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High-Intensity Focused Ultrasound (HIFU) ablation represents a rapidly advancing non-invasive treatment modality that has achieved considerable success in addressing uterine fibroids, which constitute over 50% of benign gynecological tumors. Preoperative Magnetic Resonance Imaging (MRI) plays a pivotal role in the planning and guidance of HIFU surgery for uterine fibroids, wherein the segmentation of tumors holds critical significance. The segmentation process was previously manually executed by medical experts, entailing a time-consuming and labor-intensive procedure heavily reliant on clinical expertise. This study introduced deep learning-based nnU-Net models, offering a cost-effective approach for their application in the segmentation of uterine fibroids utilizing preoperative MRI images. Furthermore, 3D reconstruction of the segmented targets was implemented to guide HIFU surgery. The evaluation of segmentation and 3D reconstruction performance was conducted with a focus on enhancing the safety and effectiveness of HIFU surgery. Results demonstrated the nnU-Net's commendable performance in the segmentation of uterine fibroids and their surrounding organs. Specifically, 3D nnU-Net achieved Dice Similarity Coefficients (DSC) of 92.55% for the uterus, 95.63% for fibroids, 92.69% for the spine, 89.63% for the endometrium, 97.75% for the bladder, and 90.45% for the urethral orifice. Compared to other state-of-the-art methods such as HIFUNet, U-Net, R2U-Net, ConvUNeXt and 2D nnU-Net, 3D nnU-Net demonstrated significantly higher DSC values, highlighting its superior accuracy and robustness. In conclusion, the efficacy of the 3D nnU-Net model for automated segmentation of the uterus and its surrounding organs was robustly validated. When integrated with intra-operative ultrasound imaging, this segmentation method and 3D reconstruction hold substantial potential to enhance the safety and efficiency of HIFU surgery in the clinical treatment of uterine fibroids. [ABSTRACT FROM AUTHOR]

Manual segmentation of brain tumors using structural magnetic resonance imaging (MRI) is an arduous and time-consuming task. Therefore, automatic and robust segmentation will considerably influence neuro-oncological clinical trials by reducing excessive manual annotation time. Herein, we propose a deep learning model that automatically segments brain tumors even in cases of missing MRI sequences, which are common in practical clinical settings. To address this issue, we enhance a generative adversarial network (GAN) by incorporating a squeeze-and-excitation (SE) attention module into its generator and a PatchGAN into its discriminator. The SE module recalibrates channel responses by explicitly modeling interdependencies, enabling the network to focus on critical regions such as tumor areas. Our proposed generative model is optimized using a combination of adversarial, structural similarity, and mean absolute error losses to synthesize missing MRI sequences more effectively. This enhancement allows our model to synthesize the missing MRI sequence (fluid attenuated inversion recovery [FLAIR]) by leveraging information from other available sequences (T1-weighted, T2-weighted, or contrast-enhanced T1-weighted [T1ce]). For the segmentation task, we employ an optimized nnU-Net model, which is trained using existing sequences and evaluated using both available and synthesized sequences (including missing ones), mimicking real-world scenarios where often only limited MRI sequences are available or usable. Our findings reveal a notable enhancement in brain tumor segmentation, as indicated by a significant increase in overall the Dice similarity coefficient (DSC) from 0.688% (when FLAIR is missing) to 0.873% (when using synthesized FLAIR derived from T2). This improvement brings the segmentation performance closer to what was achieved when real FLAIR was available, where the DSC reaches 0.901%. Moreover, our synthesizing model was also tested on two additional datasets: the BraTS 2020 validation set and BraTS Africa 2023 training set, which produces results comparable to those of BraTS 2021, thereby proving its robustness and generalizability. In addition, the resulting tumor segmentations are subsequently employed to assess the response to treatment in cases where all sequences were available and when synthesis was employed, according to response assessment in neuro-oncology criteria. [Display omitted] [ABSTRACT FROM AUTHOR]

Purpose: Addressing the challenges of unclear tumor boundaries and the confusion between cysts and tumors in liver tumor segmentation, this study aims to develop an auto-segmentation method utilizing Gaussian filter with the nnUNet architecture to effectively distinguish between tumors and cysts, enhancing the accuracy of liver tumor auto-segmentation. Methods: Firstly, 130 cases of liver tumorsegmentation challenge 2017 (LiTS2017) were used for training and validating nnU-Net-based auto-segmentation model. Then, 14 cases of 3D-IRCADb dataset and 25 liver cancer cases retrospectively collected in our hospital were used for testing. The dice similarity coefficient (DSC) was used to evaluate the accuracy of auto-segmentation model by comparing with manual contours. Results: The nnU-Net achieved an average DSC value of 0.86 for validation set (20 LiTS cases) and 0.82 for public testing set (14 3D-IRCADb cases). For clinical testing set, the standalone nnU-Net model achieved an average DSC value of 0.75, which increased to 0.81 after post-processing with the Gaussian filter (P<0.05), demonstrating its effectiveness in mitigating the influence of liver cysts on liver tumor segmentation. Conclusion: Experiments show that Gaussian filter is beneficial to improve the accuracy of liver tumor segmentation in clinic. [ABSTRACT FROM AUTHOR]

Purpose: Type A aortic dissection (TAAD) is a life-threatening aortic disease. The tear involves the ascending aorta and progresses into the separation of the layers of the aortic wall and the occurrence of a false lumen. Accurate segmentation of TAAD could provide assistance for disease assessment and guidance for clinical treatment. Methods: This study applied nnU-Net, a state-of-the-art biomedical segmentation network architecture, to segment contrast-enhanced CT images and quantify the morphological features for TAAD. CT datasets were acquired from 24 patients with TAAD. Manual segmentation and annotation of the CT images was used as the ground-truth. Two-dimensional (2D) nnU-Net and three-dimensional (3D) nnU-Net architectures with Dice- and cross entropy-based loss functions were utilized to segment the true lumen (TL), false lumen (FL), and intimal flap on the images. Four-fold cross validation was performed to evaluate the performance of the two nnU-Net architectures. Six metrics, including accuracy, precision, recall, Intersection of Union, Dice similarity coefficient (DSC), and Hausdorff distance, were calculated to evaluate the performance of the 2D and 3D nnU-Net algorithms in TAAD datasets. Aortic morphological features from both 2D and 3D nnU-Net algorithms were quantified based on the segmented results and compared. Results: Overall, 3D nnU-Net architectures had better performance in TAAD CT datasets, with TL and FL segmentation accuracy up to 99.9%. The DSCs of TLs and FLs based on the 3D nnU-Net were 88.42% and 87.10%. For the aortic TL and FL diameters, the FL area calculated from the segmentation results of the 3D nnU-Net architecture had smaller relative errors (3.89–6.80%), compared to the 2D nnU-Net architecture (relative errors: 4.35–9.48%). Conclusions: The nnU-Net architectures may serve as a basis for automatic segmentation and quantification of TAAD, which could aid in rapid diagnosis, surgical planning, and subsequent biomechanical simulation of the aorta. [ABSTRACT FROM AUTHOR]

Objective: Use microscopic video‐based tracking of laryngeal surgical instruments to investigate the effect of robot assistance on instrument tremor. Study Design: Experimental trial. Setting: Tertiary Academic Medical Center. Methods: In this randomized cross‐over trial, 36 videos were recorded from 6 surgeons performing left and right cordectomies on cadaveric pig larynges. These recordings captured 3 distinct conditions: without robotic assistance, with robot‐assisted scissors, and with robot‐assisted graspers. To assess tool tremor, we employed computer vision‐based algorithms for tracking surgical tools. Absolute tremor bandpower and normalized path length were utilized as quantitative measures. Wilcoxon rank sum exact tests were employed for statistical analyses and comparisons between trials. Additionally, surveys were administered to assess the perceived ease of use of the robotic system. Results: Absolute tremor bandpower showed a significant decrease when using robot‐assisted instruments compared to freehand instruments (P =.012). Normalized path length significantly decreased with robot‐assisted compared to freehand trials (P =.001). For the scissors, robot‐assisted trials resulted in a significant decrease in absolute tremor bandpower (P =.002) and normalized path length (P <.001). For the graspers, there was no significant difference in absolute tremor bandpower (P =.4), but there was a significantly lower normalized path length in the robot‐assisted trials (P =.03). Conclusion: This study demonstrated that computer‐vision‐based approaches can be used to assess tool motion in simulated microlaryngeal procedures. The results suggest that robot assistance is capable of reducing instrument tremor. [ABSTRACT FROM AUTHOR]

Abstract High-Intensity Focused Ultrasound (HIFU) ablation represents a rapidly advancing non-invasive treatment modality that has achieved considerable success in addressing uterine fibroids, which constitute over 50% of benign gynecological tumors. Preoperative Magnetic Resonance Imaging (MRI) plays a pivotal role in the planning and guidance of HIFU surgery for uterine fibroids, wherein the segmentation of tumors holds critical significance. The segmentation process was previously manually executed by medical experts, entailing a time-consuming and labor-intensive procedure heavily reliant on clinical expertise. This study introduced deep learning-based nnU-Net models, offering a cost-effective approach for their application in the segmentation of uterine fibroids utilizing preoperative MRI images. Furthermore, 3D reconstruction of the segmented targets was implemented to guide HIFU surgery. The evaluation of segmentation and 3D reconstruction performance was conducted with a focus on enhancing the safety and effectiveness of HIFU surgery. Results demonstrated the nnU-Net’s commendable performance in the segmentation of uterine fibroids and their surrounding organs. Specifically, 3D nnU-Net achieved Dice Similarity Coefficients (DSC) of 92.55% for the uterus, 95.63% for fibroids, 92.69% for the spine, 89.63% for the endometrium, 97.75% for the bladder, and 90.45% for the urethral orifice. Compared to other state-of-the-art methods such as HIFUNet, U-Net, R2U-Net, ConvUNeXt and 2D nnU-Net, 3D nnU-Net demonstrated significantly higher DSC values, highlighting its superior accuracy and robustness. In conclusion, the efficacy of the 3D nnU-Net model for automated segmentation of the uterus and its surrounding organs was robustly validated. When integrated with intra-operative ultrasound imaging, this segmentation method and 3D reconstruction hold substantial potential to enhance the safety and efficiency of HIFU surgery in the clinical treatment of uterine fibroids.

Manual segmentation of brain tumors using structural magnetic resonance imaging (MRI) is an arduous and time-consuming task. Therefore, automatic and robust segmentation will considerably influence neuro-oncological clinical trials by reducing excessive manual annotation time. Herein, we propose a deep learning model that automatically segments brain tumors even in cases of missing MRI sequences, which are common in practical clinical settings. To address this issue, we enhance a generative adversarial network (GAN) by incorporating a squeeze-and-excitation (SE) attention module into its generator and a PatchGAN into its discriminator. The SE module recalibrates channel responses by explicitly modeling interdependencies, enabling the network to focus on critical regions such as tumor areas. Our proposed generative model is optimized using a combination of adversarial, structural similarity, and mean absolute error losses to synthesize missing MRI sequences more effectively. This enhancement allows our model to synthesize the missing MRI sequence (fluid attenuated inversion recovery [FLAIR]) by leveraging information from other available sequences (T1-weighted, T2-weighted, or contrast-enhanced T1-weighted [T1ce]). For the segmentation task, we employ an optimized nnU-Net model, which is trained using existing sequences and evaluated using both available and synthesized sequences (including missing ones), mimicking real-world scenarios where often only limited MRI sequences are available or usable. Our findings reveal a notable enhancement in brain tumor segmentation, as indicated by a significant increase in overall the Dice similarity coefficient (DSC) from 0.688% (when FLAIR is missing) to 0.873% (when using synthesized FLAIR derived from T2). This improvement brings the segmentation performance closer to what was achieved when real FLAIR was available, where the DSC reaches 0.901%. Moreover, our synthesizing model was also tested on two additional datasets: the BraTS 2020 validation set and BraTS Africa 2023 training set, which produces results comparable to those of BraTS 2021, thereby proving its robustness and generalizability. In addition, the resulting tumor segmentations are subsequently employed to assess the response to treatment in cases where all sequences were available and when synthesis was employed, according to response assessment in neuro-oncology criteria.

Convolutional Neural Networks have emerged as a predominant tool in musculoskeletal medical image segmentation. It enables precise delineation of bone and cartilage in medical images. Recent developments in image processing and network architecture desire a reevaluation of the relationship between segmentation accuracy and the amount of training data. This study investigates the minimum sample size required to achieve clinically relevant accuracy in bone and cartilage segmentation using the nnU-Net methodology. In addition, the potential benefit of integrating available medical knowledge for data augmentation, a largely unexplored opportunity for data preprocessing, is investigated. The impact of sample size on the segmentation accuracy of the nnU-Net is studied using three distinct musculoskeletal datasets, including both MRI and CT, to segment bone and cartilage. Further, the use of model-informed augmentation is explored on two of the above datasets by generating new training samples implementing a shape model-informed approach. Results indicate that the nnU-Net can achieve remarkable segmentation accuracy with as few as 10–15 training samples on bones and 25–30 training samples on cartilage. Model-informed augmentation did not yield relevant improvements in segmentation results. The sample size findings challenge the common notion that large datasets are necessary to obtain clinically relevant segmentation outcomes in musculoskeletal applications. [ABSTRACT FROM AUTHOR]

Brain tissue segmentation plays a critical role in the diagnosis, treatment, and study of brain diseases. Accurately identifying these boundaries is essential for improving segmentation accuracy. However, distinguishing boundaries between different brain tissues can be challenging, as they often overlap. Existing deep learning methods primarily calculate the overall segmentation results without adequately addressing local regions, leading to error propagation and mis-segmentation along boundaries. In this study, we propose a novel mis-segmentation-focused loss function based on a two-stage nnU-Net framework. Our approach aims to enhance the model's ability to handle ambiguous boundaries and overlapping anatomical structures, thereby achieving more accurate brain tissue segmentation results. Specifically, the first stage targets the identification of mis-segmentation regions using a global loss function, while the second stage involves defining a mis-segmentation loss function to adaptively adjust the model, thus improving its capability to handle ambiguous boundaries and overlapping anatomical structures. Experimental evaluations on two datasets demonstrate that our proposed method outperforms existing approaches both quantitatively and qualitatively. [ABSTRACT FROM AUTHOR]

Prenatal assessment of lung size and liver position is essential to stratify congenital diaphragmatic hernia (CDH) fetuses in risk categories, guiding counseling, and patient management. Manual segmentation on fetal MRI provides a quantitative estimation of total lung volume and liver herniation. However, it is time-consuming and operator-dependent. In this study, we utilized a publicly available deep learning (DL) segmentation system (nnU-Net) to automatically contour CDH-affected fetal lungs and liver on MRI sections. Concordance between automatic and manual segmentation was assessed by calculating the Jaccard coefficient. Pyradiomics standard features were then extracted from both manually and automatically segmented regions. The reproducibility of features between the two groups was evaluated through the Wilcoxon rank-sum test and intraclass correlation coefficients (ICCs). We finally tested the reliability of the automatic-segmentation approach by building a ML classifier system for the prediction of liver herniation based on support vector machines (SVM) and trained on shape features computed both in the manual and nnU-Net-segmented organs. We compared the area under the classifier receiver operating characteristic curve (AUC) in the two cases. Pyradiomics features calculated in the manual ROIs were partly reproducible by the same features calculated in nnU-Net segmented ROIs and, when used in the ML procedure, to predict liver herniation (both AUC around 0.85). Conclusion: Our results suggest that automatic MRI segmentation is feasible, with good reproducibility of pyradiomics features, and that a ML system for liver herniation prediction offers good reliability. Trial registration: https://clinicaltrials.gov/ct2/show/NCT04609163?term=NCT04609163&draw=2&rank=1; Clinical Trial Identification no. NCT04609163. What is Known: • Magnetic resonance imaging (MRI) is crucial for prenatal congenital diaphragmatic hernia (CDH) assessment. It enables the quantification of the total lung volume and the extent of liver herniation, which are essential for stratifying the severity of CDH, guiding counseling, and patient management. • The manual segmentation of MRI scans is a time-consuming process that is heavily reliant upon the skill set of the operator. What is New: • MRI lung and liver automatic segmentation using the deep learning nnU-Net system is feasible, with good Jaccard coefficient values and satisfactory reproducibility of pyradiomics features compared to manual results. • A feasible ML system for predicting liver herniation could improve prenatal assessments and CDH patient management. [ABSTRACT FROM AUTHOR]

Machine Learning (ML) has evolved beyond being a specialized technique exclusively used by computer scientists. Besides the general ease of use, automated pipelines allow for training sophisticated ML models with minimal knowledge of computer science. In recent years, Automated ML (AutoML) frameworks have become serious competitors for specialized ML models and have even been able to outperform the latter for specific tasks. Moreover, this success is not limited to simple tasks but also complex ones, like tumor segmentation in histopathological tissue, a very time-consuming task requiring years of expertise by medical professionals. Regarding medical image segmentation, the leading AutoML frameworks are nnU-Net and deepflash2. In this work, we begin to compare those two frameworks in the area of histopathological image segmentation. This use case proves especially challenging, as tumor and healthy tissue are often not clearly distinguishable by hard borders but rather through heterogeneous transitions. A dataset of 103 whole-slide images from 56 glioblastoma patients was used for the evaluation. Training and evaluation were run on a notebook with consumer hardware, determining the suitability of the frameworks for their application in clinical scenarios rather than high-performance scenarios in research labs. [ABSTRACT FROM AUTHOR]

To validate the performance of nnU-Net in segmentation and CNN in classification for liver fibrosis using T1-weighted images. In this prospective study, animal models of liver fibrosis were induced by injecting subcutaneously a mixture of Carbon tetrachloride and olive oil. A total of 99 male Wistar rats were successfully induced and underwent MR scanning with no contrast agent to get T1-weighted images. The regions of interest (ROIs) of the whole liver were delineated layer by layer along the liver edge by 3D Slicer. For segmentation task, all T1-weighted images were randomly divided into training and test cohorts in a ratio of 7:3. For classification, images containing the hepatic maximum diameter of every rat were selected and 80% images of no liver fibrosis (NLF), early liver fibrosis (ELF) and progressive liver fibrosis (PLF) stages were randomly selected for training, while the rest were used for testing. Liver segmentation was performed by the nnU-Net model. The convolutional neural network (CNN) was used for classification task of liver fibrosis stages. The Dice similarity coefficient was used to evaluate the segmentation performance of nnU-Net. Confusion matrix, ROC curve and accuracy were used to show the classification performance of CNN. A total of 2628 images were obtained from 99 Wistar rats by MR scanning. For liver segmentation by nnU-Net, the Dice similarity coefficient in the test set was 0.8477. The accuracies of CNN in staging NLF, ELF and PLF were 0.73, 0.89 and 0.84, respectively. The AUCs were 0.76, 0.88 and 0.79, respectively. The nnU-Net architecture is of high accuracy for liver segmentation and CNN for assessment of liver fibrosis with T1-weighted images. [ABSTRACT FROM AUTHOR]

Automated brain tumor segmentation from magnetic resonance (MR) images plays a crucial role in precise diagnosis and treatment monitoring in brain tumor care. Leveraging the Brain Tumor Segmentation Challenge (BraTS) dataset, this paper introduces an extended version of the nnU-Net architecture for brain tumor segmentation, addressing both adult (Glioma) and pediatric tumors. Our methodology integrates innovative approaches to enhance segmentation accuracy. We incorporate residual blocks to capture complex spatial features, attention gates to emphasize informative regions and implement the Hausdorff distance (HD) loss for boundary-based segmentation refinement. The effectiveness of each enhancement is systematically evaluated through an ablation study using different configurations on the BraTS dataset. Results from our study highlight the significance of combining residual blocks, attention gates, and HD loss, achieving the best performance with a mean Dice and HD score of 83%, 3.8 and 71%, and 8.7 for Glioma and Pediatrics datasets, respectively. This advanced nnU-Net showcases the promising potential for accurate and robust brain tumor segmentation, offering valuable insights for enhanced clinical decision-making in pediatric brain tumor care.

Background: Adaptive MRI-guided radiotherapy (MRIgRT) requires accurate and efficient segmentation of organs and targets on MRI scans. Manual segmentation is time-consuming and variable, while deformable image registration (DIR)- based contour propagation may not account for large anatomical changes. Therefore, we developed and evaluated an automatic segmentation method using the nnU-net framework. Methods: The network was trained on 38 patients (76 scans) with localized prostate cancer and tested on 30 patients (60 scans) with localized prostate, metastatic prostate, or bladder cancer treated at a 1.5 T MRI-linac at our institution. The performance of the network was compared with the current clinical workflow based on DIR. The segmentation accuracy was evaluated using the Dice similarity coefficient (DSC), mean surface distance (MSD), and Hausdorff distance (HD) metrics. Results: The trained network successfully segmented all 600 structures in the test set. High similarity was obtained for most structures, with 90% of the contours having a DSC above 0.9 and 86% having an MSD below 1 mm. The largest discrepancies were found in the sigmoid and colon structures. Stratified analysis on cancer type showed that the best performance was seen in the same type of patients that the model was trained on (localized prostate). Especially in patients with bladder cancer, the performance was lower for the bladder and the surrounding organs. A complete automatic delineation workflow took approximately 1 minute. Compared with contour transfer based on the clinically used DIR algorithm, the nnU-net performed statistically better across all organs, with the most significant gain in using the nnU-net seen for organs subject to more considerable volumetric changes due to variation in the filling of the rectum, bladder, bowel, and sigmoid. Conclusion: We successfully trained and tested a network for automatically segmenting organs and targets for MRIgRT in the male pelvis region. Good test results were seen for the trained nnU-net, with test results outperforming the current clinical practice using DIR-based contour propagation at the 1.5 T MRIlinac. The trained network is sufficiently fast and accurate for clinical use in an online setting for MRIgRT. The model is provided as open-source. [ABSTRACT FROM AUTHOR]

Purpose: Type A aortic dissection (TAAD) is a life-threatening aortic disease. The tear involves the ascending aorta and progresses into the separation of the layers of the aortic wall and the occurrence of a false lumen. Accurate segmentation of TAAD could provide assistance for disease assessment and guidance for clinical treatment. Methods: This study applied nnU-Net, a state-of-the-art biomedical segmentation network architecture, to segment contrast-enhanced CT images and quantify the morphological features for TAAD. CT datasets were acquired from 24 patients with TAAD. Manual segmentation and annotation of the CT images was used as the ground-truth. Two-dimensional (2D) nnU-Net and three-dimensional (3D) nnU-Net architectures with Dice- and cross entropy-based loss functions were utilized to segment the true lumen (TL), false lumen (FL), and intimal flap on the images. Four-fold cross validation was performed to evaluate the performance of the two nnU-Net architectures. Six metrics, including accuracy, precision, recall, Intersection of Union, Dice similarity coefficient (DSC), and Hausdorff distance, were calculated to evaluate the performance of the 2D and 3D nnU-Net algorithms in TAAD datasets. Aortic morphological features from both 2D and 3D nnU-Net algorithms were quantified based on the segmented results and compared. Results: Overall, 3D nnU-Net architectures had better performance in TAAD CT datasets, with TL and FL segmentation accuracy up to 99.9%. The DSCs of TLs and FLs based on the 3D nnU-Net were 88.42% and 87.10%. For the aortic TL and FL diameters, the FL area calculated from the segmentation results of the 3D nnU-Net architecture had smaller relative errors (3.89–6.80%), compared to the 2D nnU-Net architecture (relative errors: 4.35–9.48%). Conclusions: The nnU-Net architectures may serve as a basis for automatic segmentation and quantification of TAAD, which could aid in rapid diagnosis, surgical planning, and subsequent biomechanical simulation of the aorta.

Brain tissue segmentation plays a critical role in the diagnosis, treatment, and study of brain diseases. Accurately identifying these boundaries is essential for improving segmentation accuracy. However, distinguishing boundaries between different brain tissues can be challenging, as they often overlap. Existing deep learning methods primarily calculate the overall segmentation results without adequately addressing local regions, leading to error propagation and mis-segmentation along boundaries. In this study, we propose a novel mis-segmentation-focused loss function based on a two-stage nnU-Net framework. Our approach aims to enhance the model’s ability to handle ambiguous boundaries and overlapping anatomical structures, thereby achieving more accurate brain tissue segmentation results. Specifically, the first stage targets the identification of mis-segmentation regions using a global loss function, while the second stage involves defining a mis-segmentation loss function to adaptively adjust the model, thus improving its capability to handle ambiguous boundaries and overlapping anatomical structures. Experimental evaluations on two datasets demonstrate that our proposed method outperforms existing approaches both quantitatively and qualitatively.

Abstract Background Segmentation of the Gross Tumor Volume (GTV) is a crucial step in the brachytherapy (BT) treatment planning workflow. Currently, radiation oncologists segment the GTV manually, which is time-consuming. The time pressure is particularly critical for BT because during the segmentation process the patient waits immobilized in bed with the applicator in place. Automatic segmentation algorithms can potentially reduce both the clinical workload and the patient burden. Although deep learning based automatic segmentation algorithms have been extensively developed for organs at risk, automatic segmentation of the targets is less common. The aim of this study was to automatically segment the cervical cancer GTV on BT MRI images using a state-of-the-art automatic segmentation framework and assess its performance. Methods A cohort of 195 cervical cancer patients treated between August 2012 and December 2021 was retrospectively collected. A total of 524 separate BT fractions were included and the axial T2-weighted (T2w) MRI sequence was used for this project. The 3D nnU-Net was used as the automatic segmentation framework. The automatic segmentations were compared with the manual segmentations used for clinical practice with Sørensen–Dice coefficient (Dice), 95th Hausdorff distance (95th HD) and mean surface distance (MSD). The dosimetric impact was defined as the difference in D98 (ΔD98) and D90 (ΔD90) between the manual segmentations and the automatic segmentations, evaluated using the clinical dose distribution. The performance of the network was also compared separately depending on FIGO stage and on GTV volume. Results The network achieved a median Dice of 0.73 (interquartile range (IQR) = 0.50–0.80), median 95th HD of 6.8 mm (IQR = 4.2–12.5 mm) and median MSD of 1.4 mm (IQR = 0.90–2.8 mm). The median ΔD90 and ΔD98 were 0.18 Gy (IQR = -1.38–1.19 Gy) and 0.20 Gy (IQR =-1.10–0.95 Gy) respectively. No significant differences in geometric or dosimetric performance were observed between tumors with different FIGO stages, however significantly improved Dice and dosimetric performance was found for larger tumors. Conclusions The nnU-Net framework achieved state-of-the-art performance in the segmentation of the cervical cancer GTV on BT MRI images. Reasonable median performance was achieved geometrically and dosimetrically but with high variability among patients.

Isocitrate dehydrogenase (IDH) mutation status has emerged as an important prognostic marker in gliomas. This study sought to develop deep learning networks for non-invasive IDH classification using T2w MR images while comparing their performance to a multi-contrast network. Methods: Multi-contrast brain tumor MRI and genomic data were obtained from The Cancer Imaging Archive (TCIA) and The Erasmus Glioma Database (EGD). Two separate 2D networks were developed using nnU-Net, a T2w-image-only network (T2-net) and a multi-contrast network (MC-net). Each network was separately trained using TCIA (227 subjects) or TCIA + EGD data (683 subjects combined). The networks were trained to classify IDH mutation status and implement single-label tumor segmentation simultaneously. The trained networks were tested on over 1100 held-out datasets including 360 cases from UT Southwestern Medical Center, 136 cases from New York University, 175 cases from the University of Wisconsin–Madison, 456 cases from EGD (for the TCIA-trained network), and 495 cases from the University of California, San Francisco public database. A receiver operating characteristic curve (ROC) was drawn to calculate the AUC value to determine classifier performance. Results: T2-net trained on TCIA and TCIA + EGD datasets achieved an overall accuracy of 85.4% and 87.6% with AUCs of 0.86 and 0.89, respectively. MC-net trained on TCIA and TCIA + EGD datasets achieved an overall accuracy of 91.0% and 92.8% with AUCs of 0.94 and 0.96, respectively. We developed reliable, high-performing deep learning algorithms for IDH classification using both a T2-image-only and a multi-contrast approach. The networks were tested on more than 1100 subjects from diverse databases, making this the largest study on image-based IDH classification to date. [ABSTRACT FROM AUTHOR]

BackgroundReproducible approaches are needed to bring AI/ML for medical image analysis closer to the bedside. Investigators wishing to shadow test cross-sectional medical imaging segmentation algorithms on new studies in real-time will benefit from simple tools that integrate PACS with on-premises image processing, allowing visualization of DICOM-compatible segmentation results and volumetric data at the radiology workstation.PurposeIn this work, we develop and release a simple containerized and easily deployable pipeline for shadow testing of segmentation algorithms within the clinical workflow.MethodsOur end-to-end automated pipeline has two major components- 1. A router/listener and anonymizer and an OHIF web viewer backstopped by a DCM4CHEE DICOM query/retrieve archive deployed in the virtual infrastructure of our secure hospital intranet, and 2. An on-premises single GPU workstation host for DICOM/NIfTI conversion steps, and image processing. DICOM images are visualized in OHIF along with their segmentation masks and associated volumetry measurements (in mL) using DICOM SEG and structured report (SR) elements. Since nnU-net has emerged as a widely-used out-of-the-box method for training segmentation models with state-of-the-art performance, feasibility of our pipleine is demonstrated by recording clock times for a traumatic pelvic hematoma nnU-net model.ResultsMean total clock time from PACS send by user to completion of transfer to the DCM4CHEE query/retrieve archive was 5 min 32 s (± SD of 1 min 26 s). This compares favorably to the report turnaround times for whole-body CT exams, which often exceed 30 min, and illustrates feasibility in the clinical setting where quantitative results would be expected prior to report sign-off. Inference times accounted for most of the total clock time, ranging from 2 min 41 s to 8 min 27 s. All other virtual and on-premises host steps combined ranged from a minimum of 34 s to a maximum of 48 s.ConclusionThe software worked seamlessly with an existing PACS and could be used for deployment of DL models within the radiology workflow for prospective testing on newly scanned patients. Once configured, the pipeline is executed through one command using a single shell script. The code is made publicly available through an open-source license at “https://github.com/vastc/,” and includes a readme file providing pipeline config instructions for host names, series filter, other parameters, and citation instructions for this work.

Background: Segmentation of the Gross Tumor Volume (GTV) is a crucial step in the brachytherapy (BT) treatment planning workflow. Currently, radiation oncologists segment the GTV manually, which is time-consuming. The time pressure is particularly critical for BT because during the segmentation process the patient waits immobilized in bed with the applicator in place. Automatic segmentation algorithms can potentially reduce both the clinical workload and the patient burden. Although deep learning based automatic segmentation algorithms have been extensively developed for organs at risk, automatic segmentation of the targets is less common. The aim of this study was to automatically segment the cervical cancer GTV on BT MRI images using a state-of-the-art automatic segmentation framework and assess its performance. Methods: A cohort of 195 cervical cancer patients treated between August 2012 and December 2021 was retrospectively collected. A total of 524 separate BT fractions were included and the axial T2-weighted (T2w) MRI sequence was used for this project. The 3D nnU-Net was used as the automatic segmentation framework. The automatic segmentations were compared with the manual segmentations used for clinical practice with Sørensen–Dice coefficient (Dice), 95th Hausdorff distance (95th HD) and mean surface distance (MSD). The dosimetric impact was defined as the difference in D98 (ΔD98) and D90 (ΔD90) between the manual segmentations and the automatic segmentations, evaluated using the clinical dose distribution. The performance of the network was also compared separately depending on FIGO stage and on GTV volume. Results: The network achieved a median Dice of 0.73 (interquartile range (IQR) = 0.50–0.80), median 95th HD of 6.8 mm (IQR = 4.2–12.5 mm) and median MSD of 1.4 mm (IQR = 0.90–2.8 mm). The median ΔD90 and ΔD98 were 0.18 Gy (IQR = -1.38–1.19 Gy) and 0.20 Gy (IQR =-1.10–0.95 Gy) respectively. No significant differences in geometric or dosimetric performance were observed between tumors with different FIGO stages, however significantly improved Dice and dosimetric performance was found for larger tumors. Conclusions: The nnU-Net framework achieved state-of-the-art performance in the segmentation of the cervical cancer GTV on BT MRI images. Reasonable median performance was achieved geometrically and dosimetrically but with high variability among patients. [ABSTRACT FROM AUTHOR]

Background: Accurate and rapid measurement of the MRI volume of meningiomas is essential in clinical practice to determine the growth rate of the tumor. Imperfect automation and disappointing performance for small meningiomas of previous automated volumetric tools limit their use in routine clinical practice. Purpose: To develop and validate a computational model for fully automated meningioma segmentation and volume measurement on contrast‐enhanced MRI scans using deep learning. Study Type: Retrospective. Population: A total of 659 intracranial meningioma patients (median age, 59.0 years; interquartile range: 53.0–66.0 years) including 554 women and 105 men. Field Strength/Sequence: The 1.0 T, 1.5 T, and 3.0 T; three‐dimensional, T1‐weighted gradient‐echo imaging with contrast enhancement. Assessment: The tumors were manually segmented by two neurosurgeons, H.K. and C.‐K.P., with 10 and 26 years of clinical experience, respectively, for use as the ground truth. Deep learning models based on U‐Net and nnU‐Net were trained using 459 subjects and tested for 100 patients from a single institution (internal validation set [IVS]) and 100 patients from other 24 institutions (external validation set [EVS]), respectively. The performance of each model was evaluated with the Sørensen‐Dice similarity coefficient (DSC) compared with the ground truth. Statistical Tests: According to the normality of the data distribution verified by the Shapiro–Wilk test, variables with three or more categories were compared by the Kruskal–Wallis test with Dunn's post hoc analysis. Results: A two‐dimensional (2D) nnU‐Net showed the highest median DSCs of 0.922 and 0.893 for the IVS and EVS, respectively. The nnU‐Nets achieved superior performance in meningioma segmentation than the U‐Nets. The DSCs of the 2D nnU‐Net for small meningiomas less than 1 cm3 were 0.769 and 0.780 with the IVS and EVS, respectively. Data Conclusion: A fully automated and accurate volumetric measurement tool for meningioma with clinically applicable performance for small meningioma using nnU‐Net was developed. Evidence Level: 3 Technical Efficacy: Stage 2 [ABSTRACT FROM AUTHOR]