Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.)最新文献

SlicerSALT: From Medical Images to Quantitative Insights of Anatomy. SlicerSALT：从医学影像到解剖学定量洞察。

Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.) Pub Date : 2023-10-01 Epub Date: 2023-10-31 DOI: 10.1007/978-3-031-46914-5_16

Jared Vicory, Ye Han, Juan Carlos Prieto, David Allemang, Mathieu Leclercq, Connor Bowley, Harald Scheirich, Jean-Christophe Fillion-Robin, Steve Pizer, James Fishbaugh, Guido Gerig, Martin Styner, Beatriz Paniagua

{"title":"SlicerSALT: From Medical Images to Quantitative Insights of Anatomy.","authors":"Jared Vicory, Ye Han, Juan Carlos Prieto, David Allemang, Mathieu Leclercq, Connor Bowley, Harald Scheirich, Jean-Christophe Fillion-Robin, Steve Pizer, James Fishbaugh, Guido Gerig, Martin Styner, Beatriz Paniagua","doi":"10.1007/978-3-031-46914-5_16","DOIUrl":"10.1007/978-3-031-46914-5_16","url":null,"abstract":"Three-dimensional (3D) shape lies at the core of understanding the physical objects that surround us. In the biomedical field, shape analysis has been shown to be powerful in quantifying how anatomy changes with time and disease. The Shape AnaLysis Toolbox (SALT) was created as a vehicle for disseminating advanced shape methodology as an open source, free, and comprehensive software tool. We present new developments in our shape analysis software package, including easy-to-interpret statistical methods to better leverage the quantitative information contained in SALT's shape representations. We also show SlicerPipelines, a module to improve the usability of SALT by facilitating the analysis of large-scale data sets, automating workflows for non-expert users, and allowing the distribution of reproducible workflows.","PeriodicalId":516531,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.)","volume":"14350 ","pages":"201-210"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10798161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139513632","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}

引用次数: 0

SADIR: Shape-Aware Diffusion Models for 3D Image Reconstruction. SADIR：用于三维图像重建的形状感知扩散模型。

Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.) Pub Date : 2023-10-01 Epub Date: 2023-10-31 DOI: 10.1007/978-3-031-46914-5_23

Nivetha Jayakumar, Tonmoy Hossain, Miaomiao Zhang

{"title":"SADIR: Shape-Aware Diffusion Models for 3D Image Reconstruction.","authors":"Nivetha Jayakumar, Tonmoy Hossain, Miaomiao Zhang","doi":"10.1007/978-3-031-46914-5_23","DOIUrl":"10.1007/978-3-031-46914-5_23","url":null,"abstract":"3D image reconstruction from a limited number of 2D images has been a long-standing challenge in computer vision and image analysis. While deep learning-based approaches have achieved impressive performance in this area, existing deep networks often fail to effectively utilize the shape structures of objects presented in images. As a result, the topology of reconstructed objects may not be well preserved, leading to the presence of artifacts such as discontinuities, holes, or mismatched connections between different parts. In this paper, we propose a shape-aware network based on diffusion models for 3D image reconstruction, named SADIR, to address these issues. In contrast to previous methods that primarily rely on spatial correlations of image intensities for 3D reconstruction, our model leverages shape priors learned from the training data to guide the reconstruction process. To achieve this, we develop a joint learning network that simultaneously learns a mean shape under deformation models. Each reconstructed image is then considered as a deformed variant of the mean shape. We validate our model, SADIR, on both brain and cardiac magnetic resonance images (MRIs). Experimental results show that our method outperforms the baselines with lower reconstruction error and better preservation of the shape structure of objects within the images.","PeriodicalId":516531,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.)","volume":"14350 ","pages":"287-300"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10977919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140320325","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}

引用次数: 0

Modeling Longitudinal Optical Coherence Tomography Images for Monitoring and Analysis of Glaucoma Progression. 为纵向光学相干断层扫描图像建模，用于监测和分析青光眼进展。

Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.) Pub Date : 2023-10-01 Epub Date: 2023-10-31 DOI: 10.1007/978-3-031-46914-5_19

James Fishbaugh, Ronald Zambrano, Joel S Schuman, Gadi Wollstein, Jared Vicory, Beatriz Paniagua

{"title":"Modeling Longitudinal Optical Coherence Tomography Images for Monitoring and Analysis of Glaucoma Progression.","authors":"James Fishbaugh, Ronald Zambrano, Joel S Schuman, Gadi Wollstein, Jared Vicory, Beatriz Paniagua","doi":"10.1007/978-3-031-46914-5_19","DOIUrl":"10.1007/978-3-031-46914-5_19","url":null,"abstract":"Glaucoma causes progressive visual field deterioration and is the leading cause of blindness worldwide. Glaucomatous damage is irreversible and greatly impacts quality of life. Therefore, it is critically important to detect glaucoma early and closely monitor progression to preserve functional vision. Glaucoma is routinely monitored in the clinical setting using optical coherence tomography (OCT) for derived measures such as the thickness of important visual structures. There is not a consensus of what measures represent the most relevant biomarkers of glaucoma progression. Further, despite the increasing availability of longitudinal OCT data, a quantitative model of 3D structural change over time associated with glaucoma does not exist. In this paper we present an algorithm that will perform hierarchical geodesic modeling at the imaging level, considering 3D OCT images as observations of structural change over time. Hierarchical modeling includes subject-wise trajectories as geodesics in the space of diffeomorphisms and population level (glaucoma vs control) trajectories are also geodesics which explain subject-wise trajectories as deviations from the mean. Our preliminary experiments demonstrate a greater magnitude of structural change associated with glaucoma compared to normal aging. Our algorithm has the potential application in patient-specific monitoring and analysis of glaucoma progression as well as a statistical model of population trends and population variability.","PeriodicalId":516531,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.)","volume":"14350 ","pages":"236-247"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10798144/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139513631","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}

引用次数: 0

Geodesic Logistic Analysis of Lumbar Spine Intervertebral Disc Shapes in Supine and Standing Positions. 仰卧位和站立位腰椎间盘形状的测地逻辑分析

Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.) Pub Date : 2023-10-01 Epub Date: 2023-10-31 DOI: 10.1007/978-3-031-46914-5_15

Ye Han, James Fishbaugh, Christian E Gonzalez, Donald A Aboyotes, Jared Vicory, Simon Y Tang, Beatriz Paniagua

{"title":"Geodesic Logistic Analysis of Lumbar Spine Intervertebral Disc Shapes in Supine and Standing Positions.","authors":"Ye Han, James Fishbaugh, Christian E Gonzalez, Donald A Aboyotes, Jared Vicory, Simon Y Tang, Beatriz Paniagua","doi":"10.1007/978-3-031-46914-5_15","DOIUrl":"10.1007/978-3-031-46914-5_15","url":null,"abstract":"Non-specific lower back pain (LBP) is a world-wide public health problem that affects people of all ages. Despite the high prevalence of non-specific LBP and the associated economic burdens, the pathoanatomical mechanisms for the development and course of the condition remain unclear. While intervertebral disc degeneration (IDD) is associated with LBP, there is overlapping occurrence of IDD in symptomatic and asymptomatic individuals, suggesting that degeneration alone cannot identify LBP populations. Previous work has been done trying to relate linear measurements of compression obtained from Magnetic Resonance Imaging (MRI) to pain unsuccessfully. To bridge this gap, we propose to use advanced non-Euclidean statistical shape analysis methods to develop biomarkers that can help identify symptomatic and asymptomatic adults who might be susceptible to standing-induced LBP. We scanned 4 male and 7 female participants who exhibited lower back pain after prolonged standing using an Open Upright MRI. Supine and standing MRIs were obtained for each participant. Patients reported their pain intensity every fifteen minutes within a period of 2 h. Using our proposed geodesic logistic regression, we related the structure of their lower spine to pain and computed a regression model that can delineate lower spine structures using reported pain intensities. These results indicate the feasibility of identifying individuals who may suffer from lower back pain solely based on their spinal anatomy. Our proposed spinal shape analysis methodology have the potential to provide powerful information to the clinicians so they can make better treatment decisions.","PeriodicalId":516531,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.)","volume":"14350 ","pages":"188-200"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10801698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139522017","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}

引用次数: 0

ADASSM: Adversarial Data Augmentation in Statistical Shape Models From Images. ADASSM：图像统计形状模型中的对抗性数据增强。

Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.) Pub Date : 2023-10-01 Epub Date: 2023-10-31 DOI: 10.1007/978-3-031-46914-5_8

Mokshagna Sai Teja Karanam, Tushar Kataria, Krithika Iyer, Shireen Y Elhabian

{"title":"ADASSM: Adversarial Data Augmentation in Statistical Shape Models From Images.","authors":"Mokshagna Sai Teja Karanam, Tushar Kataria, Krithika Iyer, Shireen Y Elhabian","doi":"10.1007/978-3-031-46914-5_8","DOIUrl":"10.1007/978-3-031-46914-5_8","url":null,"abstract":"Statistical shape models (SSM) have been well-established as an excellent tool for identifying variations in the morphology of anatomy across the underlying population. Shape models use consistent shape representation across all the samples in a given cohort, which helps to compare shapes and identify the variations that can detect pathologies and help in formulating treatment plans. In medical imaging, computing these shape representations from CT/MRI scans requires time-intensive preprocessing operations, including but not limited to anatomy segmentation annotations, registration, and texture denoising. Deep learning models have demonstrated exceptional capabilities in learning shape representations directly from volumetric images, giving rise to highly effective and efficient Image-to-SSM networks. Nevertheless, these models are data-hungry and due to the limited availability of medical data, deep learning models tend to overfit. Offline data augmentation techniques, that use kernel density estimation based (KDE) methods for generating shape-augmented samples, have successfully aided Image-to-SSM networks in achieving comparable accuracy to traditional SSM methods. However, these augmentation methods focus on shape augmentation, whereas deep learning models exhibit image-based texture bias resulting in sub-optimal models. This paper introduces a novel strategy for on-the-fly data augmentation for the Image-to-SSM framework by leveraging data-dependent noise generation or texture augmentation. The proposed framework is trained as an adversary to the Image-to-SSM network, augmenting diverse and challenging noisy samples. Our approach achieves improved accuracy by encouraging the model to focus on the underlying geometry rather than relying solely on pixel values.","PeriodicalId":516531,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.)","volume":"14350 ","pages":"90-104"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11251192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141636371","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}

引用次数: 0

IcoConv : Explainable brain cortical surface analysis for ASD classification. IcoConv : 用于 ASD 分类的可解释大脑皮层表面分析。

Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.) Pub Date : 2023-10-01 Epub Date: 2023-10-31 DOI: 10.1007/978-3-031-46914-5_20

Ugo Rodriguez, Tahya Deddah, Sun Hyung Kim, Mark Shen, Kelly N Botteron, D Louis Collins, Stephen R Dager, Annette M Estes, Alan C Evans, Heather C Hazlett, Robert McKinstry, Robert T Shultz, Joseph Piven, Quyen Dang, Martin Styner, Juan Carlos Prieto

{"title":"IcoConv : Explainable brain cortical surface analysis for ASD classification.","authors":"Ugo Rodriguez, Tahya Deddah, Sun Hyung Kim, Mark Shen, Kelly N Botteron, D Louis Collins, Stephen R Dager, Annette M Estes, Alan C Evans, Heather C Hazlett, Robert McKinstry, Robert T Shultz, Joseph Piven, Quyen Dang, Martin Styner, Juan Carlos Prieto","doi":"10.1007/978-3-031-46914-5_20","DOIUrl":"10.1007/978-3-031-46914-5_20","url":null,"abstract":"In this study, we introduce a novel approach for the analysis and interpretation of 3D shapes, particularly applied in the context of neuroscientific research. Our method captures 2D perspectives from various vantage points of a 3D object. These perspectives are subsequently analyzed using 2D Convolutional Neural Networks (CNNs), uniquely modified with custom pooling mechanisms. We sought to assess the efficacy of our approach through a binary classification task involving subjects at high risk for Autism Spectrum Disorder (ASD). The task entailed differentiating between high-risk positive and high-risk negative ASD cases. To do this, we employed brain attributes like cortical thickness, surface area, and extra-axial cerebral spinal measurements. We then mapped these measurements onto the surface of a sphere and subsequently analyzed them via our bespoke method. One distinguishing feature of our method is the pooling of data from diverse views using our icosahedron convolution operator. This operator facilitates the efficient sharing of information between neighboring views. A significant contribution of our method is the generation of gradient-based explainability maps, which can be visualized on the brain surface. The insights derived from these explainability images align with prior research findings, particularly those detailing the brain regions typically impacted by ASD. Our innovative approach thereby substantiates the known understanding of this disorder while potentially unveiling novel areas of study.","PeriodicalId":516531,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.)","volume":"14350 ","pages":"248-258"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10902712/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139998750","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}

引用次数: 0

Progressive DeepSSM: Training Methodology for Image-To-Shape Deep Models. 渐进式 DeepSSM：图像到形状深度模型的训练方法。

Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.) Pub Date : 2023-10-01 Epub Date: 2023-10-31 DOI: 10.1007/978-3-031-46914-5_13

Abu Zahid Bin Aziz, Jadie Adams, Shireen Elhabian

{"title":"Progressive DeepSSM: Training Methodology for Image-To-Shape Deep Models.","authors":"Abu Zahid Bin Aziz, Jadie Adams, Shireen Elhabian","doi":"10.1007/978-3-031-46914-5_13","DOIUrl":"10.1007/978-3-031-46914-5_13","url":null,"abstract":"Statistical shape modeling (SSM) is an enabling quantitative tool to study anatomical shapes in various medical applications. However, directly using 3D images in these applications still has a long way to go. Recent deep learning methods have paved the way for reducing the substantial preprocessing steps to construct SSMs directly from unsegmented images. Nevertheless, the performance of these models is not up to the mark. Inspired by multiscale/multiresolution learning, we propose a new training strategy, progressive DeepSSM, to train image-to-shape deep learning models. The training is performed in multiple scales, and each scale utilizes the output from the previous scale. This strategy enables the model to learn coarse shape features in the first scales and gradually learn detailed fine shape features in the later scales. We leverage shape priors via segmentation-guided multi-task learning and employ deep supervision loss to ensure learning at each scale. Experiments show the superiority of models trained by the proposed strategy from both quantitative and qualitative perspectives. This training methodology can be employed to improve the stability and accuracy of any deep learning method for inferring statistical representations of anatomies from medical images and can be adopted by existing deep learning methods to improve model accuracy and training stability.","PeriodicalId":516531,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2023, held in conjunction with MICCAI 2023, Vancouver, BC, Canada, October 8, 2023, Proceedings. ShapeMI (Workshop) (2023 : Vancouver, B.C.)","volume":"14350 ","pages":"157-172"},"PeriodicalIF":0.0,"publicationDate":"2023-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11090218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923504","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}

引用次数: 0