Search

We developed a deep ensemble learning model with a radiomics spatial encoding execution for improved glioma segmentation accuracy using multi-parametric MRI (mp-MRI). This model was developed using 369 glioma patients with a 4-modality mp-MRI protocol: T1, contrast-enhanced T1 (T1-Ce), T2, and FLAIR. In each modality volume, a 3D sliding kernel was implemented across the brain to capture image heterogeneity: fifty-six radiomic features were extracted within the kernel, resulting in a 4th order tensor. Each radiomic feature can then be encoded as a 3D image volume, namely a radiomic feature map (RFM). PCA was employed for data dimension reduction and the first 4 PCs were selected. Four deep neural networks as sub-models following the U-Net architecture were trained for the segmenting of a region-of-interest (ROI): each sub-model utilizes the mp-MRI and 1 of the 4 PCs as a 5-channel input for a 2D execution. The 4 softmax probability results given by the U-net ensemble were superimposed and binarized by Otsu method as the segmentation result. Three ensemble models were trained to segment enhancing tumor (ET), tumor core (TC), and whole tumor (WT). The adopted radiomics spatial encoding execution enriches the image heterogeneity information that leads to the successful demonstration of the proposed deep ensemble model, which offers a new tool for mp-MRI based medical image segmentation.

PurposeTo develop a method of biologically guided deep learning for post-radiation 18FDG-PET image outcome prediction based on pre-radiation images and radiotherapy dose information.MethodsBased on the classic reaction-diffusion mechanism, a novel biological model was proposed using a partial differential equation that incorporates spatial radiation dose distribution as a patient-specific treatment information variable. A 7-layer encoder-decoder-based convolutional neural network (CNN) was designed and trained to learn the proposed biological model. As such, the model could generate post-radiation 18FDG-PET image outcome predictions with breakdown biological components for enhanced explainability. The proposed method was developed using 64 oropharyngeal patients with paired 18FDG-PET studies before and after 20-Gy delivery (2 Gy/day fraction) by intensity-modulated radiotherapy (IMRT). In a two-branch deep learning execution, the proposed CNN learns specific terms in the biological model from paired 18FDG-PET images and spatial dose distribution in one branch, and the biological model generates post-20-Gy 18FDG-PET image prediction in the other branch. As in 2D execution, 718/233/230 axial slices from 38/13/13 patients were used for training/validation/independent test. The prediction image results in test cases were compared with the ground-truth results quantitatively.ResultsThe proposed method successfully generated post-20-Gy 18FDG-PET image outcome prediction with breakdown illustrations of biological model components. Standardized uptake value (SUV) mean values in 18FDG high-uptake regions of predicted images (2.45 ± 0.25) were similar to ground-truth results (2.51 ± 0.33). In 2D-based Gamma analysis, the median/mean Gamma Index (<1) passing rate of test images was 96.5%/92.8% using the 5%/5 mm criterion; such result was improved to 99.9%/99.6% when 10%/10 mm was adopted.ConclusionThe developed biologically guided deep learning method achieved post-20-Gy 18

PurposeTo develop a method of biologically guided deep learning for post-radiation 18FDG-PET image outcome prediction based on pre-radiation images and radiotherapy dose information.MethodsBased on the classic reaction-diffusion mechanism, a novel biological model was proposed using a partial differential equation that incorporates spatial radiation dose distribution as a patient-specific treatment information variable. A 7-layer encoder-decoder-based convolutional neural network (CNN) was designed and trained to learn the proposed biological model. As such, the model could generate post-radiation 18FDG-PET image outcome predictions with breakdown biological components for enhanced explainability. The proposed method was developed using 64 oropharyngeal patients with paired 18FDG-PET studies before and after 20-Gy delivery (2 Gy/day fraction) by intensity-modulated radiotherapy (IMRT). In a two-branch deep learning execution, the proposed CNN learns specific terms in the biological model from paired 18FDG-PET images and spatial dose distribution in one branch, and the biological model generates post-20-Gy 18FDG-PET image prediction in the other branch. As in 2D execution, 718/233/230 axial slices from 38/13/13 patients were used for training/validation/independent test. The prediction image results in test cases were compared with the ground-truth results quantitatively.ResultsThe proposed method successfully generated post-20-Gy 18FDG-PET image outcome prediction with breakdown illustrations of biological model components. Standardized uptake value (SUV) mean values in 18FDG high-uptake regions of predicted images (2.45 ± 0.25) were similar to ground-truth results (2.51 ± 0.33). In 2D-based Gamma analysis, the median/mean Gamma Index (<1) passing rate of test images was 96.5%/92.8% using the 5%/5 mm criterion; such result was improved to 99.9%/99.6% when 10%/10 mm was adopted.ConclusionThe developed biologically guided deep learning method achieved post-20-Gy 18

The projection of planar MRI data onto a spherical surface is equivalent to a nonlinear image transformation that retains global anatomical information. By incorporating this image transformation process in our proposed spherical projection-based U-Net (SPU-Net) segmentation model design, multiple independent segmentation predictions can be obtained from a single MRI. The final segmentation is the average of all available results, and the variation can be visualized as a pixel-wise uncertainty map. An uncertainty score was introduced to evaluate and compare the performance of uncertainty measurements. The proposed SPU-Net model was implemented on the basis of 369 glioma patients with MP-MRI scans (T1, T1-Ce, T2, and FLAIR). Three SPU-Net models were trained to segment enhancing tumor (ET), tumor core (TC), and whole tumor (WT), respectively. The SPU-Net model was compared with (1) the classic U-Net model with test-time augmentation (TTA) and (2) linear scaling-based U-Net (LSU-Net) segmentation models in terms of both segmentation accuracy (Dice coefficient, sensitivity, specificity, and accuracy) and segmentation uncertainty (uncertainty map and uncertainty score). The developed SPU-Net model successfully achieved low uncertainty for correct segmentation predictions (e.g., tumor interior or healthy tissue interior) and high uncertainty for incorrect results (e.g., tumor boundaries). This model could allow the identification of missed tumor targets or segmentation errors in U-Net. Quantitatively, the SPU-Net model achieved the highest uncertainty scores for three segmentation targets (ET/TC/WT): 0.826/0.848/0.936, compared to 0.784/0.643/0.872 using the U-Net with TTA and 0.743/0.702/0.876 with the LSU-Net (scaling factor = 2). The SPU-Net also achieved statistically significantly higher Dice coefficients, underscoring the improved segmentation accuracy., Comment: 31 pages, 9 figures, 1 table

Purpose: To develop a neural ordinary differential equation (ODE) model for visualizing deep neural network (DNN) behavior during multi-parametric MRI (mp-MRI) based glioma segmentation as a method to enhance deep learning explainability. Methods: By hypothesizing that deep feature extraction can be modeled as a spatiotemporally continuous process, we designed a novel deep learning model, neural ODE, in which deep feature extraction was governed by an ODE without explicit expression. The dynamics of 1) MR images after interactions with DNN and 2) segmentation formation can be visualized after solving ODE. An accumulative contribution curve (ACC) was designed to quantitatively evaluate the utilization of each MRI by DNN towards the final segmentation results. The proposed neural ODE model was demonstrated using 369 glioma patients with a 4-modality mp-MRI protocol: T1, contrast-enhanced T1 (T1-Ce), T2, and FLAIR. Three neural ODE models were trained to segment enhancing tumor (ET), tumor core (TC), and whole tumor (WT). The key MR modalities with significant utilization by DNN were identified based on ACC analysis. Segmentation results by DNN using only the key MR modalities were compared to the ones using all 4 MR modalities. Results: All neural ODE models successfully illustrated image dynamics as expected. ACC analysis identified T1-Ce as the only key modality in ET and TC segmentations, while both FLAIR and T2 were key modalities in WT segmentation. Compared to the U-Net results using all 4 MR modalities, Dice coefficient of ET (0.784->0.775), TC (0.760->0.758), and WT (0.841->0.837) using the key modalities only had minimal differences without significance. Conclusion: The neural ODE model offers a new tool for optimizing the deep learning model inputs with enhanced explainability. The presented methodology can be generalized to other medical image-related deep learning applications., Comment: 30 pages, 7 figures, 2 tables

This paper develops a method of biologically guided deep learning for post-radiation FDG-PET image outcome prediction based on pre-radiation images and radiotherapy dose information. Based on the classic reaction-diffusion mechanism, a novel biological model was proposed using a partial differential equation that incorporates spatial radiation dose distribution as a patient-specific treatment information variable. A 7-layer encoder-decoder-based convolutional neural network (CNN) was designed and trained to learn the proposed biological model. As such, the model could generate post-radiation FDG-PET image outcome predictions with possible time-series transition from pre-radiotherapy image states to post-radiotherapy states. The proposed method was developed using 64 oropharyngeal patients with paired FDG-PET studies before and after 20Gy delivery (2Gy/daily fraction) by IMRT. In a two-branch deep learning execution, the proposed CNN learns specific terms in the biological model from paired FDG-PET images and spatial dose distribution as in one branch, and the biological model generates post-20Gy FDG-PET image prediction in the other branch. The proposed method successfully generated post-20Gy FDG-PET image outcome prediction with breakdown illustrations of biological model components. Time-series FDG-PET image predictions were generated to demonstrate the feasibility of disease response rendering. The developed biologically guided deep learning method achieved post-20Gy FDG-PET image outcome predictions in good agreement with ground-truth results. With break-down biological modeling components, the outcome image predictions could be used in adaptive radiotherapy decision-making to optimize personalized plans for the best outcome in the future., Comment: 26 pages, 5 figures

PurposeTo assess stereotactic radiotherapy (SRT)/stereotactic body radiotherapy (SBRT) practices by polling clinics participating in multi-institutional clinical trials.MethodsThe NRG Oncology Medical Physics Subcommittee distributed a survey consisting of 23 questions, which covered general technologies, policies, and procedures used in the Radiation Oncology field for the delivery of SRT/SBRT (9 questions), and site-specific questions for brain SRT, lung SBRT, and prostate SBRT (14 questions). Surveys were distributed to 1,996 radiotherapy institutions included on the membership rosters of the five National Clinical Trials Network (NCTN) groups. Patient setup, motion management, target localization, prescriptions, and treatment delivery technique data were reported back by 568 institutions (28%).Results97.5% of respondents treat lung SBRT patients, 77.0% perform brain SRT, and 29.1% deliver prostate SBRT. 48.8% of clinics require a physicist present for every fraction of SBRT, 18.5% require a physicist present for the initial SBRT fraction only, and 14.9% require a physicist present for the entire first fraction, including set-up approval for all subsequent fractions. 55.3% require physician approval for all fractions, and 86.7% do not reposition without x-ray imaging. For brain SRT, most institutions (83.9%) use a planning target volume (PTV) margin of 2 mm or less. Lung SBRT PTV margins of 3 mm or more are used in 80.6% of clinics. Volumetric modulated arc therapy (VMAT) is the dominant delivery method in 62.8% of SRT treatments, 70.9% of lung SBRT, and 68.3% of prostate SBRT.ConclusionThis report characterizes SRT/SBRT practices in radiotherapy clinics participating in clinical trials. Data made available here allows the radiotherapy community to compare their practice with that of other clinics, determine what is achievable, and assess areas for improvement.

Contemporary medical imaging is becoming increasingly more quantitative. The emerging field of radiomics is a leading example. By translating unstructured data (i.e., images) into structured data (i.e., imaging features), radiomics can potentially characterize clinically useful imaging phenotypes. In this paper, an exploratory radiomics approach is used to investigate the potential association between quantitative imaging features and pulmonary function in CT images. Thirty-nine radiomic features were extracted from the lungs of 64 patients as potential imaging biomarkers for pulmonary function. Collectively, these features capture the morphology of the lungs, as well as intensity variations, fine-texture, and coarse-texture of the pulmonary tissue. The extracted lung radiomics data was compared to conventional pulmonary function tests. In general, patients with larger lungs of homogeneous, low attenuating pulmonary tissue (as measured via radiomics) were found to be associated with poor spirometry performance and a lower diffusing capacity for carbon monoxide. Unsupervised dynamic data clustering revealed subsets of patients with similar lung radiomic patterns that were found to be associated with similar forced expiratory volume in one second (FEV1) measurements. This implies that patients with similar radiomic feature vectors also presented with comparable spirometry performance, and were separable by varying degrees of pulmonary function as measured by imaging.

Contemporary medical imaging is becoming increasingly more quantitative. The emerging field of radiomics is a leading example. By translating unstructured data (i.e., images) into structured data (i.e., imaging features), radiomics can potentially characterize clinically useful imaging phenotypes. In this paper, an exploratory radiomics approach is used to investigate the potential association between quantitative imaging features and pulmonary function in CT images. Thirty-nine radiomic features were extracted from the lungs of 64 patients as potential imaging biomarkers for pulmonary function. Collectively, these features capture the morphology of the lungs, as well as intensity variations, fine-texture, and coarse-texture of the pulmonary tissue. The extracted lung radiomics data was compared to conventional pulmonary function tests. In general, patients with larger lungs of homogeneous, low attenuating pulmonary tissue (as measured via radiomics) were found to be associated with poor spirometry performance and a lower diffusing capacity for carbon monoxide. Unsupervised dynamic data clustering revealed subsets of patients with similar lung radiomic patterns that were found to be associated with similar forced expiratory volume in one second (FEV1) measurements. This implies that patients with similar radiomic feature vectors also presented with comparable spirometry performance, and were separable by varying degrees of pulmonary function as measured by imaging.

Contemporary medical imaging is becoming increasingly more quantitative. The emerging field of radiomics is a leading example. By translating unstructured data (i.e., images) into structured data (i.e., imaging features), radiomics can potentially characterize clinically useful imaging phenotypes. In this paper, an exploratory radiomics approach is used to investigate the potential association between quantitative imaging features and pulmonary function in CT images. Thirty-nine radiomic features were extracted from the lungs of 64 patients as potential imaging biomarkers for pulmonary function. Collectively, these features capture the morphology of the lungs, as well as intensity variations, fine-texture, and coarse-texture of the pulmonary tissue. The extracted lung radiomics data was compared to conventional pulmonary function tests. In general, patients with larger lungs of homogeneous, low attenuating pulmonary tissue (as measured via radiomics) were found to be associated with poor spirometry performance and a lower diffusing capacity for carbon monoxide. Unsupervised dynamic data clustering revealed subsets of patients with similar lung radiomic patterns that were found to be associated with similar forced expiratory volume in one second (FEV1) measurements. This implies that patients with similar radiomic feature vectors also presented with comparable spirometry performance, and were separable by varying degrees of pulmonary function as measured by imaging.

Purpose: Often, the inverse deformation vector field (DVF) is needed together with the corresponding forward DVF in 4D reconstruction and dose calculation, adaptive radiation therapy, and simultaneous deformable registration. This study aims at improving both accuracy and efficiency of iterative algorithms for DVF inversion, and advancing our understanding of divergence and latency conditions. Method: We introduce a framework of fixed-point iteration algorithms with active feedback control for DVF inversion. Based on rigorous convergence analysis, we design control mechanisms for modulating the inverse consistency (IC) residual of the current iterate, to be used as feedback into the next iterate. The control is designed adaptively to the input DVF with the objective to enlarge the convergence area and expedite convergence. Three particular settings of feedback control are introduced: constant value over the domain throughout the iteration; alternating values between iteration steps; and spatially variant values. We also introduce three spectral measures of the displacement Jacobian for characterizing a DVF. These measures reveal the critical role of what we term the non-translational displacement component (NTDC) of the DVF. We carry out inversion experiments with an analytical DVF pair, and with DVFs associated with thoracic CT images of 6 patients at end of expiration and end of inspiration. Results: NTDC-adaptive iterations are shown to attain a larger convergence region at a faster pace compared to previous non-adaptive DVF inversion iteration algorithms. By our numerical experiments, alternating control yields smaller IC residuals and inversion errors than constant control. Spatially variant control renders smaller residuals and errors by at least an order of magnitude, compared to other schemes, in no more than 10 steps. Inversion results also show remarkable quantitative agreement with analysis-based predictions. Conclusion: Our analysis captures properties o

This report describes the current state of flattening filter-free (FFF) radiotherapy beams implemented on conventional linear accelerators, and is aimed primarily at practicing medical physicists. The Therapy Emerging Technology Assessment Work Group of the American Association of Physicists in Medicine (AAPM) formed a writing group to assess FFF technology. The published literature on FFF technology was reviewed, along with technical specifications provided by vendors. Based on this information, supplemented by the clinical experience of the group members, consensus guidelines and recommendations for implementation of FFF technology were developed. Areas in need of further investigation were identified. Removing the flattening filter increases beam intensity, especially near the central axis. Increased intensity reduces treatment time, especially for high-dose stereotactic radiotherapy/radiosurgery (SRT/SRS). Furthermore, removing the flattening filter reduces out-of-field dose and improves beam modeling accuracy. FFF beams are advantageous for small field (e.g., SRS) treatments and are appropriate for intensity-modulated radiotherapy (IMRT). For conventional 3D radiotherapy of large targets, FFF beams may be disadvantageous compared to flattened beams because of the heterogeneity of FFF beam across the target (unless modulation is employed). For any application, the nonflat beam characteristics and substantially higher dose rates require consideration during the commissioning and quality assurance processes relative to flattened beams, and the appropriate clinical use of the technology needs to be identified. Consideration also needs to be given to these unique characteristics when undertaking facility planning. Several areas still warrant further research and development. Recommendations pertinent to FFF technology, including acceptance testing, commissioning, quality assurance, radiation safety, and facility planning, are presented. Examples of clinical applicat