Convolutional Neural Network Addresses the Confounding Impact of CT Reconstruction Kernels on Radiomics Studies.
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ABSTRACT:
SUBMITTER: Yoon JH
PROVIDER: S-EPMC8707549 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A novel hermetic detector composed of 200 bismuth germanium oxide crystal scintillators and 393 channel silicon photomultipliers has been developed for positronium (Ps) annihilation studies. This compact 4π detector is capable of simultaneously detecting γ-ray decay in all directions, enabling not only the study of visible and invisible exotic decay processes but also tumor localization in positron emission tomography for small animals. In this study, we investigate the use of a convolutional neural network (CNN) for the localization of Ps annihilation synonymous with tumor localization. Two-γ decay systems of the Ps annihilation from 22Na and 18F radioactive sources are simulated using a GEANT4 simulation. The simulated datasets are preprocessed by applying energy cutoffs. The spatial error in the XY plane from the CNN is compared to that from the classical weighted k-means algorithm centroiding, and the feasibility of CNN-based Ps annihilation reconstruction with tumor localization is discussed.
| S-EPMC9122910 | biostudies-literature
Project description:Interventions: None
Primary outcome(s): The primary outcome of the study is the accuracy of the CAD-CNN system for predicting histology of diminutive colorectal polyps (1-5mm) compared with the accuracy of the prediction of the endoscopist. Both the CAD-CNN system and the endoscopist will use NBI for their predictions.
Accuracy is defined as the percentage of correctly predicted optical diagnoses of the CAD-CNN system and/or endoscopist compared to the gold standard pathology. For the calculation of the accuracy, adenomas and SSLs will be dichotomised as neoplastic polyps, while HPs and other non-neoplastic histology are considered non-neoplastic.
Study Design: N/A: single arm study, Open (masking not used), N/A , unknown, Other
| 2443187 | ecrin-mdr-crc
Project description:Background and purpose4D and midposition MRI could inform plan adaptation in lung and abdominal MR-guided radiotherapy. We present deep learning-based solutions to overcome long 4D-MRI reconstruction times while maintaining high image quality and short scan times.MethodsTwo 3D U-net deep convolutional neural networks were trained to accelerate the 4D joint MoCo-HDTV reconstruction. For the first network, gridded and joint MoCo-HDTV-reconstructed 4D-MRI were used as input and target data, respectively, whereas the second network was trained to directly calculate the midposition image. For both networks, input and target data had dimensions of 256 × 256 voxels (2D) and 16 respiratory phases. Deep learning-based MRI were verified against joint MoCo-HDTV-reconstructed MRI using the structural similarity index (SSIM) and the naturalness image quality evaluator (NIQE). Moreover, two experienced observers contoured the gross tumour volume and scored the images in a blinded study.ResultsFor 12 subjects, previously unseen by the networks, high-quality 4D and midposition MRI (1.25 × 1.25 × 3.3 mm3) were each reconstructed from gridded images in only 28 seconds per subject. Excellent agreement was found between deep-learning-based and joint MoCo-HDTV-reconstructed MRI (average SSIM ≥ 0.96, NIQE scores 7.94 and 5.66). Deep-learning-based 4D-MRI were clinically acceptable for target and organ-at-risk delineation. Tumour positions agreed within 0.7 mm on midposition images.ConclusionOur results suggest that the joint MoCo-HDTV and midposition algorithms can each be approximated by a deep convolutional neural network. This rapid reconstruction of 4D and midposition MRI facilitates online treatment adaptation in thoracic or abdominal MR-guided radiotherapy.
| S-EPMC8216429 | biostudies-literature
Project description:ObjectiveTo identify confounding variables influencing the accuracy of a convolutional neural network (CNN) specific for infrarenal abdominal aortic aneurysms (AAAs) on computed tomography angiograms (CTAs).MethodsA Health Insurance Portability and Accountability Act-compliant, institutional review board-approved, retrospective study analyzed abdominopelvic CTA scans from 200 patients with infrarenal AAAs and 200 propensity-matched control patients. An AAA-specific trained CNN was developed by the application of transfer learning to the VGG-16 base model using model training, validation, and testing techniques. Model accuracy and area under the curve were analyzed based on data sets (selected, balanced, or unbalanced), aneurysm size, extra-abdominal extension, dissections, and mural thrombus. Misjudgments were analyzed by review of heatmaps, via gradient weighted class activation, overlaid on CTA images.ResultsThe trained custom CNN model reported high test group accuracies of 94.1%, 99.1%, and 99.6% and area under the curve of 0.9900, 0.9998, and 0.9993 in selected (n = 120), balanced (n = 3704), and unbalanced image sets (n = 31,899), respectively. Despite an eightfold difference between balanced and unbalanced image sets, the CNN model demonstrated high test group sensitivities (98.7% vs 98.9%) and specificities (99.7% vs 99.3%) in unbalanced and balanced image sets, respectively. For aneurysm size, the CNN model demonstrates decreasing misjudgments as aneurysm size increases: 47% (16/34) for aneurysms <3.3 cm, 32% (11/34) for aneurysms 3.3 to 5 cm, and 20% (7/34) for aneurysms >5 cm. Aneurysms containing measurable mural thrombus were over-represented within type II (false-negative) misjudgments compared with type I (false-positive) misjudgments (71% vs 15%, P < .05). Inclusion of extra-abdominal aneurysm extension (thoracic or iliac artery) or dissection flaps in these imaging sets did not decrease the model's overall accuracy, indicating that the model performance was excellent without the need to clean the data set of confounding or comorbid diagnoses.ConclusionsAnalysis of an AAA-specific CNN model can accurately screen and identify infrarenal AAAs on CTA despite varying pathology and quantitative data sets. The highest anatomic misjudgments were with small aneurysms (<3.3 cm) or the presence of mural thrombus. Accuracy of the CNN model is maintained despite the inclusion of extra-abdominal pathology and imbalanced data sets.
| S-EPMC10245322 | biostudies-literature
Project description:In the last two decades, it has been shown that anatomically-guided PET reconstruction can lead to improved bias-noise characteristics in brain PET imaging. However, despite promising results in simulations and first studies, anatomically-guided PET reconstructions are not yet available for use in routine clinical because of several reasons. In light of this, we investigate whether the improvements of anatomically-guided PET reconstruction methods can be achieved entirely in the image domain with a convolutional neural network (CNN). An entirely image-based CNN post-reconstruction approach has the advantage that no access to PET raw data is needed and, moreover, that the prediction times of trained CNNs are extremely fast on state of the art GPUs which will substantially facilitate the evaluation, fine-tuning and application of anatomically-guided PET reconstruction in real-world clinical settings. In this work, we demonstrate that anatomically-guided PET reconstruction using the asymmetric Bowsher prior can be well-approximated by a purely shift-invariant convolutional neural network in image space allowing the generation of anatomically-guided PET images in almost real-time. We show that by applying dedicated data augmentation techniques in the training phase, in which 16 [18F]FDG and 10 [18F]PE2I data sets were used, lead to a CNN that is robust against the used PET tracer, the noise level of the input PET images and the input MRI contrast. A detailed analysis of our CNN in 36 [18F]FDG, 18 [18F]PE2I, and 7 [18F]FET test data sets demonstrates that the image quality of our trained CNN is very close to the one of the target reconstructions in terms of regional mean recovery and regional structural similarity.
| S-EPMC7812485 | biostudies-literature
Project description:Remarkable progress has been made in image classification and segmentation, due to the recent study of deep convolutional neural networks (CNNs). To solve the similar problem of diagnostic lung nodule detection in low-dose computed tomography (CT) scans, we propose a new Computer-Aided Detection (CAD) system using CNNs and CT image segmentation techniques. Unlike former studies focusing on the classification of malignant nodule types or relying on prior image processing, in this work, we put raw CT image patches directly in CNNs to reduce the complexity of the system. Specifically, we split each CT image into several patches, which are divided into 6 types consisting of 3 nodule types and 3 non-nodule types. We compare the performance of ResNet with different CNNs architectures on CT images from a publicly available dataset named the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI). Results show that our best model reaches a high detection sensitivity of 92.8% with 8 false positives per scan (FPs/scan). Compared with related work, our work obtains a state-of-the-art effect.
| S-EPMC6841817 | biostudies-literature
Project description:PurposeTo assess feasibility of training a convolutional neural network (CNN) to automate liver segmentation across different imaging modalities and techniques used in clinical practice and apply this to enable automation of liver biometry.MethodsWe trained a 2D U-Net CNN for liver segmentation in two stages using 330 abdominal MRI and CT exams acquired at our institution. First, we trained the neural network with non-contrast multi-echo spoiled-gradient-echo (SGPR)images with 300 MRI exams to provide multiple signal-weightings. Then, we used transfer learning to generalize the CNN with additional images from 30 contrast-enhanced MRI and CT exams.We assessed the performance of the CNN using a distinct multi-institutional data set curated from multiple sources (n = 498 subjects). Segmentation accuracy was evaluated by computing Dice scores. Utilizing these segmentations, we computed liver volume from CT and T1-weighted (T1w) MRI exams, and estimated hepatic proton- density-fat-fraction (PDFF) from multi-echo T2*w MRI exams. We compared quantitative volumetry and PDFF estimates between automated and manual segmentation using Pearson correlation and Bland-Altman statistics.ResultsDice scores were 0.94 ± 0.06 for CT (n = 230), 0.95 ± 0.03 (n = 100) for T1w MR, and 0.92 ± 0.05 for T2*w MR (n = 169). Liver volume measured by manual and automated segmentation agreed closely for CT (95% limit-of-agreement (LoA) = [-298 mL, 180 mL]) and T1w MR (LoA = [-358 mL, 180 mL]). Hepatic PDFF measured by the two segmentations also agreed closely (LoA = [-0.62%, 0.80%]).ConclusionsUtilizing a transfer-learning strategy, we have demonstrated the feasibility of a CNN to be generalized to perform liver segmentations across different imaging techniques and modalities. With further refinement and validation, CNNs may have broad applicability for multimodal liver volumetry and hepatic tissue characterization.
| S-EPMC7314107 | biostudies-literature
Project description:This work presents the application of an Encoder-Decoder convolutional neural network (ED-CNN) model to automatically segment COVID-19 computerised tomography (CT) data. By doing so we are producing an alternative model to current literature, which is easy to follow and reproduce, making it more accessible for real-world applications as little training would be required to use this. Our simple approach achieves results comparable to those of previously published studies, which use more complex deep-learning networks. We demonstrate a high-quality automated segmentation prediction of thoracic CT scans that correctly delineates the infected regions of the lungs. This segmentation automation can be used as a tool to speed up the contouring process, either to check manual contouring in place of a peer checking, when not possible or to give a rapid indication of infection to be referred for further treatment, thus saving time and resources. In contrast, manual contouring is a time-consuming process in which a professional would contour each patient one by one to be later checked by another professional. The proposed model uses approximately 49 k parameters while others average over 1,000 times more parameters. As our approach relies on a very compact model, shorter training times are observed, which make it possible to easily retrain the model using other data and potentially afford "personalised medicine" workflows. The model achieves similarity scores of Specificity (Sp) = 0.996 ± 0.001, Accuracy (Acc) = 0.994 ± 0.002 and Mean absolute error (MAE) = 0.0075 ± 0.0005.
| S-EPMC11323195 | biostudies-literature
Project description:ObjectiveThe research aims to develop an advanced and precise lung cancer screening model based on Convolutional Neural Networks (CNN).MethodsBased on the health medical big data platform of Shandong University, we developed a VGG16-Based CNN lung cancer screening model. This model was trained using the Computed Tomography scans data of patients from Pingyi Traditional Chinese Medicine Hospital in Shandong Province, from January to February 2023. Data augmentation techniques, including random resizing, cropping, horizontal flipping, color jitter, random rotation and normalization, were applied to improve model generalization. We used five-fold cross-validation to robustly assess performance. The model was fine-tuned with an SGD optimizer (learning rate 0.001, momentum 0.9, and L2 regularization) and a learning rate scheduler. Dropout layers were added to prevent the model from relying too heavily on specific neurons, enhancing its ability to generalize. Early stopping was implemented when validation loss did not decrease over 10 epochs. In addition, we evaluated the model's performance with Area Under the Curve (AUC), Classification accuracy, Positive Predictive Value (PPV), and Negative Predictive Value (NPV), Sensitivity, Specificity and F1 score. External validation used an independent dataset from the same hospital, covering January to February 2022.ResultsThe training and validation loss and accuracy over iterations show that both accuracy metrics peak at over 0.9 by iteration 15, prompting early stopping to prevent overfitting. Based on five-fold cross-validation, the ROC curves for the VGG16-Based CNN model, demonstrate an AUC of 0.963 ± 0.004, highlighting its excellent diagnostic capability. Confusion matrices provide average metrics with a classification accuracy of 0.917 ± 0.004, PPV of 0.868 ± 0.015, NPV of 0.931 ± 0.003, Sensitivity of 0.776 ± 0.01, Specificity of 0.962 ± 0.005 and F1 score of 0.819 ± 0.008, respectively. External validation confirmed the model's robustness across different patient populations and imaging conditions.ConclusionThe VGG16-Based CNN lung screening model constructed in this study can effectively identify lung tumors, demonstrating reliability and effectiveness in real-world medical settings, and providing strong theoretical and empirical support for its use in lung cancer screening.
| S-EPMC11369893 | biostudies-literature
Project description:To improve the network performance of radial basis function (RBF) and back-propagation (BP) networks on complex nonlinear problems, an integrated neural network model with pre-RBF kernels is proposed. The proposed method is based on the framework of a single optimized BP network and an RBF network. By integrating and connecting the RBF kernel mapping layer and BP neural network, the local features of a sample set can be effectively extracted to improve separability; subsequently, the connected BP network can be used to perform learning and classification in the kernel space. Experiments on an artificial dataset and three benchmark datasets show that the proposed model combines the advantages of RBF and BP networks, as well as improves the performances of the two networks. Finally, the effectiveness of the proposed method is verified.
| S-EPMC10450702 | biostudies-literature