Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...最新文献

{"title":"Head and Neck Tumor Segmentation and Outcome Prediction: Third Challenge, HECKTOR 2022, Held in Conjunction with MICCAI 2022, Singapore, September 22, 2022, Proceedings","authors":"","doi":"10.1007/978-3-031-27420-6","DOIUrl":"https://doi.org/10.1007/978-3-031-27420-6","url":null,"abstract":"","PeriodicalId":93561,"journal":{"name":"Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83592290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Head and Neck Tumor Segmentation and Outcome Prediction: Second Challenge, HECKTOR 2021, Held in Conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings","authors":"","doi":"10.1007/978-3-030-98253-9","DOIUrl":"https://doi.org/10.1007/978-3-030-98253-9","url":null,"abstract":"","PeriodicalId":93561,"journal":{"name":"Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...","volume":"112 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77218136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Head and Neck Cancer Primary Tumor Auto Segmentation Using Model Ensembling of Deep Learning in PET/CT Images.","authors":"Mohamed A Naser, Kareem A Wahid, Lisanne V van Dijk, Renjie He, Moamen Abobakr Abdelaal, Cem Dede, Abdallah S R Mohamed, Clifton D Fuller","doi":"10.1007/978-3-030-98253-9_11","DOIUrl":"https://doi.org/10.1007/978-3-030-98253-9_11","url":null,"abstract":"<p><p>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 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. Our DSC and 95% HD test results are within 0.01 and 0.06 mm of the top ranked model in the competition, respectively. 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. Future investigations should target the ideal combination of channel combinations and label fusion strategies to maximize segmentation performance.</p>","PeriodicalId":93561,"journal":{"name":"Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...","volume":"13209 ","pages":"121-132"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8991449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142086464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combining Tumor Segmentation Masks with PET/CT Images and Clinical Data in a Deep Learning Framework for Improved Prognostic Prediction in Head and Neck Squamous Cell Carcinoma.","authors":"Kareem A Wahid, Renjie He, Cem Dede, Abdallah S R Mohamed, Moamen Abobakr Abdelaal, Lisanne V van Dijk, Clifton D Fuller, Mohamed A Naser","doi":"10.1007/978-3-030-98253-9_28","DOIUrl":"https://doi.org/10.1007/978-3-030-98253-9_28","url":null,"abstract":"<p><p>PET/CT images provide a rich data source for clinical prediction models in head and neck squamous cell carcinoma (HNSCC). Deep learning models often use images in an end-to-end fashion with clinical data or no additional input for predictions. However, in the context of HNSCC, the tumor region of interest may be an informative prior in the generation of improved prediction performance. In this study, we utilize a deep learning framework based on a DenseNet architecture to combine PET images, CT images, primary tumor segmentation masks, and clinical data as separate channels to predict progression-free survival (PFS) in days for HNSCC patients. Through internal validation (10-fold cross-validation) based on a large set of training data provided by the 2021 HECKTOR Challenge, we achieve a mean C-index of 0.855 ± 0.060 and 0.650 ± 0.074 when observed events are and are not included in the C-index calculation, respectively. Ensemble approaches applied to cross-validation folds yield C-index values up to 0.698 in the independent test set (external validation), leading to a 1^st place ranking on the competition leaderboard. Importantly, the value of the added segmentation mask is underscored in both internal and external validation by an improvement of the C-index when compared to models that do not utilize the segmentation mask. These promising results highlight the utility of including segmentation masks as additional input channels in deep learning pipelines for clinical outcome prediction in HNSCC.</p>","PeriodicalId":93561,"journal":{"name":"Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...","volume":"13209 ","pages":"300-307"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8991448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142086463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Head and Neck Cancer Primary Tumor Auto Segmentation using Model Ensembling of Deep Learning in PET-CT Images","authors":"M. Naser, K. Wahid, L. V. Dijk, R. He, M. A. Abdelaal, C. Dede, A. Mohamed, C. Fuller","doi":"10.1101/2021.10.14.21264953","DOIUrl":"https://doi.org/10.1101/2021.10.14.21264953","url":null,"abstract":"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 seg-mentation performance.","PeriodicalId":93561,"journal":{"name":"Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...","volume":"117 1","pages":"121-132"},"PeriodicalIF":0.0,"publicationDate":"2021-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77144792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combining Tumor Segmentation Masks with PET/CT Images and Clinical Data in a Deep Learning Framework for Improved Prognostic Prediction in Head and Neck Squamous Cell Carcinoma","authors":"K. Wahid, R. He, C. Dede, A. Mohamed, M. A. Abdelaal, L. V. Dijk, C. Fuller, M. Naser","doi":"10.1101/2021.10.14.21264958","DOIUrl":"https://doi.org/10.1101/2021.10.14.21264958","url":null,"abstract":"PET/CT images provide a rich data source for clinical prediction models in head and neck squamous cell carcinoma (HNSCC). Deep learning models often use images in an end-to-end fashion with clinical data or no additional input for predictions. However, in the context of HNSCC, the tumor region of interest may be an informative prior in the generation of improved prediction performance. In this study, we utilize a deep learning framework based on a DenseNet architecture to combine PET images, CT images, primary tumor segmentation masks, and clinical data as separate channels to predict progression-free survival (PFS) in days for HNSCC patients. Through internal validation (10-fold cross-validation) based on a large set of training data provided by the 2021 HECKTOR Challenge, we achieve a mean C-index of 0.855 +- 0.060 and 0.650 +- 0.074 when observed events are and are not included in the C-index calculation, respectively. Ensemble approaches applied to cross-validation folds yield C-index values up to 0.698 in the independent test set (external validation). Importantly, the value of the added segmentation mask is underscored in both internal and external validation by an improvement of the C-index when compared to models that do not utilize the segmentation mask. These promising results highlight the utility of including segmentation masks as additional input channels in deep learning pipelines for clinical outcome prediction in HNSCC.","PeriodicalId":93561,"journal":{"name":"Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...","volume":"84 1","pages":"300-307"},"PeriodicalIF":0.0,"publicationDate":"2021-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80460043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Progression Free Survival Prediction for Head and Neck Cancer using Deep Learning based on Clinical and PET-CT Imaging Data","authors":"M. Naser, K. Wahid, A. Mohamed, M. A. Abdelaal, R. He, C. Dede, L. V. Dijk, C. Fuller","doi":"10.1101/2021.10.14.21264955","DOIUrl":"https://doi.org/10.1101/2021.10.14.21264955","url":null,"abstract":"Determining progression-free survival (PFS) for head and neck squamous cell carcinoma (HNSCC) patients is a challenging but pertinent task that could help stratify patients for improved overall outcomes. PET/CT images provide a rich source of anatomical and metabolic data for potential clinical biomarkers that would inform treatment decisions and could help improve PFS. In this study, we participate in the 2021 HECKTOR Challenge to predict PFS in a large dataset of HNSCC PET/CT images using deep learning approaches. We develop a series of deep learning models based on the DenseNet architecture using a negative log-likelihood loss function that utilizes PET/CT images and clinical data as separate input channels to predict PFS in days. Internal model validation based on 10-fold cross-validation using the training data (N=224) yielded C-index values up to 0.622 (without) and 0.842 (with) censoring status considered in C-index computation, respectively. We then implemented model ensembling approaches based on the training data cross-validation folds to predict the PFS of the test set patients (N=101). External validation on the test set for the best ensembling method yielded a C-index value of 0.694. Our results are a promising example of how deep learning approaches can effectively utilize imaging and clinical data for medical outcome prediction in HNSCC, but further work in optimizing these processes is needed.","PeriodicalId":93561,"journal":{"name":"Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...","volume":"1 1","pages":"287-299"},"PeriodicalIF":0.0,"publicationDate":"2021-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77815003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Head and Neck Tumor Segmentation: First Challenge, HECKTOR 2020, Held in Conjunction with MICCAI 2020, Lima, Peru, October 4, 2020, Proceedings","authors":"","doi":"10.1007/978-3-030-67194-5","DOIUrl":"https://doi.org/10.1007/978-3-030-67194-5","url":null,"abstract":"","PeriodicalId":93561,"journal":{"name":"Head and neck tumor segmentation and outcome prediction : second challenge, HECKTOR 2021, held in conjunction with MICCAI 2021, Strasbourg, France, September 27, 2021, Proceedings. Head and Neck Tumor Segmentation Challenge (2nd : 2021 ...","volume":"96 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76021487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}