swoboda PP, Captur G, Treibel TA, Augusto JB, Knott KD, Seraphim A, Cole GD, Petersen SE, Edwards NC, Greenwood JP, Bucciarelli-Ducci C, Hughes AD, Rueckert D, Moon JC, Manisty CHet al., 2019, A multicenter, scan-rescan, human and machine learning CMR study to test generalizability and precision in imaging biomarker analysis, Circulation: Cardiovascular Imaging, Vol: 12, Pages: 1-11, ISSN: 1941-9651

Background:Automated analysis of cardiac structure and function using machine learning (ML) has great potential, but is currently hindered by poor generalizability. Comparison is traditionally against clinicians as a reference, ignoring inherent human inter- and intraobserver error, and ensuring that ML cannot demonstrate superiority. Measuring precision (scan:rescan reproducibility) addresses this. We compared precision of ML and humans using a multicenter, multi-disease, scan:rescan cardiovascular magnetic resonance data set.Methods:One hundred ten patients (5 disease categories, 5 institutions, 2 scanner manufacturers, and 2 field strengths) underwent scan:rescan cardiovascular magnetic resonance (96% within one week). After identification of the most precise human technique, left ventricular chamber volumes, mass, and ejection fraction were measured by an expert, a trained junior clinician, and a fully automated convolutional neural network trained on 599 independent multicenter disease cases. Scan:rescan coefficient of variation and 1000 bootstrapped 95% CIs were calculated and compared using mixed linear effects models.Results:Clinicians can be confident in detecting a 9% change in left ventricular ejection fraction, with greater than half of coefficient of variation attributable to intraobserver variation. Expert, trained junior, and automated scan:rescan precision were similar (for left ventricular ejection fraction, coefficient of variation 6.1 [5.2%–7.1%], P=0.2581; 8.3 [5.6%–10.3%], P=0.3653; 8.8 [6.1%–11.1%], P=0.8620). Automated analysis was 186× faster than humans (0.07 versus 13 minutes).Conclusions:Automated ML analysis is faster with similar precision to the most precise human techniques, even when challenged with real-world scan:rescan data. Assessment of multicenter, multi-vendor, multi-field strength scan:rescan data (available at www.thevolumesresource.com) permits a generalizable assessment of ML precision and may facili

Journal article

Ktena SI, Schirmer MD, Etherton MR, Giese A-K, Tuozzo C, Mills BB, Rueckert D, Wu O, Rost NSet al., 2019, Brain Connectivity Measures Improve Modeling of Functional Outcome After Acute Ischemic Stroke, STROKE, Vol: 50, Pages: 2761-2767, ISSN: 0039-2499

Journal article

Chen C, Biffi C, Tarroni G, Petersen S, Bai W, Rueckert Det al., 2019, Learning shape priors for robust cardiac MR segmentation from multi-view images, International Conference on Medical Image Computing and Computer-Assisted Intervention, Publisher: Springer International Publishing, Pages: 523-531, ISSN: 0302-9743

Cardiac MR image segmentation is essential for the morphological and functional analysis of the heart. Inspired by how experienced clinicians assess the cardiac morphology and function across multiple standard views (i.e. long- and short-axis views), we propose a novel approach which learns anatomical shape priors across different 2D standard views and leverages these priors to segment the left ventricular (LV) myocardium from short-axis MR image stacks. The proposed segmentation method has the advantage of being a 2D network but at the same time incorporates spatial context from multiple, complementary views that span a 3D space. Our method achieves accurate and robust segmentation of the myocardium across different short-axis slices (from apex to base), outperforming baseline models (e.g. 2D U-Net, 3D U-Net) while achieving higher data efficiency. Compared to the 2D U-Net, the proposed method reduces the mean Hausdorff distance (mm) from 3.24 to 2.49 on the apical slices, from 2.34 to 2.09 on the middle slices and from 3.62 to 2.76 on the basal slices on the test set, when only 10% of the training data was used.

Conference paper

Steyerberg EW, Wiegers E, Sewalt C, Buki A, Citerio G, De Keyser V, Ercole A, Kunzmann K, Lanyon L, Lecky F, Lingsma H, Manley G, Nelson D, Peul W, Stocchetti N, von Steinbüchel N, Vande Vyvere T, Verheyden J, Wilson L, Maas AIR, Menon DK, CENTER-TBI Participants and Investigatorset al., 2019, Case-mix, care pathways, and outcomes in patients with traumatic brain injury in CENTER-TBI: a European prospective, multicentre, longitudinal, cohort study., Lancet Neurol, Vol: 18, Pages: 923-934

BACKGROUND: The burden of traumatic brain injury (TBI) poses a large public health and societal problem, but the characteristics of patients and their care pathways in Europe are poorly understood. We aimed to characterise patient case-mix, care pathways, and outcomes of TBI. METHODS: CENTER-TBI is a Europe-based, observational cohort study, consisting of a core study and a registry. Inclusion criteria for the core study were a clinical diagnosis of TBI, presentation fewer than 24 h after injury, and an indication for CT. Patients were differentiated by care pathway and assigned to the emergency room (ER) stratum (patients who were discharged from an emergency room), admission stratum (patients who were admitted to a hospital ward), or intensive care unit (ICU) stratum (patients who were admitted to the ICU). Neuroimages and biospecimens were stored in repositories and outcome was assessed at 6 months after injury. We used the IMPACT core model for estimating the expected mortality and proportion with unfavourable Glasgow Outcome Scale Extended (GOSE) outcomes in patients with moderate or severe TBI (Glasgow Coma Scale [GCS] score ≤12). The core study was registered with ClinicalTrials.gov, number NCT02210221, and with Resource Identification Portal (RRID: SCR_015582). FINDINGS: Data from 4509 patients from 18 countries, collected between Dec 9, 2014, and Dec 17, 2017, were analysed in the core study and from 22 782 patients in the registry. In the core study, 848 (19%) patients were in the ER stratum, 1523 (34%) in the admission stratum, and 2138 (47%) in the ICU stratum. In the ICU stratum, 720 (36%) patients had mild TBI (GCS score 13-15). Compared with the core cohort, the registry had a higher proportion of patients in the ER (9839 [43%]) and admission (8571 [38%]) strata, with more than 95% of patients classified as having mild TBI. Patients in the core study were older than those in previous studies (median age 50 years [IQR 30-66], 1254 [28%] aged >65

Journal article

Balaban G, Halliday BP, Bai W, Porter B, Malvuccio C, Lamata P, Rinaldi CA, Plank G, Rueckert D, Prasad SK, Bishop MJet al., 2019, Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort., PLoS Computational Biology, Vol: 15, Pages: 1-18, ISSN: 1553-734X

This paper presents a morphological analysis of fibrotic scarring in non-ischemic dilated cardiomyopathy, and its relationship to electrical instabilities which underlie reentrant arrhythmias. Two dimensional electrophysiological simulation models were constructed from a set of 699 late gadolinium enhanced cardiac magnetic resonance images originating from 157 patients. Areas of late gadolinium enhancement (LGE) in each image were assigned one of 10 possible microstructures, which modelled the details of fibrotic scarring an order of magnitude below the MRI scan resolution. A simulated programmed electrical stimulation protocol tested each model for the possibility of generating either a transmural block or a transmural reentry. The outcomes of the simulations were compared against morphological LGE features extracted from the images. Models which blocked or reentered, grouped by microstructure, were significantly different from one another in myocardial-LGE interface length, number of components and entropy, but not in relative area and transmurality. With an unknown microstructure, transmurality alone was the best predictor of block, whereas a combination of interface length, transmurality and number of components was the best predictor of reentry in linear discriminant analysis.

Journal article

Monteiro M, Kamnitsas K, Ferrante E, Mathieu F, McDonagh S, Cook S, Stevenson S, Das T, Khetani A, Newman T, Zeiler F, Digby R, Coles J, Rueckert D, Menon D, Newcombe V, Glocker Bet al., 2019, TBI lesion segmentation in head CT: impact of preprocessing and data augmentation, MICCAI Brain Lesion Workshop, Publisher: Springer Verlag, ISSN: 0302-9743

Automatic segmentation of lesions in head CT provides keyinformation for patient management, prognosis and disease monitoring.Despite its clinical importance, method development has mostly focusedon multi-parametric MRI. Analysis of the brain in CT is challengingdue to limited soft tissue contrast and its mono-modal nature. We studythe under-explored problem of fine-grained CT segmentation of multiplelesion types (core, blood, oedema) in traumatic brain injury (TBI). Weobserve that preprocessing and data augmentation choices greatly impactthe segmentation accuracy of a neural network, yet these factors arerarely thoroughly assessed in prior work. We design an empirical studythat extensively evaluates the impact of different data preprocessing andaugmentation methods. We show that these choices can have an impactof up to 18% DSC. We conclude that resampling to isotropic resolutionyields improved performance, skull-stripping can be replaced by using theright intensity window, and affine-to-atlas registration is not necessaryif we use sufficient spatial augmentation. Since both skull-stripping andaffine-to-atlas registration are susceptible to failure, we recommend theiralternatives to be used in practice. We believe this is the first work toreport results for fine-grained multi-class segmentation of TBI in CT. Ourfindings may inform further research in this under-explored yet clinicallyimportant task of automatic head CT lesion segmentation.

Conference paper

Duan J, Schlemper J, Qin C, Ouyang C, Bai W, Biffi C, Bello G, Statton B, O’Regan DP, Rueckert Det al., 2019, VS-Net: variable splitting network for accelerated parallel MRI reconstruction, International Conference on Medical Image Computing and Computer-Assisted Intervention, Publisher: Springer International Publishing, Pages: 713-722, ISSN: 0302-9743

In this work, we propose a deep learning approach for parallel magnetic resonance imaging (MRI) reconstruction, termed a variable splitting network (VS-Net), for an efficient, high-quality reconstruction of undersampled multi-coil MR data. We formulate the generalized parallel compressed sensing reconstruction as an energy minimization problem, for which a variable splitting optimization method is derived. Based on this formulation we propose a novel, end-to-end trainable deep neural network architecture by unrolling the resulting iterative process of such variable splitting scheme. VS-Net is evaluated on complex valued multi-coil knee images for 4-fold and 6-fold acceleration factors. We show that VS-Net outperforms state-of-the-art deep learning reconstruction algorithms, in terms of reconstruction accuracy and perceptual quality. Our code is publicly available at https://github.com/j-duan/VS-Net.

Conference paper

Duan J, Bello G, Schlemper J, Bai W, Dawes TJW, Biffi C, Marvao AD, Doumou G, O'Regan DP, Rueckert Det al., 2019, Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach, IEEE Transactions on Medical Imaging, Vol: 38, Pages: 2151-2164, ISSN: 0278-0062

Deep learning approaches have achieved state-of-the-art performance incardiac magnetic resonance (CMR) image segmentation. However, most approaches have focused on learning image intensity features for segmentation, whereas the incorporation of anatomical shape priors has received less attention. In this paper, we combine a multi-task deep learning approach with atlas propagation to develop a shape-constrained bi-ventricular segmentation pipeline for short-axis CMR volumetric images. The pipeline first employs a fully convolutional network (FCN) that learns segmentation and landmark localisation tasks simultaneously. The architecture of the proposed FCN uses a 2.5D representation, thus combining the computational advantage of 2D FCNs networks and the capability of addressing 3D spatial consistency without compromising segmentation accuracy. Moreover, the refinement step is designed to explicitly enforce a shape constraint and improve segmentation quality. This step is effective for overcoming image artefacts (e.g. due to different breath-hold positions and large slice thickness), which preclude the creation of anatomically meaningful 3D cardiac shapes. The proposed pipeline is fully automated, due to network's ability to infer landmarks, which are then used downstream in the pipeline to initialise atlas propagation. We validate the pipeline on 1831 healthy subjects and 649 subjects with pulmonary hypertension. Extensive numerical experiments on the two datasets demonstrate that our proposed method is robust and capable of producing accurate, high-resolution and anatomically smooth bi-ventricular3D models, despite the artefacts in input CMR volumes.

Journal article

Cerrolaza JJ, Lopez Picazo M, Humbert L, Sato Y, Rueckert D, Gonzalez Ballester MA, Linguraru MGet al., 2019, Computational anatomy for multi-organ analysis in medical imaging: A review, MEDICAL IMAGE ANALYSIS, Vol: 56, Pages: 44-67, ISSN: 1361-8415

Journal article

Xavier IRR, Giraldi GA, Gibson SJ, Gattas GJF, Rueckert D, Thomaz CEet al., 2019, Age-related craniofacial differences based on spatio-temporal face image atlases, IET IMAGE PROCESSING, Vol: 13, Pages: 1561-1568, ISSN: 1751-9659

Journal article

Biffi C, Cerrolaza JJ, Tarroni G, de Marvao A, Cook SA, O'Regan DP, Rueckert Det al., 2019, 3D high-resolution cardiac segmentation reconstruction from 2D views using conditional variational autoencoders, 16th IEEE International Symposium on Biomedical Imaging (ISBI), Publisher: IEEE, Pages: 1643-1646, ISSN: 1945-7928

Accurate segmentation of heart structures imaged by cardiac MR is key for the quantitative analysis of pathology. High-resolution 3D MR sequences enable whole-heart structural imaging but are time-consuming, expensive to acquire and they often require long breath holds that are not suitable for patients. Consequently, multiplanar breath-hold 2D cines sequences are standard practice but are disadvantaged by lack of whole-heart coverage and low through-plane resolution. To address this, we propose a conditional variational autoencoder architecture able to learn a generative model of 3D high-resolution left ventricular (LV) segmentations which is conditioned on three 2D LV segmentations of one short-axis and two long-axis images. By only employing these three 2D segmentations, our model can efficiently reconstruct the 3D high-resolution LV segmentation of a subject. When evaluated on 400 unseen healthy volunteers, our model yielded an average Dice score of 87.92 ± 0.15 and outperformed competing architectures (TL-net, Dice score = 82.60 ± 0.23, p = 2.2 · 10 -16 ).

Conference paper

Bai W, Chen C, Tarroni G, Duan J, Guitton F, Petersen SE, Guo Y, Matthews PM, Rueckert Det al., 2019, Self-supervised learning for cardiac MR image segmentation by anatomicalposition prediction, International Conference on Medical Image Computing and Computer Assisted Intervention, Publisher: Springer

In the recent years, convolutional neural networks have transformed the field of medical image analysis due to their capacity to learn discriminative image features for a variety of classification and regression tasks. However, successfully learning these features requires a large amount of manuallyannotated data, which is expensive to acquire and limited by the availableresources of expert image analysts. Therefore, unsupervised, weakly-supervised and self-supervised feature learning techniques receive a lot of attention, which aim to utilise the vast amount of available data, while at the same time avoid or substantially reduce the effort of manual annotation. In this paper, we propose a novel way for training a cardiac MR image segmentation network, in which features are learnt in a self-supervised manner by predicting anatomical positions. The anatomical positions serve as a supervisory signal and do not require extra manual annotation. We demonstrate that this seemingly simple task provides a strong signal for feature learning and with self-supervised learning, we achieve a high segmentation accuracy that is better than or comparable to a U-net trained from scratch, especially at a small data setting. When only five annotated subjects are available, the proposed method improves the mean Dice metric from 0.811 to 0.852 for short-axis image segmentation, compared to the baseline U-net.

Conference paper

Oksuz I, Ruijsink B, Puyol-Anton E, Clough JR, Cruz G, Bustin A, Prieto C, Botnar R, Rueckert D, Schnabel JA, King APet al., 2019, Automatic CNN-based detection of cardiac MR motion artefacts using k-space data augmentation and curriculum learning, MEDICAL IMAGE ANALYSIS, Vol: 55, Pages: 136-147, ISSN: 1361-8415

Journal article

Tournier J-D, Christiaens D, Hutter J, Price AN, Cordero-Grande L, Hughes E, Bastiani M, Sotiropoulos SN, Smith SM, Rueckert D, Counsell SJ, Edwards AD, Hajnal JVet al., 2019, A data-driven approach to optimising the encoding for multi-shell diffusion MRI with application to neonatal imaging

<jats:title>Abstract</jats:title><jats:p>Diffusion MRI has the potential to provide important information about the connectivity and microstructure of the human brain during normal and abnormal development, non-invasively and in vivo. Recent developments in MRI hardware and reconstruction methods now permit the acquisition of large amounts of data within relatively short scan times. This makes it possible to acquire more informative multi-shell data, with diffusion-sensitisation applied along many directions over multiple <jats:italic>b</jats:italic>-value shells. Such schemes are characterised by the number of shells acquired, and the specific <jats:italic>b</jats:italic>-value and number of directions sampled for each shell. However, there is currently no clear consensus as to how to optimise these parameters. In this work, we propose a means of optimising multi-shell acquisition schemes by estimating the information content of the diffusion MRI signal, and optimising the acquisition parameters for sensitivity to the observed effects, in a manner agnostic to any particular diffusion analysis method that might subsequently be applied to the data. This method was used to design the acquisition scheme for the neonatal diffusion MRI sequence used in the developing Human Connectome Project, which aims to acquire high quality data and make it freely available to the research community. The final protocol selected by the algorithm, and currently in use within the dHCP, consists of <jats:italic>b =</jats:italic> 0, 400, 1000, 2600 s/mm<jats:sup>2</jats:sup> with 20, 64, 88 &amp; 128 DW directions per shell respectively.</jats:p><jats:sec><jats:title>Highlights</jats:title><jats:list list-type="bullet"><jats:list-item><jats:p>A data driven method is presented to design multi-shell diffusion MRI acquisition schemes (<jats:italic>b</jats:italic&g

Journal article

Attard M, Dawes T, Simoes Monteiro de Marvao A, Biffi C, Shi W, Wharton J, Rhodes C, Ghataorhe P, Gibbs J, Howard L, Rueckert D, Wilkins M, O'Regan Det al., 2019, Metabolic pathways associated with right ventricular adaptation to pulmonary hypertension: Three dimensional analysis of cardiac magnetic resonance imaging, EHJ Cardiovascular Imaging / European Heart Journal - Cardiovascular Imaging, Vol: 20, Pages: 668-676, ISSN: 2047-2412

AimsWe sought to identify metabolic pathways associated with right ventricular (RV) adaptation to pulmonary hypertension (PH). We evaluated candidate metabolites, previously associated with survival in pulmonary arterial hypertension, and used automated image segmentation and parametric mapping to model their relationship to adverse patterns of remodelling and wall stress.Methods and resultsIn 312 PH subjects (47.1% female, mean age 60.8 ± 15.9 years), of which 182 (50.5% female, mean age 58.6 ± 16.8 years) had metabolomics, we modelled the relationship between the RV phenotype, haemodynamic state, and metabolite levels. Atlas-based segmentation and co-registration of cardiac magnetic resonance imaging was used to create a quantitative 3D model of RV geometry and function—including maps of regional wall stress. Increasing mean pulmonary artery pressure was associated with hypertrophy of the basal free wall (β = 0.29) and reduced relative wall thickness (β = −0.38), indicative of eccentric remodelling. Wall stress was an independent predictor of all-cause mortality (hazard ratio = 1.27, P = 0.04). Six metabolites were significantly associated with elevated wall stress (β = 0.28–0.34) including increased levels of tRNA-specific modified nucleosides and fatty acid acylcarnitines, and decreased levels (β = −0.40) of sulfated androgen.ConclusionUsing computational image phenotyping, we identify metabolic profiles, reporting on energy metabolism and cellular stress-response, which are associated with adaptive RV mechanisms to PH.

Journal article

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