70 research outputs found
DeepMesh: Mesh-based Cardiac Motion Tracking using Deep Learning
3D motion estimation from cine cardiac magnetic resonance (CMR) images is
important for the assessment of cardiac function and the diagnosis of
cardiovascular diseases. Current state-of-the art methods focus on estimating
dense pixel-/voxel-wise motion fields in image space, which ignores the fact
that motion estimation is only relevant and useful within the anatomical
objects of interest, e.g., the heart. In this work, we model the heart as a 3D
mesh consisting of epi- and endocardial surfaces. We propose a novel learning
framework, DeepMesh, which propagates a template heart mesh to a subject space
and estimates the 3D motion of the heart mesh from CMR images for individual
subjects. In DeepMesh, the heart mesh of the end-diastolic frame of an
individual subject is first reconstructed from the template mesh. Mesh-based 3D
motion fields with respect to the end-diastolic frame are then estimated from
2D short- and long-axis CMR images. By developing a differentiable
mesh-to-image rasterizer, DeepMesh is able to leverage 2D shape information
from multiple anatomical views for 3D mesh reconstruction and mesh motion
estimation. The proposed method estimates vertex-wise displacement and thus
maintains vertex correspondences between time frames, which is important for
the quantitative assessment of cardiac function across different subjects and
populations. We evaluate DeepMesh on CMR images acquired from the UK Biobank.
We focus on 3D motion estimation of the left ventricle in this work.
Experimental results show that the proposed method quantitatively and
qualitatively outperforms other image-based and mesh-based cardiac motion
tracking methods
Automatic 3D bi-ventricular segmentation of cardiac images by a shape-refined multi-task deep learning approach
Deep learning approaches have achieved state-of-the-art performance in
cardiac 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-ventricular
3D models, despite the artefacts in input CMR volumes
Deep learning cardiac motion analysis for human survival prediction
Motion analysis is used in computer vision to understand the behaviour of
moving objects in sequences of images. Optimising the interpretation of dynamic
biological systems requires accurate and precise motion tracking as well as
efficient representations of high-dimensional motion trajectories so that these
can be used for prediction tasks. Here we use image sequences of the heart,
acquired using cardiac magnetic resonance imaging, to create time-resolved
three-dimensional segmentations using a fully convolutional network trained on
anatomical shape priors. This dense motion model formed the input to a
supervised denoising autoencoder (4Dsurvival), which is a hybrid network
consisting of an autoencoder that learns a task-specific latent code
representation trained on observed outcome data, yielding a latent
representation optimised for survival prediction. To handle right-censored
survival outcomes, our network used a Cox partial likelihood loss function. In
a study of 302 patients the predictive accuracy (quantified by Harrell's
C-index) was significantly higher (p < .0001) for our model C=0.73 (95 CI:
0.68 - 0.78) than the human benchmark of C=0.59 (95 CI: 0.53 - 0.65). This
work demonstrates how a complex computer vision task using high-dimensional
medical image data can efficiently predict human survival
Data-driven generation of 4D velocity profiles in the aneurysmal ascending aorta
Numerical simulations of blood flow are a valuable tool to investigate the
pathophysiology of ascending thoracic aortic aneurysms (ATAA). To accurately
reproduce hemodynamics, computational fluid dynamics (CFD) models must employ
realistic inflow boundary conditions (BCs). However, the limited availability
of in vivo velocity measurements still makes researchers resort to idealized
BCs. In this study we generated and thoroughly characterized a large dataset of
synthetic 4D aortic velocity profiles suitable to be used as BCs for CFD
simulations. 4D flow MRI scans of 30 subjects with ATAA were processed to
extract cross-sectional planes along the ascending aorta, ensuring spatial
alignment among all planes and interpolating all velocity fields to a reference
configuration. Velocity profiles of the clinical cohort were extensively
characterized by computing flow morphology descriptors of both spatial and
temporal features. By exploiting principal component analysis (PCA), a
statistical shape model (SSM) of 4D aortic velocity profiles was built and a
dataset of 437 synthetic cases with realistic properties was generated.
Comparison between clinical and synthetic datasets showed that the synthetic
data presented similar characteristics as the clinical population in terms of
key morphological parameters. The average velocity profile qualitatively
resembled a parabolic-shaped profile, but was quantitatively characterized by
more complex flow patterns which an idealized profile would not replicate.
Statistically significant correlations were found between PCA principal modes
of variation and flow descriptors. We built a data-driven generative model of
4D aortic velocity profiles, suitable to be used in computational studies of
blood flow. The proposed software system also allows to map any of the
generated velocity profiles to the inlet plane of any virtual subject given its
coordinate set.Comment: 21 pages, 5 figures, 2 tables To be submitted to "Computer methods
and programs in biomedicine" Scripts: https://github.com/saitta-s/flow4D
Synthetic velocity profiles: //doi.org/10.5281/zenodo.725198
Genetic and environmental determinants of diastolic heart function
Diastole is the sequence of physiological events that occur in the heart during ventricular filling and principally depends on myocardial relaxation and chamber stiffness. Abnormal diastolic function is related to many cardiovascular disease processes and is predictive of health outcomes, but its genetic architecture is largely unknown. Here, we use machine learning cardiac motion analysis to measure diastolic functional traits in 39,559 participants of the UK Biobank and perform a genome-wide association study. We identified 9 significant, independent loci near genes that are associated with maintaining sarcomeric function under biomechanical stress and genes implicated in the development of cardiomyopathy. Age, sex and diabetes were independent predictors of diastolic function and we found a causal relationship between genetically-determined ventricular stiffness and incident heart failure. Our results provide insights into the genetic and environmental factors influencing diastolic function that are relevant for identifying causal relationships and potential tractable targets
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