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Purpose To study the performance of a proposed deep learning-based autocontouring system in delineating organs at risk (OARs) in breast radiotherapy with a group of experts. Methods Eleven experts from two institutions delineated nine OARs in 10 cases of adjuvant radiotherapy after breast-conserving surgery. Autocontours were then provided to the experts for correction. Overall, 110 manual contours, 110 corrected autocontours, and 10 autocontours of each type of OAR were analyzed. The Dice similarity coefficient (DSC) and Hausdorff distance (HD) were used to compare the degree of agreement between the best manual contour (chosen by an independent expert committee) and each autocontour, corrected autocontour, and manual contour. Higher DSCs and lower HDs indicated a better geometric overlap. The amount of time reduction using the autocontouring system was examined. User satisfaction was evaluated using a survey. Results Manual contours, corrected autocontours, and autocontours had a similar accuracy in the average DSC value (0.88 vs. 0.90 vs. 0.90). The accuracy of autocontours ranked the second place, based on DSCs, and the first place, based on HDs among the manual contours. Interphysician variations among the experts were reduced in corrected autocontours, compared to variations in manual contours (DSC: 0.89–0.90 vs. 0.87–0.90; HD: 4.3–5.8 mm vs. 5.3–7.6 mm). Among the manual delineations, the breast contours had the largest variations, which improved most significantly with the autocontouring system. The total mean times for nine OARs were 37 min for manual contours and 6 min for corrected autocontours. The results of the survey revealed good user satisfaction. Conclusions The autocontouring system had a similar performance in OARs as that of the experts’ manual contouring. This system can be valuable in improving the quality of breast radiotherapy and reducing interphysician variability in clinical practice.

Purpose: This study was conducted to develop a deep learning-based automatic segmentation (DLBAS) model of head and neck organs for radiotherapy (RT) in dogs, and to evaluate the feasibility for delineating the RT planning.Materials and Methods: The segmentation indicated that there were potentially 15 organs at risk (OARs) in the head and neck of dogs. Post-contrast computed tomography (CT) was performed in 90 dogs. The training and validation sets comprised 80 CT data sets, including 20 test sets. The accuracy of the segmentation was assessed using both the Dice similarity coefficient (DSC) and the Hausdorff distance (HD), and by referencing the expert contours as the ground truth. An additional 10 clinical test sets with relatively large displacement or deformation of organs were selected for verification in cancer patients. To evaluate the applicability in cancer patients, and the impact of expert intervention, three methods–HA, DLBAS, and the readjustment of the predicted data obtained via the DLBAS of the clinical test sets (HA_DLBAS)–were compared.Results: The DLBAS model (in the 20 test sets) showed reliable DSC and HD values; it also had a short contouring time of ~3 s. The average (mean ± standard deviation) DSC (0.83 ± 0.04) and HD (2.71 ± 1.01 mm) values were similar to those of previous human studies. The DLBAS was highly accurate and had no large displacement of head and neck organs. However, the DLBAS in the 10 clinical test sets showed lower DSC (0.78 ± 0.11) and higher HD (4.30 ± 3.69 mm) values than those of the test sets. The HA_DLBAS was comparable to both the HA (DSC: 0.85 ± 0.06 and HD: 2.74 ± 1.18 mm) and DLBAS presented better comparison metrics and decreased statistical deviations (DSC: 0.94 ± 0.03 and HD: 2.30 ± 0.41 mm). In addition, the contouring time of HA_DLBAS (30 min) was less than that of HA (80 min).Conclusion: In conclusion, HA_DLBAS method and the proposed DLBAS was highly consistent and robust in its performance. Thus, DLBAS has great potential as a single or supportive tool to the key process in RT planning.

PURPOSE The purpose of this study was to present real-time three-dimensional (3D) magnetic resonance imaging (MRI) in the presence of motion for MRI-guided radiotherapy (MRgRT) using dynamic keyhole imaging for high-temporal acquisition and super-resolution generative (SRG) model for high-spatial reconstruction. METHOD We propose a unique real-time 3D MRI technique by combining a data sharing technique (3D dynamic keyhole imaging) with a SRG model using cascaded deep learning technique. 3D dynamic keyhole imaging utilizes the data sharing mechanism by combining keyhole central k-space data acquired in real-time with high-spatial, high-temporal resolution prior peripheral k-space data at various motion positions prepared by the SRG model. The efficacy of the 3D dynamic keyhole imaging with super-resolution (SR_dKeyhole) was compared to the ground-truth super-resolution images with the original full k-space data. It was also compared with the zero-filling reconstruction (zero-filling), conventional keyhole reconstruction with low-spatial high-temporal prior data (LR_cKeyhole), and conventional keyhole reconstruction with super-resolution prior data (SR_cKeyhole). RESULTS High-spatial, high-temporal resolution 3D MRI datasets (1.5 × 1.5 × 6 mm3 ) were generated from low-spatial, high-temporal resolution 3D MRI datasets (6 × 6 × 6 mm3 ) using the cascaded deep learning SRG framework (

Purpose The superior soft-tissue contrast achieved using magnetic resonance imaging (MRI) compared to x-ray computed tomography (CT) has led to the popularization of MRI-guided radiation therapy (MR-IGRT), especially in recent years with the advent of first and second generation MRI-based therapy delivery systems for MR-IGRT. The expanding use of these systems is driving interest in MRI-only RT workflows in which MRI is the sole imaging modality used for treatment planning and dose calculations. To enable such a workflow, synthetic CT (sCT) data must be generated based on a patient's MRI data so that dose calculations may be performed using the electron density information derived from CT images. In this study, we propose a novel deep spatial pyramid convolutional framework for the MRI-to-CT image-to-image translation task and compare its performance to the well established U-Net architecture in a generative adversarial network (GAN) framework. Methods Our proposed framework utilizes atrous convolution in a method named atrous spatial pyramid pooling (ASPP) to significantly reduce the total number of parameters required to describe the model while effectively capturing rich, multi-scale structural information in a manner that is not possible in the conventional framework. The proposed framework consists of a generative model composed of stacked encoders and decoders separated by the ASPP module, where atrous convolution is applied at increasing rates in parallel to encode large-scale features. The performance of the proposed method is compared to that of the conventional GAN framework in terms of the time required to train the model and the image quality of the generated sCT as measured by the root mean square error (RMSE), structural similarity index (SSIM), and peak signal-to-noise ratio (PSNR) depending on the size of the training data set. Dose calculations based on sCT data generated using the proposed architecture are also compared to clinical plans to evaluate the dosimetric accuracy of the method. Results Significant reductions in training time and improvements in image quality are observed at every training data set size when the proposed framework is adopted instead of the conventional framework. Over 1042 test images, values of 17.7 ± 4.3 HU, 0.9995 ± 0.0003, and 71.7 ± 2.3 are observed for the RMSE, SSIM, and PSNR metrics, respectively. Dose distributions calculated based on sCT data generated using the proposed framework demonstrate passing rates equal to or greater than 98% using the 3D gamma index with a 2%/2 mm criterion. Conclusions The deep spatial pyramid convolutional framework proposed here demonstrates improved performance compared to the conventional GAN framework that has been applied to the image-to-image translation task of sCT generation. Adopting the method is a first step toward an MRI-only RT workflow that enables widespread clinical applications for MR-IGRT including online adaptive therapy.

MR-guided radiotherapy (MRgRT) systems provide excellent soft tissue imaging immediately prior to and in real time during radiation delivery for cancer treatment. However, 2D cine MRI often has limited spatial resolution due to high temporal resolution. This work applies a super resolution machine learning framework to 3.5 mm pixel edge length, low resolution (LR), sagittal 2D cine MRI images acquired on a MRgRT system to generate 0.9 mm pixel edge length, super resolution (SR), images originally acquired at 4 frames per second (FPS). LR images were collected from 50 pancreatic cancer patients treated on a ViewRay MR-LINAC. SR images were evaluated using three methods. 1) The first method utilized intrinsic image quality metrics for evaluation. 2) The second used relative metrics including edge detection and structural similarity index (SSIM). 3) Finally, automatically generated tumor contours were created on both low resolution and super resolution images to evaluate target delineation and compared with DICE and SSIM. Intrinsic image quality metrics all had statistically significant improvements for SR images versus LR images, with mean (±1 SD) BRISQUE scores of 29.65 ± 2.98 and 42.48 ± 0.98 for SR and LR, respectively. SR images showed good agreement with LR images in SSIM evaluation, indicating there was not significant distortion of the images. Comparison of LR and SR images with paired high resolution (HR) 3D images showed that SR images had a mean (±1 SD) SSIM value of 0.633 ± 0.063 and LR a value of 0.587 ± 0.067 (p ≪ 0.05). Contours generated on SR images were also more robust to noise addition than those generated on LR images. This study shows that super resolution with a machine learning framework can generate high spatial resolution images from 4fps low spatial resolution cine MRI acquired on the ViewRay MR-LINAC while maintaining tumor contour quality and without significant acquisition or post processing delay.

PURPOSE Applications of deep learning (DL) are essential to realizing an effective adaptive radiotherapy (ART) workflow. Despite the promise demonstrated by DL approaches in several critical ART tasks, there remain unsolved challenges to achieve satisfactory generalizability of a trained model in a clinical setting. Foremost among these is the difficulty of collecting a task-specific training dataset with high-quality, consistent annotations for supervised learning applications. In this study, we propose a tailored DL framework for patient-specific performance that leverages the behavior of a model intentionally overfitted to a patient-specific training dataset augmented from the prior information available in an ART workflow-an approach we term Intentional Deep Overfit Learning (IDOL). METHODS Implementing the IDOL framework in any task in radiotherapy consists of two training stages: (1) training a generalized model with a diverse training dataset of N patients, just as in the conventional DL approach, and (2) intentionally overfitting this general model to a small training dataset-specific the patient of interest ( N+1 ) generated through perturbations and augmentations of the available task- and patient-specific prior information to establish a personalized IDOL model. The IDOL framework itself is task-agnostic and is, thus, widely applicable to many components of the ART workflow, three of which we use as a proof of concept here: the autocontouring task on replanning CTs for traditional ART, the MRI super-resolution (SR) task for MRI-guided ART, and the synthetic CT (sCT) reconstruction task for MRI-only ART. RESULTS In the replanning CT autocontouring task, the accuracy measured by the Dice similarity coefficient improves from 0.847 with the general model to 0.935 by adopting the IDOL model. In the case of MRI SR, the mean absolute error (MAE) is improved by 40% using the IDOL framework over the conventional model. Finally, in the sCT reconstruction task, the MAE is reduced from 68 to 22 HU by utilizing the IDOL framework. CONCLUSIONS In this study, we propose a novel IDOL framework for ART and demonstrate its feasibility using three ART tasks. We expect the IDOL framework to be especially useful in creating personally tailored models in situations with limited availability of training data but existing prior information, which is usually true in the medical setting in general and is especially true in ART.

This study investigated the feasibility of deep learning-based segmentation (DLS) and continual training for adaptive radiotherapy (RT) of head and neck (H&amp, N) cancer. One-hundred patients treated with definitive RT were included. Based on 23 organs-at-risk (OARs) manually segmented in initial planning computed tomography (CT), modified FC-DenseNet was trained for DLS: (i) using data obtained from 60 patients, with 20 matched patients in the test set (DLSm), (ii) using data obtained from 60 identical patients with 20 unmatched patients in the test set (DLSu). Manually contoured OARs in adaptive planning CT for independent 20 patients were provided as test sets. Deformable image registration (DIR) was also performed. All 23 OARs were compared using quantitative measurements, and nine OARs were also evaluated via subjective assessment from 26 observers using the Turing test. DLSm achieved better performance than both DLSu and DIR (mean Dice similarity coefficient, 0.83 vs. 0.80 vs. 0.70), mainly for glandular structures, whose volume significantly reduced during RT. Based on subjective measurements, DLS is often perceived as a human (49.2%). Furthermore, DLSm is preferred over DLSu (67.2%) and DIR (96.7%), with a similar rate of required revision to that of manual segmentation (28.0% vs. 29.7%). In conclusion, DLS was effective and preferred over DIR. Additionally, continual DLS training is required for an effective optimization and robustness in personalized adaptive RT.

Background In breast cancer patients receiving radiotherapy (RT), accurate target delineation and reduction of radiation doses to the nearby normal organs is important. However, manual clinical target volume (CTV) and organs-at-risk (OARs) segmentation for treatment planning increases physicians’ workload and inter-physician variability considerably. In this study, we evaluated the potential benefits of deep learning-based auto-segmented contours by comparing them to manually delineated contours for breast cancer patients. Methods CTVs for bilateral breasts, regional lymph nodes, and OARs (including the heart, lungs, esophagus, spinal cord, and thyroid) were manually delineated on planning computed tomography scans of 111 breast cancer patients who received breast-conserving surgery. Subsequently, a two-stage convolutional neural network algorithm was used. Quantitative metrics, including the Dice similarity coefficient (DSC) and 95% Hausdorff distance, and qualitative scoring by two panels from 10 institutions were used for analysis. Inter-observer variability and delineation time were assessed; furthermore, dose-volume histograms and dosimetric parameters were also analyzed using another set of patient data. Results The correlation between the auto-segmented and manual contours was acceptable for OARs, with a mean DSC higher than 0.80 for all OARs. In addition, the CTVs showed favorable results, with mean DSCs higher than 0.70 for all breast and regional lymph node CTVs. Furthermore, qualitative subjective scoring showed that the results were acceptable for all CTVs and OARs, with a median score of at least 8 (possible range: 0–10) for (1) the differences between manual and auto-segmented contours and (2) the extent to which auto-segmentation would assist physicians in clinical practice. The differences in dosimetric parameters between the auto-segmented and manual contours were minimal. Conclusions The feasibility of deep learning-based auto-segmentation in breast RT planning was demonstrated. Although deep learning-based auto-segmentation cannot be a substitute for radiation oncologists, it is a useful tool with excellent potential in assisting radiation oncologists in the future. Trial registration Retrospectively registered.

Manual segmentation is the gold standard method for radiation therapy planning; however, it is time-consuming and prone to inter- and intra-observer variation, giving rise to interests in auto-segmentation methods. We evaluated the feasibility of deep learning-based auto-segmentation (DLBAS) in comparison to commercially available atlas-based segmentation solutions (ABAS) for breast cancer radiation therapy. This study used contrast-enhanced planning computed tomography scans from 62 patients with breast cancer who underwent breast-conservation surgery. Contours of target volumes (CTVs), organs, and heart substructures were generated using two commercial ABAS solutions and DLBAS using fully convolutional DenseNet. The accuracy of the segmentation was assessed using 14 test patients using the Dice Similarity Coefficient and Hausdorff Distance referencing the expert contours. A sensitivity analysis was performed using non-contrast planning CT from 14 additional patients. Compared to ABAS, the proposed DLBAS model yielded more consistent results and the highest average Dice Similarity Coefficient values and lowest Hausdorff Distances, especially for CTVs and the substructures of the heart. ABAS showed limited performance in soft-tissue-based regions, such as the esophagus, cardiac arteries, and smaller CTVs. The results of sensitivity analysis between contrast and non-contrast CT test sets showed little difference in the performance of DLBAS and conversely, a large discrepancy for ABAS. The proposed DLBAS algorithm was more consistent and robust in its performance than ABAS across the majority of structures when examining both CTVs and normal organs. DLBAS has great potential to aid a key process in the radiation therapy workflow, helping optimise and reduce the clinical workload.

Purpose/Objective(s) A large inter-physician variation can be seen when delineating organ-at-risks (OARs) for breast radiotherapy. This study aimed to externally validate the performance of deep learning-based auto-contouring system (ACS) for breast radiotherapy. Materials/Methods Eleven experts from two institutions were asked to delineate 9 OARs of 10 cases of breast radiotherapy. Then, auto-contours were provided to the experts for correction. To compare the performance of auto-, corrected-auto-, and experts’ manual contours, Dice similarity coefficient (DSC) and Hausdorff distance (HD) between each contour and the best manual contour were used, where higher DSC and lower HD means better geometric overlap. Results Total mean time for 9 OARs was 37 ± 20 min for manual and 6 ± 5 min for corrected-auto-contours. Among the DSC of experts’ manual contours and an auto-contour, DSC of an auto-contour ranked the second place and HD ranked the first place. Better performance was shown in corrected-auto-contours than in manual contours (median DSC: 0.90 vs. 0.88; median HD: 4.5 vs. 6.5 mm). The inter-physician variations among experts were reduced in corrected-auto-contours, compared with manual contours (DSC range: 0.86–0.90 vs. 0.89–0.90; HD range: 5.1–9.1 mm vs. 4.3–5.7 mm). Among manual OARs, breast contours had the largest variations, which were most significantly improved with an aid of ACS. Conclusion ACS showed at least similar performance in OARs compared with experts’ manual contouring, which anticipates further applications of ACS to target volumes. ACS can be a valuable tool for improving the quality of breast radiotherapy and reducing inter-physician variability in clinical practice.

PURPOSE Deep learning (DL)-based super-resolution (SR) reconstruction for magnetic resonance imaging (MRI) has recently been receiving attention due to the significant improvement in spatial resolution compared to conventional SR techniques. Challenges hindering the widespread implementation of these approaches remain, however. Low-resolution (LR) MRIs captured in the clinic exhibit complex tissue structures obfuscated by noise that are difficult for a simple DL framework to handle. Moreover, training a robust network for a SR task requires abundant, perfectly matched pairs of LR and high-resolution (HR) images that are often unavailable or difficult to collect. The purpose of this study is to develop a novel SR technique for MRI based on the concept of cascaded DL that allows for the reconstruction of high-quality SR images in the presence of insufficient training data, an unknown translation model, and noise. METHODS The proposed framework, based on the concept named cascaded deep learning, consists of three components: (a) a denoising autoencoder (DAE) trained using clinical LR noisy MRI scans that have been processed with a nonlocal means filter that generates denoised LR data; (b) a down-sampling network (DSN) trained with a small amount of paired LR/HR data from volunteers that allows for the generation of perfectly paired LR/HR data for the training of a generative model; and (c) the proposed SR generative model (p-SRG) trained with data generated by the DSN that maps from LR inputs to HR outputs. After training, LR clinical images may be fed through the DAE and p-SRG to yield SR reconstructions of the LR input. The application of this framework was explored in two settings: 3D breath-hold MRI axial SR reconstruction from LR axial scans (

The aim of this study is to develop a 3D registration algorithm for positron emission tomography/computed tomography (PET/CT) and magnetic resonance (MR) images acquired from independent PET/CT and MR imaging systems. Combined PET/CT images provide anatomic and functional information, and MR images have high resolution for soft tissue. With the registration technique, the strengths of each modality image can be combined to achieve higher performance in diagnosis and radiotherapy planning. The proposed method consists of two stages: normalized mutual information (NMI)-based global matching and independent component analysis (ICA)-based refinement. In global matching, the field of view of the CT and MR images are adjusted to the same size in the preprocessing step. Then, the target image is geometrically transformed, and the similarities between the two images are measured with NMI. The optimization step updates the transformation parameters to efficiently find the best matched parameter set. In the refinement stage, ICA planes from the windowed image slices are extracted and the similarity between the images is measured to determine the transformation parameters of the control points. B-spline–based freeform deformation is performed for the geometric transformation. The results show good agreement between PET/CT and MR images.