1,624 research outputs found
Automatic Segmentation and Disease Classification Using Cardiac Cine MR Images
Segmentation of the heart in cardiac cine MR is clinically used to quantify
cardiac function. We propose a fully automatic method for segmentation and
disease classification using cardiac cine MR images. A convolutional neural
network (CNN) was designed to simultaneously segment the left ventricle (LV),
right ventricle (RV) and myocardium in end-diastole (ED) and end-systole (ES)
images. Features derived from the obtained segmentations were used in a Random
Forest classifier to label patients as suffering from dilated cardiomyopathy,
hypertrophic cardiomyopathy, heart failure following myocardial infarction,
right ventricular abnormality, or no cardiac disease. The method was developed
and evaluated using a balanced dataset containing images of 100 patients, which
was provided in the MICCAI 2017 automated cardiac diagnosis challenge (ACDC).
The segmentation and classification pipeline were evaluated in a four-fold
stratified cross-validation. Average Dice scores between reference and
automatically obtained segmentations were 0.94, 0.88 and 0.87 for the LV, RV
and myocardium. The classifier assigned 91% of patients to the correct disease
category. Segmentation and disease classification took 5 s per patient. The
results of our study suggest that image-based diagnosis using cine MR cardiac
scans can be performed automatically with high accuracy.Comment: Accepted in STACOM Automated Cardiac Diagnosis Challenge 201
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Deep learning for cardiac image segmentation: A review
Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research
Deep learning tools for outcome prediction in a trial fibrilation from cardiac MRI
Tese de mestrado integrado em Engenharia Biomédica e Biofísica (Engenharia Clínica e Instrumentação Médica), Universidade de Lisboa, Faculdade de Ciências, 2021Atrial fibrillation (AF), is the most frequent sustained cardiac arrhythmia, described by an irregular and rapid contraction of the two upper chambers of the heart (the atria). AF development is promoted and predisposed by atrial dilation, which is a consequence of atria adaptation to AF. However, it is not clear whether atrial dilation appears similarly over the cardiac cycle and how it affects ventricular volumes. Catheter ablation is arguably the AF gold standard treatment. In their current form, ablations are capable of directly terminating AF in selected patients but are only first-time effective in approximately 50% of the cases. In the first part of this work, volumetric functional markers of the left atrium (LA) and left ventricle (LV) of AF patients were studied. More precisely, a customised convolutional neural network (CNN) was proposed to segment, across the cardiac cycle, the LA from short axis CINE MRI images acquired with full cardiac coverage in AF patients. Using the proposed automatic LA segmentation, volumetric time curves were plotted and ejection fractions (EF) were automatically calculated for both chambers. The second part of the project was dedicated to developing classification models based on cardiac MR images. The EMIDEC STACOM 2020 challenge was used as an initial project and basis to create binary classifiers based on fully automatic classification neural networks (NNs), since it presented a relatively simple binary classification task (presence/absence of disease) and a large dataset. For the challenge, a deep learning NN was proposed to automatically classify myocardial disease from delayed enhancement cardiac MR (DE-CMR) and patient clinical information. The highest classification accuracy (100%) was achieved with Clinic-NET+, a NN that used information from images, segmentations and clinical annotations. For the final goal of this project, the previously referred NNs were re-trained to predict AF recurrence after catheter ablation (CA) in AF patients using pre-ablation LA short axis in CINE MRI images. In this task, the best overall performance was achieved by Clinic-NET+ with a test accuracy of 88%. This work shown the potential of NNs to interpret and extract clinical information from cardiac MRI. If more data is available, in the future, these methods can potentially be used to help and guide clinical AF prognosis and diagnosis
Explainable cardiac pathology classification on cine MRI with motion characterization by semi-supervised learning of apparent flow
We propose a method to classify cardiac pathology based on a novel approach
to extract image derived features to characterize the shape and motion of the
heart. An original semi-supervised learning procedure, which makes efficient
use of a large amount of non-segmented images and a small amount of images
segmented manually by experts, is developed to generate pixel-wise apparent
flow between two time points of a 2D+t cine MRI image sequence. Combining the
apparent flow maps and cardiac segmentation masks, we obtain a local apparent
flow corresponding to the 2D motion of myocardium and ventricular cavities.
This leads to the generation of time series of the radius and thickness of
myocardial segments to represent cardiac motion. These time series of motion
features are reliable and explainable characteristics of pathological cardiac
motion. Furthermore, they are combined with shape-related features to classify
cardiac pathologies. Using only nine feature values as input, we propose an
explainable, simple and flexible model for pathology classification. On ACDC
training set and testing set, the model achieves 95% and 94% respectively as
classification accuracy. Its performance is hence comparable to that of the
state-of-the-art. Comparison with various other models is performed to outline
some advantages of our model
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
Automated segmentation on the entire cardiac cycle using a deep learning work-flow
The segmentation of the left ventricle (LV) from CINE MRI images is essential
to infer important clinical parameters. Typically, machine learning algorithms
for automated LV segmentation use annotated contours from only two cardiac
phases, diastole, and systole. In this work, we present an analysis work-flow
for fully-automated LV segmentation that learns from images acquired through
the cardiac cycle. The workflow consists of three components: first, for each
image in the sequence, we perform an automated localization and subsequent
cropping of the bounding box containing the cardiac silhouette. Second, we
identify the LV contours using a Temporal Fully Convolutional Neural Network
(T-FCNN), which extends Fully Convolutional Neural Networks (FCNN) through a
recurrent mechanism enforcing temporal coherence across consecutive frames.
Finally, we further defined the boundaries using either one of two components:
fully-connected Conditional Random Fields (CRFs) with Gaussian edge potentials
and Semantic Flow. Our initial experiments suggest that significant improvement
in performance can potentially be achieved by using a recurrent neural network
component that explicitly learns cardiac motion patterns whilst performing LV
segmentation.Comment: 6 pages, 2 figures, published on IEEE Xplor
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