Convolutional Neural Networks and Geometric Moments to Identify the Bilateral Symmetric Midplane in Facial Skeletons from CT Scans.
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ABSTRACT:
SUBMITTER: Dalvit Carvalho da Silva R
PROVIDER: S-EPMC7999007 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The Convolutional Neural Network algorithm achieved a sensitivity of 94% and specificity of 93% in identifying scans with vertebral fractures (VFs). The external validation results suggest that the algorithm provides an opportunity to aid radiologists with the early identification of VFs in routine CT scans of abdomen and chest.PurposeTo evaluate the performance of a previously trained Convolutional Neural Network (CNN) model to automatically detect vertebral fractures (VFs) in CT scans in an external validation cohort.MethodsTwo Chinese studies and clinical data were used to retrospectively select CT scans of the chest, abdomen and thoracolumbar spine in men and women aged ≥50 years. The CT scans were assessed using the semiquantitative (SQ) Genant classification for prevalent VFs in a process blinded to clinical information. The performance of the CNN model was evaluated against reference standard readings by the area under the receiver operating characteristics curve (AUROC), accuracy, Cohen's kappa, sensitivity, and specificity.ResultsA total of 4,810 subjects were included, with a median age of 62 years (IQR 56-67), of which 2,654 (55.2%) were females. The scans were acquired between January 2013 and January 2019 on 16 different CT scanners from three different manufacturers. 2,773 (57.7%) were abdominal CTs. A total of 628 scans (13.1%) had ≥1 VF (grade 2-3), representing 899 fractured vertebrae out of a total of 48,584 (1.9%) visualized vertebral bodies. The CNN's performance in identifying scans with ≥1 moderate or severe fractures achieved an AUROC of 0.94 (95% CI: 0.93-0.95), accuracy of 93% (95% CI: 93%-94%), kappa of 0.75 (95% CI: 0.72-0.77), a sensitivity of 94% (95% CI: 92-96%) and a specificity of 93% (95% CI: 93-94%).ConclusionThe algorithm demonstrated excellent performance in the identification of vertebral fractures in a cohort of chest and abdominal CT scans of Chinese patients ≥50 years.
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Project description:BackgroundStructural changes of the brain's third ventricle have been acknowledged as an indicative measure of the brain atrophy progression in neurodegenerative and endocrinal diseases. To investigate the ventricular enlargement in relation to the atrophy of the surrounding structures, shape analysis is a promising approach. However, there are hurdles in modeling the third ventricle shape. First, it has topological variations across individuals due to the inter-thalamic adhesion. In addition, as an interhemispheric structure, it needs to be aligned to the midsagittal plane to assess its asymmetric and regional deformation.MethodTo address these issues, we propose a model-based shape assessment. Our template model of the third ventricle consists of a midplane and a symmetric mesh of generic shape. By mapping the template's midplane to the individuals' brain midsagittal plane, we align the symmetric mesh on the midline of the brain before quantifying the third ventricle shape. To build the vertex-wise correspondence between the individual third ventricle and the template mesh, we employ a minimal-distortion surface deformation framework. In addition, to account for topological variations, we implement geometric constraints guiding the template mesh to have zero width where the inter-thalamic adhesion passes through, preventing vertices crossing between left and right walls of the third ventricle. The individual shapes are compared using a vertex-wise deformity from the symmetric template.ResultsExperiments on imaging and demographic data from a study of aging showed that our model was sensitive in assessing morphological differences between individuals in relation to brain volume (i.e. proxy for general brain atrophy), gender and the fluid intelligence at age 72. It also revealed that the proposed method can detect the regional and asymmetrical deformation unlike the conventional measures: volume (median 1.95ml, IQR 0.96ml) and width of the third ventricle. Similarity measures between binary masks and the shape model showed that the latter reconstructed shape details with high accuracy (Dice coefficient ?0.9, mean distance 0.5mm and Hausdorff distance 2.7mm).ConclusionsWe have demonstrated that our approach is suitable to morphometrical analyses of the third ventricle, providing high accuracy and inter-subject consistency in the shape quantification. This shape modeling method with geometric constraints based on anatomical landmarks could be extended to other brain structures which require a consistent measurement basis in the morphometry.
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Project description:COVID-19 is a respiratory disease that, as of July 15th, 2021, has infected more than 187 million people worldwide and is responsible for more than 4 million deaths. An accurate diagnosis of COVID-19 is essential for the treatment and control of the disease. The use of computed tomography (CT) has shown to be promising for evaluating patients suspected of COVID-19 infection. The analysis of a CT examination is complex, and requires attention from a specialist. This paper presents a methodology for detecting COVID-19 from CT images. We first propose a convolutional neural network architecture to extract features from CT images, and then optimize the hyperparameters of the network using a tree Parzen estimator to choose the best parameters. Following this, we apply a selection of features using a genetic algorithm. Finally, classification is performed using four classifiers with different approaches. The proposed methodology achieved an accuracy of 0.997, a kappa index of 0.995, an AUROC of 0.997, and an AUPRC of 0.997 on the SARS-CoV-2 CT-Scan dataset, and an accuracy of 0.987, a kappa index of 0.975, an AUROC of 0.989, and an AUPRC of 0.987 on the COVID-CT dataset, using our CNN after optimization of the hyperparameters, the selection of features and the multi-layer perceptron classifier. Compared with pretrained CNNs and related state-of-the-art works, the results achieved by the proposed methodology were superior. Our results show that the proposed method can assist specialists in screening and can aid in diagnosing patients with suspected COVID-19.
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Project description:Accurately detecting and examining lung nodules early is key in diagnosing lung cancers and thus one of the best ways to prevent lung cancer deaths. Radiologists spend countless hours detecting small spherical-shaped nodules in computed tomography (CT) images. In addition, even after detecting nodule candidates, a considerable amount of effort and time is required for them to determine whether they are real nodules. The aim of this paper is to introduce a high performance nodule classification method that uses three dimensional deep convolutional neural networks (DCNNs) and an ensemble method to distinguish nodules between non-nodules. In this paper, we use a three dimensional deep convolutional neural network (3D DCNN) with shortcut connections and a 3D DCNN with dense connections for lung nodule classification. The shortcut connections and dense connections successfully alleviate the gradient vanishing problem by allowing the gradient to pass quickly and directly. Connections help deep structured networks to obtain general as well as distinctive features of lung nodules. Moreover, we increased the dimension of DCNNs from two to three to capture 3D features. Compared with shallow 3D CNNs used in previous studies, deep 3D CNNs more effectively capture the features of spherical-shaped nodules. In addition, we use an alternative ensemble method called the checkpoint ensemble method to boost performance. The performance of our nodule classification method is compared with that of the state-of-the-art methods which were used in the LUng Nodule Analysis 2016 Challenge. Our method achieves higher competition performance metric (CPM) scores than the state-of-the-art methods using deep learning. In the experimental setup ESB-ALL, the 3D DCNN with shortcut connections and the 3D DCNN with dense connections using the checkpoint ensemble method achieved the highest CPM score of 0.910. The result demonstrates that our method of using a 3D DCNN with shortcut connections, a 3D DCNN with dense connections, and the checkpoint ensemble method is effective for capturing 3D features of nodules and distinguishing nodules between non-nodules.
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Project description:The aim of this study was to determine whether quantitative analyses ("radiomics") of low-dose computed tomography lung cancer screening images at baseline can predict subsequent emergence of cancer.Public data from the National Lung Screening Trial (ACRIN 6684) were assembled into two cohorts of 104 and 92 patients with screen-detected lung cancer and then matched with cohorts of 208 and 196 screening subjects with benign pulmonary nodules. Image features were extracted from each nodule and used to predict the subsequent emergence of cancer.The best models used 23 stable features in a random forests classifier and could predict nodules that would become cancerous 1 and 2 years hence with accuracies of 80% (area under the curve 0.83) and 79% (area under the curve 0.75), respectively. Radiomics outperformed the Lung Imaging Reporting and Data System and volume-only approaches. The performance of the McWilliams risk assessment model was commensurate.The radiomics of lung cancer screening computed tomography scans at baseline can be used to assess risk for development of cancer.
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