209 research outputs found
Automated Scar Segmentation from CMR-LGE Images Using a Deep Learning Approach
Aim. The presence of myocardial scar is a strong predictor of ventricular remodeling, cardiac dysfunction and mortality. Our aim was to assess quantitatively the presence of scar tissue from cardiac-magnetic-resonance (CMR) with late-Gadolinium-enhancement (LGE) images using a deep-learning (DL) approach. Methods. Scar segmentation was performed automatically with a DL approach based on ENet, a deep fully-convolutional neural network (FCNN). We investigated three different ENet configurations. The first configuration (C1) exploited ENet to retrieve directly scar segmentation from the CMR-LGE images. The second (C2) and third (C3) configurations performed scar segmentation in the myocardial region, which was previously obtained in a manual or automatic way with a state-of-the-art DL method, respectively. Results. When tested on 250 CMR-LGE images from 30 patients, the best-performing configuration (C2) achieved 97% median accuracy (inter-quartile (IQR) range = 4%) and 71% median Dice similarity coefficient (IQR = 32%). Conclusions. DL approaches using ENet are promising in automatically segmenting scars in CMR-LGE images, achieving higher performance when limiting the search area to the manually-defined myocardial region
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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
ScarGAN: Chained Generative Adversarial Networks to Simulate Pathological Tissue on Cardiovascular MR Scans
Medical images with specific pathologies are scarce, but a large amount of
data is usually required for a deep convolutional neural network (DCNN) to
achieve good accuracy. We consider the problem of segmenting the left
ventricular (LV) myocardium on late gadolinium enhancement (LGE) cardiovascular
magnetic resonance (CMR) scans of which only some of the scans have scar
tissue. We propose ScarGAN to simulate scar tissue on healthy myocardium using
chained generative adversarial networks (GAN). Our novel approach factorizes
the simulation process into 3 steps: 1) a mask generator to simulate the shape
of the scar tissue; 2) a domain-specific heuristic to produce the initial
simulated scar tissue from the simulated shape; 3) a refining generator to add
details to the simulated scar tissue. Unlike other approaches that generate
samples from scratch, we simulate scar tissue on normal scans resulting in
highly realistic samples. We show that experienced radiologists are unable to
distinguish between real and simulated scar tissue. Training a U-Net with
additional scans with scar tissue simulated by ScarGAN increases the percentage
of scar pixels correctly included in LV myocardium prediction from 75.9% to
80.5%.Comment: 12 pages, 5 figures. To appear in MICCAI DLMIA 201
Automated Diagnosis of Cardiovascular Diseases from Cardiac Magnetic Resonance Imaging Using Deep Learning Models: A Review
In recent years, cardiovascular diseases (CVDs) have become one of the
leading causes of mortality globally. CVDs appear with minor symptoms and
progressively get worse. The majority of people experience symptoms such as
exhaustion, shortness of breath, ankle swelling, fluid retention, and other
symptoms when starting CVD. Coronary artery disease (CAD), arrhythmia,
cardiomyopathy, congenital heart defect (CHD), mitral regurgitation, and angina
are the most common CVDs. Clinical methods such as blood tests,
electrocardiography (ECG) signals, and medical imaging are the most effective
methods used for the detection of CVDs. Among the diagnostic methods, cardiac
magnetic resonance imaging (CMR) is increasingly used to diagnose, monitor the
disease, plan treatment and predict CVDs. Coupled with all the advantages of
CMR data, CVDs diagnosis is challenging for physicians due to many slices of
data, low contrast, etc. To address these issues, deep learning (DL) techniques
have been employed to the diagnosis of CVDs using CMR data, and much research
is currently being conducted in this field. This review provides an overview of
the studies performed in CVDs detection using CMR images and DL techniques. The
introduction section examined CVDs types, diagnostic methods, and the most
important medical imaging techniques. In the following, investigations to
detect CVDs using CMR images and the most significant DL methods are presented.
Another section discussed the challenges in diagnosing CVDs from CMR data.
Next, the discussion section discusses the results of this review, and future
work in CVDs diagnosis from CMR images and DL techniques are outlined. The most
important findings of this study are presented in the conclusion section
An accurate and time-efficient deep learning-based system for automated segmentation and reporting of cardiac magnetic resonance-detected ischemic scar
Background and objectives: Myocardial infarction scar (MIS) assessment by cardiac magnetic resonance provides prognostic information and guides patients' clinical management. However, MIS segmentation is time-consuming and not performed routinely. This study presents a deep-learning-based computational workflow for the segmentation of left ventricular (LV) MIS, for the first time performed on state-of-the-art dark-blood late gadolinium enhancement (DB-LGE) images, and the computation of MIS transmurality and extent.Methods: DB-LGE short-axis images of consecutive patients with myocardial infarction were acquired at 1.5T in two centres between Jan 1, 2019, and June 1, 2021. Two convolutional neural network (CNN) mod-els based on the U-Net architecture were trained to sequentially segment the LV and MIS, by processing an incoming series of DB-LGE images. A 5-fold cross-validation was performed to assess the performance of the models. Model outputs were compared respectively with manual (LV endo-and epicardial border) and semi-automated (MIS, 4-Standard Deviation technique) ground truth to assess the accuracy of the segmentation. An automated post-processing and reporting tool was developed, computing MIS extent (expressed as relative infarcted mass) and transmurality.Results: The dataset included 1355 DB-LGE short-axis images from 144 patients (MIS in 942 images). High performance (> 0.85) as measured by the Intersection over Union metric was obtained for both the LV and MIS segmentations on the training sets. The performance for both LV and MIS segmentations was 0.83 on the test sets.Compared to the 4-Standard Deviation segmentation technique, our system was five times quicker ( <1 min versus 7 +/- 3 min), and required minimal user interaction. Conclusions: Our solution successfully addresses different issues related to automatic MIS segmentation, including accuracy, time-effectiveness, and the automatic generation of a clinical report.(c) 2022 Elsevier B.V. All rights reserved
Myocardial Infarction Quantification From Late Gadolinium Enhancement MRI Using Top-hat Transforms and Neural Networks
Significance: Late gadolinium enhanced magnetic resonance imaging (LGE-MRI)
is the gold standard technique for myocardial viability assessment. Although
the technique accurately reflects the damaged tissue, there is no clinical
standard for quantifying myocardial infarction (MI), demanding most algorithms
to be expert dependent. Objectives and Methods: In this work a new automatic
method for MI quantification from LGE-MRI is proposed. Our novel segmentation
approach is devised for accurately detecting not only hyper-enhanced lesions,
but also microvascular-obstructed areas. Moreover, it includes a myocardial
disease detection step which extends the algorithm for working under healthy
scans. The method is based on a cascade approach where firstly, diseased slices
are identified by a convolutional neural network (CNN). Secondly, by means of
morphological operations a fast coarse scar segmentation is obtained. Thirdly,
the segmentation is refined by a boundary-voxel reclassification strategy using
an ensemble of CNNs. For its validation, reproducibility and further comparison
against other methods, we tested the method on a big multi-field expert
annotated LGE-MRI database including healthy and diseased cases. Results and
Conclusion: In an exhaustive comparison against nine reference algorithms, the
proposal achieved state-of-the-art segmentation performances and showed to be
the only method agreeing in volumetric scar quantification with the expert
delineations. Moreover, the method was able to reproduce the intra- and
inter-observer variability ranges. It is concluded that the method could
suitably be transferred to clinical scenarios.Comment: Submitted to IEE
Automated Method for the Volumetric Evaluation of Myocardial Scar from Cardiac Magnetic Resonance Images
In most western countries cardiovascular diseases are the leading cause of death, and for the survivors of ischemic attack an accurate quantification of the extent of the damage is required to correctly assess its impact and for
risk stratification, and to select the best treatment for the patient. Moreover, a fast and reliable tool for the assessment of the cardiac function and the measurement of clinical indexes is highly desirable. The aim of this thesis is to provide computational approaches to better detect and assess the presence of myocardial fibrosis in the heart, particularly but not only in the left ventricle, by performing a fusion of the information from different magnetic resonance imaging sequences. We also developed and provided a semiautomatic tool useful for the fast evaluation and quantification of clinical indexes derived from heart chambers volumes. The thesis is composed by five chapters. The first chapter introduces the most common cardiac diseases such as ischemic cardiomyopathy and describes in detail the cellular and structural remodelling phenomena stemming from heart failure. The second chapter regards the detection of the left ventricle through the development of a semi-automated approach for both endocardial and epicardial surfaces, and myocardial mask extraction. In the third chapter the workflow for scar assessment is presented, in which the previously described approach is used to obtain the 3D left ventricle patient-specific geometry; a registration algorithm is then used to superimpose the fibrosis information derived from the late gadolinium enhancement magnetic resonance imaging to obtain a patientspecific 3D map of fibrosis extension and location on the left ventricle myocardium. Focus of the fourth chapter is on the left atrium, and fibrotic tissue detection for gaining insight on atrial fibrillation. In the fifth chapter some conclusive remarks are presented with possible future developments of the presented work
Multi-Modality Pathology Segmentation Framework: Application to Cardiac Magnetic Resonance Images
Multi-sequence of cardiac magnetic resonance (CMR) images can provide
complementary information for myocardial pathology (scar and edema). However,
it is still challenging to fuse these underlying information for pathology
segmentation effectively. This work presents an automatic cascade pathology
segmentation framework based on multi-modality CMR images. It mainly consists
of two neural networks: an anatomical structure segmentation network (ASSN) and
a pathological region segmentation network (PRSN). Specifically, the ASSN aims
to segment the anatomical structure where the pathology may exist, and it can
provide a spatial prior for the pathological region segmentation. In addition,
we integrate a denoising auto-encoder (DAE) into the ASSN to generate
segmentation results with plausible shapes. The PRSN is designed to segment
pathological region based on the result of ASSN, in which a fusion block based
on channel attention is proposed to better aggregate multi-modality information
from multi-modality CMR images. Experiments from the MyoPS2020 challenge
dataset show that our framework can achieve promising performance for
myocardial scar and edema segmentation.Comment: 12 pages,MyoPS 202
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