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  • Conference paper
    Sridharan S, Raffel J, Nandoskar A, Record C, Brooks D, Owen D, Sharp D, Muraro P, Gunn R, Nicholas Ret al., 2018,

    Confirmation of specific binding of the 18 kDa translocator protein (TSPO) radioligand [F-18]GE-180: a blocking study using XDB173 in multiple sclerosis

    , 34th Congress of the European-Committee-for-Treatment-and-Research-in-Multiple-Sclerosis (ECTRIMS), Publisher: SAGE PUBLICATIONS LTD, Pages: 421-422, ISSN: 1352-4585
  • Journal article
    Grant JE, Daws R, Hampshire A, Chamberlain SRet al., 2018,

    An fMRI Pilot Study of Cognitive Flexibility in Trichotillomania.

    , J Neuropsychiatry Clin Neurosci, Vol: 30, Pages: 318-324

    Trichotillomania is a relatively common psychiatric condition, although its neurobiological basis is unknown. Abnormalities of flexible responding have been implicated in the pathophysiology of obsessive-compulsive disorder and thus may be relevant in trichotillomania. The purpose of this study was to probe reversal learning and attentional set-shifting in trichotillomania. Twelve adults with trichotillomania and 13 matched healthy control subjects undertook a functional MRI task of cognitive flexibility. Group-level activation maps for extradimensional and reversal switches were independently parcellated into discrete regions of interest using a custom watershed algorithm. Activation magnitudes were extracted from each region of interest and study subject and compared at the group level. Reversal events evoked the expected patterns of insula and parietal regions and activity in the frontal dorsal cortex extending anterior to the frontal poles, whereas extradimensional shifts evoked the expected frontal dorsolateral and parietal pattern of activity. Trichotillomania was associated with significantly increased right middle frontal and reduced right occipital cortex activation during reversal and set-shifting. Elevated frontal activation coupled with reduced activation in more posterior brain regions was identified. These pilot data suggest potentially important neural dysfunction associated with trichotillomania.

  • Conference paper
    Alansary A, Le Folgoc L, Vaillant G, Oktay O, Li Y, Bai W, Passerat-Palmbach J, Guerrero R, Kamnitsas K, Hou B, McDonagh S, Glocker B, Kainz B, Rueckert Det al., 2018,

    Automatic view planning with multi-scale deep reinforcement learning agents

    , International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Publisher: Springer Verlag, Pages: 277-285, ISSN: 0302-9743

    We propose a fully automatic method to find standardizedview planes in 3D image acquisitions. Standard view images are impor-tant in clinical practice as they provide a means to perform biometricmeasurements from similar anatomical regions. These views are often constrained to the native orientation of a 3D image acquisition. Navigating through target anatomy to find the required view plane is tedious and operator-dependent. For this task, we employ a multi-scale reinforcement learning (RL) agent framework and extensively evaluate several DeepQ-Network (DQN) based strategies. RL enables a natural learning paradigm by interaction with the environment, which can be used to mimic experienced operators. We evaluate our results using the distance between the anatomical landmarks and detected planes, and the angles between their normal vector and target. The proposed algorithm is assessed on the mid-sagittal and anterior-posterior commissure planes of brain MRI, and the 4-chamber long-axis plane commonly used in cardiac MRI, achieving accuracy of 1.53mm, 1.98mm and 4.84mm, respectively.

  • Conference paper
    Tarroni G, Oktay O, Sinclair M, Bai W, Schuh A, Suzuki H, de Marvao A, O'Regan D, Cook S, Rueckert Det al., 2018,

    A comprehensive approach for learning-based fully-automated inter-slice motion correction for short-axis cine cardiac MR image stacks

    , 21st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI) / 8th Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), Publisher: SPRINGER INTERNATIONAL PUBLISHING AG, Pages: 268-276, ISSN: 0302-9743

    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.

  • Conference paper
    Schlemper J, Castro DC, Bai W, Qin C, Oktay O, Duan J, Price AN, Hajnal J, Rueckert Det 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.

  • Conference paper
    Biffi C, Oktay O, Tarroni G, Bai W, De Marvao A, Doumou G, Rajchl M, Bedair R, Prasad S, Cook S, O’Regan D, Rueckert Det al., 2018,

    Learning interpretable anatomical features through deep generative models: Application to cardiac remodeling

    , International Conference On Medical Image Computing & Computer Assisted Intervention, Publisher: Springer, Pages: 464-471, ISSN: 0302-9743

    Alterations in the geometry and function of the heart define well-established causes of cardiovascular disease. However, current approaches to the diagnosis of cardiovascular diseases often rely on subjective human assessment as well as manual analysis of medical images. Both factors limit the sensitivity in quantifying complex structural and functional phenotypes. Deep learning approaches have recently achieved success for tasks such as classification or segmentation of medical images, but lack interpretability in the feature extraction and decision processes, limiting their value in clinical diagnosis. In this work, we propose a 3D convolutional generative model for automatic classification of images from patients with cardiac diseases associated with structural remodeling. The model leverages interpretable task-specific anatomic patterns learned from 3D segmentations. It further allows to visualise and quantify the learned pathology-specific remodeling patterns in the original input space of the images. This approach yields high accuracy in the categorization of healthy and hypertrophic cardiomyopathy subjects when tested on unseen MR images from our own multi-centre dataset (100%) as well on the ACDC MICCAI 2017 dataset (90%). We believe that the proposed deep learning approach is a promising step towards the development of interpretable classifiers for the medical imaging domain, which may help clinicians to improve diagnostic accuracy and enhance patient risk-stratification.

  • Conference paper
    Qin C, Bai W, Schlemper J, Petersen SE, Piechnik SK, Neubauer S, Rueckert Det 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.

  • Conference paper
    Schlemper J, Oktay O, Bai W, Castro DC, Duan J, Qin C, Hajnal JV, Rueckert Det 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.

  • Conference paper
    Qin C, Bai W, Schlemper J, Petersen SE, Piechnik SK, Neubauer S, Rueckert Det 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.

  • Conference paper
    Robinson R, Oktay O, Bai W, Valindria V, Sanghvi MM, Aung N, Paiva JM, Zemrak F, Fung K, Lukaschuk E, Lee AM, Carapella V, Kim YJ, Kainz B, Piechnik SK, Neubauer S, Petersen SE, Page C, Rueckert D, Glocker Bet 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.

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