Shape in medical imaging : International Workshop, ShapeMI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 20, 2018 : proceedings. ShapeMI (Workshop) (2018 : Granada, Spain)最新文献

{"title":"DeepSSM: A Deep Learning Framework for Statistical Shape Modeling from Raw Images.","authors":"Riddhish Bhalodia, Shireen Y Elhabian, Ladislav Kavan, Ross T Whitaker","doi":"10.1007/978-3-030-04747-4_23","DOIUrl":"10.1007/978-3-030-04747-4_23","url":null,"abstract":"<p><p>Statistical shape modeling is an important tool to characterize variation in anatomical morphology. Typical shapes of interest are measured using 3D imaging and a subsequent pipeline of registration, segmentation, and some extraction of shape features or projections onto some lower-dimensional shape space, which facilitates subsequent statistical analysis. Many methods for constructing compact shape representations have been proposed, but are often impractical due to the sequence of image preprocessing operations, which involve significant parameter tuning, manual delineation, and/or quality control by the users. We propose DeepSSM: a deep learning approach to extract a low-dimensional shape representation directly from 3D images, requiring virtually no parameter tuning or user assistance. DeepSSM uses a convolutional neural network (CNN) that simultaneously localizes the biological structure of interest, establishes correspondences, and projects these points onto a low-dimensional shape representation in the form of PCA loadings within a point distribution model. To overcome the challenge of the limited availability of training images with dense correspondences, we present a novel data augmentation procedure that uses existing correspondences on a relatively small set of processed images with shape statistics to create plausible training samples with known shape parameters. In this way, we leverage the limited CT/MRI scans (40-50) into thousands of images needed to train a deep neural net. After the training, the CNN automatically produces accurate low-dimensional shape representations for unseen images. We validate DeepSSM for three different applications pertaining to modeling pediatric cranial CT for characterization of metopic craniosynostosis, femur CT scans identifying morphologic deformities of the hip due to femoroacetabular impingement, and left atrium MRI scans for atrial fibrillation recurrence prediction.</p>","PeriodicalId":74795,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 20, 2018 : proceedings. ShapeMI (Workshop) (2018 : Granada, Spain)","volume":" ","pages":"244-257"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385885/pdf/nihms-1006323.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36999187","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":"Organ-At-Risk Segmentation in Brain MRI using Model-Based Segmentation: Benefits of Deep Learning-Based Boundary Detectors.","authors":"Eliza Orasanu,&nbsp;Tom Brosch,&nbsp;Carri Glide-Hurst,&nbsp;Steffen Renisch","doi":"10.1007/978-3-030-04747-4_27","DOIUrl":"https://doi.org/10.1007/978-3-030-04747-4_27","url":null,"abstract":"<p><p>Organ-at-risk (OAR) segmentation is a key step for radiotherapy treatment planning. Model-based segmentation (MBS) has been successfully used for the fully automatic segmentation of anatomical structures and it has proven to be robust to noise due to its incorporated shape prior knowledge. In this work, we investigate the advantages of combining neural networks with the prior anatomical shape knowledge of the model-based segmentation of organs-at-risk for brain radiotherapy (RT) on Magnetic Resonance Imaging (MRI). We train our boundary detectors using two different approaches: classic strong gradients as described in [4] and as a locally adaptive regression task, where for each triangle a convolutional neural network (CNN) was trained to estimate the distances between the mesh triangles and organ boundary, which were then combined into a single network, as described by [1]. We evaluate both methods using a 5-fold cross- validation on both T1w and T2w brain MRI data from sixteen primary and metastatic brain cancer patients (some post-surgical). Using CNN-based boundary detectors improved the results for all structures in both T1w and T2w data. The improvements were statistically significant (<i>p</i> < 0.05) for all segmented structures in the T1w images and only for the auditory system in the T2w images.</p>","PeriodicalId":74795,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 20, 2018 : proceedings. ShapeMI (Workshop) (2018 : Granada, Spain)","volume":" ","pages":"291-299"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-030-04747-4_27","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37243845","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":"Nonparametric Aggregation of Geodesic Trends for Longitudinal Data Analysis.","authors":"Kristen M Campbell,&nbsp;P Thomas Fletcher","doi":"10.1007/978-3-030-04747-4_22","DOIUrl":"https://doi.org/10.1007/978-3-030-04747-4_22","url":null,"abstract":"<p><p>We propose a technique for analyzing longitudinal imaging data that models individual changes with diffeomorphic geodesic regression and aggregates these geodesics into a nonparametric group average trend. Our model is specifically tailored to the unbalanced and sparse characteristics of longitudinal imaging studies. That is, each individual has few data points measured over a short period of time, while the study population as a whole spans a wide age range. We use geodesic regression to estimate individual trends, which is an appropriate model for capturing shape changes over a short time window, as is typically found within an individual. Geodesics are also adept at handling the low sample sizes found within individuals, and can model the change between as few as two timepoints. However, geodesics are limited for modeling longer-term trends, where constant velocity may not be appropriate. Therefore, we develop a novel nonparametric regression to aggregate individual trends into an average group trend. We demonstrate the power of our method to capture non-geodesic group trends on hippocampal volume (real-valued data) and diffeomorphic registration of full 3D MRI from the longitudinal OASIS data.</p>","PeriodicalId":74795,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 20, 2018 : proceedings. ShapeMI (Workshop) (2018 : Granada, Spain)","volume":" ","pages":"232-243"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-030-04747-4_22","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38732337","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":"SlicerSALT: Shape AnaLysis Toolbox.","authors":"Jared Vicory,&nbsp;Laura Pascal,&nbsp;Pablo Hernandez,&nbsp;James Fishbaugh,&nbsp;Juan Prieto,&nbsp;Mahmoud Mostapha,&nbsp;Chao Huang,&nbsp;Hina Shah,&nbsp;Junpyo Hong,&nbsp;Zhiyuan Liu,&nbsp;Loic Michoud,&nbsp;Jean-Christophe Fillion-Robin,&nbsp;Guido Gerig,&nbsp;Hongtu Zhu,&nbsp;Stephen M Pizer,&nbsp;Martin Styner,&nbsp;Beatriz Paniagua","doi":"10.1007/978-3-030-04747-4_6","DOIUrl":"https://doi.org/10.1007/978-3-030-04747-4_6","url":null,"abstract":"<p><p>SlicerSALT is an open-source platform for disseminating state-of-the-art methods for performing statistical shape analysis. These methods are developed as 3D Slicer extensions to take advantage of its powerful underlying libraries. SlicerSALT itself is a heavily customized 3D Slicer package that is designed to be easy to use for shape analysis researchers. The packaged methods include powerful techniques for creating and visualizing shape representations as well as performing various types of analysis.</p>","PeriodicalId":74795,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 20, 2018 : proceedings. ShapeMI (Workshop) (2018 : Granada, Spain)","volume":"11167 ","pages":"65-72"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-030-04747-4_6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9133883","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":"On the Evaluation and Validation of Off-the-shelf Statistical Shape Modeling Tools: A Clinical Application.","authors":"Anupama Goparaju,&nbsp;Ibolya Csecs,&nbsp;Alan Morris,&nbsp;Evgueni Kholmovski,&nbsp;Nassir Marrouche,&nbsp;Ross Whitaker,&nbsp;Shireen Elhabian","doi":"10.1007/978-3-030-04747-4_2","DOIUrl":"https://doi.org/10.1007/978-3-030-04747-4_2","url":null,"abstract":"<p><p>Statistical shape modeling (SSM) has proven useful in many areas of biology and medicine as a new generation of morphometric approaches for the quantitative analysis of anatomical shapes. Recently, the increased availability of high-resolution in vivo images of anatomy has led to the development and distribution of open-source computational tools to model anatomical shapes and their variability within populations with unprecedented detail and statistical power. Nonetheless, there is little work on the evaluation and validation of such tools as related to clinical applications that rely on morphometric quantifications for treatment planning. To address this lack of validation, we systematically assess the outcome of widely used off-the-shelf SSM tools, namely ShapeWorks, SPHARM-PDM, and Deformetrica, in the context of designing closure devices for left atrium appendage (LAA) in atrial fibrillation (AF) patients to prevent stroke, where an incomplete LAA closure may be worse than no closure. This study is motivated by the potential role of SSM in the geometric design of closure devices, which could be informed by population-level statistics, and patient-specific device selection, which is driven by anatomical measurements that could be automated by relating patient-level anatomy to population-level morphometrics. Hence, understanding the consequences of different SSM tools for the final analysis is critical for the careful choice of the tool to be deployed in real clinical scenarios. Results demonstrate that estimated measurements from ShapeWorks model are more consistent compared to models from Deformetrica and SPHARM-PDM. Furthermore, ShapeWorks and Deformetrica shape models capture clinically relevant population-level variability compared to SPHARM-PDM models.</p>","PeriodicalId":74795,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 20, 2018 : proceedings. ShapeMI (Workshop) (2018 : Granada, Spain)","volume":" ","pages":"14-27"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/978-3-030-04747-4_2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36999186","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":"Characterizing Anatomical Variability And Alzheimer's Disease Related Cortical Thinning in the Medial Temporal Lobe Using Graph-Based Groupwise Registration And Point Set Geodesic Shooting.","authors":"Long Xie, Laura E M Wisse, Sandhitsu R Das, Ranjit Ittyerah, Jiancong Wang, David A Wolk, Paul A Yushkevich","doi":"10.1007/978-3-030-04747-4_3","DOIUrl":"10.1007/978-3-030-04747-4_3","url":null,"abstract":"<p><p>The perirhinal cortex (PRC) is a site of early neurofibrillary tangle (NFT) pathology in Alzheimer's disease (AD). Subtle morphological changes in the PRC have been reported in MRI studies of early AD, which has significance for clinical trials targeting preclinical AD. However, the PRC exhibits considerable anatomical variability with multiple <i>discrete variants</i> described in the neuroanatomy literature. We hypothesize that different anatomical variants are associated with different patterns of AD-related effects in the PRC. Single-template approaches conventionally used for automated image-based brain morphometry are ill-equipped to test this hypothesis. This study uses graph-based groupwise registration and diffeomorphic landmark matching with geodesic shooting to build statistical shape models of discrete PRC variants and examine variant-specific effects of AD on PRC shape and thickness. Experimental results demonstrate that the statistical models recover the folding patterns of the known PRC variants and capture the expected shape variability within the population. By applying the proposed pipeline to a large dataset with subjects from different stages in the AD spectrum, we find 1) a pattern of cortical thinning consistent with the NFT pathology progression, 2) different patterns of the initial spatial distribution of cortical thinning between anatomical variants, and 3) an effect of AD on medial temporal lobe shape. As such, the proposed pipeline could have important utility in the early detection and monitoring of AD.</p>","PeriodicalId":74795,"journal":{"name":"Shape in medical imaging : International Workshop, ShapeMI 2018, held in conjunction with MICCAI 2018, Granada, Spain, September 20, 2018 : proceedings. ShapeMI (Workshop) (2018 : Granada, Spain)","volume":" ","pages":"28-37"},"PeriodicalIF":0.0,"publicationDate":"2018-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6469499/pdf/nihms-1021758.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37348476","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}