Knowledge of vertebra location, shape, and orientation is crucial in many medical applications such as orthopedics or interventional procedures. Computed tomography (CT) offers a high contrast between bone and soft tissues, but automatic vertebra segmentation remains difficult. Hence, the wide range of shapes, aging, and degenerative joint disease alterations as well as the variety of pathological cases encountered in an aging population make automatic segmentation sometimes challenging. Besides, daily practice implies a need for affordable computation time. This paper aims to present a new automated vertebra segmentation method (using a first bounding box for initialization) for CT 3D data which tackles these problems. This method is based on two consecutive steps. The first one is a new coarse-to-fine method efficiently reducing the data amount to obtain a coarse shape of the vertebra. The second step consists in a hidden Markov chain (HMC) segmentation using a specific volume transformation within a Bayesian framework. Our method does not introduce any prior on the expected shape of the vertebra within the bounding box and thus deals with the most frequent pathological cases encountered in daily practice. We experiment this method on a set of standard lumbar, thoracic, and cervical vertebrae and on a public dataset, on pathological cases, and in a simple integration example. Quantitative and qualitative results show that our method is robust to changes in shapes and luminance and provides correct segmentation with respect to pathological cases.
{"title":"Vertebra segmentation based on two-step refinement.","authors":"Jean-Baptiste Courbot, Edmond Rust, Emmanuel Monfrini, Christophe Collet","doi":"10.1186/s40244-016-0018-0","DOIUrl":"https://doi.org/10.1186/s40244-016-0018-0","url":null,"abstract":"<p><p>Knowledge of vertebra location, shape, and orientation is crucial in many medical applications such as orthopedics or interventional procedures. Computed tomography (CT) offers a high contrast between bone and soft tissues, but automatic vertebra segmentation remains difficult. Hence, the wide range of shapes, aging, and degenerative joint disease alterations as well as the variety of pathological cases encountered in an aging population make automatic segmentation sometimes challenging. Besides, daily practice implies a need for affordable computation time. This paper aims to present a new automated vertebra segmentation method (using a first bounding box for initialization) for CT 3D data which tackles these problems. This method is based on two consecutive steps. The first one is a new coarse-to-fine method efficiently reducing the data amount to obtain a coarse shape of the vertebra. The second step consists in a hidden Markov chain (HMC) segmentation using a specific volume transformation within a Bayesian framework. Our method does not introduce any prior on the expected shape of the vertebra within the bounding box and thus deals with the most frequent pathological cases encountered in daily practice. We experiment this method on a set of standard lumbar, thoracic, and cervical vertebrae and on a public dataset, on pathological cases, and in a simple integration example. Quantitative and qualitative results show that our method is robust to changes in shapes and luminance and provides correct segmentation with respect to pathological cases.</p>","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"4 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40244-016-0018-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34360252","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}
Pub Date : 2015-08-11DOI: 10.1186/S40244-015-0017-6
A. Hostettler, Wenwu Zhu, S. Nicolau, L. Soler, J. Marescaux
{"title":"Methodology for fast interactive segmentation of the peritoneum and diaphragm in multi-modal 3D medical image","authors":"A. Hostettler, Wenwu Zhu, S. Nicolau, L. Soler, J. Marescaux","doi":"10.1186/S40244-015-0017-6","DOIUrl":"https://doi.org/10.1186/S40244-015-0017-6","url":null,"abstract":"","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"60 1","pages":"1-17"},"PeriodicalIF":0.0,"publicationDate":"2015-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78236164","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}
Pub Date : 2015-07-18DOI: 10.1186/S40244-015-0016-7
M. Garbey, G. Joerger, Albert Y Huang, Remi Salmon, Jin-Ju Kim, V. Sherman, B. Dunkin, B. Bass
{"title":"An intelligent hospital operating room to improve patient health care","authors":"M. Garbey, G. Joerger, Albert Y Huang, Remi Salmon, Jin-Ju Kim, V. Sherman, B. Dunkin, B. Bass","doi":"10.1186/S40244-015-0016-7","DOIUrl":"https://doi.org/10.1186/S40244-015-0016-7","url":null,"abstract":"","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"35 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2015-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85739184","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}
Pub Date : 2015-05-01Epub Date: 2015-05-07DOI: 10.1186/s40244-015-0015-8
Saurabh Dargar, Rebecca Kennedy, WeiXuan Lai, Venkata Arikatla, Suvranu De
Surgery is characterized by complex tasks performed in stressful environments. To enhance patient safety and reduce errors, surgeons must be trained in environments that mimic the actual clinical setting. Rasmussen's model of human behavior indicates that errors in surgical procedures may be skill-, rule-, or knowledge-based. While skill-based behavior and some rule-based behavior may be taught using box trainers and ex vivo or in vivo animal models, we posit that multimodal immersive virtual reality (iVR) that includes high-fidelity visual as well as other sensory feedback in a seamless fashion provides the only means of achieving true surgical expertise by addressing all three levels of human behavior. While the field of virtual reality is not new, realization of the goals of complete immersion is challenging and has been recognized as a Grand Challenge by the National Academy of Engineering. Recent technological advances in both interface and computational hardware have generated significant enthusiasm in this field. In this paper, we discuss convergence of some of these technologies and possible evolution of the field in the near term.
{"title":"Towards immersive virtual reality (iVR): a route to surgical expertise.","authors":"Saurabh Dargar, Rebecca Kennedy, WeiXuan Lai, Venkata Arikatla, Suvranu De","doi":"10.1186/s40244-015-0015-8","DOIUrl":"https://doi.org/10.1186/s40244-015-0015-8","url":null,"abstract":"<p><p>Surgery is characterized by complex tasks performed in stressful environments. To enhance patient safety and reduce errors, surgeons must be trained in environments that mimic the actual clinical setting. Rasmussen's model of human behavior indicates that errors in surgical procedures may be skill-, rule-, or knowledge-based. While skill-based behavior and some rule-based behavior may be taught using box trainers and <i>ex vivo</i> or <i>in vivo</i> animal models, we posit that multimodal immersive virtual reality (iVR) that includes high-fidelity visual as well as other sensory feedback in a seamless fashion provides the only means of achieving true surgical expertise by addressing all three levels of human behavior. While the field of virtual reality is not new, realization of the goals of complete immersion is challenging and has been recognized as a Grand Challenge by the National Academy of Engineering. Recent technological advances in both interface and computational hardware have generated significant enthusiasm in this field. In this paper, we discuss convergence of some of these technologies and possible evolution of the field in the near term.</p>","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"2 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40244-015-0015-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34164959","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}
Pub Date : 2015-02-04DOI: 10.1186/S40244-014-0014-1
T. Colin, F. Cornelis, Julien Jouganous, J. Palussiere, Olivier Saut
{"title":"Patient-specific simulation of tumor growth, response to the treatment, and relapse of a lung metastasis: a clinical case","authors":"T. Colin, F. Cornelis, Julien Jouganous, J. Palussiere, Olivier Saut","doi":"10.1186/S40244-014-0014-1","DOIUrl":"https://doi.org/10.1186/S40244-014-0014-1","url":null,"abstract":"","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"79 1","pages":"1-17"},"PeriodicalIF":0.0,"publicationDate":"2015-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86092693","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}
Pub Date : 2014-11-22DOI: 10.1186/S40244-014-0013-2
G. Valenza, O. Akeju, Kara J. Pavone, L. Citi, Katharine E. Hartnack, A. Sampson, P. Purdon, E. Brown, R. Barbieri
{"title":"Instantaneous monitoring of heart beat dynamics during anesthesia and sedation","authors":"G. Valenza, O. Akeju, Kara J. Pavone, L. Citi, Katharine E. Hartnack, A. Sampson, P. Purdon, E. Brown, R. Barbieri","doi":"10.1186/S40244-014-0013-2","DOIUrl":"https://doi.org/10.1186/S40244-014-0013-2","url":null,"abstract":"","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"17 1","pages":"1-18"},"PeriodicalIF":0.0,"publicationDate":"2014-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89614159","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}
Pub Date : 2014-11-01DOI: 10.1186/s40244-014-0012-3
Giljae Lee, Andréa M. Matsunaga, S. Dura-Bernal, W. Zhang, W. Lytton, J. Francis, J. Fortes
{"title":"Towards real-time communication between in vivo neurophysiological data sources and simulator-based brain biomimetic models","authors":"Giljae Lee, Andréa M. Matsunaga, S. Dura-Bernal, W. Zhang, W. Lytton, J. Francis, J. Fortes","doi":"10.1186/s40244-014-0012-3","DOIUrl":"https://doi.org/10.1186/s40244-014-0012-3","url":null,"abstract":"","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"15 1","pages":"1 - 23"},"PeriodicalIF":0.0,"publicationDate":"2014-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75483938","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}
Pub Date : 2014-10-07DOI: 10.1186/S40244-014-0011-4
N. Lepoutre, M. Gilles, Remi Salmon, C. Collet, B. Bass, M. Garbey
{"title":"A robust method and affordable system for the 3D-surface reconstruction of patient torso to evaluate cosmetic outcome after Breast Conservative Therapy","authors":"N. Lepoutre, M. Gilles, Remi Salmon, C. Collet, B. Bass, M. Garbey","doi":"10.1186/S40244-014-0011-4","DOIUrl":"https://doi.org/10.1186/S40244-014-0011-4","url":null,"abstract":"","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"1 1","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2014-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89070894","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}
Pub Date : 2014-08-06DOI: 10.1186/S40244-014-0010-5
K. Endo, N. Sata, Y. Ishiguro, A. Miki, H. Sasanuma, Y. Sakuma, A. Shimizu, M. Hyodo, A. Lefor, Y. Yasuda
{"title":"A patient-specific surgical simulator using preoperative imaging data: an interactive simulator using a three-dimensional tactile mouse","authors":"K. Endo, N. Sata, Y. Ishiguro, A. Miki, H. Sasanuma, Y. Sakuma, A. Shimizu, M. Hyodo, A. Lefor, Y. Yasuda","doi":"10.1186/S40244-014-0010-5","DOIUrl":"https://doi.org/10.1186/S40244-014-0010-5","url":null,"abstract":"","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"75 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2014-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86323336","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}
S. Zaunseder, M. Riedl, J. Kurths, H. Malberg, R. Bauernschmitt, N. Wessel
{"title":"Impact of cardiac surgery on the autonomic cardiovascular function","authors":"S. Zaunseder, M. Riedl, J. Kurths, H. Malberg, R. Bauernschmitt, N. Wessel","doi":"10.1186/2194-3990-1-9","DOIUrl":"https://doi.org/10.1186/2194-3990-1-9","url":null,"abstract":"","PeriodicalId":91110,"journal":{"name":"Journal of computational surgery","volume":"9 1","pages":"1-16"},"PeriodicalIF":0.0,"publicationDate":"2014-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88110457","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}
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