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Effective 3D Humerus and Scapula Extraction using Low-contrast and High-shape-variability MR Data [article]

Xiaoxiao He, Chaowei Tan, Yuting Qiao, Virak Tan, Dimitris Metaxas, Kang Li
2019 arXiv   pre-print
In this paper, we present a joint segmentation for the humerus and scapula bones on a small dataset with low-contrast and high-shape-variability 3D MR images.  ...  Therefore, it is practical to consider the bone extraction on low-resolution data which may influence imaging contrast and make the segmentation work difficult.  ...  Thus, the proposed method has higher robustness to segment the small dataset with low-contrast and high-shape-variability 3D MR Data.  ... 
arXiv:1902.08527v1 fatcat:aeeugmk46fb4vfcftsdrngjlba

Recursive 3D Segmentation of Shoulder Joint with Coarse-scanned MR Image [article]

Xiaoxiao He, Chaowei Tan, Virak Tan, Kang Li
2022 arXiv   pre-print
In order to combat all obstacles stated above, we develop a fully automated algorithm for segmenting the humerus and scapula bone from coarsely scanned and low-resolution MR images and a recursive learning  ...  The proposed neural network and the recursive learning scheme improve the overall quality of the segmentation on humerus and scapula on the low-resolution dataset and reduced incorrect segmentation in  ...  The task of 3D segmentation with low resolution, limited amount of data and high shape variability is addressed for the first time.  ... 
arXiv:2203.07846v1 fatcat:gztzga6umvh3np4sya3upc7otq

A Three-Dimensional Analysis of Morphological Evolution and Locomotor Performance of the Carnivoran Forelimb

Alberto Martín-Serra, Borja Figueirido, Paul Palmqvist, Andrew Iwaniuk
2014 PLoS ONE  
In this study, three-dimensional landmark-based methods of geometric morphometrics are used for estimating the influence of phylogeny, allometry and locomotor performance on forelimb shape in living and  ...  Results indicate that both size and phylogeny have strong effects on the anatomy of all forelimb bones.  ...  Almécija for providing us the bone scanning surfaces. We thank J. Galkin and E.  ... 
doi:10.1371/journal.pone.0085574 pmid:24454891 pmcid:PMC3893248 fatcat:xhd3mqvszjdvngyg344zsh6f6y

Deep learning-based segmentation and fat fraction analysis of the shoulder muscles using quantitative MRI

Michael Herren, Nicolas Gerber, Hanspeter Hess, Kate Gerber
2022 Zenodo  
To segment the SSP muscle and the humerus and scapula bones, we employed nnU-Net, a state-of-the-art convolutional neural network for medical image segmentation.  ...  work required to extract such a metric has limited their use in clinical routine.  ...  Acknowledgements I have received a great deal of support and assistance throughout this project. I want to thank my supervisors and examiners Dr. Nicolas Gerber, MSc Hanspeter Hess, and Dr.  ... 
doi:10.5281/zenodo.6397485 fatcat:hhfaboug5re5npvhsr3okuzmqi

Multi-structure bone segmentation in pediatric MR images with combined regularization from shape priors and adversarial network [article]

Arnaud Boutillon, Bhushan Borotikar, Valérie Burdin, Pierre-Henri Conze
2022 arXiv   pre-print
Morphological and diagnostic evaluation of pediatric musculoskeletal system is crucial in clinical practice. However, most segmentation models do not perform well on scarce pediatric imaging data.  ...  In order to obtain globally consistent predictions, we incorporate a shape priors based regularization, derived from a non-linear shape representation learnt by an auto-encoder.  ...  Christelle Pons from Ildys Foundation, Brest, France for her involvement in clinical data collection and patient enrolment process.  ... 
arXiv:2009.07092v5 fatcat:dpd2vsoipnejnbzgxqt4rmc6cm

Generalizable multi-task, multi-domain deep segmentation of sparse pediatric imaging datasets via multi-scale contrastive regularization and multi-joint anatomical priors [article]

Arnaud Boutillon, Pierre-Henri Conze, Christelle Pons, Valérie Burdin, Bhushan Borotikar
2022 arXiv   pre-print
We evaluate our contributions for performing bone segmentation using three scarce and pediatric imaging datasets of the ankle, knee, and shoulder joints.  ...  Unlike previous approaches, we simultaneously consider multiple intensity domains and segmentation tasks to overcome the inherent scarcity of pediatric data while leveraging shared features between imaging  ...  For deep learning based medical image segmentation, incorporating shape or anatomical priors has already proven to be useful in reducing the effect of noise, low contrast, and artefacts (Ravishankar et  ... 
arXiv:2207.13502v1 fatcat:qe4stepkqnd2rjgtii4cwxsk34

Shape Covariation (or the Lack Thereof) Between Vertebrae and Other Skeletal Traits in Felids: The Whole is Not Always Greater than the Sum of Parts

Marcela Randau, Anjali Goswami
2018 Evolutionary biology  
We accomplish this comparison by performing pairwise tests of integration between vertebral and other osteological units, quantified with 3D geometric morphometric data and analysed both with and without  ...  Results demonstrate a functionally-partitioned vertebral column, with regions varying greatly in level of correlation between shape and ecology.  ...  Cuff for allowing us to use two of his beautiful 3D reconstructions in one of our figures. We also thank Dr. John R. Hutchinson and Dr. Andrew R. Cuff, who are members of the 'Team Cat', and Dr.  ... 
doi:10.1007/s11692-017-9443-6 pmid:29755151 pmcid:PMC5938317 fatcat:qw6z5qqt3zh2jaaogxucczjfvq

Multimodal Correlative Preclinical Whole Body Imaging and Segmentation

Ayelet Akselrod-Ballin, Hagit Dafni, Yoseph Addadi, Inbal Biton, Reut Avni, Yafit Brenner, Michal Neeman
2016 Scientific Reports  
Specifically for MRI, field dependent effects provide incentive for registration of data acquired at different field strength.  ...  Automatic segmentation of anatomical structures in medical images remains challenging due to issues such as noise, intensity non-uniformity, partial volume effect, shape complexity of the various structures  ...  Acknowledgements The authors would like to thank Nava Nevo for her help in tumor injection and advice on tumor delineation.  ... 
doi:10.1038/srep27940 pmid:27325178 pmcid:PMC4914843 fatcat:y3z32ebeonegxaa6fy4mkdaw2a

Measuring and Establishing the Accuracy and Reproducibility of 3D Printed Medical Models

Elizabeth George, Peter Liacouras, Frank J. Rybicki, Dimitrios Mitsouras
2017 Radiographics  
These metrics can be used to define the accuracy of a model, as compared with the reference standard, and to measure the variability of models created by different observers or using different workflows  ...  Radiologists' understanding of the factors that influence 3D printed model accuracy and the metrics used to measure this accuracy is key in directing appropriate practices and establishing reference standards  ...  performing chest MR imaging with a volumetric (ie, 3D) sequence and combined segmentation with CT and MR imaging in parallel Consider performing ECG-gated contrast-enhanced and contrast-enhanced MR  ... 
doi:10.1148/rg.2017160165 pmid:28800287 pmcid:PMC5621728 fatcat:zfygnblgtbe3nhjsrgm5uwcqde

Trabecular architecture and joint loading of the proximal humerus in extant hominoids, Ateles , and Australopithecus africanus

Tracy L. Kivell, Rebecca Davenport, Jean-Jacques Hublin, J. Francis Thackeray, Matthew M. Skinner
2018 American Journal of Physical Anthropology  
of aspects of bony 9 morphology that are more sensitive to loading during life than external bone shape and size. 10  ...  proximal humerus of extant hominoids, Ateles and A. africanus (StW 328).  ...  Knuckle-walking also generates 12 high compressive joint reaction forces in the humerus due to the combined effect of muscle 13 contraction and gravitational forces acting on the body mass (Carlson and  ... 
doi:10.1002/ajpa.23635 pmid:30129074 fatcat:5ya53p2wlzbgte6c7tiovj2pta

Fabric Image Representation Encoding Networks for Large-scale 3D Medical Image Analysis [article]

Siyu Liu, Wei Dai, Craig Engstrom, Jurgen Fripp, Peter B. Greer, Stuart Crozier, Jason A. Dowling, Shekhar S. Chandra
2020 arXiv   pre-print
The fabric network uses Atrous Spatial Pyramid Pooling (ASPP) extended to 3D to extract local and image-level features at a fine selection of scales.  ...  FIRENet was also simultaneously trained on MR (Magnatic Resonance) images acquired from 3D examinations of musculoskeletal elements in the (hip, knee, shoulder) joints and a public OAI knee dataset to  ...  , contrast, scale, shape, orientation and object coverage.  ... 
arXiv:2006.15578v2 fatcat:txa2zt4d35dg3apyecnsoglliy

Cross Platform Comparison of Imaging Technologies for Measuring Musculoskeletal Motion [chapter]

Richard M. Smith, Frances T. Sheehan
2017 Handbook of Human Motion  
Human movement is integral to daily life, it defines our species (the ability to walk upright and manipulate objects using an opposable thumb), and it is central to our ability to interact with our environment  ...  Accuracies are presented throughout this chapter if they were reported as maximum average absolute or root mean squared errors for accuracy data for translational (in millimeters) and rotational data (  ...  Acknowledgments We thank Judith Welsh for her help and support toward this project.  ... 
doi:10.1007/978-3-319-30808-1_194-1 fatcat:ogjspujmizc5zotaht62qbwacm

Problems and solutions for the Accurate 3d Functional Modelling of the Hip and Shoulder [chapter]

Nadia Magnenat-Thalmann, MyungJin Kang, Taro Goto
2002 Advances in Modelling, Animation and Rendering  
properties, and planning system, and give a solution for individual accurate surface models by using an inter-patient registration method.  ...  The survey of functional modelling and our proposal, in order to obtain individual accurate model from MR Image dataset of several living people, are described.  ...  Acknowledgement This work is supported by CO-ME (Computer Aided and Image Guided Medical Interventions) project funded by Swiss National Research Foundation.  ... 
doi:10.1007/978-1-4471-0103-1_1 fatcat:3fazooo6tfbfjmip5rlgjs5jae

Articulated Whole-Body Atlases for Small Animal Image Analysis: Construction and Applications

Artem Khmelinskii, Martin Baiker, Eric L. Kaijzel, Josette Chen, Johan H. C. Reiber, Boudewijn P. F. Lelieveldt
2010 Molecular Imaging and Biology  
This eliminates the postural variability (e.g., of the head, back, and front limbs) that occurs in different time steps and due to modality differences and nonstandardized acquisition protocols.  ...  Purpose: Using three publicly available small-animal atlases (Sprague-Dawley rat, MOBY, and Digimouse), we built three articulated atlases and present several applications in the scope of molecular imaging  ...  ., and Bai et al. We would also like to thank Ivo Que from Clemens Löwik's group and Josette Chen from Mark Henkelman's group for providing the data used to validate the proposed algorithms.  ... 
doi:10.1007/s11307-010-0386-x pmid:20824510 pmcid:PMC3179580 fatcat:zfijpwlp65hyzot5jvwwwczzze

Image-based biomechanical models of the musculoskeletal system

Fabio Galbusera, Andrea Cina, Matteo Panico, Domenico Albano, Carmelo Messina
2020 European Radiology Experimental  
This paper presents a brief overview of the techniques used for image segmentation, meshing, and assessing the mechanical properties of biological tissues, with focus on finite element models of the musculoskeletal  ...  Both consolidated methods and recent advances such as those based on artificial intelligence are described.  ...  Moreover, segmentation can be used for the study of tissue diseases such as osteoarthritis, for example, by extracting important geometrical features from the 3D shape and size of the joint that are useful  ... 
doi:10.1186/s41747-020-00172-3 pmid:32789547 pmcid:PMC7423821 fatcat:w5wl67lvgvbxvmna43xkjxliyu
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