241 research outputs found
Autoadaptive motion modelling for MR-based respiratory motion estimation
© 2016 The Authors.Respiratory motion poses significant challenges in image-guided interventions. In emerging treatments such as MR-guided HIFU or MR-guided radiotherapy, it may cause significant misalignments between interventional road maps obtained pre-procedure and the anatomy during the treatment, and may affect intra-procedural imaging such as MR-thermometry. Patient specific respiratory motion models provide a solution to this problem. They establish a correspondence between the patient motion and simpler surrogate data which can be acquired easily during the treatment. Patient motion can then be estimated during the treatment by acquiring only the simpler surrogate data.In the majority of classical motion modelling approaches once the correspondence between the surrogate data and the patient motion is established it cannot be changed unless the model is recalibrated. However, breathing patterns are known to significantly change in the time frame of MR-guided interventions. Thus, the classical motion modelling approach may yield inaccurate motion estimations when the relation between the motion and the surrogate data changes over the duration of the treatment and frequent recalibration may not be feasible.We propose a novel methodology for motion modelling which has the ability to automatically adapt to new breathing patterns. This is achieved by choosing the surrogate data in such a way that it can be used to estimate the current motion in 3D as well as to update the motion model. In particular, in this work, we use 2D MR slices from different slice positions to build as well as to apply the motion model. We implemented such an autoadaptive motion model by extending our previous work on manifold alignment.We demonstrate a proof-of-principle of the proposed technique on cardiac gated data of the thorax and evaluate its adaptive behaviour on realistic synthetic data containing two breathing types generated from 6 volunteers, and real data from 4 volunteers. On synthetic data the autoadaptive motion model yielded 21.45% more accurate motion estimations compared to a non-adaptive motion model 10 min after a change in breathing pattern. On real data we demonstrated the methods ability to maintain motion estimation accuracy despite a drift in the respiratory baseline. Due to the cardiac gating of the imaging data, the method is currently limited to one update per heart beat and the calibration requires approximately 12 min of scanning. Furthermore, the method has a prediction latency of 800 ms. These limitations may be overcome in future work by altering the acquisition protocol
Deep Learning using K-space Based Data Augmentation for Automated Cardiac MR Motion Artefact Detection
Quality assessment of medical images is essential for complete automation of
image processing pipelines. For large population studies such as the UK
Biobank, artefacts such as those caused by heart motion are problematic and
manual identification is tedious and time-consuming. Therefore, there is an
urgent need for automatic image quality assessment techniques. In this paper,
we propose a method to automatically detect the presence of motion-related
artefacts in cardiac magnetic resonance (CMR) images. As this is a highly
imbalanced classification problem (due to the high number of good quality
images compared to the low number of images with motion artefacts), we propose
a novel k-space based training data augmentation approach in order to address
this problem. Our method is based on 3D spatio-temporal Convolutional Neural
Networks, and is able to detect 2D+time short axis images with motion artefacts
in less than 1ms. We test our algorithm on a subset of the UK Biobank dataset
consisting of 3465 CMR images and achieve not only high accuracy in detection
of motion artefacts, but also high precision and recall. We compare our
approach to a range of state-of-the-art quality assessment methods.Comment: Accepted for MICCAI2018 Conferenc
Self-supervised Contrastive Video-Speech Representation Learning for Ultrasound
In medical imaging, manual annotations can be expensive to acquire and
sometimes infeasible to access, making conventional deep learning-based models
difficult to scale. As a result, it would be beneficial if useful
representations could be derived from raw data without the need for manual
annotations. In this paper, we propose to address the problem of
self-supervised representation learning with multi-modal ultrasound
video-speech raw data. For this case, we assume that there is a high
correlation between the ultrasound video and the corresponding narrative speech
audio of the sonographer. In order to learn meaningful representations, the
model needs to identify such correlation and at the same time understand the
underlying anatomical features. We designed a framework to model the
correspondence between video and audio without any kind of human annotations.
Within this framework, we introduce cross-modal contrastive learning and an
affinity-aware self-paced learning scheme to enhance correlation modelling.
Experimental evaluations on multi-modal fetal ultrasound video and audio show
that the proposed approach is able to learn strong representations and
transfers well to downstream tasks of standard plane detection and eye-gaze
prediction.Comment: MICCAI 2020 (early acceptance
Uncertainty quantification in medical image segmentation with normalizing flows
Medical image segmentation is inherently an ambiguous task due to factors
such as partial volumes and variations in anatomical definitions. While in most
cases the segmentation uncertainty is around the border of structures of
interest, there can also be considerable inter-rater differences. The class of
conditional variational autoencoders (cVAE) offers a principled approach to
inferring distributions over plausible segmentations that are conditioned on
input images. Segmentation uncertainty estimated from samples of such
distributions can be more informative than using pixel level probability
scores. In this work, we propose a novel conditional generative model that is
based on conditional Normalizing Flow (cFlow). The basic idea is to increase
the expressivity of the cVAE by introducing a cFlow transformation step after
the encoder. This yields improved approximations of the latent posterior
distribution, allowing the model to capture richer segmentation variations.
With this we show that the quality and diversity of samples obtained from our
conditional generative model is enhanced. Performance of our model, which we
call cFlow Net, is evaluated on two medical imaging datasets demonstrating
substantial improvements in both qualitative and quantitative measures when
compared to a recent cVAE based model.Comment: 12 pages. Accepted to be presented at 11th International Workshop on
Machine Learning in Medical Imaging. Source code will be updated at
https://github.com/raghavian/cFlo
Disentangled Representations for Domain-generalized Cardiac Segmentation
Robust cardiac image segmentation is still an open challenge due to the
inability of the existing methods to achieve satisfactory performance on unseen
data of different domains. Since the acquisition and annotation of medical data
are costly and time-consuming, recent work focuses on domain adaptation and
generalization to bridge the gap between data from different populations and
scanners. In this paper, we propose two data augmentation methods that focus on
improving the domain adaptation and generalization abilities of
state-to-the-art cardiac segmentation models. In particular, our "Resolution
Augmentation" method generates more diverse data by rescaling images to
different resolutions within a range spanning different scanner protocols.
Subsequently, our "Factor-based Augmentation" method generates more diverse
data by projecting the original samples onto disentangled latent spaces, and
combining the learned anatomy and modality factors from different domains. Our
extensive experiments demonstrate the importance of efficient adaptation
between seen and unseen domains, as well as model generalization ability, to
robust cardiac image segmentation.Comment: Accepted by STACOM 202
Surface agnostic metrics for cortical volume segmentation and regression
The cerebral cortex performs higher-order brain functions and is thus implicated in a range of cognitive disorders. Current analysis of cortical variation is typically performed by fitting surface mesh models to inner and outer cortical boundaries and investigating metrics such as surface area and cortical curvature or thickness. These, however, take a long time to run, and are sensitive to motion and image and surface resolution, which can prohibit their use in clinical settings. In this paper, we instead propose a machine learning solution, training a novel architecture to predict cortical thickness and curvature metrics from T2 MRI images, while additionally returning metrics of prediction uncertainty. Our proposed model is tested on a clinical cohort (Down Syndrome) for which surface-based modelling often fails. Results suggest that deep convolutional neural networks are a viable option to predict cortical metrics across a range of brain development stages and pathologies
Compare and Contrast: How to Assess the Completeness of Mechanistic Explanation
Opponents of the new mechanistic account of scientific explanation argue that the new mechanists are committed to a ‘More Details Are Better’ claim: adding details about the mechanism always improves an explanation. Due to this commitment, the mechanistic account cannot be descriptively adequate as actual scientific explanations usually leave out details about the mechanism. In reply to this objection, defenders of the new mechanistic account have highlighted that only adding relevant mechanistic details improves an explanation and that relevance is to be determined relative to the phenomenon-to-be-explained. Craver and Kaplan (B J Philos Sci 71:287–319, 2020) provide a thorough reply along these lines specifying that the phenomena at issue are contrasts. In this paper, we will discuss Craver and Kaplan’s reply. We will argue that it needs to be modified in order to avoid three problems, i.e., what we will call the Odd Ontology Problem, the Multiplication of Mechanisms Problem, and the Ontic Completeness Problem. However, even this modification is confronted with two challenges: First, it remains unclear how explanatory relevance is to be determined for contrastive explananda within the mechanistic framework. Second, it remains to be shown as to how the new mechanistic account can avoid what we will call the ‘Vertical More Details are Better’ objection. We will provide answers to both challenges
Automated detection of congenital heart disease in fetal ultrasound screening
Prenatal screening with ultrasound can lower neonatal mortality significantly for selected cardiac abnormalities. However, the need for human expertise, coupled with the high volume of screening cases, limits the practically achievable detection rates. In this paper we discuss the potential for deep learning techniques to aid in the detection of congenital heart disease (CHD) in fetal ultrasound. We propose a pipeline for automated data curation and classification. During both training and inference, we exploit an auxiliary view classification task to bias features toward relevant cardiac structures. This bias helps to improve in F1-scores from 0.72 and 0.77 to 0.87 and 0.85 for healthy and CHD classes respectively
Combining Multi-Sequence and Synthetic Images for Improved Segmentation of Late Gadolinium Enhancement Cardiac MRI
© Springer Nature Switzerland AG 2020. Accurate segmentation of the cardiac boundaries in late gadolinium enhancement magnetic resonance images (LGE-MRI) is a fundamental step for accurate quantification of scar tissue. However, while there are many solutions for automatic cardiac segmentation of cine images, the presence of scar tissue can make the correct delineation of the myocardium in LGE-MRI challenging even for human experts. As part of the Multi-Sequence Cardiac MR Segmentation Challenge, we propose a solution for LGE-MRI segmentation based on two components. First, a generative adversarial network is trained for the task of modality-to-modality translation between cine and LGE-MRI sequences to obtain extra synthetic images for both modalities. Second, a deep learning model is trained for segmentation with different combinations of original, augmented and synthetic sequences. Our results based on three magnetic resonance sequences (LGE, bSSFP and T2) from 45 different patients show that the multi-sequence model training integrating synthetic images and data augmentation improves in the segmentation over conventional training with real datasets. In conclusion, the accuracy of the segmentation of LGE-MRI images can be improved by using complementary information provided by non-contrast MRI sequences
Automatic Probe Movement Guidance for Freehand Obstetric Ultrasound
We present the first system that provides real-time probe movement guidance
for acquiring standard planes in routine freehand obstetric ultrasound
scanning. Such a system can contribute to the worldwide deployment of obstetric
ultrasound scanning by lowering the required level of operator expertise. The
system employs an artificial neural network that receives the ultrasound video
signal and the motion signal of an inertial measurement unit (IMU) that is
attached to the probe, and predicts a guidance signal. The network termed
US-GuideNet predicts either the movement towards the standard plane position
(goal prediction), or the next movement that an expert sonographer would
perform (action prediction). While existing models for other ultrasound
applications are trained with simulations or phantoms, we train our model with
real-world ultrasound video and probe motion data from 464 routine clinical
scans by 17 accredited sonographers. Evaluations for 3 standard plane types
show that the model provides a useful guidance signal with an accuracy of 88.8%
for goal prediction and 90.9% for action prediction.Comment: Accepted at the 23rd International Conference on Medical Image
Computing and Computer Assisted Intervention (MICCAI 2020
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