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Medical Physics

Wiley

All preprints, ranked by how well they match Medical Physics's content profile, based on 14 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

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Heart-centered positioning and tailored beam-shaping filtration for reduced radiation dose in coronary artery calcium imaging: a MESA study

Colvert, B.; Rigolli, M.; Craine, A.; Criqui, M.; Contijoch, F.

2021-07-22 radiology and imaging 10.1101/2021.07.18.21259666 medRxiv
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PurposeCardiac CT has a clear clinical role in the evaluation of coronary artery disease and assessment of coronary artery calcium (CAC) but the use of ionizing radiation limits clinical use. Beam shaping "bow-tie" filters determine the radiation dose and the effective scan field-of-view diameter (SFOV) by delivering higher X-ray fluence to a region centered at the isocenter. A method for positioning the heart near the isocenter could enable reduced SFOV imaging and reduce dose in cardiac scans. However, a predictive approach to center the heart, the extent to which heart centering can reduce the SFOV, and the associated dose reductions have not been assessed. The purpose of this study is to build a heart-centered patient positioning model, to test whether it reduces the SFOV required for accurate CAC scoring, and to quantify the associated reduction in radiation dose. MethodsThe location of 38,184 calcium lesions (3,151 studies) in the Multi-Ethnic Study of Atherosclerosis (MESA) were utilized to build a predictive heart-centered positioning model and compare the impact of SFOV on CAC scoring accuracy in heart-centered and conventional body-centered scanning. Then, the positioning model was applied retrospectively to an independent, contemporary cohort of 118 individuals (81 with CAC>0) at our institution to validate the models ability to maintain CAC accuracy while reducing the SFOV. In these patients, the reduction in dose associated with a reduced SFOV beam-shaping filter was quantified. ResultsHeart centering reduced the SFOV diameter 25.7% relative to body centering while maintaining high CAC scoring accuracy (0.82% risk reclassification rate). In our validation cohort, imaging at this reduced SFOV with heart-centered positioning and tailored beam-shaping filtration led to a 26.9% median dose reduction (25-75th percentile: 21.6 to 29.8%) without any calcium risk reclassification. ConclusionsHeart-centered patient positioning enables a significant radiation dose reduction while maintaining CAC accuracy.

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Radiation-induced disruption of cardiac mitochondrial bioenergetics and nucleotide homeostasis in mice

Stawarska, K.; Kawecka, A.; Urbanowicz, K.; Kaminska, J.; Posiewnik, M.; Braczko, A.; Michnowska, W.; Kutryb-Zajac, B.; Tomasik, B.

2026-06-10 biochemistry 10.64898/2026.06.08.730816 medRxiv
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AimsCardiac stereotactic body radiotherapy (SBRT) has emerged as a promising non-invasive treatment for refractory ventricular tachycardia (VT). Intriguingly, the clinical benefit of SBRT often occurs within days of treatment, preceding the development of radiation-induced fibrosis, suggesting alternative underlying mechanisms. This study aimed to investigate the acute and persistent effects of ionizing radiation on cardiac bioenergetics and mitochondrial function, providing mechanistic insights into early cardiac responses to radiation exposure. Methods and resultsWe employed a translational multi-model approach, including HL-1 mouse cardiomyocytes and ex vivo mouse left ventricular living myocardial slices (LMS). Bioenergetic profiling, assessment of mitochondrial respiration and calcium handling were performed following exposure to clinically relevant radiation doses (10 Gy and 25 Gy). In HL-1 cardiomyocytes, 10 Gy induced acute bioenergetic stress, characterized by reduced adenylate energy charge, cytoskeletal disorganization, and impaired mitochondrial respiration, accompanied by increased calcium oscillation amplitude. 25 Gy exposure led to NAD+ depletion but paradoxically enhanced mitochondrial respiratory capacity, suggesting an adaptive metabolic response. Murine myocardial slices demonstrated reduced creatine content while preserving energy balance as indicated by phosphocreatine/ATP ratio, indicating tissue-level metabolic resilience. These findings reveal model-specific metabolic perturbations induced by cardiac irradiation, underscoring the importance of tissue complexity in modulating the cardiac response to radiation. ConclusionThis study demonstrates that ionizing radiation at 10 Gy and 25 Gy induced dose- and model-dependent bioenergetic alterations in cardiac cells and tissues, including changes in mitochondrial respiration, nucleotide levels, and redox balance. While 10 Gy exacerbated metabolic disruption, 25 Gy triggered partial recovery, highlighting differential responses across cellular and tissue levels. These metabolic changes may contribute to the immediate effects of cardiac SBRT and potentially to long-term cardiotoxicity. Translational PerspectiveOur study provides novel mechanistic insights into the metabolic effects of cardiac irradiation, revealing acute mitochondrial stress, redox imbalance and alterations in calcium homeostasis in cardiomyocytes. These early bioenergetic changes may contribute to both the immediate anti-arrhythmic effects and the potential long-term cardiotoxicity of stereotactic body radiation therapy. Understanding these molecular responses is essential to optimize the therapeutic window of cardiac radioablation and minimize adverse effects. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/730816v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@d963d3org.highwire.dtl.DTLVardef@28e03dorg.highwire.dtl.DTLVardef@19a0165org.highwire.dtl.DTLVardef@1d1ca34_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Organ Finder a new AI-based organ segmentation tool for CT

Edenbrandt, L.; Enqvist, O.; Larsson, M.; Ulen, J.

2022-11-18 radiology and imaging 10.1101/2022.11.15.22282357 medRxiv
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BackgroundAutomated organ segmentation in computed tomography (CT) is a vital component in many artificial intelligence-based tools in medical imaging. This study presents a new organ segmentation tool called Organ Finder 2.0. In contrast to most existing methods, Organ Finder was trained and evaluated on a rich multi-origin dataset with both contrast and non-contrast studies from different vendors and patient populations. ApproachA total of 1,171 CT studies from seven different publicly available CT databases were retrospectively included. Twenty CT studies were used as test set and the remaining 1,151 were used to train a convolutional neural network. Twenty-two different organs were studied. Professional annotators segmented a total of 5,826 organs and segmentation quality was assured manually for each of these organs. ResultsOrgan Finder showed high agreement with manual segmentations in the test set. The average Dice index over all organs was 0.93 and the same high performance was found for four different subgroups of the test set based on the presence or absence of intravenous and oral contrast. ConclusionsAn AI-based tool can be used to accurately segment organs in both contrast and non-contrast CT studies. The results indicate that a large training set and high-quality manual segmentations should be used to handle common variations in the appearance of clinical CT studies.

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Convolutional Encoder-Decoder Networks for Volumetric Computed Tomography Surviews from Single- and Dual-View Topograms

Shapira, N.; Bharthulwar, S.; Noel, P. B.

2022-05-21 radiology and imaging 10.1101/2022.05.17.22275229 medRxiv
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Computed tomography (CT) is an extensively used imaging modality capable of generating detailed images of a patients internal anatomy for diagnostic and interventional procedures. High-resolution volumes are created by measuring and combining information along many radiographic projection angles. In current medical practice, single and dual-view two-dimensional (2D) topograms are utilized for planning the proceeding diagnostic scans and for selecting favorable acquisition parameters, either manually or automatically, as well as for dose modulation calculations. In this study, we develop modified 2D to three-dimensional (3D) encoder-decoder neural network architectures to generate CT-like volumes from single and dual-view topograms. We validate the developed neural networks on synthesized topograms from publicly available thoracic CT datasets. Finally, we assess the viability of the proposed transformational encoder-decoder architecture on both common image similarity metrics and quantitative clinical use case metrics, a first for 2D-to-3D CT reconstruction research. According to our findings, both single-input and dual-input neural networks are able to provide accurate volumetric anatomical estimates. The proposed technology will allow for improved (i) planning of diagnostic CT acquisitions, (ii) input for various dose modulation techniques, and (iii) recommendations for acquisition parameters and/or automatic parameter selection. It may also provide for an accurate attenuation correction map for positron emission tomography (PET) with only a small fraction of the radiation dose utilized.

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Application of simultaneous uncertainty quantification for image segmentation with probabilistic deep learning: Performance benchmarking of oropharyngeal cancer target delineation as a use-case

Sahlsten, J.; Jaskari, J.; Wahid, K. A.; Ahmed, S.; Glerean, E.; He, R.; Kann, B.; Makitie, A. A.; Fuller, C. D.; Naser, M. A.; Kaski, K.

2023-02-24 radiology and imaging 10.1101/2023.02.20.23286188 medRxiv
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BackgroundOropharyngeal cancer (OPC) is a widespread disease, with radiotherapy being a core treatment modality. Manual segmentation of the primary gross tumor volume (GTVp) is currently employed for OPC radiotherapy planning, but is subject to significant interobserver variability. Deep learning (DL) approaches have shown promise in automating GTVp segmentation, but comparative (auto)confidence metrics of these models predictions has not been well-explored. Quantifying instance-specific DL model uncertainty is crucial to improving clinician trust and facilitating broad clinical implementation. Therefore, in this study, probabilistic DL models for GTVp auto-segmentation were developed using large-scale PET/CT datasets, and various uncertainty auto-estimation methods were systematically investigated and benchmarked. MethodsWe utilized the publicly available 2021 HECKTOR Challenge training dataset with 224 co-registered PET/CT scans of OPC patients with corresponding GTVp segmentations as a development set. A separate set of 67 co-registered PET/CT scans of OPC patients with corresponding GTVp segmentations was used for external validation. Two approximate Bayesian deep learning methods, the MC Dropout Ensemble and Deep Ensemble, both with five submodels, were evaluated for GTVp segmentation and uncertainty performance. The segmentation performance was evaluated using the volumetric Dice similarity coefficient (DSC), mean surface distance (MSD), and Hausdorff distance at 95% (95HD). The uncertainty was evaluated using four measures from literature: coefficient of variation (CV), structure expected entropy, structure predictive entropy, and structure mutual information, and additionally with our novel Dice-risk measure. The utility of uncertainty information was evaluated with the accuracy of uncertainty-based segmentation performance prediction using the Accuracy vs Uncertainty (AvU) metric, and by examining the linear correlation between uncertainty estimates and DSC. In addition, batch-based and instance-based referral processes were examined, where the patients with high uncertainty were rejected from the set. In the batch referral process, the area under the referral curve with DSC (R-DSC AUC) was used for evaluation, whereas in the instance referral process, the DSC at various uncertainty thresholds were examined. ResultsBoth models behaved similarly in terms of the segmentation performance and uncertainty estimation. Specifically, the MC Dropout Ensemble had 0.776 DSC, 1.703 mm MSD, and 5.385 mm 95HD. The Deep Ensemble had 0.767 DSC, 1.717 mm MSD, and 5.477 mm 95HD. The uncertainty measure with the highest DSC correlation was structure predictive entropy with correlation coefficients of 0.699 and 0.692 for the MC Dropout Ensemble and the Deep Ensemble, respectively. The highest AvU value was 0.866 for both models. The best performing uncertainty measure for both models was the CV which had R-DSC AUC of 0.783 and 0.782 for the MC Dropout Ensemble and Deep Ensemble, respectively. With referring patients based on uncertainty thresholds from 0.85 validation DSC for all uncertainty measures, on average the DSC improved from the full dataset by 4.7% and 5.0% while referring 21.8% and 22% patients for MC Dropout Ensemble and Deep Ensemble, respectively. ConclusionWe found that many of the investigated methods provide overall similar but distinct utility in terms of predicting segmentation quality and referral performance. These findings are a critical first-step towards more widespread implementation of uncertainty quantification in OPC GTVp segmentation.

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Investigation of Autosegmentation Techniques on T2-Weighted MRI for Off-line Dose Reconstruction in MR-Linac Adapt to Position Workflow for Head and Neck Cancers

McDonald, B. A.; Cardenas, C.; O'Connell, N.; Ahmed, S.; Naser, M. A.; Wahid, K. A.; Xu, J.; Thill, D.; Zuhour, R.; Mesko, S.; Augustyn, A.; Buszek, S. M.; Grant, S.; Chapman, B. V.; Bagley, A.; He, R.; Mohamed, A. S. R.; Christodouleas, J. P.; Brock, K. K.; Fuller, C. D.

2021-10-01 radiology and imaging 10.1101/2021.09.30.21264327 medRxiv
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PurposeIn order to accurately accumulate delivered dose for head and neck cancer patients treated with the Adapt to Position workflow on the 1.5T magnetic resonance imaging (MRI)-linear accelerator (MR-linac), the low-resolution T2-weighted MRIs used for daily setup must be segmented to enable reconstruction of the delivered dose at each fraction. In this study, our goal is to evaluate various autosegmentation methods for head and neck organs at risk (OARs) on on-board setup MRIs from the MR-linac for off-line reconstruction of delivered dose. MethodsSeven OARs (parotid glands, submandibular glands, mandible, spinal cord, and brainstem) were contoured on 43 images by seven observers each. Ground truth contours were generated using a simultaneous truth and performance level estimation (STAPLE) algorithm. 20 autosegmentation methods were evaluated in ADMIRE: 1-9) atlas-based autosegmentation using a population atlas library (PAL) of 5/10/15 patients with STAPLE, patch fusion (PF), random forest (RF) for label fusion; 10-19) autosegmentation using images from a patients 1-4 prior fractions (individualized patient prior (IPP)) using STAPLE/PF/RF; 20) deep learning (DL) (3D ResUNet trained on 43 ground truth structure sets plus 45 contoured by one observer). Execution time was measured for each method. Autosegmented structures were compared to ground truth structures using the Dice similarity coefficient, mean surface distance, Hausdorff distance, and Jaccard index. For each metric and OAR, performance was compared to the inter-observer variability using Dunns test with control. Methods were compared pairwise using the Steel-Dwass test for each metric pooled across all OARs. Further dosimetric analysis was performed on three high-performing autosegmentation methods (DL, IPP with RF and 4 fractions (IPP_RF_4), IPP with 1 fraction (IPP_1)), and one low-performing (PAL with STAPLE and 5 atlases (PAL_ST_5)). For five patients, delivered doses from clinical plans were recalculated on setup images with ground truth and autosegmented structure sets. Differences in maximum and mean dose to each structure between the ground truth and autosegmented structures were calculated and correlated with geometric metrics. ResultsDL and IPP methods performed best overall, all significantly outperforming inter-observer variability and with no significant difference between methods in pairwise comparison. PAL methods performed worst overall; most were not significantly different from the inter-observer variability or from each other. DL was the fastest method (33 seconds per case) and PAL methods the slowest (3.7 - 13.8 minutes per case). Execution time increased with number of prior fractions/atlases for IPP and PAL. For DL, IPP_1, and IPP_RF_4, the majority (95%) of dose differences were within {+/-}250 cGy from ground truth, but outlier differences up to 785 cGy occurred. Dose differences were much higher for PAL_ST_5, with outlier differences up to 1920 cGy. Dose differences showed weak but significant correlations with all geometric metrics (R2 between 0.030 and 0.314). ConclusionsThe autosegmentation methods offering the best combination of performance and execution time are DL and IPP_1. Dose reconstruction on on-board T2-weighted MRIs is feasible with autosegmented structures with minimal dosimetric variation from ground truth, but contours should be visually inspected prior to dose reconstruction in an end-to-end dose accumulation workflow.

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Deep learning-assisted multiple organ segmentation from whole-body CT images

Salimi, y.; Shiri, I.; MAnsouri, Z.; Zaidi, H.

2023-10-21 radiology and imaging 10.1101/2023.10.20.23297331 medRxiv
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BackgroundAutomated organ segmentation from computed tomography (CT) images facilitates a number of clinical applications, including clinical diagnosis, monitoring of treatment response, quantification, radiation therapy treatment planning, and radiation dosimetry. PurposeTo develop a novel deep learning framework to generate multi-organ masks from CT images for 23 different body organs. MethodsA dataset consisting of 3106 CT images (649,398 axial 2D CT slices, 13,640 images/segment pairs) and ground-truth manual segmentation from various online available databases were collected. After cropping them to body contour, they were resized, normalized and used to train separate models for 23 organs. Data were split to train (80%) and test (20%) covering all the databases. A Res-UNET model was trained to generate segmentation masks from the input normalized CT images. The model output was converted back to the original dimensions and compared with ground-truth segmentation masks in terms of Dice and Jaccard coefficients. The information about organ positions was implemented during post-processing by providing six anchor organ segmentations as input. Our model was compared with the online available "TotalSegmentator" model through testing our model on their test datasets and their model on our test datasets. ResultsThe average Dice coefficient before and after post-processing was 84.28% and 83.26% respectively. The average Jaccard index was 76.17 and 70.60 before and after post-processing respectively. Dice coefficients over 90% were achieved for the liver, heart, bones, kidneys, spleen, femur heads, lungs, aorta, eyes, and brain segmentation masks. Post-processing improved the performance in only nine organs. Our model on the TotalSegmentator dataset was better than their models on our dataset in five organs out of 15 common organs and achieved almost similar performance for two organs. ConclusionsThe availability of a fast and reliable multi-organ segmentation tool leverages implementation in clinical setting. In this study, we developed deep learning models to segment multiple body organs and compared the performance of our models with different algorithms. Our model was trained on images presenting with large variability emanating from different databases producing acceptable results even in cases with unusual anatomies and pathologies, such as splenomegaly. We recommend using these algorithms for organs providing good performance. One of the main merits of our proposed models is their lightweight nature with an average inference time of 1.67 seconds per case per organ for a total-body CT image, which facilitates their implementation on standard computers.

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Deep learning models to predict mammographic density jointly on standard dose and low dose images

Squires, S.; Mackenzie, A.; Evans, D. G.; Howell, S. J.; Astley, S. M.

2024-04-12 radiology and imaging 10.1101/2024.04.10.24305572 medRxiv
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ObjectivesMammographic density is associated with increased risk of developing breast cancer. Automated estimation of density in women below normal screening age would enable earlier risk stratification. We are piloting the use of low dose mammograms combined with models that can make accurate mammographic density estimates. MethodsThree models were trained on a joint set (107,619) of standard dose mammograms with associated density scores and their simulated low dose counterparts such that the models made predictions on standard and low dose mammograms. A second set of models was trained separately on the standard and simulated low dose mammograms. All models were tested on a held-out set from the training data and an independent dataset with 294 pairs of standard and real low dose mammograms. ResultsThe root mean squared errors (RMSE) between the model predictions and density scores on standard and simulated low dose images were 8.26 (8.16-8.36) and 8.27 (8.17-8.38) respectively. The RMSE between predictions on standard and simulated low dose images for the jointly trained models was 1.91 (1.88-1.96). The RMSE of the predictions on the real low dose images compared to the standard dose images is 3.79 (2.75-4.99). ConclusionsDeep learning models make density predictions on low dose images with similar quality as on standard dose images. Such automated analysis of low dose mammograms could contribute to accurate breast cancer risk estimation in younger women enabling stratification for further monitoring and preventative therapy. Advances in knowledgeMammographic density can be estimated in low dose mammograms with similar quality to standard dose mammograms.

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Evaluating clinical acceptability of organ-at-risk segmentation In head & neck cancer using a compendium of open-source 3D convolutional neural networks

Marsilla, J.; Won Kim, J.; Kim, S.; Tkachuck, D.; Rey-McIntyre, K.; Patel, T.; Tadic, T.; Liu, F.-F.; Bratman, S.; Hope, A.; Haibe-Kains, B.

2022-01-25 radiology and imaging 10.1101/2022.01.15.22269276 medRxiv
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Background and PurposeAuto-segmentation of organs at risk (OAR) in cancer patients is essential for enhancing radiotherapy planning efficacy and reducing inter-observer variability. Deep learning auto-segmentation models have shown promise, but their lack of transparency and reproducibility hinders their generalizability and clinical acceptability, limiting their use in clinical settings. Materials and MethodsThis study introduces SCARF (auto-Segmentation Clinical Acceptability & Reproducibility Framework), a comprehensive six-stage reproducible framework designed to benchmark open-source convolutional neural networks for auto-segmentation of 19 essential OARs in head and neck cancer (HNC). ResultsSCARF offers an easily implementable framework for designing and reproducibly benchmarking auto-segmentation tools, along with thorough expert assessment capabilities. Expert assessment labelled 16/19 AI-generated OAR categories as acceptable with minor revisions. Boundary distance metrics, such as 95th Percentile Hausdorff Distance (95HD), were found to be 2x more correlated to Mean Acceptability Rating (MAR) than volumetric overlap metrics (DICE). ConclusionsThe introduction of SCARF, our auto-Segmentation Clinical Acceptability & Reproducibility Framework, represents a significant step forward in systematically assessing the performance of AI models for auto-segmentation in radiation therapy planning. By providing a comprehensive and reproducible framework, SCARF facilitates benchmarking and expert assessment of AI-driven auto-segmentation tools, addressing the need for transparency and reproducibility in this domain. The robust foundation laid by SCARF enables the progression towards the creation of usable AI tools in the field of radiation therapy. Through its emphasis on clinical acceptability and expert assessment, SCARF fosters the integration of AI models into clinical environments, paving the way for more randomised clinical trials to evaluate their real-world impact. O_TEXTBOXHighlightsO_LIOur study highlights the significance of both quantitative and qualitative controls for benchmarking new auto-segmentation systems effectively, promoting a more robust evaluation process of AI tools. C_LIO_LIWe address the lack of baseline models for medical image segmentation benchmarking by presenting SCARF, a comprehensive and reproducible six-stage framework, which serves as a valuable resource for advancing auto-segmentation research and contributing to the foundation of AI tools in radiation therapy planning. C_LIO_LISCARF enables benchmarking of 11 open-source convolutional neural networks (CNN) against 19 essential organs-at-risk (OARs) for radiation therapy in head and neck cancer, fostering transparency and facilitating external validation. C_LIO_LITo accurately assess the performance of auto-segmentation models, we introduce a clinical assessment toolkit based on the open-source QUANNOTATE platform, further promoting the use of external validation tools and expert assessment. C_LIO_LIOur study emphasises the importance of clinical acceptability testing and advocates its integration into developing validated AI tools for radiation therapy planning and beyond, bridging the gap between AI research and clinical practice. C_LI C_TEXTBOX

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PixelPrint: Three-dimensional printing of realistic patient-specific lung phantoms for validation of computed tomography post-processing and inference algorithms

Shapira, N.; Donovan, K.; Mei, K.; Geagan, M.; Roshkovan, L.; Gang, G.; Abed, M.; Linna, N. B.; Cranston, C. P.; Leary, C. N.; Dhanaliwala, A. H.; Kontos, D.; Litt, H. I.; Stayman, J. W.; Shinohara, R. T.; Noël, P. B.

2022-05-10 radiology and imaging 10.1101/2022.05.06.22274739 medRxiv
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BackgroundRadiomics and other modern clinical decision-support algorithms are emerging as the next frontier for diagnostic and prognostic medical imaging. However, heterogeneities in image characteristics due to variations in imaging systems and protocols hamper the advancement of reproducible feature extraction pipelines. There is a growing need for realistic patient-based phantoms that accurately mimic human anatomy and disease manifestations to provide consistent ground-truth targets when comparing different feature extraction or image cohort normalization techniques. Materials and MethodsPixelPrint was developed for 3D-printing lifelike lung phantoms for computed tomography (CT) by directly translating clinical images into printer instructions that control the density on a voxel-by-voxel basis. CT datasets of three COVID-19 pneumonia patients served as input for 3D-printing lung phantoms. Five radiologists rated patient and phantom images for imaging characteristics and diagnostic confidence in a blinded reader study. Linear mixed models were utilized to evaluate effect sizes of evaluating phantom as opposed to patient images. Finally, PixelPrints reproducibility was evaluated by producing four phantoms from the same clinical images. ResultsEstimated mean differences between patient and phantom images were small (0.03-0.29, using a 1-5 scale). Effect size assessment with respect to rating variabilities revealed that the effect of having a phantom in the image is within one-third of the inter- and intra-reader variabilities. PixelPrints production reproducibility tests showed high correspondence among four phantoms produced using the same patient images, with higher similarity scores between high-dose scans of the different phantoms than those measured between clinical-dose scans of a single phantom. ConclusionsWe demonstrated PixelPrints ability to produce lifelike 3D-printed CT lung phantoms reliably. These can provide ground-truth targets for validating the generalizability of inference-based decision-support algorithms between different health centers and imaging protocols, as well as for optimizing scan protocols with realistic patient-based phantoms.

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Head and Neck Cancer Primary Tumor Auto Segmentation using Model Ensembling of Deep Learning in PET-CT Images

Naser, M. A.; Wahid, K. A.; van Dijk, L. V.; He, R.; Abdelaal, M. A.; Dede, C.; Mohamed, A. S. R.; Fuller, C. D.

2021-10-18 radiology and imaging 10.1101/2021.10.14.21264953 medRxiv
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Auto-segmentation of primary tumors in oropharyngeal cancer using PET/CT images is an unmet need that has the potential to improve radiation oncology workflows. In this study, we develop a series of deep learning models based on a 3D Residual Unet (ResUnet) architecture that can segment oropharyngeal tumors with high performance as demonstrated through internal and external validation of large-scale datasets (training size = 224 patients, testing size = 101 patients) as part of the 2021 HECKTOR Challenge. Specifically, we leverage ResUNet models with either 256 or 512 bottleneck layer channels that are able to demonstrate internal validation (10-fold cross-validation) mean Dice similarity coefficient (DSC) up to 0.771 and median 95% Hausdorff distance (95% HD) as low as 2.919 mm. We employ label fusion ensemble approaches, including Simultaneous Truth and Performance Level Estimation (STAPLE) and a voxel-level threshold approach based on majority voting (AVERAGE), to generate consensus segmentations on the test data by combining the segmentations produced through different trained cross-validation models. We demonstrate that our best performing ensembling approach (256 channels AVERAGE) achieves a mean DSC of 0.770 and median 95% HD of 3.143 mm through independent external validation on the test set. Concordance of internal and external validation results suggests our models are robust and can generalize well to unseen PET/CT data. We advocate that ResUNet models coupled to label fusion ensembling approaches are promising candidates for PET/CT oropharyngeal primary tumors auto-segmentation, with future investigations targeting the ideal combination of channel combinations and label fusion strategies to maximize segmentation performance.

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FLASH Radiotherapy is faster than a heartbeat: A compartmental model to illustrate the interplay between tissue oxygen perfusion and ultra-high dose rate effects.

Ballesteros-Zebadua, P.; Jansen, J.; Grilij, V.; Franco-Perez, J.; Vozenin, M.-C.; Abolfath, R.

2026-03-16 biochemistry 10.64898/2026.03.12.711443 medRxiv
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Ultra-high-dose-rate therapy enhances the protection of normal tissues and reduces side effects while effectively controlling tumors. This biological phenomenon is called the FLASH effect, and when observed, therapy is called FLASH Radiotherapy (FLASH-RT). Various hypotheses have been proposed to explain how ultra-high dose rates achieve these effects under different conditions, with the impact of tissue oxygen perfusion still needing further investigation. FLASH-RT involves brief exposure to radiation, which results in fewer heartbeats occurring during the irradiation period, which could lead to reduced tissue oxygen perfusion occurring during the treatment timeframe. Therefore, we developed a compartmental model to simulate oxygen transfer and its interaction with radiation. The proposed model consists of three compartments: 1) the heart and arteries; 2) the irradiated brains blood vessels and capillaries; and 3) the irradiated brain tissue. We employed a system of differential equations, incorporating experimental data from in vivo oxygen measurements using the Oxyphor probe in the brain, to fit the model parameters to the experimental results. This model shows how dose rate and oxygen perfusion could influence chemical processes such as lipid peroxidation, potentially leading to differential biological effects. Our analysis of lipid peroxidation as a function of dose rate revealed a sigmoidal dose-rate-response curve that correlates well with several published biological response datasets. Our results indicate that the differential chemical effects of FLASH-RT compared with conventional dose rates may depend on factors such as oxygen perfusion, consumption, and tissue oxygen tension. This suggests that the temporal dynamics of oxygen could play a crucial role in enhancing the therapeutic window for FLASH-RT treatments. Furthermore, it suggests that the magnitude of some observed FLASH effects may vary across tissues or tumors and across experimental models, given differential oxygen dynamics.

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The Effect of Image Resolution on the Performance of Deep Learning Algorithms in Detecting Calcaneus Fractures on X-Ray

Yee, N. J.; Taseh, A.; Ghandour, S.; Sirls, E.; Halai, M.; Whyne, C.; DiGiovanni, C. W.; Kwon, J. Y.; Ashkani-Esfahani, S. J.

2025-09-07 orthopedics 10.1101/2025.09.04.25334786 medRxiv
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PurposeTo evaluate convolutional neural network (CNN) model training strategies that optimize the performance of calcaneus fracture detection on radiographs at different image resolutions. Materials and MethodsThis retrospective study included foot radiographs from a single hospital between 2015 and 2022 for a total of 1,775 x-ray series (551 fractures; 1,224 without) and was split into training (70%), validation (15%), and testing (15%). ImageNet pre-trained ResNet models were fine-tuned on the dataset. Three training strategies were evaluated: 1) single size: trained exclusively on 128x128, 256x256, 512x512, 640x640, or 900x900 radiographs (5 model sets); 2) curriculum learning: trained exclusively on 128x128 radiographs then exclusively on 256x256, then 512x512, then 640x640, and finally on 900x900 (5 model sets); and 3) multi-scale augmentation: trained on x-ray images resized along continuous dimensions between 128x128 to 900x900 (1 model set). Inference time and training time were compared. ResultsMulti-scale augmentation trained models achieved the highest average area under the Receiver Operating Characteristic curve of 0.938 [95% CI: 0.936 - 0.939] for a single model across image resolutions compared to the other strategies without prolonging training or inference time. Using the optimal model sets, curriculum learning had the highest sensitivity on in-distribution low-resolution images (85.4% to 90.1%) and on out-of-distribution high-resolution images (78.2% to 89.2%). However, curriculum learning models took significantly longer to train (11.8 [IQR: 11.1-16.4] hours; P<.001). ConclusioWhile 512x512 images worked well for fracture identification, curriculum learning and multi-scale augmentation training strategies algorithmically improved model robustness towards different image resolutions without requiring additional annotated data. Summary statementDifferent deep learning training strategies affect performance in detecting calcaneus fractures on radiographs across in- and out-of-distribution image resolutions, with a multi-scale augmentation strategy conferring the greatest overall performance improvement in a single model. Key pointsO_LITraining strategies addressing differences in radiograph image resolution (or pixel dimensions) could improve deep learning performance. C_LIO_LIThe highest average performance across different image resolutions in a single model was achieved by multi-scale augmentation, where the sampled training dataset is uniformly resized between square resolutions of 128x128 to 900x900. C_LIO_LICompared to model training on a single image resolution, sequentially training on increasingly higher resolution images up to 900x900 (i.e., curriculum learning) resulted in higher fracture detection performance on images resolutions between 128x128 and 2048x2048. C_LI

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Deep Learning-powered CT-less Multi-tracer Organ Segmentation from PET Images: A solution for unreliable CT segmentation in PET/CT Imaging

Salimi, Y.; Mansouri, Z.; Shiri, I.; Mainta, I.; Zaidi, H.

2024-08-28 radiology and imaging 10.1101/2024.08.27.24312482 medRxiv
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IntroductionThe common approach for organ segmentation in hybrid imaging relies on co-registered CT (CTAC) images. This method, however, presents several limitations in real clinical workflows where mismatch between PET and CT images are very common. Moreover, low-dose CTAC images have poor quality, thus challenging the segmentation task. Recent advances in CT-less PET imaging further highlight the necessity for an effective PET organ segmentation pipeline that does not rely on CT images. Therefore, the goal of this study was to develop a CT-less multi-tracer PET segmentation framework. MethodsWe collected 2062 PET/CT images from multiple scanners. The patients were injected with either 18F-FDG (1487) or 68Ga-PSMA (575). PET/CT images with any kind of mismatch between PET and CT images were detected through visual assessment and excluded from our study. Multiple organs were delineated on CT components using previously trained in-house developed nnU-Net models. The segmentation masks were resampled to co-registered PET images and used to train four different deep-learning models using different images as input, including non-corrected PET (PET-NC) and attenuation and scatter-corrected PET (PET-ASC) for 18F-FDG (tasks #1 and #2, respectively using 22 organs) and PET-NC and PET-ASC for 68Ga tracers (tasks #3 and #4, respectively, using 15 organs). The models performance was evaluated in terms of Dice coefficient, Jaccard index, and segment volume difference. ResultsThe average Dice coefficient over all organs was 0.81{+/-}0.15, 0.82{+/-}0.14, 0.77{+/-}0.17, and 0.79{+/-}0.16 for tasks #1, #2, #3, and #4, respectively. PET-ASC models outperformed PET-NC models (P-value < 0.05). The highest Dice values were achieved for the brain (0.93 to 0.96 in all four tasks), whereas the lowest values were achieved for small organs, such as the adrenal glands. The trained models showed robust performance on dynamic noisy images as well. ConclusionDeep learning models allow high performance multi-organ segmentation for two popular PET tracers without the use of CT information. These models may tackle the limitations of using CT segmentation in PET/CT image quantification, kinetic modeling, radiomics analysis, dosimetry, or any other tasks that require organ segmentation masks.

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Dual-energy computed tomography imaging with megavoltage and kilovoltage x-ray spectra

Jadick, G.; Schlafly, G.; La Riviere, P.

2023-06-29 radiology and imaging 10.1101/2023.06.22.23291766 medRxiv
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PurposeSingle-energy computed tomography (CT) often suffers from poor contrast, yet it remains critical for effec-tive radiotherapy treatment. Modern therapy systems are often equipped with both megavoltage (MV) and kilovoltage (kV) x-ray sources and thus already possess the hardware needed for dual-energy (DE) CT. There exists an unexplored potential for enhanced image contrast using MV-kV DE-CT in radiotherapy contexts. ApproachA toy model comprising a single-line integral through a two-material object was designed for computing basis material signal-to-noise ratio (SNR) using estimation theory. Five dose-matched spectra (three kV, two MV) and three variables were considered: spectral combination, spectral dose allocation, and object material composition. The single-line model was extended to a simulated fan-beam CT acquisition of an anthropomorphic phantom with and without a metal implant. Basis material sinograms were computed and synthesized into virtual monoenergetic images (VMIs). MV-kV and kV-kV VMIs were compared with single-energy images. ResultsThe 80kV-140kV pair typically yielded the best SNRs, but for bone thicknesses greater than 8 cm, the detunedMV-80kV pair surpassed it. Peak MV-kV SNR was achieved with approximately 90% dose allocated to the MV spectrum. For the CT simulations, MV-kV VMIs yielded a higher contrast-to-noise ratio (CNR) than single-energy CT at specific monoenergies. With the metal implant, MV-kV produced a higher maximum CNR and lower minimum root-mean-square-error than kV-kV. ConclusionsThis work quantitatively analyzes MV-kV DE-CT imaging and assesses its potential advantages. This technique may yield improved contrast and accuracy relative to dose-matched single-energy CT or kV-kV DE-CT, depending on object composition.

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Capability and reliability of deep learning models to make density predictions on low dose mammograms

Squires, S.; Mackenzie, A.; Evans, D. G.; Howell, S. J.; Astley, S. M.

2024-01-02 radiology and imaging 10.1101/2024.01.01.23300313 medRxiv
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PurposeBreast density is associated with risk of developing cancer and can be automatically estimated, using deep learning models, from digital mammograms. Our aim is to estimate the capacity and reliability of such models to estimate density from low dose mammograms taken to enable risk estimates for younger women. MethodsWe trained deep learning models on standard and simulated low dose mammograms. The models were then tested on a mammography data-set with paired standard and low-dose image. The effect of different factors (including age, density and dose ratio) on the differences between predictions on standard and low dose are analysed. Methods to improve performance are assessed and factors that reduce model quality are demonstrated. ResultsWe showed that whilst many factors have no significant effect on the quality of low dose density prediction both density and breast area have an impact. For example correlation between density predictions on low and standard dose images of breasts with the largest breast area is 0.985 (0.949-0.995) while with the smallest is 0.882 (0.697-0.961). We also demonstrated that averaging across CC-MLO images and across repeatedly trained models can improve predictive performance. ConclusionLow dose mammography can be used to produce density and risk estimates that are comparable to standard dose images. Averaging across CC-MLO and across model predictions should improve this performance. Model quality is reduced when making predictions on denser and smaller breasts. Code is available at: https://github.com/stevensquires/

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Precise prostate contours: setting the bar and meticulously evaluating AI performance

Song, Y.; Dornisch, A. M.; Dess, R. T.; Margolis, D. J.; Weinberg, E.; Barrett, T.; Cornell, M.; Fan, R. E.; Harisinghani, M.; Kamran, S. C.; Lee, J. H.; Li, C. X.; Liss, M. A.; Rusu, M.; Santos, J.; Sonn, G. A.; Vidic, I.; Woolen, S. A.; Dale, A.; Seibert, T. M.

2024-10-22 radiology and imaging 10.1101/2024.10.21.24315771 medRxiv
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IntroductionEvaluation of artificial intelligence (AI) algorithms for prostate segmentation is challenging because ground truth is lacking. We aimed to (1) create a reference standard dataset with precise prostate contours by expert consensus and (2) evaluate various AI tools against this standard. Materials and methodsWe obtained prostate MRI cases from six institutions from the Quantitative Prostate Imaging Consortium. A panel of four experts (two genitourinary radiologists, two prostate radiation oncologists) meticulously developed consensus prostate segmentations on axial T2-weighted series. We evaluated the performance of six AI tools (three commercially available, three academic) using Dice scores, distance from reference contour, and volume error. ResultsThe panel achieved consensus prostate segmentation on each slice of all 68 patient cases included in the reference dataset. We present two patient examples to serve as contouring guides. Depending on the AI tool, median Dice scores (across patients) ranged from 0.80 to 0.94 for whole prostate segmentation. For a typical (median) patient, AI tools had a mean error over the prostate surface ranging from 1.3 to 2.4 mm. They maximally deviated 3.0 to 9.4 mm outside the prostate and 3.0 to 8.5 mm inside the prostate for a typical patient. Error in prostate volume measurement for a typical patient ranged from 4.3% to 31.4%. DiscussionWe established an expert consensus benchmark for prostate segmentation. The best-performing AI tools have typical accuracy greater than that reported for radiation oncologists using CT scans (most common clinical approach for radiotherapy planning). Physician review remains essential to detect occasional major errors.

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Multicenter Comparison of AI Deep Learning Reconstruction, Iterative Reconstruction, and Filtered Back Projection for Coronary Artery Calcification Scoring

Winkler, A. R.; Campos, J. D.; Winkler, M. L.

2024-11-01 radiology and imaging 10.1101/2024.10.30.24316447 medRxiv
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ObjectiveTo validate the feasibility of AI Deep Learning Reconstruction for Coronary Artery Calcification Scoring in order to decrease radiation exposure on a 4cm detector CT scanner. This is the first such validation on devices that are most commonly utilized for this procedure. MethodsData from 105 consecutive patients referred for Coronary Artery Calcification Scoring (CACS) in 4 centers was reconstructed with Filtered Back Projection (FBP), Iterative Reconstruction (Hybrid-IR), and AI Deep Learning Reconstruction (AI DLR), and analyzed both quantitatively and qualitatively to determine if AI DLR can be routinely used for this purpose. Additional phantom testing was performed to determine if further dose reduction can be accomplished with AI DLR while maintaining or improving image quality compared to current Hybrid-IR reconstruction. ResultsQuantitively, there was excellent agreement between the three reconstructions (FBP, Hybrid IR and AI DLR) with an interclass coefficient of 0.99. The mean CACS for Filtered Back Projection Reconstructions was 111.05. The mean CACS for Hybrid-IR was 91.30. The mean CACS for AI Deep Learning Reconstructions was 93.50. Qualitatively, image quality was consistently better with AI DLR than with Hybrid-IR at both soft tissue and lung windowing. Based on our phantom experiments, AI DLR allows for dose reduction of at least a 37% without any image quality penalty compared to Hybrid-IR. ConclusionsThe use of AI DLR for use in CACS on 4 cm coverage CT scanner has been quantitatively and qualitatively validated for use for the first time. AI DLR produces qualitatively and quantitively better image quality than Hybrid-IR at the same dose level, and produces good agreement in categorization of Agatston scores. In vivo and in vitro evaluations show that AI DLR will allow for an at least a 37% further dose reduction on a 4 cm coverage CT scanner.

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Nationwide Organ Volume Reference Standards and Aging-Related Changes in Abdominal CT from Japan

Kikuchi, T.; Yamamoto, K.; Yamagishi, Y.; Akashi, T.; Hanaoka, S.; Yoshikawa, T.; Fujii, H.; Mori, H.; Makimoto, H.; Kohro, T.

2026-02-03 radiology and imaging 10.64898/2026.01.30.26345246 medRxiv
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BackgroundLarge-scale CT-based reference standards for abdominal organ volume, incorporating age, sex, and body size, are limited. PurposeTo establish sex- and age-specific reference distributions for major abdominal organ volumes on non-contrast abdominopelvic CT in a nationwide Japanese cohort to provide a foundation for automated clinical assessment and dose optimization. Materials and MethodsIn this retrospective, multicenter study, using the Japan Medical Image Database, we identified all non-contrast abdominopelvic CT examinations performed in 2024. Unique adults with available data on age, sex, height, and weight were included in this study. The final sample comprised 49,764 examinations (26,456 men and 23,308 women) conducted at nine institutions. Automated segmentation (TotalSegmentator v2.10.0) was used to produce organ volumes, excluding hollow viscera. The sex-specific 10th, 25th, 50th, 75th, and 90th percentiles were calculated. Age-volume relationships of body surface area (BSA)-normalized volumes (mL/m2) were modeled using natural cubic splines (four degrees of freedom) separately by sex. ResultsMedian (mL) male vs female volumes were as follows: liver, 1194.7 vs 1024.0; pancreas, 63.6 vs 52.2; spleen, 118.1 vs 95.1; kidneys (total), 268.3 vs 221.2; adrenals (total), 6.6 vs 4.2; iliopsoas (total), 483.4 vs 317.7; prostate, 24.9 (men only). Age-volume relationships of BSA-normalized volumes showed convex patterns for the liver, pancreas, and kidneys in both sexes and for male adrenal glands; lower values in older age groups for the spleen and iliopsoas in both sexes; and higher values in older age groups for the prostate and female adrenal glands. ConclusionThis nationwide Japanese CT cohort provides sex- and age-resolved volumetric reference standards. These standards enable objective identification of abnormalities, support personalized medicine, and facilitate automated AI-based reporting to reduce radiologist workload and optimize radiation dose protocols. Key ResultsO_LIMedian volumes (men vs women, mL): liver 1195/1024; pancreas 64/52; spleen 118/95; kidneys 268/221; adrenals 6.6/4.2; iliopsoas 483/318; prostate 25. C_LIO_LIBody surface area-normalized age-volume relationships were convex for liver, pancreas, and kidneys in both sexes and for male adrenal glands. C_LIO_LISpleen and iliopsoas declined monotonically with age in both sexes, whereas prostate and female adrenal glands increased monotonically. C_LI

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Evaluation of Photon-Counting CT for Spectral Imaging in Cardiovascular Applications: Impact of Lumen Size, Dose, and Patient Habitus

Rybertt, M. V.; Liu, L. P.; Mathew, M.; Sahbaee, P.; Litt, H. I.; Noel, P. B.

2025-01-08 radiology and imaging 10.1101/2025.01.07.25320150 medRxiv
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ObjectivesThis study evaluates the performance of a clinical dual-source photon-counting computed tomography (PCCT) system in quantifying iodine within calcified vessels, using 3D- printed phantoms with vascular-like structures lined with calcium. MethodsParameters assessed include lumen diameters (4, 6, 8, 10, and 12 mm), phantom sizes (S: 20x20 cm, M: 25x25 cm, L: 30x40 cm, XL: 40x50 cm, representing the 99th percentile of US patient sizes), and iodine concentrations (2, 5, and 10 mg/mL). Scans were performed at radiation dose levels of 5, 10, 15, and 20 mGy to systematically evaluate iodine quantification accuracy and spectral imaging performance. ResultsThe results indicate that for lumen diameters [&ge;]6 mm, iodine quantification remains stable across all dose levels and phantom sizes, with deviations consistently below 0.6 mg/mL. Whereas, for 4 mm lumens, stability is observed primarily in smaller to medium phantoms, highlighting the influence of patient size and radiation dose on quantification accuracy. Virtual Monoenergetic Imaging (VMI) at 70 keV showed stable performance for larger lumens ([&ge;]6 mm) with variations of 13 {+/-} 2 HU across all conditions, while smaller lumens remained stable in medium to small phantoms. ConclusionsThese findings highlight the influence of lumen diameter, patient size, and radiation dose in optimizing PCCT protocols for spectral imaging. Importantly, the study demonstrates that PCCT delivers stable and highly accurate imaging across nearly the entire range of patient sizes in the U.S.. Advances in knowledgeThis study demonstrates PCCTs potential to enhance spectral imaging in vascular applications, surpassing conventional or Dual Energy CT.