{"id":2436,"date":"2024-05-03T16:35:35","date_gmt":"2024-05-03T16:35:35","guid":{"rendered":"https:\/\/labs.cs.queensu.ca\/perklab\/members\/csaba-pinter\/"},"modified":"2024-05-03T16:35:35","modified_gmt":"2024-05-03T16:35:35","slug":"csaba-pinter","status":"publish","type":"qsc_member","link":"https:\/\/labs.cs.queensu.ca\/perklab\/members\/csaba-pinter\/","title":{"rendered":"Csaba Pinter"},"content":{"rendered":"<div class=\"wp-block-columns is-layout-flex wp-block-columns-is-layout-flex qsc-member-single-core-info-container\">\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow qsc-member-single-photo-column\">\n\t\t<img decoding=\"async\" src=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/plugins\/qsc-members\/\/images\/missing-image-placeholder.png\" class=\"qsc-member-single-photo\"\/>\n\t<\/div>\n<div class=\"wp-block-column is-layout-flow wp-block-column-is-layout-flow qsc-member-single-info-column\">\n<div class=\"qsc-member-name\">\n<h1>Csaba Pinter<\/h1>\n<\/div>\n<div class=\"qsc-member-position\">Staff<\/div>\n<div class=\"qsc-member-department\">School of Computing<\/div>\n<div class=\"qsc-member-organization\">Queen&#8217;s University<\/div>\n<div class=\"qsc-member-date-range\">Member from <em>2011<\/em> to <em>2019<\/em><\/div>\n<div class=\"qsc-member-contact\">\n<div class=\"qsc-member-socials\">\n\t\t\t<\/div>\n<\/p><\/div>\n<\/p><\/div>\n<\/div>\n<div class=\"qsc-member-bio\">\n\tCsaba Pinter graduated at the University of Szeged, Hungary in 2006 as Computer Program Designer (MSc in Image Processing). He participated various medical image processing related research projects first at the university, then in the industry at companies in the field of radiology, nuclear medicine, and digital microscopy. His main interests are medical image segmentation and the design of innovative medical applications.<br \/>\n<div class=\"teachpress_pub_list\"><form name=\"tppublistform\" method=\"get\"><a name=\"tppubs\" id=\"tppubs\"><\/a><\/form><div class=\"tablenav\"><div class=\"tablenav-pages\"><span class=\"displaying-num\">83 entries<\/span> <a class=\"page-numbers button disabled\">&laquo;<\/a> <a class=\"page-numbers button disabled\">&lsaquo;<\/a> 1 of 2 <a href=\"https:\/\/labs.cs.queensu.ca\/perklab\/members\/csaba-pinter\/?limit=2&amp;tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=&amp;tsr=#tppubs\" title=\"next page\" class=\"page-numbers button\">&rsaquo;<\/a> <a href=\"https:\/\/labs.cs.queensu.ca\/perklab\/members\/csaba-pinter\/?limit=2&amp;tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=&amp;tsr=#tppubs\" title=\"last page\" class=\"page-numbers button\">&raquo;<\/a> <\/div><\/div><div class=\"teachpress_publication_list\"><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Lasso, Andras;  Herz, Christian;  Nam, Hannah;  Cianciulli, Alana;  Pieper, Steve;  Drouin, Simon;  Pinter, Csaba;  St-Onge, Samuelle;  Vigil, Chad;  Ching, Stephen;  Sunderland, Kyle;  Fichtinger, Gabor;  Kikinis, Ron;  Jolley, Matthew A<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcvm.2022.886549\/full\" title=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcvm.2022.886549\/full\" target=\"blank\">SlicerHeart: An open-source computing platform for cardiac image analysis and modeling<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_volume\">vol. 9, <\/span><span class=\"tp_pub_additional_pages\">pp. 886549, <\/span><span class=\"tp_pub_additional_year\">2022<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_801\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('801','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_801\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('801','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_801\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('801','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_801\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2022c,<br \/>\r\ntitle = {SlicerHeart: An open-source computing platform for cardiac image analysis and modeling},<br \/>\r\nauthor = {Andras Lasso and Christian Herz and Hannah Nam and Alana Cianciulli and Steve Pieper and Simon Drouin and Csaba Pinter and Samuelle St-Onge and Chad Vigil and Stephen Ching and Kyle Sunderland and Gabor Fichtinger and Ron Kikinis and Matthew A Jolley},<br \/>\r\nurl = {https:\/\/www.frontiersin.org\/articles\/10.3389\/fcvm.2022.886549\/full},<br \/>\r\nyear  = {2022},<br \/>\r\ndate = {2022-01-01},<br \/>\r\nvolume = {9},<br \/>\r\npages = {886549},<br \/>\r\npublisher = {Frontiers},<br \/>\r\nabstract = {Cardiovascular disease is a significant cause of morbidity and mortality in the developed world. 3D imaging of the heart\u2019s structure is critical to the understanding and treatment of cardiovascular disease. However, open-source tools for image analysis of cardiac images, particularly 3D echocardiographic (3DE) data, are limited. We describe the rationale, development, implementation, and application of SlicerHeart, a cardiac-focused toolkit for image analysis built upon 3D Slicer, an open-source image computing platform. We designed and implemented multiple Python scripted modules within 3D Slicer to import, register, and view 3DE data, including new code to volume render and crop 3DE. In addition, we developed dedicated workflows for the modeling and quantitative analysis of multi-modality image-derived heart models, including heart valves. Finally, we created and integrated new functionality to facilitate the planning of cardiac interventions and surgery. We demonstrate application of SlicerHeart to a diverse range of cardiovascular modeling and simulation including volume rendering of 3DE images, mitral valve modeling, transcatheter device modeling, and planning of complex surgical intervention such as cardiac baffle creation. SlicerHeart is an evolving open-source image processing platform based on 3D Slicer initiated to support the investigation and treatment of congenital heart disease. The technology in SlicerHeart provides a robust foundation for 3D image-based investigation in cardiovascular medicine.},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('801','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_801\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Cardiovascular disease is a significant cause of morbidity and mortality in the developed world. 3D imaging of the heart\u2019s structure is critical to the understanding and treatment of cardiovascular disease. However, open-source tools for image analysis of cardiac images, particularly 3D echocardiographic (3DE) data, are limited. We describe the rationale, development, implementation, and application of SlicerHeart, a cardiac-focused toolkit for image analysis built upon 3D Slicer, an open-source image computing platform. We designed and implemented multiple Python scripted modules within 3D Slicer to import, register, and view 3DE data, including new code to volume render and crop 3DE. In addition, we developed dedicated workflows for the modeling and quantitative analysis of multi-modality image-derived heart models, including heart valves. Finally, we created and integrated new functionality to facilitate the planning of cardiac interventions and surgery. We demonstrate application of SlicerHeart to a diverse range of cardiovascular modeling and simulation including volume rendering of 3DE images, mitral valve modeling, transcatheter device modeling, and planning of complex surgical intervention such as cardiac baffle creation. SlicerHeart is an evolving open-source image processing platform based on 3D Slicer initiated to support the investigation and treatment of congenital heart disease. The technology in SlicerHeart provides a robust foundation for 3D image-based investigation in cardiovascular medicine.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('801','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_801\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcvm.2022.886549\/full\" title=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcvm.2022.886549\/full\" target=\"_blank\">https:\/\/www.frontiersin.org\/articles\/10.3389\/fcvm.2022.886549\/full<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('801','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Cianciulli, Alana;  Lasso, Andras;  Pinter, Csaba;  Ching, Stephen;  Ghosh, Reena M;  Chen, Tiffany;  Herz, Christian;  Vigil, Chad;  Drouin, Simon;  Rogers, Lindsay S;  Quartermain, Michael D;  Biko, David M;  Whitehead, Kevin K;  Fichtinger, Gabor;  Gillespie, Matthew J;  Jolley, Matthew A<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.onlinejase.com\/article\/S0894-7317(21)00588-5\/abstract\" title=\"https:\/\/www.onlinejase.com\/article\/S0894-7317(21)00588-5\/abstract\" target=\"blank\">Simulation of delivery of clip-based therapies within multimodality images to facilitate preprocedural planning<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Journal of the American Society of Echocardiography, <\/span><span class=\"tp_pub_additional_volume\">vol. 34, <\/span><span class=\"tp_pub_additional_issue\">iss. 10, <\/span><span class=\"tp_pub_additional_pages\">pp. 1111-1114, <\/span><span class=\"tp_pub_additional_year\">2021<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_880\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('880','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_880\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('880','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_880\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('880','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_880\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2021g,<br \/>\r\ntitle = {Simulation of delivery of clip-based therapies within multimodality images to facilitate preprocedural planning},<br \/>\r\nauthor = {Alana Cianciulli and Andras Lasso and Csaba Pinter and Stephen Ching and Reena M Ghosh and Tiffany Chen and Christian Herz and Chad Vigil and Simon Drouin and Lindsay S Rogers and Michael D Quartermain and David M Biko and Kevin K Whitehead and Gabor Fichtinger and Matthew J Gillespie and Matthew A Jolley},<br \/>\r\nurl = {https:\/\/www.onlinejase.com\/article\/S0894-7317(21)00588-5\/abstract},<br \/>\r\nyear  = {2021},<br \/>\r\ndate = {2021-01-01},<br \/>\r\njournal = {Journal of the American Society of Echocardiography},<br \/>\r\nvolume = {34},<br \/>\r\nissue = {10},<br \/>\r\npages = {1111-1114},<br \/>\r\npublisher = {Elsevier},<br \/>\r\nabstract = {Brief Research Communications 1111 repair (TEER) has emerged as a therapeutic option for the treatment of severe mitral regurgitation and tricuspid regurgitation and avoids the morbidity and mortality associated with open heart surgery. 1, 2 One challenge to the successful application of this therapy is delivering the clip to a precise location within the constraints of the unique anatomy and resulting geometry of an individual patient. Threedimensional echocardiography (3DE) is typically used to plan and execute TEER using catheter delivery systems designed to access a specific anatomic location (mitral valve, tricuspid valve) via a known path. These systems are then empirically validated and iteratively improved via large clinical trials and clinical practice. However, there has been little work on modeling the catheter path and approach to deliver the clip to the desired location in atypical or surgically altered \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('880','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_880\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Brief Research Communications 1111 repair (TEER) has emerged as a therapeutic option for the treatment of severe mitral regurgitation and tricuspid regurgitation and avoids the morbidity and mortality associated with open heart surgery. 1, 2 One challenge to the successful application of this therapy is delivering the clip to a precise location within the constraints of the unique anatomy and resulting geometry of an individual patient. Threedimensional echocardiography (3DE) is typically used to plan and execute TEER using catheter delivery systems designed to access a specific anatomic location (mitral valve, tricuspid valve) via a known path. These systems are then empirically validated and iteratively improved via large clinical trials and clinical practice. However, there has been little work on modeling the catheter path and approach to deliver the clip to the desired location in atypical or surgically altered \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('880','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_880\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.onlinejase.com\/article\/S0894-7317(21)00588-5\/abstract\" title=\"https:\/\/www.onlinejase.com\/article\/S0894-7317(21)00588-5\/abstract\" target=\"_blank\">https:\/\/www.onlinejase.com\/article\/S0894-7317(21)00588-5\/abstract<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('880','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Hu, Zoe;  Brastianos, Harry;  Ungi, Tamas;  Pinter, Csaba;  Olding, Tim;  Korzeniowski, Martin;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11598\/115980Z\/Automated-catheter-segmentation-using-3D-ultrasound-images-in-high-dose\/10.1117\/12.2581966.short\" title=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11598\/115980Z\/Automated-catheter-segmentation-using-3D-ultrasound-images-in-high-dose\/10.1117\/12.2581966.short\" target=\"blank\">Automated catheter segmentation using 3D ultrasound images in high-dose-rate prostate brachytherapy<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_volume\">vol. 11598, <\/span><span class=\"tp_pub_additional_pages\">pp. 252-259, <\/span><span class=\"tp_pub_additional_year\">2021<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_947\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('947','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_947\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('947','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_947\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('947','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_947\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2021o,<br \/>\r\ntitle = {Automated catheter segmentation using 3D ultrasound images in high-dose-rate prostate brachytherapy},<br \/>\r\nauthor = {Zoe Hu and Harry Brastianos and Tamas Ungi and Csaba Pinter and Tim Olding and Martin Korzeniowski and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11598\/115980Z\/Automated-catheter-segmentation-using-3D-ultrasound-images-in-high-dose\/10.1117\/12.2581966.short},<br \/>\r\nyear  = {2021},<br \/>\r\ndate = {2021-01-01},<br \/>\r\nvolume = {11598},<br \/>\r\npages = {252-259},<br \/>\r\npublisher = {SPIE},<br \/>\r\nabstract = {PURPOSE <br \/>\r\nHigh-dose-rate brachytherapy (HDR-BT) is an important treatment modality for prostate cancer that maximizes radiation dose to cancerous tissue while sparing surrounding organs. Currently, treatment planning during HDR-BT is manually completed by medical physicists, a time-consuming and observer dependent process. We propose using deep learning through a U-Net architecture to automatically segment catheters in HDR prostate brachytherapy treatment planning. <br \/>\r\nMETHODS <br \/>\r\n3D Ultrasound data along with the corresponding manual contours were obtained from 49 patients undergoing HDR prostate brachytherapy. The dataset was preprocessed and then exported for training and evaluation. The resulting model was assessed both quantitatively with binary segmentation metrics and qualitatively through 3D reconstructions. <br \/>\r\nRESULTS <br \/>\r\nThe output segmentations demonstrated consistency on \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('947','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_947\" style=\"display:none;\"><div class=\"tp_abstract_entry\">PURPOSE <br \/>\r\nHigh-dose-rate brachytherapy (HDR-BT) is an important treatment modality for prostate cancer that maximizes radiation dose to cancerous tissue while sparing surrounding organs. Currently, treatment planning during HDR-BT is manually completed by medical physicists, a time-consuming and observer dependent process. We propose using deep learning through a U-Net architecture to automatically segment catheters in HDR prostate brachytherapy treatment planning. <br \/>\r\nMETHODS <br \/>\r\n3D Ultrasound data along with the corresponding manual contours were obtained from 49 patients undergoing HDR prostate brachytherapy. The dataset was preprocessed and then exported for training and evaluation. The resulting model was assessed both quantitatively with binary segmentation metrics and qualitatively through 3D reconstructions. <br \/>\r\nRESULTS <br \/>\r\nThe output segmentations demonstrated consistency on \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('947','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_947\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11598\/115980Z\/Automated-catheter-segmentation-using-3D-ultrasound-images-in-high-dose\/10.1117\/12.2581966.short\" title=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11598\/115980Z\/[...]\" target=\"_blank\">https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11598\/115980Z\/[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('947','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Olding, Tim;  Schreiner, L. John;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1007\/s00500-020-05126-w\" title=\"Using Fuzzy Logics to Determine Optimal Oversampling Factor for Voxelizing 3D Surfaces in Radiation Therapy\" target=\"blank\">Using Fuzzy Logics to Determine Optimal Oversampling Factor for Voxelizing 3D Surfaces in Radiation Therapy<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Soft Computing, <\/span><span class=\"tp_pub_additional_year\">2020<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_58\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('58','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_58\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('58','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_58\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Pinter2020a,<br \/>\r\ntitle = {Using Fuzzy Logics to Determine Optimal Oversampling Factor for Voxelizing 3D Surfaces in Radiation Therapy},<br \/>\r\nauthor = {Csaba Pinter and Tim Olding and L. John Schreiner and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/03\/Pinter2020a_0.pdf},<br \/>\r\ndoi = {10.1007\/s00500-020-05126-w},<br \/>\r\nyear  = {2020},<br \/>\r\ndate = {2020-06-01},<br \/>\r\nurldate = {2020-06-01},<br \/>\r\njournal = {Soft Computing},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('58','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_58\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w\" title=\"https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w\" target=\"_blank\">https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/03\/Pinter2020a_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/03\/Pinter2020[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/03\/Pinter2020[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1007\/s00500-020-05126-w\" title=\"Follow DOI:10.1007\/s00500-020-05126-w\" target=\"_blank\">doi:10.1007\/s00500-020-05126-w<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('58','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Lasso, Andras;  Choueib, Saleh;  Asselin, Mark;  Fillion-Robin, Jean-ChristopheC.;  Vimort, Jean-Baptiste;  Martin, Ken;  Jolley, MatthewA;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1109\/TMRB.2020.2983199\" title=\"SlicerVR for Medical Intervention Training and Planning in Immersive Virtual Reality\" target=\"blank\">SlicerVR for Medical Intervention Training and Planning in Immersive Virtual Reality<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">IEEE Transactions on Medical Robotics and Bionics, <\/span><span class=\"tp_pub_additional_volume\">vol. 2, <\/span><span class=\"tp_pub_additional_number\">no. 2, <\/span><span class=\"tp_pub_additional_pages\">pp. 108-117, <\/span><span class=\"tp_pub_additional_year\">2020<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_56\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('56','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_56\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('56','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_56\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('56','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_56\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Pinter2020,<br \/>\r\ntitle = {SlicerVR for Medical Intervention Training and Planning in Immersive Virtual Reality},<br \/>\r\nauthor = {Csaba Pinter and Andras Lasso and Saleh Choueib and Mark Asselin and Jean-ChristopheC. Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and MatthewA Jolley and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/03\/Pinter2020a_0.pdf},<br \/>\r\ndoi = {10.1109\/TMRB.2020.2983199},<br \/>\r\nyear  = {2020},<br \/>\r\ndate = {2020-03-01},<br \/>\r\nurldate = {2020-03-01},<br \/>\r\njournal = {IEEE Transactions on Medical Robotics and Bionics},<br \/>\r\nvolume = {2},<br \/>\r\nnumber = {2},<br \/>\r\npages = {108-117},<br \/>\r\nabstract = {&lt;p&gt;Virtual reality (VR) provides immersive visualization that has proved to be useful in a variety of medical applications. Currently, however, no free open-source software platform exists that would provide comprehensive support for translational clinical researchers in prototyping experimental VR scenarios in training, planning or guiding medical interventions. By integrating VR functions in 3D Slicer, an established medical image analysis and visualization platform, SlicerVR enables virtual reality experience by a single click. It provides functions to navigate and manipulate the virtual scene, as well as various settings to abate the feeling of motion sickness. SlicerVR allows for shared collaborative VR experience both locally and remotely. We present illustrative scenarios created with SlicerVR in a wide spectrum of applications, including echocardiography, neurosurgery, spine surgery, brachytherapy, intervention training and personalized patient education. SlicerVR is freely available under BSD type license as an extension to 3D Slicer and it has been downloaded over 7,800 times at the time of writing this article.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('56','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_56\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;Virtual reality (VR) provides immersive visualization that has proved to be useful in a variety of medical applications. Currently, however, no free open-source software platform exists that would provide comprehensive support for translational clinical researchers in prototyping experimental VR scenarios in training, planning or guiding medical interventions. By integrating VR functions in 3D Slicer, an established medical image analysis and visualization platform, SlicerVR enables virtual reality experience by a single click. It provides functions to navigate and manipulate the virtual scene, as well as various settings to abate the feeling of motion sickness. SlicerVR allows for shared collaborative VR experience both locally and remotely. We present illustrative scenarios created with SlicerVR in a wide spectrum of applications, including echocardiography, neurosurgery, spine surgery, brachytherapy, intervention training and personalized patient education. SlicerVR is freely available under BSD type license as an extension to 3D Slicer and it has been downloaded over 7,800 times at the time of writing this article.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('56','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_56\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/03\/Pinter2020a_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/03\/Pinter2020[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/03\/Pinter2020[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1109\/TMRB.2020.2983199\" title=\"Follow DOI:10.1109\/TMRB.2020.2983199\" target=\"_blank\">doi:10.1109\/TMRB.2020.2983199<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('56','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Santilli, Alice;  Pinter, Csaba;  Jiang, Bote;  Kronreif, Gernot;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11315\/1131526\/Open-source-software-platform-for-interstitial-ablation-treatment-planning\/10.1117\/12.2549577.short\" title=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11315\/1131526\/Open-source-software-platform-for-interstitial-ablation-treatment-planning\/10.1117\/12.2549577.short\" target=\"blank\">Open source software platform for interstitial ablation treatment planning<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_volume\">vol. 11315, <\/span><span class=\"tp_pub_additional_pages\">pp. 566-571, <\/span><span class=\"tp_pub_additional_year\">2020<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_951\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('951','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_951\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('951','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_951\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('951','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_951\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2020n,<br \/>\r\ntitle = {Open source software platform for interstitial ablation treatment planning},<br \/>\r\nauthor = {Alice Santilli and Csaba Pinter and Bote Jiang and Gernot Kronreif and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11315\/1131526\/Open-source-software-platform-for-interstitial-ablation-treatment-planning\/10.1117\/12.2549577.short},<br \/>\r\nyear  = {2020},<br \/>\r\ndate = {2020-01-01},<br \/>\r\nvolume = {11315},<br \/>\r\npages = {566-571},<br \/>\r\npublisher = {SPIE},<br \/>\r\nabstract = {PURPOSE <br \/>\r\nThere are several interstitial (needle based) image-guided ablation planning systems available, but most of them are closed or unsupported. We propose an open source software platform for the planning of image-guided interstitial ablation procedures, providing generic functionality and support for specialized plug-ins. <br \/>\r\nMETHODS <br \/>\r\nThe patient\u2019s image data is loaded or streamed into the system and the relevant structures are segmented. The user places fiducial points as ablation needle entries and tips, sets the ablation times, and the thermal dose is calculated by a dose engine. The thermal dose is then visualized on the 2D image slices and 3D rendering using a combination of isodose lines and surfaces. Quantitative feedback is provided by dose volume histograms. The treatment plan can be iteratively edited until satisfactory dose distribution is achieved. We performed a usability study with eight \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('951','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_951\" style=\"display:none;\"><div class=\"tp_abstract_entry\">PURPOSE <br \/>\r\nThere are several interstitial (needle based) image-guided ablation planning systems available, but most of them are closed or unsupported. We propose an open source software platform for the planning of image-guided interstitial ablation procedures, providing generic functionality and support for specialized plug-ins. <br \/>\r\nMETHODS <br \/>\r\nThe patient\u2019s image data is loaded or streamed into the system and the relevant structures are segmented. The user places fiducial points as ablation needle entries and tips, sets the ablation times, and the thermal dose is calculated by a dose engine. The thermal dose is then visualized on the 2D image slices and 3D rendering using a combination of isodose lines and surfaces. Quantitative feedback is provided by dose volume histograms. The treatment plan can be iteratively edited until satisfactory dose distribution is achieved. We performed a usability study with eight \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('951','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_951\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11315\/1131526\/Open-source-software-platform-for-interstitial-ablation-treatment-planning\/10.1117\/12.2549577.short\" title=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11315\/1131526\/[...]\" target=\"_blank\">https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/11315\/1131526\/[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('951','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Olding, Tim;  Schreiner, L John;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w\" title=\"https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w\" target=\"blank\">Using fuzzy logics to determine optimal oversampling factor for voxelizing 3D surfaces in radiation therapy<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Soft Computing, <\/span><span class=\"tp_pub_additional_volume\">vol. 24, <\/span><span class=\"tp_pub_additional_pages\">pp. 18959-18970, <\/span><span class=\"tp_pub_additional_year\">2020<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_1019\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('1019','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_1019\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('1019','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_1019\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('1019','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_1019\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2020q,<br \/>\r\ntitle = {Using fuzzy logics to determine optimal oversampling factor for voxelizing 3D surfaces in radiation therapy},<br \/>\r\nauthor = {Csaba Pinter and Tim Olding and L John Schreiner and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w},<br \/>\r\nyear  = {2020},<br \/>\r\ndate = {2020-01-01},<br \/>\r\njournal = {Soft Computing},<br \/>\r\nvolume = {24},<br \/>\r\npages = {18959-18970},<br \/>\r\npublisher = {Springer Berlin Heidelberg},<br \/>\r\nabstract = {Voxelizing three-dimensional surfaces into binary image volumes is a frequently performed operation in medical applications. In radiation therapy (RT), dose-volume histograms (DVHs) calculated within such surfaces are used to assess the quality of an RT treatment plan in both clinical and research settings. To calculate a DVH, the 3D surfaces need to be voxelized into binary volumes. The voxelization parameters may considerably influence the output DVH. An effective way to improve the quality of the voxelized volume (i.e., increasing similarity between that and the original structure) is to apply oversampling to increase the resolution of the output binary volume. However, increasing the oversampling factor raises computational and storage demand. This paper introduces a fuzzy inference system that determines an optimal oversampling factor based on relative structure size and complexity, finding the balance \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('1019','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_1019\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Voxelizing three-dimensional surfaces into binary image volumes is a frequently performed operation in medical applications. In radiation therapy (RT), dose-volume histograms (DVHs) calculated within such surfaces are used to assess the quality of an RT treatment plan in both clinical and research settings. To calculate a DVH, the 3D surfaces need to be voxelized into binary volumes. The voxelization parameters may considerably influence the output DVH. An effective way to improve the quality of the voxelized volume (i.e., increasing similarity between that and the original structure) is to apply oversampling to increase the resolution of the output binary volume. However, increasing the oversampling factor raises computational and storage demand. This paper introduces a fuzzy inference system that determines an optimal oversampling factor based on relative structure size and complexity, finding the balance \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('1019','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_1019\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w\" title=\"https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w\" target=\"_blank\">https:\/\/link.springer.com\/article\/10.1007\/s00500-020-05126-w<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('1019','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Lasso, Andras;  Choueib, Saleh;  Asselin, Mark;  Fillion-Robin, Jean-Christophe;  Vimort, Jean-Baptiste;  Martin, Ken;  Jolley, Matthew A;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/ieeexplore.ieee.org\/abstract\/document\/9047949\/\" title=\"https:\/\/ieeexplore.ieee.org\/abstract\/document\/9047949\/\" target=\"blank\">SlicerVR for medical intervention training and planning in immersive virtual reality<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">IEEE transactions on medical robotics and bionics, <\/span><span class=\"tp_pub_additional_volume\">vol. 2, <\/span><span class=\"tp_pub_additional_issue\">iss. 2, <\/span><span class=\"tp_pub_additional_pages\">pp. 108-117, <\/span><span class=\"tp_pub_additional_year\">2020<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_757\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('757','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_757\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('757','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_757\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('757','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_757\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2020,<br \/>\r\ntitle = {SlicerVR for medical intervention training and planning in immersive virtual reality},<br \/>\r\nauthor = {Csaba Pinter and Andras Lasso and Saleh Choueib and Mark Asselin and Jean-Christophe Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and Matthew A Jolley and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/ieeexplore.ieee.org\/abstract\/document\/9047949\/},<br \/>\r\nyear  = {2020},<br \/>\r\ndate = {2020-01-01},<br \/>\r\njournal = {IEEE transactions on medical robotics and bionics},<br \/>\r\nvolume = {2},<br \/>\r\nissue = {2},<br \/>\r\npages = {108-117},<br \/>\r\npublisher = {IEEE},<br \/>\r\nabstract = {Virtual reality (VR) provides immersive visualization that has proved to be useful in a variety of medical applications. Currently, however, no free open-source software platform exists that would provide comprehensive support for translational clinical researchers in prototyping experimental VR scenarios in training, planning or guiding medical interventions. By integrating VR functions in 3D Slicer, an established medical image analysis and visualization platform, SlicerVR enables virtual reality experience by a single click. It provides functions to navigate and manipulate the virtual scene, as well as various settings to abate the feeling of motion sickness. SlicerVR allows for shared collaborative VR experience both locally and remotely. We present illustrative scenarios created with SlicerVR in a wide spectrum of applications, including echocardiography, neurosurgery, spine surgery, brachytherapy, intervention \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('757','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_757\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Virtual reality (VR) provides immersive visualization that has proved to be useful in a variety of medical applications. Currently, however, no free open-source software platform exists that would provide comprehensive support for translational clinical researchers in prototyping experimental VR scenarios in training, planning or guiding medical interventions. By integrating VR functions in 3D Slicer, an established medical image analysis and visualization platform, SlicerVR enables virtual reality experience by a single click. It provides functions to navigate and manipulate the virtual scene, as well as various settings to abate the feeling of motion sickness. SlicerVR allows for shared collaborative VR experience both locally and remotely. We present illustrative scenarios created with SlicerVR in a wide spectrum of applications, including echocardiography, neurosurgery, spine surgery, brachytherapy, intervention \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('757','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_757\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/ieeexplore.ieee.org\/abstract\/document\/9047949\/\" title=\"https:\/\/ieeexplore.ieee.org\/abstract\/document\/9047949\/\" target=\"_blank\">https:\/\/ieeexplore.ieee.org\/abstract\/document\/9047949\/<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('757','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Fedorov, Andriy;  Beichel, Reinhard;  Kalpathy-Cramer, Jayashree;  Clunie, David;  Onken, Michael;  Riesmeier, J\u00f6rg;  Herz, Christian;  Bauer, Christian;  Beers, Andrew;  Fillion-Robin, Jean-ChristopheC.;  Lasso, Andras;  Pinter, Csaba;  Pieper, Steve;  Nolden, Marco;  Maier-Hein, Klaus;  Herrmann, Markus D.;  Saltz, Joel;  Prior, Fred;  Fennessy, Fiona M.;  Buatti, John;  Kikinis, Ron<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10. 1200\/CCI.19.00165\" title=\"Quantitative Imaging Informatics for Cancer Research\" target=\"blank\">Quantitative Imaging Informatics for Cancer Research<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">JCO Clinical Cancer Informatics, <\/span><span class=\"tp_pub_additional_volume\">vol. 4, <\/span><span class=\"tp_pub_additional_pages\">pp. 444-453., <\/span><span class=\"tp_pub_additional_year\">2020<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_52\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('52','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_52\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('52','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_52\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Fedorov2020,<br \/>\r\ntitle = {Quantitative Imaging Informatics for Cancer Research},<br \/>\r\nauthor = {Andriy Fedorov and Reinhard Beichel and Jayashree Kalpathy-Cramer and David Clunie and Michael Onken and J\u00f6rg Riesmeier and Christian Herz and Christian Bauer and Andrew Beers and Jean-ChristopheC. Fillion-Robin and Andras Lasso and Csaba Pinter and Steve Pieper and Marco Nolden and Klaus Maier-Hein and Markus D. Herrmann and Joel Saltz and Fred Prior and Fiona M. Fennessy and John Buatti and Ron Kikinis},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Fedorov2020.pdf},<br \/>\r\ndoi = {https:\/\/doi.org\/10. 1200\/CCI.19.00165},<br \/>\r\nyear  = {2020},<br \/>\r\ndate = {2020-01-01},<br \/>\r\nurldate = {2020-01-01},<br \/>\r\njournal = {JCO Clinical Cancer Informatics},<br \/>\r\nvolume = {4},<br \/>\r\npages = {444-453.},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('52','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_52\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Fedorov2020.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Fedorov202[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Fedorov202[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10. 1200\/CCI.19.00165\" title=\"Follow DOI:https:\/\/doi.org\/10. 1200\/CCI.19.00165\" target=\"_blank\">doi:https:\/\/doi.org\/10. 1200\/CCI.19.00165<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('52','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Lasso, Andras;  Pinter, Csaba;  Choueib, Saleh;  Ungi, Tamas;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2019.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2019.pdf\" target=\"blank\">Enhance medical software applications with immersive virtual reality experience<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">Techna Symposium, <\/span><span class=\"tp_pub_additional_address\">Toronto, ON, Canada, <\/span><span class=\"tp_pub_additional_year\">2019<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_70\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('70','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_70\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('70','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_70\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Lasso2019,<br \/>\r\ntitle = {Enhance medical software applications with immersive virtual reality experience},<br \/>\r\nauthor = {Andras Lasso and Csaba Pinter and Saleh Choueib and Tamas Ungi and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2019.pdf},<br \/>\r\nyear  = {2019},<br \/>\r\ndate = {2019-10-01},<br \/>\r\nurldate = {2019-10-01},<br \/>\r\nbooktitle = {Techna Symposium},<br \/>\r\naddress = {Toronto, ON, Canada},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('70','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_70\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2019.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2019.[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2019.[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('70','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Lasso, Andras;  Asselin, Mark;  Fillion-Robin, Jean-ChristopheC.;  Vimort, Jean-Baptiste;  Martin, Ken;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019a_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019a_0.pdf\" target=\"blank\">SlicerVR for image-guided therapy planning in immersive virtual reality<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">The 12th Hamlyn Symposium on Medical Robotics, 23-26 June 2019, Imperial College, London, UK, <\/span><span class=\"tp_pub_additional_address\">London, UK, <\/span><span class=\"tp_pub_additional_year\">2019<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_80\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('80','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_80\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('80','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_80\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Pinter2019a,<br \/>\r\ntitle = {SlicerVR for image-guided therapy planning in immersive virtual reality},<br \/>\r\nauthor = {Csaba Pinter and Andras Lasso and Mark Asselin and Jean-ChristopheC. Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019a_0.pdf},<br \/>\r\nyear  = {2019},<br \/>\r\ndate = {2019-06-01},<br \/>\r\nurldate = {2019-06-01},<br \/>\r\nbooktitle = {The 12th Hamlyn Symposium on Medical Robotics, 23-26 June 2019, Imperial College, London, UK},<br \/>\r\npages = {91-92},<br \/>\r\naddress = {London, UK},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('80','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_80\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019a_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('80','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Choueib, Saleh;  Pinter, Csaba;  Lasso, Andras;  Fillion-Robin, Jean-ChristopheC.;  Vimort, Jean-Baptiste;  Martin, Ken;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib2019a.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib2019a.pdf\" target=\"blank\">Evaluation of 3D Slicer as a medical virtual reality visualization platform<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling, <\/span><span class=\"tp_pub_additional_volume\">vol. 10951, <\/span><span class=\"tp_pub_additional_number\">no. 38, <\/span><span class=\"tp_pub_additional_organization\">SPIE Medical Imaging <\/span><span class=\"tp_pub_additional_publisher\">SPIE Medical Imaging, <\/span><span class=\"tp_pub_additional_address\">San Diego, California, <\/span><span class=\"tp_pub_additional_year\">2019<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_71\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('71','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_71\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('71','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_71\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Choueib2019a,<br \/>\r\ntitle = {Evaluation of 3D Slicer as a medical virtual reality visualization platform},<br \/>\r\nauthor = {Saleh Choueib and Csaba Pinter and Andras Lasso and Jean-ChristopheC. Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib2019a.pdf},<br \/>\r\nyear  = {2019},<br \/>\r\ndate = {2019-03-01},<br \/>\r\nurldate = {2019-03-01},<br \/>\r\nbooktitle = {SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling},<br \/>\r\nvolume = {10951},<br \/>\r\nnumber = {38},<br \/>\r\npublisher = {SPIE Medical Imaging},<br \/>\r\naddress = {San Diego, California},<br \/>\r\norganization = {SPIE Medical Imaging},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('71','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_71\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib2019a.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib201[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib201[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('71','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Choueib, Saleh;  Pinter, Csaba;  Lasso, Andras;  Fillion-Robin, Jean-ChristopheC.;  Vimort, Jean-Baptiste;  Martin, Ken;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib2019b.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib2019b.pdf\" target=\"blank\">Assessment of immersive medical virtual reality visualization using 3D Slicer<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">17th Annual Imaging Network Ontario Symposium (ImNO), <\/span><span class=\"tp_pub_additional_address\">London, Ontario, <\/span><span class=\"tp_pub_additional_year\">2019<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_62\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('62','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_62\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('62','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_62\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Choueib2019b,<br \/>\r\ntitle = {Assessment of immersive medical virtual reality visualization using 3D Slicer},<br \/>\r\nauthor = {Saleh Choueib and Csaba Pinter and Andras Lasso and Jean-ChristopheC. Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib2019b.pdf},<br \/>\r\nyear  = {2019},<br \/>\r\ndate = {2019-03-01},<br \/>\r\nurldate = {2019-03-01},<br \/>\r\nbooktitle = {17th Annual Imaging Network Ontario Symposium (ImNO)},<br \/>\r\naddress = {London, Ontario},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('62','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_62\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib2019b.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib201[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Choueib201[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('62','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Lasso, Andras;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1016\/j.cmpb.2019.02.011\" title=\"Polymorph Segmentation Representation for Medical Image Computing\" target=\"blank\">Polymorph Segmentation Representation for Medical Image Computing<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Computer Methods and Programs in Biomedicine, <\/span><span class=\"tp_pub_additional_volume\">vol. 171, <\/span><span class=\"tp_pub_additional_pages\">pp. 19-26, <\/span><span class=\"tp_pub_additional_year\">2019<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_76\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('76','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_76\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('76','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_76\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('76','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_76\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Pinter2019,<br \/>\r\ntitle = {Polymorph Segmentation Representation for Medical Image Computing},<br \/>\r\nauthor = {Csaba Pinter and Andras Lasso and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019_Manuscript.pdf},<br \/>\r\ndoi = {https:\/\/doi.org\/10.1016\/j.cmpb.2019.02.011},<br \/>\r\nyear  = {2019},<br \/>\r\ndate = {2019-02-01},<br \/>\r\nurldate = {2019-02-01},<br \/>\r\njournal = {Computer Methods and Programs in Biomedicine},<br \/>\r\nvolume = {171},<br \/>\r\npages = {19-26},<br \/>\r\nabstract = {&lt;p&gt;&lt;strong&gt;Background and Objective: &lt;\/strong&gt;Segmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: &lt;a name=\"OLE_LINK3\"&gt;&lt;\/a&gt;&lt;a name=\"OLE_LINK2\"&gt;conversion &lt;\/a&gt;method selection, data provenance, data consistency, and coherence of in-memory objects. &lt;strong&gt;Methods:&lt;\/strong&gt; A complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable software tool to manage segmentation data in multiple data representations. A low-level core library called PolySeg implemented in The Visualization Toolkit (VTK) manages the data objects and conversions. It is used by a high-level application layer, which has been implemented in the medical image visualization and analysis platform 3D Slicer. The application layer provides advanced visualization, transformation, interoperability, and other functions. &lt;strong&gt;Results: &lt;\/strong&gt;The core conversion algorithms comprising the graph were validated. Several applications were implemented based on the library, demonstrating advantages in terms of usability and ease of software development in each case. The Segment Editor application provides fast, comprehensive, and easy-to-use manual and semi-automatic segmentation workflows. Clinical applications for gel dosimetry, external beam planning, and MRI-ultrasound image fusion in brachytherapy were rapidly prototyped resulting robust applications that are already in use in clinical research. The conversion algorithms were found to be accurate and reliable using these applications. &lt;strong&gt;Conclusions:&lt;\/strong&gt;  A generic software library has been designed and developed for automatic management of multiple data formats in segmentation tasks. It enhances both user and developer experience, enabling fast and convenient manual workflows and quicker and more robust software prototyping. The software\u2019s BSD-style open-source license allows complete freedom of use of the library.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('76','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_76\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;&lt;strong&gt;Background and Objective: &lt;\/strong&gt;Segmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: &lt;a name=&quot;OLE_LINK3&quot;&gt;&lt;\/a&gt;&lt;a name=&quot;OLE_LINK2&quot;&gt;conversion &lt;\/a&gt;method selection, data provenance, data consistency, and coherence of in-memory objects. &lt;strong&gt;Methods:&lt;\/strong&gt; A complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable software tool to manage segmentation data in multiple data representations. A low-level core library called PolySeg implemented in The Visualization Toolkit (VTK) manages the data objects and conversions. It is used by a high-level application layer, which has been implemented in the medical image visualization and analysis platform 3D Slicer. The application layer provides advanced visualization, transformation, interoperability, and other functions. &lt;strong&gt;Results: &lt;\/strong&gt;The core conversion algorithms comprising the graph were validated. Several applications were implemented based on the library, demonstrating advantages in terms of usability and ease of software development in each case. The Segment Editor application provides fast, comprehensive, and easy-to-use manual and semi-automatic segmentation workflows. Clinical applications for gel dosimetry, external beam planning, and MRI-ultrasound image fusion in brachytherapy were rapidly prototyped resulting robust applications that are already in use in clinical research. The conversion algorithms were found to be accurate and reliable using these applications. &lt;strong&gt;Conclusions:&lt;\/strong&gt;&amp;nbsp; A generic software library has been designed and developed for automatic management of multiple data formats in segmentation tasks. It enhances both user and developer experience, enabling fast and convenient manual workflows and quicker and more robust software prototyping. The software\u2019s BSD-style open-source license allows complete freedom of use of the library.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('76','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_76\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019_Manuscript.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2019[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1016\/j.cmpb.2019.02.011\" title=\"Follow DOI:https:\/\/doi.org\/10.1016\/j.cmpb.2019.02.011\" target=\"_blank\">doi:https:\/\/doi.org\/10.1016\/j.cmpb.2019.02.011<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('76','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Lasso, Andras;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0169260718313038\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0169260718313038\" target=\"blank\">Polymorph segmentation representation for medical image computing<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Computer methods and programs in biomedicine, <\/span><span class=\"tp_pub_additional_volume\">vol. 171, <\/span><span class=\"tp_pub_additional_pages\">pp. 19-26, <\/span><span class=\"tp_pub_additional_year\">2019<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_704\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('704','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_704\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('704','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_704\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('704','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_704\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2019b,<br \/>\r\ntitle = {Polymorph segmentation representation for medical image computing},<br \/>\r\nauthor = {Csaba Pinter and Andras Lasso and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0169260718313038},<br \/>\r\nyear  = {2019},<br \/>\r\ndate = {2019-01-01},<br \/>\r\njournal = {Computer methods and programs in biomedicine},<br \/>\r\nvolume = {171},<br \/>\r\npages = {19-26},<br \/>\r\npublisher = {Elsevier},<br \/>\r\nabstract = {Background and objective <br \/>\r\nSegmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: conversion method selection, data provenance, data consistency, and coherence of in-memory objects. <br \/>\r\nMethods <br \/>\r\nA complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('704','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_704\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Background and objective <br \/>\r\nSegmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: conversion method selection, data provenance, data consistency, and coherence of in-memory objects. <br \/>\r\nMethods <br \/>\r\nA complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('704','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_704\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0169260718313038\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0169260718313038\" target=\"_blank\">https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0169260718313038<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('704','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Socorro-Marrero, Guillermo V;  Luque, Carlos;  Pinter, Csaba;  Diao, Babacar;  Ungi, Tamas;  Lasso, Andras;  Fichtinger, Gabor;  Ruiz-Alzola, Juan<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/ieeexplore.ieee.org\/abstract\/document\/9033036\/\" title=\"https:\/\/ieeexplore.ieee.org\/abstract\/document\/9033036\/\" target=\"blank\">Affordable medical ultrasound navigation training<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_pages\">pp. 1-4, <\/span><span class=\"tp_pub_additional_year\">2019<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_920\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('920','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_920\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('920','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_920\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('920','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_920\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2019j,<br \/>\r\ntitle = {Affordable medical ultrasound navigation training},<br \/>\r\nauthor = {Guillermo V Socorro-Marrero and Carlos Luque and Csaba Pinter and Babacar Diao and Tamas Ungi and Andras Lasso and Gabor Fichtinger and Juan Ruiz-Alzola},<br \/>\r\nurl = {https:\/\/ieeexplore.ieee.org\/abstract\/document\/9033036\/},<br \/>\r\nyear  = {2019},<br \/>\r\ndate = {2019-01-01},<br \/>\r\npages = {1-4},<br \/>\r\npublisher = {IEEE},<br \/>\r\nabstract = {In recent years, image-assisted medical procedures have been widely adopted, since they reduce patient risk and medical cost. The use of ultrasound imaging is noteworthy, as it is safe and easy to acquire. In medical intervention navigation systems, image guidance is combined with real-time position tracking of interventional tools. These techniques allow to improve the safety and accuracy of the procedures. However, the complexity of the systems and equipment cost hinder their adaptation, especially in regions with limited resources. In this paper we report part of our collaborative work within the framework of the European INTERREG MACbioIDi project, devoted to promoting sustainable development through medical technology in some African countries, with the participations of collaborators from Europe, Africa and the Americas. To this extent a medical technology training and development hub has been set \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('920','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_920\" style=\"display:none;\"><div class=\"tp_abstract_entry\">In recent years, image-assisted medical procedures have been widely adopted, since they reduce patient risk and medical cost. The use of ultrasound imaging is noteworthy, as it is safe and easy to acquire. In medical intervention navigation systems, image guidance is combined with real-time position tracking of interventional tools. These techniques allow to improve the safety and accuracy of the procedures. However, the complexity of the systems and equipment cost hinder their adaptation, especially in regions with limited resources. In this paper we report part of our collaborative work within the framework of the European INTERREG MACbioIDi project, devoted to promoting sustainable development through medical technology in some African countries, with the participations of collaborators from Europe, Africa and the Americas. To this extent a medical technology training and development hub has been set \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('920','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_920\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/ieeexplore.ieee.org\/abstract\/document\/9033036\/\" title=\"https:\/\/ieeexplore.ieee.org\/abstract\/document\/9033036\/\" target=\"_blank\">https:\/\/ieeexplore.ieee.org\/abstract\/document\/9033036\/<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('920','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Choueib, Saleh;  Pinter, Csaba;  Lasso, Andras;  Fillion-Robin, Jean-Christophe;  Vimort, Jean-Batiste;  Martin, Ken;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/10951\/1095113\/Evaluation-of-3D-slicer-as-a-medical-virtual-reality-visualization\/10.1117\/12.2513053.short\" title=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/10951\/1095113\/Evaluation-of-3D-slicer-as-a-medical-virtual-reality-visualization\/10.1117\/12.2513053.short\" target=\"blank\">Evaluation of 3D slicer as a medical virtual reality visualization platform<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_volume\">vol. 10951, <\/span><span class=\"tp_pub_additional_pages\">pp. 279-286, <\/span><span class=\"tp_pub_additional_year\">2019<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_818\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('818','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_818\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('818','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_818\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('818','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_818\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2019f,<br \/>\r\ntitle = {Evaluation of 3D slicer as a medical virtual reality visualization platform},<br \/>\r\nauthor = {Saleh Choueib and Csaba Pinter and Andras Lasso and Jean-Christophe Fillion-Robin and Jean-Batiste Vimort and Ken Martin and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/10951\/1095113\/Evaluation-of-3D-slicer-as-a-medical-virtual-reality-visualization\/10.1117\/12.2513053.short},<br \/>\r\nyear  = {2019},<br \/>\r\ndate = {2019-01-01},<br \/>\r\nvolume = {10951},<br \/>\r\npages = {279-286},<br \/>\r\npublisher = {SPIE},<br \/>\r\nabstract = {PURPOSE <br \/>\r\nThere is a lack of open-source or free virtual reality (VR) software that can be utilized for research by medical professionals and researchers. We propose the design and implementation of such software. We also aim to assess the feasibility of using VR as a modality for navigating 3D visualizations of medical scenes. <br \/>\r\nMETHODS <br \/>\r\nTo achieve our goal, we added VR capabilities to the open-source medical image analysis and visualization platform, 3D Slicer. We designed the VR extension by basing the software architecture on VTK\u2019s vtkRenderingOpenVR software module. We extended this module by adding features such as full interactivity between 3D Slicer and the VR extension during VR use, variable volume rendering quality based on user headset motion etc. Furthermore, the VR extension was tested in a feasibility study in which participants were asked to complete specific tasks using bot the \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('818','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_818\" style=\"display:none;\"><div class=\"tp_abstract_entry\">PURPOSE <br \/>\r\nThere is a lack of open-source or free virtual reality (VR) software that can be utilized for research by medical professionals and researchers. We propose the design and implementation of such software. We also aim to assess the feasibility of using VR as a modality for navigating 3D visualizations of medical scenes. <br \/>\r\nMETHODS <br \/>\r\nTo achieve our goal, we added VR capabilities to the open-source medical image analysis and visualization platform, 3D Slicer. We designed the VR extension by basing the software architecture on VTK\u2019s vtkRenderingOpenVR software module. We extended this module by adding features such as full interactivity between 3D Slicer and the VR extension during VR use, variable volume rendering quality based on user headset motion etc. Furthermore, the VR extension was tested in a feasibility study in which participants were asked to complete specific tasks using bot the \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('818','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_818\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/10951\/1095113\/Evaluation-of-3D-slicer-as-a-medical-virtual-reality-visualization\/10.1117\/12.2513053.short\" title=\"https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/10951\/1095113\/[...]\" target=\"_blank\">https:\/\/www.spiedigitallibrary.org\/conference-proceedings-of-spie\/10951\/1095113\/[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('818','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Alexander, Kevin;  Pinter, Csaba;  Fichtinger, Gabor;  Olding, Tim;  Schreiner, L. John<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1088\/2057-1976\/aad0cf\" title=\"Streamlined open-source gel dosimetry analysis in 3D slicer\" target=\"blank\">Streamlined open-source gel dosimetry analysis in 3D slicer<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Biomedical Physics &amp; Engineering Express, <\/span><span class=\"tp_pub_additional_volume\">vol. 4, <\/span><span class=\"tp_pub_additional_number\">no. 4, <\/span><span class=\"tp_pub_additional_pages\">pp. 045041, <\/span><span class=\"tp_pub_additional_year\">2018<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_103\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('103','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_103\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('103','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_103\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('103','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_103\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Alexander2018,<br \/>\r\ntitle = {Streamlined open-source gel dosimetry analysis in 3D slicer},<br \/>\r\nauthor = {Kevin Alexander and Csaba Pinter and Gabor Fichtinger and Tim Olding and L. John Schreiner},<br \/>\r\nurl = {http:\/\/stacks.iop.org\/2057-1976\/4\/i=4\/a=045041<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2018.pdf},<br \/>\r\ndoi = {https:\/\/doi.org\/10.1088\/2057-1976\/aad0cf},<br \/>\r\nyear  = {2018},<br \/>\r\ndate = {2018-07-01},<br \/>\r\nurldate = {2018-07-01},<br \/>\r\njournal = {Biomedical Physics & Engineering Express},<br \/>\r\nvolume = {4},<br \/>\r\nnumber = {4},<br \/>\r\npages = {045041},<br \/>\r\nabstract = {&lt;p&gt;Three dimensional dosimetry is being used in an increasingly wide variety of clinical applications as more gel and radiochromic plastic dosimeters become available. However, accessible 3D dosimetry analysis tools have not kept pace. 3D dosimetry data analysis is time consuming and laborious, creating a barrier to entry for busy clinical environments. To help in the adoption of 3D dosimetry, we have produced a streamlined, open-source dosimetry analysis system by developing a custom extension in 3D Slicer, called the Gel Dosimetry Analysis slicelet, which enables rapid and accurate data analysis. To assist those interested in adopting 3D dosimetry in their clinic or those unfamiliar with what is involved in a 3D dosimeter experiment, we first present the workflow of a typical gel dosimetry experiment. This is followed by the results of experiments used to validate, step-wise, each component of our software. Overall, our software has made a full 3D gel dosimeter analysis roughly 20 times faster than previous analysis systems.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('103','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_103\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;Three dimensional dosimetry is being used in an increasingly wide variety of clinical applications as more gel and radiochromic plastic dosimeters become available. However, accessible 3D dosimetry analysis tools have not kept pace. 3D dosimetry data analysis is time consuming and laborious, creating a barrier to entry for busy clinical environments. To help in the adoption of 3D dosimetry, we have produced a streamlined, open-source dosimetry analysis system by developing a custom extension in 3D Slicer, called the Gel Dosimetry Analysis slicelet, which enables rapid and accurate data analysis. To assist those interested in adopting 3D dosimetry in their clinic or those unfamiliar with what is involved in a 3D dosimeter experiment, we first present the workflow of a typical gel dosimetry experiment. This is followed by the results of experiments used to validate, step-wise, each component of our software. Overall, our software has made a full 3D gel dosimeter analysis roughly 20 times faster than previous analysis systems.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('103','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_103\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/stacks.iop.org\/2057-1976\/4\/i=4\/a=045041\" title=\"http:\/\/stacks.iop.org\/2057-1976\/4\/i=4\/a=045041\" target=\"_blank\">http:\/\/stacks.iop.org\/2057-1976\/4\/i=4\/a=045041<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2018.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/https:\/\/doi.org\/10.1088\/2057-1976\/aad0cf\" title=\"Follow DOI:https:\/\/doi.org\/10.1088\/2057-1976\/aad0cf\" target=\"_blank\">doi:https:\/\/doi.org\/10.1088\/2057-1976\/aad0cf<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('103','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Travers, Bryan;  Baum, Zachary M C;  Ungi, Tamas;  Lasso, Andras;  Church, Ben;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018a.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018a.pdf\" target=\"blank\">Real-time transverse process delineation in tracked ultrasound for scoliosis measurement<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">Imaging Network Ontario Symposium (ImNO 2018), <\/span><span class=\"tp_pub_additional_address\">Toronto, Canada, <\/span><span class=\"tp_pub_additional_year\">2018<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_98\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('98','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_98\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('98','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_98\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Pinter2018a,<br \/>\r\ntitle = {Real-time transverse process delineation in tracked ultrasound for scoliosis measurement},<br \/>\r\nauthor = {Csaba Pinter and Bryan Travers and Zachary M C Baum and Tamas Ungi and Andras Lasso and Ben Church and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018a.pdf},<br \/>\r\nyear  = {2018},<br \/>\r\ndate = {2018-03-01},<br \/>\r\nurldate = {2018-03-01},<br \/>\r\nbooktitle = {Imaging Network Ontario Symposium (ImNO 2018)},<br \/>\r\naddress = {Toronto, Canada},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('98','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_98\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018a.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('98','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Ilina, Anna;  Pinter, Csaba;  Lasso, Andras;  Lai, Ingrid;  Joshi, C. P.;  Alexander, Kevin;  Schreiner, L. John;  Hanna, Timothy;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a_0.pdf\" target=\"blank\">3D Surface Scanning for Tumour Localization in Non-Melanoma Skin Cancer<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">16th Annual Imaging Network Ontario Symposium (ImNO), <\/span><span class=\"tp_pub_additional_address\">Toronto, Canada, <\/span><span class=\"tp_pub_additional_year\">2018<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_87\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('87','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_87\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('87','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_87\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Ilina2018a,<br \/>\r\ntitle = {3D Surface Scanning for Tumour Localization in Non-Melanoma Skin Cancer},<br \/>\r\nauthor = {Anna Ilina and Csaba Pinter and Andras Lasso and Ingrid Lai and C. P. Joshi and Kevin Alexander and L. John Schreiner and Timothy Hanna and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a_0.pdf<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a-poster.pdf},<br \/>\r\nyear  = {2018},<br \/>\r\ndate = {2018-03-01},<br \/>\r\nurldate = {2018-03-01},<br \/>\r\nbooktitle = {16th Annual Imaging Network Ontario Symposium (ImNO)},<br \/>\r\naddress = {Toronto, Canada},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('87','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_87\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a[...]<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a-poster.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018a[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('87','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Travers, Bryan;  Baum, Zachary M C;  Kamali, Shahrokh;  Ungi, Tamas;  Lasso, Andras;  Church, Ben;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018.pdf\" target=\"blank\">Real-time transverse process detection in ultrasound<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">SPIE Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling, <\/span><span class=\"tp_pub_additional_address\">Houston, Texas, <\/span><span class=\"tp_pub_additional_year\">2018<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_99\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('99','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_99\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('99','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_99\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Pinter2018,<br \/>\r\ntitle = {Real-time transverse process detection in ultrasound},<br \/>\r\nauthor = {Csaba Pinter and Bryan Travers and Zachary M C Baum and Shahrokh Kamali and Tamas Ungi and Andras Lasso and Ben Church and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018.pdf},<br \/>\r\nyear  = {2018},<br \/>\r\ndate = {2018-03-01},<br \/>\r\nurldate = {2018-03-01},<br \/>\r\nbooktitle = {SPIE Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling},<br \/>\r\naddress = {Houston, Texas},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('99','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_99\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2018[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('99','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Ilina, Anna;  Pinter, Csaba;  Lasso, Andras;  Lai, Ingrid;  Joshi, C. P.;  Alexander, Kevin;  Schreiner, L. John;  Hanna, Timothy;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018b.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018b.pdf\" target=\"blank\">Target Definition with 3D Surface Scanning for Orthovoltage Radiation Therapy Planning<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">CARS, <\/span><span class=\"tp_pub_additional_address\">Berlin, Germany, <\/span><span class=\"tp_pub_additional_year\">2018<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_104\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('104','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_104\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('104','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_104\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Ilina2018b,<br \/>\r\ntitle = {Target Definition with 3D Surface Scanning for Orthovoltage Radiation Therapy Planning},<br \/>\r\nauthor = {Anna Ilina and Csaba Pinter and Andras Lasso and Ingrid Lai and C. P. Joshi and Kevin Alexander and L. John Schreiner and Timothy Hanna and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018b.pdf},<br \/>\r\nyear  = {2018},<br \/>\r\ndate = {2018-01-01},<br \/>\r\nurldate = {2018-01-01},<br \/>\r\nbooktitle = {CARS},<br \/>\r\naddress = {Berlin, Germany},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('104','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_104\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018b.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018b[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Ilina2018b[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('104','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Lasso, Andras;  Nam, HannahH;  Dinh, Patrick V.;  Pinter, Csaba;  Fillion-Robin, Jean-ChristopheC.;  Pieper, Steve;  Jhaveri, Sankhesh;  Vimort, Jean-Baptiste;  Martin, Ken;  Asselin, Mark;  McGowan, FrancisX;  Kikinis, Ron;  Fichtinger, Gabor;  Jolley, MatthewA<\/p><p class=\"tp_pub_title\">Interaction with Volume-Rendered Three-Dimensional Echocardiographic Images in Virtual Reality <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">J Am Soc Echocardiogr, <\/span><span class=\"tp_pub_additional_volume\">vol. 31, <\/span><span class=\"tp_pub_additional_number\">no. 10, <\/span><span class=\"tp_pub_additional_pages\">pp. 1158-60\u2013, <\/span><span class=\"tp_pub_additional_year\">2018<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_95\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('95','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_95\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('95','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_95\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Lasso2018,<br \/>\r\ntitle = {Interaction with Volume-Rendered Three-Dimensional Echocardiographic Images in Virtual Reality},<br \/>\r\nauthor = {Andras Lasso and HannahH Nam and Patrick V. Dinh and Csaba Pinter and Jean-ChristopheC. Fillion-Robin and Steve Pieper and Sankhesh Jhaveri and Jean-Baptiste Vimort and Ken Martin and Mark Asselin and FrancisX McGowan and Ron Kikinis and Gabor Fichtinger and MatthewA Jolley},<br \/>\r\nyear  = {2018},<br \/>\r\ndate = {2018-01-01},<br \/>\r\nurldate = {2018-01-01},<br \/>\r\njournal = {J Am Soc Echocardiogr},<br \/>\r\nvolume = {31},<br \/>\r\nnumber = {10},<br \/>\r\npages = {1158-60\u2013},<br \/>\r\nabstract = {&lt;p&gt;Three-dimensional (3D) imaging is increasingly important in echocardiography. However, viewing of 3D images on a flat, two-dimensional screen is a barrier to comprehension of latent information. There have been previous attempts to visualize the full 3D nature of the data, but they have not been widely adopted. For example, 3D printing offers realistic interaction but is time consuming, has limited means for the observer to move into or through the model, and is not yet practical for routine clinical use. Furthermore, the heart beats, and 3D printed models are static. Stereoscopic viewing on 2D screens (as at a movie theater) is possible but is expensive, may not provide an immersive experience, and does not have integrated 3D input devices (controllers).&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('95','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_95\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;Three-dimensional (3D) imaging is increasingly important in echocardiography. However, viewing of 3D images on a flat, two-dimensional screen is a barrier to comprehension of latent information. There have been previous attempts to visualize the full 3D nature of the data, but they have not been widely adopted. For example, 3D printing offers realistic interaction but is time consuming, has limited means for the observer to move into or through the model, and is not yet practical for routine clinical use. Furthermore, the heart beats, and 3D printed models are static. Stereoscopic viewing on 2D screens (as at a movie theater) is possible but is expensive, may not provide an immersive experience, and does not have integrated 3D input devices (controllers).&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('95','tp_abstract')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Poulin, Eric;  Boudam, Karim;  Pinter, Csaba;  Kadoury, Samuel;  Lasso, Andras;  Fichtinger, Gabor;  M\u00e9nard, Cynthia<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1538472117305391\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1538472117305391\" target=\"blank\">Validation of MRI to TRUS registration for high-dose-rate prostate brachytherapy<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Brachytherapy, <\/span><span class=\"tp_pub_additional_volume\">vol. 17, <\/span><span class=\"tp_pub_additional_issue\">iss. 2, <\/span><span class=\"tp_pub_additional_pages\">pp. 283-290, <\/span><span class=\"tp_pub_additional_year\">2018<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_776\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('776','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_776\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('776','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_776\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('776','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_776\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2018e,<br \/>\r\ntitle = {Validation of MRI to TRUS registration for high-dose-rate prostate brachytherapy},<br \/>\r\nauthor = {Eric Poulin and Karim Boudam and Csaba Pinter and Samuel Kadoury and Andras Lasso and Gabor Fichtinger and Cynthia M\u00e9nard},<br \/>\r\nurl = {https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1538472117305391},<br \/>\r\nyear  = {2018},<br \/>\r\ndate = {2018-01-01},<br \/>\r\njournal = {Brachytherapy},<br \/>\r\nvolume = {17},<br \/>\r\nissue = {2},<br \/>\r\npages = {283-290},<br \/>\r\npublisher = {Elsevier},<br \/>\r\nabstract = {Purpose <br \/>\r\nThe objective of this study was to develop and validate an open-source module for MRI to transrectal ultrasound (TRUS) registration to support tumor-targeted prostate brachytherapy. <br \/>\r\nMethods and Materials <br \/>\r\nIn this study, 15 patients with prostate cancer lesions visible on multiparametric MRI were selected for the validation. T2-weighted images with 1-mm isotropic voxel size and diffusion weighted images were acquired on a 1.5T Siemens imager. Three-dimensional (3D) TRUS images with 0.5-mm slice thickness were acquired. The investigated registration module was incorporated in the open-source 3D Slicer platform, which can compute rigid and deformable transformations. An extension of 3D Slicer, SlicerRT, allows import of and export to DICOM-RT formats. For validation, similarity indices, prostate volumes, and centroid positions were determined in addition to registration errors for common 3D points \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('776','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_776\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Purpose <br \/>\r\nThe objective of this study was to develop and validate an open-source module for MRI to transrectal ultrasound (TRUS) registration to support tumor-targeted prostate brachytherapy. <br \/>\r\nMethods and Materials <br \/>\r\nIn this study, 15 patients with prostate cancer lesions visible on multiparametric MRI were selected for the validation. T2-weighted images with 1-mm isotropic voxel size and diffusion weighted images were acquired on a 1.5T Siemens imager. Three-dimensional (3D) TRUS images with 0.5-mm slice thickness were acquired. The investigated registration module was incorporated in the open-source 3D Slicer platform, which can compute rigid and deformable transformations. An extension of 3D Slicer, SlicerRT, allows import of and export to DICOM-RT formats. For validation, similarity indices, prostate volumes, and centroid positions were determined in addition to registration errors for common 3D points \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('776','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_776\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1538472117305391\" title=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1538472117305391\" target=\"_blank\">https:\/\/www.sciencedirect.com\/science\/article\/pii\/S1538472117305391<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('776','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Lasso, Andras;  Nam, Hannah H;  Dinh, Patrick V;  Pinter, Csaba;  Fillion-Robin, Jean-Christophe;  Pieper, Steve;  Jhaveri, Sankhesh;  Vimort, Jean-Baptiste;  Martin, Ken;  Asselin, Mark;  McGowan, Francis X;  Kikinis, Ron;  Fichtinger, Gabor;  Jolley, Matthew A<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.onlinejase.com\/article\/S0894-7317(18)30343-2\/abstract\" title=\"https:\/\/www.onlinejase.com\/article\/S0894-7317(18)30343-2\/abstract\" target=\"blank\">Interaction with volume-rendered three-dimensional echocardiographic images in virtual reality<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Journal of the American Society of Echocardiography, <\/span><span class=\"tp_pub_additional_volume\">vol. 31, <\/span><span class=\"tp_pub_additional_issue\">iss. 10, <\/span><span class=\"tp_pub_additional_pages\">pp. 1158-1160, <\/span><span class=\"tp_pub_additional_year\">2018<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_789\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('789','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_789\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('789','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_789\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('789','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_789\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2018f,<br \/>\r\ntitle = {Interaction with volume-rendered three-dimensional echocardiographic images in virtual reality},<br \/>\r\nauthor = {Andras Lasso and Hannah H Nam and Patrick V Dinh and Csaba Pinter and Jean-Christophe Fillion-Robin and Steve Pieper and Sankhesh Jhaveri and Jean-Baptiste Vimort and Ken Martin and Mark Asselin and Francis X McGowan and Ron Kikinis and Gabor Fichtinger and Matthew A Jolley},<br \/>\r\nurl = {https:\/\/www.onlinejase.com\/article\/S0894-7317(18)30343-2\/abstract},<br \/>\r\nyear  = {2018},<br \/>\r\ndate = {2018-01-01},<br \/>\r\njournal = {Journal of the American Society of Echocardiography},<br \/>\r\nvolume = {31},<br \/>\r\nissue = {10},<br \/>\r\npages = {1158-1160},<br \/>\r\npublisher = {Elsevier},<br \/>\r\nabstract = {Three-dimensional (3D) imaging is increasingly important in echocardiography. However, viewing of 3D images on a flat, two-dimensional screen is a barrier to comprehension of latent information. There have been previous attempts to visualize the full 3D nature of the data, but they have not been widely adopted. For example, 3D printing offers realistic interaction but is time consuming, has limited means for the observer to move into or through the model, and is not yet practical for routine clinical use. Furthermore, the heart beats, and 3D printed models are static. Stereoscopic viewing on 2D screens (as at a movie theater) is possible but is expensive, may not provide an immersive experience, and does not have integrated 3D input devices (controllers). <br \/>\r\nStereoscopic virtual reality (VR) is developing rapidly but is being driven by the video gaming industry, with features not directly applicable to the visualization of \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('789','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_789\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Three-dimensional (3D) imaging is increasingly important in echocardiography. However, viewing of 3D images on a flat, two-dimensional screen is a barrier to comprehension of latent information. There have been previous attempts to visualize the full 3D nature of the data, but they have not been widely adopted. For example, 3D printing offers realistic interaction but is time consuming, has limited means for the observer to move into or through the model, and is not yet practical for routine clinical use. Furthermore, the heart beats, and 3D printed models are static. Stereoscopic viewing on 2D screens (as at a movie theater) is possible but is expensive, may not provide an immersive experience, and does not have integrated 3D input devices (controllers). <br \/>\r\nStereoscopic virtual reality (VR) is developing rapidly but is being driven by the video gaming industry, with features not directly applicable to the visualization of \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('789','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_789\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.onlinejase.com\/article\/S0894-7317(18)30343-2\/abstract\" title=\"https:\/\/www.onlinejase.com\/article\/S0894-7317(18)30343-2\/abstract\" target=\"_blank\">https:\/\/www.onlinejase.com\/article\/S0894-7317(18)30343-2\/abstract<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('789','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Herz, Christian;  Fillion-Robin, Jean-ChristopheC.;  Onken, Michael;  Riesmeier, J\u00f6rg;  Lasso, Andras;  Pinter, Csaba;  Fichtinger, Gabor;  Pieper, Steve;  Clunie, David;  Kikinis, Ron;  Fedorov, Andriy<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1158\/0008-5472.CAN-17-0336\" title=\"dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM\" target=\"blank\">dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Cancer Research, <\/span><span class=\"tp_pub_additional_volume\">vol. 77, <\/span><span class=\"tp_pub_additional_number\">no. 21, <\/span><span class=\"tp_pub_additional_pages\">pp. e87\u2013e90, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0008-5472<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_119\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('119','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_119\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('119','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_119\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('119','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_119\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Herz2017,<br \/>\r\ntitle = {dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM},<br \/>\r\nauthor = {Christian Herz and Jean-ChristopheC. Fillion-Robin and Michael Onken and J\u00f6rg Riesmeier and Andras Lasso and Csaba Pinter and Gabor Fichtinger and Steve Pieper and David Clunie and Ron Kikinis and Andriy Fedorov},<br \/>\r\nurl = {http:\/\/cancerres.aacrjournals.org\/content\/77\/21\/e87<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Herz2017_1.pdf},<br \/>\r\ndoi = {10.1158\/0008-5472.CAN-17-0336},<br \/>\r\nissn = {0008-5472},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-11-01},<br \/>\r\nurldate = {2017-11-01},<br \/>\r\njournal = {Cancer Research},<br \/>\r\nvolume = {77},<br \/>\r\nnumber = {21},<br \/>\r\npages = {e87\u2013e90},<br \/>\r\nabstract = {&lt;p&gt;Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology. dcmqi (DICOM for Quantitative Imaging) is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation. dcmqi source code is distributed under BSD-style license. It is freely available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. Installation and usage instructions are provided in the GitHub repository at https:\/\/github.com\/qiicr\/dcmqi. Cancer Res; 77(21); e87\u201390. \u00a92017 AACR.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('119','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_119\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology. dcmqi (DICOM for Quantitative Imaging) is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation. dcmqi source code is distributed under BSD-style license. It is freely available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. Installation and usage instructions are provided in the GitHub repository at https:\/\/github.com\/qiicr\/dcmqi. Cancer Res; 77(21); e87\u201390. \u00a92017 AACR.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('119','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_119\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/cancerres.aacrjournals.org\/content\/77\/21\/e87\" title=\"http:\/\/cancerres.aacrjournals.org\/content\/77\/21\/e87\" target=\"_blank\">http:\/\/cancerres.aacrjournals.org\/content\/77\/21\/e87<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Herz2017_1.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Herz2017_1[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Herz2017_1[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1158\/0008-5472.CAN-17-0336\" title=\"Follow DOI:10.1158\/0008-5472.CAN-17-0336\" target=\"_blank\">doi:10.1158\/0008-5472.CAN-17-0336<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('119','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Moult, Eric;  Lasso, Andras;  Ungi, Tamas;  Pinter, Csaba;  Welch, Mattea;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Moult2017.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Moult2017.pdf\" target=\"blank\">Improved temporal calibration of tracked ultrasound: an open-source solution<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">ImNO2013 - Imaging Network Ontario Symposium, <\/span><span class=\"tp_pub_additional_volume\">vol. 2, <\/span><span class=\"tp_pub_additional_number\">no. 04, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_126\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('126','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_126\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('126','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_126\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('126','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_126\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Moult2017,<br \/>\r\ntitle = {Improved temporal calibration of tracked ultrasound: an open-source solution},<br \/>\r\nauthor = {Eric Moult and Andras Lasso and Tamas Ungi and Csaba Pinter and Mattea Welch and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Moult2017.pdf<br \/>\r\n},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-07-01},<br \/>\r\nurldate = {2017-07-01},<br \/>\r\nbooktitle = {ImNO2013 - Imaging Network Ontario Symposium},<br \/>\r\njournal = {Journal of Medical Robotics Research},<br \/>\r\nvolume = {2},<br \/>\r\nnumber = {04},<br \/>\r\npages = {1750008},<br \/>\r\nabstract = {&lt;p&gt;In tracked ultrasound systems, temporal misalignment between image and tracker data results in incorrect image pose. We present a fully automatic temporal calibration. We image a flat plate in water with a tracked probe undergoing periodic uniaxial freehand translation. Using robust line detection scheme, we compute temporal misalignment as difference between probe and corresponding image position. From 240 sequences, standard deviation was under 5ms for standard imaging parameters. Source code is available in Public Library for Ultrasound Research, PLUS (www.plustoolkit.org).&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('126','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_126\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;In tracked ultrasound systems, temporal misalignment between image and tracker data results in incorrect image pose. We present a fully automatic temporal calibration. We image a flat plate in water with a tracked probe undergoing periodic uniaxial freehand translation. Using robust line detection scheme, we compute temporal misalignment as difference between probe and corresponding image position. From 240 sequences, standard deviation was under 5ms for standard imaging parameters. Source code is available in Public Library for Ultrasound Research, PLUS (www.plustoolkit.org).&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('126','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_126\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Moult2017.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Moult2017.[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Moult2017.[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('126','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Sharp, Gregory C;  Pinter, Csaba;  Unkelbach, Jan;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\">Open Source Proton Treatment Planning in 3D Slicer: Status Update <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">Proceedings to the 56 Annual Meeting of the Particle Therapy Cooperative Group (PTCOG), <\/span><span class=\"tp_pub_additional_volume\">vol. 4, <\/span><span class=\"tp_pub_additional_number\">no. 1, <\/span><span class=\"tp_pub_additional_publisher\">International Journal of Particle Therapy: Summer 2017, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_129\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('129','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_129\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Sharp2017,<br \/>\r\ntitle = {Open Source Proton Treatment Planning in 3D Slicer: Status Update},<br \/>\r\nauthor = {Gregory C Sharp and Csaba Pinter and Jan Unkelbach and Gabor Fichtinger},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-05-01},<br \/>\r\nurldate = {2017-05-01},<br \/>\r\nbooktitle = {Proceedings to the 56 Annual Meeting of the Particle Therapy Cooperative Group (PTCOG)},<br \/>\r\nvolume = {4},<br \/>\r\nnumber = {1},<br \/>\r\npages = {14-83},<br \/>\r\npublisher = {International Journal of Particle Therapy: Summer 2017},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('129','tp_bibtex')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Poulin, Eric<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/http:\/\/dx.doi.org\/10.1016\/j.brachy.2017.04.093\" title=\"Validation Of MRI To US Registration For Focal Hdr Prostate Brachytherapy Treatment\" target=\"blank\">Validation Of MRI To US Registration For Focal Hdr Prostate Brachytherapy Treatment<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">Annual Scientific Meeting of the American Brachytherapy Society, <\/span><span class=\"tp_pub_additional_volume\">vol. 16, <\/span><span class=\"tp_pub_additional_number\">no. 3, <\/span><span class=\"tp_pub_additional_organization\">Elsevier <\/span><span class=\"tp_pub_additional_publisher\">Elsevier, <\/span><span class=\"tp_pub_additional_address\">Boston, MA, USA, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1538-4721<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_145\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('145','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_145\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('145','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_145\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Poulin2017,<br \/>\r\ntitle = {Validation Of MRI To US Registration For Focal Hdr Prostate Brachytherapy Treatment},<br \/>\r\nauthor = {Eric Poulin},<br \/>\r\neditor = {Karim Boudam and Csaba Pinter and Samuel Kadoury and Andras Lasso and Gabor Fichtinger and Cynthia Menard},<br \/>\r\nurl = {http:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/fulltext<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2017.pdf},<br \/>\r\ndoi = {http:\/\/dx.doi.org\/10.1016\/j.brachy.2017.04.093},<br \/>\r\nissn = {1538-4721},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-01-01},<br \/>\r\nurldate = {2017-01-01},<br \/>\r\nbooktitle = {Annual Scientific Meeting of the American Brachytherapy Society},<br \/>\r\nvolume = {16},<br \/>\r\nnumber = {3},<br \/>\r\npages = {S56-S57},<br \/>\r\npublisher = {Elsevier},<br \/>\r\naddress = {Boston, MA, USA},<br \/>\r\norganization = {Elsevier},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('145','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_145\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/fulltext\" title=\"http:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/fulltext\" target=\"_blank\">http:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/fulltext<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2017.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2017[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2017[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/http:\/\/dx.doi.org\/10.1016\/j.brachy.2017.04.093\" title=\"Follow DOI:http:\/\/dx.doi.org\/10.1016\/j.brachy.2017.04.093\" target=\"_blank\">doi:http:\/\/dx.doi.org\/10.1016\/j.brachy.2017.04.093<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('145','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Poulin, Eric;  Boudam, Karim;  Pinter, Csaba;  Kadoury, Samuel;  Lasso, Andras;  Fichtinger, Gabor;  Menard, Cynthia<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2018.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2018.pdf\" target=\"blank\">Validation of MRI to TRUS registration for HDR prostate brachytherapy<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Brachytherapy, <\/span><span class=\"tp_pub_additional_volume\">vol. 17, <\/span><span class=\"tp_pub_additional_number\">no. 2, <\/span><span class=\"tp_pub_additional_pages\">pp. 283-290, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_111\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('111','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_111\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('111','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_111\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('111','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_111\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Poulin2017b,<br \/>\r\ntitle = {Validation of MRI to TRUS registration for HDR prostate brachytherapy},<br \/>\r\nauthor = {Eric Poulin and Karim Boudam and Csaba Pinter and Samuel Kadoury and Andras Lasso and Gabor Fichtinger and Cynthia Menard},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2018.pdf},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-01-01},<br \/>\r\nurldate = {2017-01-01},<br \/>\r\njournal = {Brachytherapy},<br \/>\r\nvolume = {17},<br \/>\r\nnumber = {2},<br \/>\r\npages = {283-290},<br \/>\r\nabstract = {&lt;p&gt;Purpose: The objective of this study was to develop and&lt;br \/&gt; <br \/>\r\nvalidate an open-source module for MRI to transrectal ultrasound (TRUS)&lt;br \/&gt; <br \/>\r\nregistration to support tumor-targeted prostate brachytherapy.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;Methods and Materials: In this study, fifteen patients with prostate&lt;br \/&gt; <br \/>\r\ncancer lesions visible on multiparametric MRI were selected for the&lt;br \/&gt; <br \/>\r\nvalidation. T2-weighted images with 1 mm isotropic voxel size and&lt;br \/&gt; <br \/>\r\ndiffusion weighted images were acquired on a 1.5T Siemens. Three&lt;br \/&gt; <br \/>\r\ndimensional (3D) TRUS images with 0.5 mm slice thickness were acquired.&lt;br \/&gt; <br \/>\r\nThe investigated registration module was incorporated in the open-source&lt;br \/&gt; <br \/>\r\n3D Slicer platform and can compute rigid and deformable transformations.&lt;br \/&gt; <br \/>\r\nAn extension of 3D Slicer, SlicerRT, allows import and export to DICOM-RT&lt;br \/&gt; <br \/>\r\nformats. For validation, similarity indices, prostate volumes and&lt;br \/&gt; <br \/>\r\ncentroid positions were determined in addition to registration errors for&lt;br \/&gt; <br \/>\r\ncommon 3D points identified by an experienced radiation oncologist.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;Results: The average time to compute the registration was 35\u00b13 seconds.&lt;br \/&gt; <br \/>\r\nFor the deformable and rigid registration respectively, Dice similarity&lt;br \/&gt; <br \/>\r\ncoefficients were 0.93\u00b10.01 and 0.87\u00b10.05 while the 95% Hausdorff&lt;br \/&gt; <br \/>\r\ndistance was 2.2\u00b10.3 and 4.2\u00b11.0 mm. MRI volumes obtained after the rigid&lt;br \/&gt; <br \/>\r\nand deformable registration were not statistically different (p&gt;0.05)&lt;br \/&gt; <br \/>\r\nfrom reference TRUS volumes. For the deformable and rigid registration&lt;br \/&gt; <br \/>\r\nrespectively, 3D distance error between centroid positions were 0.4\u00b10.1&lt;br \/&gt; <br \/>\r\nand 2.1\u00b11.0 mm while registration errors between common points were&lt;br \/&gt; <br \/>\r\n2.3\u00b11.1 and 3.5\u00b13.2 mm. Deformable registration was found significantly&lt;br \/&gt; <br \/>\r\nbetter (p&lt;0.05) than rigid registration in all parameters.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;Conclusions: An open-source MRI to TRUS registration platform was&lt;br \/&gt; <br \/>\r\nvalidated for integration in the brachytherapy workflow.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('111','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_111\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;Purpose: The objective of this study was to develop and&lt;br \/&gt; <br \/>\r\nvalidate an open-source module for MRI to transrectal ultrasound (TRUS)&lt;br \/&gt; <br \/>\r\nregistration to support tumor-targeted prostate brachytherapy.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;Methods and Materials: In this study, fifteen patients with prostate&lt;br \/&gt; <br \/>\r\ncancer lesions visible on multiparametric MRI were selected for the&lt;br \/&gt; <br \/>\r\nvalidation. T2-weighted images with 1 mm isotropic voxel size and&lt;br \/&gt; <br \/>\r\ndiffusion weighted images were acquired on a 1.5T Siemens. Three&lt;br \/&gt; <br \/>\r\ndimensional (3D) TRUS images with 0.5 mm slice thickness were acquired.&lt;br \/&gt; <br \/>\r\nThe investigated registration module was incorporated in the open-source&lt;br \/&gt; <br \/>\r\n3D Slicer platform and can compute rigid and deformable transformations.&lt;br \/&gt; <br \/>\r\nAn extension of 3D Slicer, SlicerRT, allows import and export to DICOM-RT&lt;br \/&gt; <br \/>\r\nformats. For validation, similarity indices, prostate volumes and&lt;br \/&gt; <br \/>\r\ncentroid positions were determined in addition to registration errors for&lt;br \/&gt; <br \/>\r\ncommon 3D points identified by an experienced radiation oncologist.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;Results: The average time to compute the registration was 35\u00b13 seconds.&lt;br \/&gt; <br \/>\r\nFor the deformable and rigid registration respectively, Dice similarity&lt;br \/&gt; <br \/>\r\ncoefficients were 0.93\u00b10.01 and 0.87\u00b10.05 while the 95% Hausdorff&lt;br \/&gt; <br \/>\r\ndistance was 2.2\u00b10.3 and 4.2\u00b11.0 mm. MRI volumes obtained after the rigid&lt;br \/&gt; <br \/>\r\nand deformable registration were not statistically different (p&amp;gt;0.05)&lt;br \/&gt; <br \/>\r\nfrom reference TRUS volumes. For the deformable and rigid registration&lt;br \/&gt; <br \/>\r\nrespectively, 3D distance error between centroid positions were 0.4\u00b10.1&lt;br \/&gt; <br \/>\r\nand 2.1\u00b11.0 mm while registration errors between common points were&lt;br \/&gt; <br \/>\r\n2.3\u00b11.1 and 3.5\u00b13.2 mm. Deformable registration was found significantly&lt;br \/&gt; <br \/>\r\nbetter (p&amp;lt;0.05) than rigid registration in all parameters.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;Conclusions: An open-source MRI to TRUS registration platform was&lt;br \/&gt; <br \/>\r\nvalidated for integration in the brachytherapy workflow.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('111','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_111\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2018.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2018[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Poulin2018[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('111','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Sunderland, Kyle R.;  Pinter, Csaba;  Lasso, Andras;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2017a.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2017a.pdf\" target=\"blank\">Fractional labelmaps for computing accurate dose volume histograms<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">SPIE Medical Imaging, <\/span><span class=\"tp_pub_additional_organization\">International Society for Optics and Photonics <\/span><span class=\"tp_pub_additional_publisher\">International Society for Optics and Photonics, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_124\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('124','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_124\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('124','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_124\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('124','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_124\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{sunderland2017a,<br \/>\r\ntitle = {Fractional labelmaps for computing accurate dose volume histograms},<br \/>\r\nauthor = {Kyle R. Sunderland and Csaba Pinter and Andras Lasso and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2017a.pdf},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-01-01},<br \/>\r\nurldate = {2017-01-01},<br \/>\r\nbooktitle = {SPIE Medical Imaging},<br \/>\r\npublisher = {International Society for Optics and Photonics},<br \/>\r\norganization = {International Society for Optics and Photonics},<br \/>\r\nabstract = {&lt;p&gt;&lt;strong&gt;PURPOSE:&lt;\/strong&gt; In radiation therapy treatment planning systems, structures are represented as parallel 2D contours. For treatment planning algorithms, structures must be converted into labelmap (i.e. 3D image denoting structure inside\/outside) representations. This is often done by triangulated a surface from contours, which is converted into a binary labelmap. This surface to binary labelmap conversion can cause large errors in small structures. Binary labelmaps are often represented using one byte per voxel, meaning a large amount of memory is unused. Our goal is to develop a fractional labelmap representation containing non-binary values, allowing more information to be stored in the same amount of memory.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;METHODS:&lt;\/strong&gt; We implemented an algorithm in 3D Slicer, which converts surfaces to fractional labelmaps by creating 216 binary labelmaps, changing the labelmap origin on each iteration. The binary labelmap values are summed to create the fractional labelmap. In addition, an algorithm is implemented in the SlicerRT toolkit that calculates dose volume histograms (DVH) using fractional labelmaps.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;RESULTS:&lt;\/strong&gt; We found that with manually segmented RANDO\u00ae head and neck structures, fractional labelmaps represented structure volume up to 19.07% (average 6.81%) more accurately than binary labelmaps, while occupying the same amount of memory. When compared to baseline DVH from treatment planning software, DVH from fractional labelmaps had agreement acceptance percent (1% \u0394D, 1% \u0394V) up to 57.46% higher (average 4.33%) than DVH from binary labelmaps.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;CONCLUSION:&lt;\/strong&gt; Fractional labelmaps promise to be an effective method for structure representation, allowing considerably more information to be stored in the same amount of memory&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('124','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_124\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;&lt;strong&gt;PURPOSE:&lt;\/strong&gt; In radiation therapy treatment planning systems, structures are represented as parallel 2D contours. For treatment planning algorithms, structures must be converted into labelmap (i.e. 3D image denoting structure inside\/outside) representations. This is often done by triangulated a surface from contours, which is converted into a binary labelmap. This surface to binary labelmap conversion can cause large errors in small structures. Binary labelmaps are often represented using one byte per voxel, meaning a large amount of memory is unused. Our goal is to develop a fractional labelmap representation containing non-binary values, allowing more information to be stored in the same amount of memory.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;METHODS:&lt;\/strong&gt; We implemented an algorithm in 3D Slicer, which converts surfaces to fractional labelmaps by creating 216 binary labelmaps, changing the labelmap origin on each iteration. The binary labelmap values are summed to create the fractional labelmap. In addition, an algorithm is implemented in the SlicerRT toolkit that calculates dose volume histograms (DVH) using fractional labelmaps.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;RESULTS:&lt;\/strong&gt; We found that with manually segmented RANDO\u00ae head and neck structures, fractional labelmaps represented structure volume up to 19.07% (average 6.81%) more accurately than binary labelmaps, while occupying the same amount of memory. When compared to baseline DVH from treatment planning software, DVH from fractional labelmaps had agreement acceptance percent (1% \u0394D, 1% \u0394V) up to 57.46% higher (average 4.33%) than DVH from binary labelmaps.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;CONCLUSION:&lt;\/strong&gt; Fractional labelmaps promise to be an effective method for structure representation, allowing considerably more information to be stored in the same amount of memory&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('124','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_124\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2017a.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('124','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Suriyakumar, Vinith M.;  Xu, Renee;  Pinter, Csaba;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017a.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017a.pdf\" target=\"blank\">Open-source software for collision detection in external beam radiation therapy<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">SPIE Medical Imaging 2017, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_130\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('130','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_130\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('130','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_130\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Suriyakumar2017a,<br \/>\r\ntitle = {Open-source software for collision detection in external beam radiation therapy},<br \/>\r\nauthor = {Vinith M. Suriyakumar and Renee Xu and Csaba Pinter and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017a.pdf},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-01-01},<br \/>\r\nurldate = {2017-01-01},<br \/>\r\nbooktitle = {SPIE Medical Imaging 2017},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('130','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_130\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017a.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakuma[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakuma[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('130','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Suriyakumar, Vinith M.;  Xu, Renee;  Pinter, Csaba;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017b-poster_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017b-poster_0.pdf\" target=\"blank\">Collision detection for external beam radiation therapy applications in SlicerRT<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">15th Annual Imaging Network Ontario Symposiuim, <\/span><span class=\"tp_pub_additional_publisher\">Imaging Network Ontario (ImNO), <\/span><span class=\"tp_pub_additional_address\">London, Ontario, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_116\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('116','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_116\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('116','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_116\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Suriyakumar2017b,<br \/>\r\ntitle = {Collision detection for external beam radiation therapy applications in SlicerRT},<br \/>\r\nauthor = {Vinith M. Suriyakumar and Renee Xu and Csaba Pinter and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017b-poster_0.pdf<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017b-poster_0.pdf},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-01-01},<br \/>\r\nurldate = {2017-01-01},<br \/>\r\nbooktitle = {15th Annual Imaging Network Ontario Symposiuim},<br \/>\r\npublisher = {Imaging Network Ontario (ImNO)},<br \/>\r\naddress = {London, Ontario},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('116','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_116\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017b-poster_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakuma[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakuma[...]<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakumar2017b-poster_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakuma[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Suriyakuma[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('116','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Herz, Christian;  Fillion-Robin, Jean-Christophe;  Onken, Michael;  Riesmeier, J\u00f6rg;  Lasso, Andras;  Pinter, Csaba;  Fichtinger, Gabor;  Pieper, Steve;  Clunie, David;  Kikinis, Ron;  Fedorov, Andriy<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/aacrjournals.org\/cancerres\/article-abstract\/77\/21\/e87\/662591\" title=\"https:\/\/aacrjournals.org\/cancerres\/article-abstract\/77\/21\/e87\/662591\" target=\"blank\">DCMQI: an open source library for standardized communication of quantitative image analysis results using DICOM<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Cancer research, <\/span><span class=\"tp_pub_additional_volume\">vol. 77, <\/span><span class=\"tp_pub_additional_issue\">iss. 21, <\/span><span class=\"tp_pub_additional_pages\">pp. e87-e90, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_742\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('742','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_742\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('742','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_742\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('742','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_742\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2017,<br \/>\r\ntitle = {DCMQI: an open source library for standardized communication of quantitative image analysis results using DICOM},<br \/>\r\nauthor = {Christian Herz and Jean-Christophe Fillion-Robin and Michael Onken and J\u00f6rg Riesmeier and Andras Lasso and Csaba Pinter and Gabor Fichtinger and Steve Pieper and David Clunie and Ron Kikinis and Andriy Fedorov},<br \/>\r\nurl = {https:\/\/aacrjournals.org\/cancerres\/article-abstract\/77\/21\/e87\/662591},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-01-01},<br \/>\r\njournal = {Cancer research},<br \/>\r\nvolume = {77},<br \/>\r\nissue = {21},<br \/>\r\npages = {e87-e90},<br \/>\r\npublisher = {American Association for Cancer Research},<br \/>\r\nabstract = {Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology. dcmqi (DICOM for Quantitative Imaging) is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation. dcmqi source code is distributed under BSD-style license. It is freely available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('742','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_742\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology. dcmqi (DICOM for Quantitative Imaging) is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation. dcmqi source code is distributed under BSD-style license. It is freely available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('742','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_742\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/aacrjournals.org\/cancerres\/article-abstract\/77\/21\/e87\/662591\" title=\"https:\/\/aacrjournals.org\/cancerres\/article-abstract\/77\/21\/e87\/662591\" target=\"_blank\">https:\/\/aacrjournals.org\/cancerres\/article-abstract\/77\/21\/e87\/662591<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('742','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Poulin, Eric;  Boudam, Karim;  Pinter, Csaba;  Kadoury, Samuel;  Lasso, Andras;  Fichtinger, Gabor;  M\u00e9nard, Cynthia<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/abstract\" title=\"https:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/abstract\" target=\"blank\">Validation of MRI to US registration for focal HDR prostate brachytherapy<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Brachytherapy, <\/span><span class=\"tp_pub_additional_volume\">vol. 16, <\/span><span class=\"tp_pub_additional_issue\">iss. 3, <\/span><span class=\"tp_pub_additional_pages\">pp. S56-S57, <\/span><span class=\"tp_pub_additional_year\">2017<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_872\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('872','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_872\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('872','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_872\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('872','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_872\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2017i,<br \/>\r\ntitle = {Validation of MRI to US registration for focal HDR prostate brachytherapy},<br \/>\r\nauthor = {Eric Poulin and Karim Boudam and Csaba Pinter and Samuel Kadoury and Andras Lasso and Gabor Fichtinger and Cynthia M\u00e9nard},<br \/>\r\nurl = {https:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/abstract},<br \/>\r\nyear  = {2017},<br \/>\r\ndate = {2017-01-01},<br \/>\r\njournal = {Brachytherapy},<br \/>\r\nvolume = {16},<br \/>\r\nissue = {3},<br \/>\r\npages = {S56-S57},<br \/>\r\npublisher = {Elsevier},<br \/>\r\nabstract = {Purpose <br \/>\r\nHigh dose rate (HDR) prostate brachytherapy can achieve long-term disease control. Multiparametric Magnetic Resonance Imaging (mpMRI) allows identification of gross tumor (GTV) in order to boost or target lesions. However, a significant number of clinics are using ultrasound (US) as their planning imaging modality due to its low cost and real time capability; but can\u2019t identify the position of the GTV. Therefore, a registration is needed between mpMRI and US images to accurately delineate the GTV. The goal of the study was to develop and validate a new 3D Slicer MRI to US registration module for focal HDR prostate brachytherapy treatment. <br \/>\r\nMaterials and Methods <br \/>\r\nIn this study, eleven patients with prostate cancer who underwent HDR brachytherapy, with lesions visible on mpMRI, were selected for the validation. T2-weighted 3D variable-flip-angle TSE images with 1mm isotropic voxel and diffusion \u2026},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('872','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_872\" style=\"display:none;\"><div class=\"tp_abstract_entry\">Purpose <br \/>\r\nHigh dose rate (HDR) prostate brachytherapy can achieve long-term disease control. Multiparametric Magnetic Resonance Imaging (mpMRI) allows identification of gross tumor (GTV) in order to boost or target lesions. However, a significant number of clinics are using ultrasound (US) as their planning imaging modality due to its low cost and real time capability; but can\u2019t identify the position of the GTV. Therefore, a registration is needed between mpMRI and US images to accurately delineate the GTV. The goal of the study was to develop and validate a new 3D Slicer MRI to US registration module for focal HDR prostate brachytherapy treatment. <br \/>\r\nMaterials and Methods <br \/>\r\nIn this study, eleven patients with prostate cancer who underwent HDR brachytherapy, with lesions visible on mpMRI, were selected for the validation. T2-weighted 3D variable-flip-angle TSE images with 1mm isotropic voxel and diffusion \u2026<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('872','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_872\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/abstract\" title=\"https:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/abstract\" target=\"_blank\">https:\/\/www.brachyjournal.com\/article\/S1538-4721(17)30154-X\/abstract<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('872','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Kapur, Tina;  Pieper, Steve;  Lasso, Andras;  Ungi, Tamas;  Pinter, Csaba;  Fichtinger, Gabor;  Kikinis, Ron<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/http:\/\/doi.org\/10.1016\/j.media.2016.06.035\" title=\"Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience\" target=\"blank\">Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">Medical Image Analysis, <\/span><span class=\"tp_pub_additional_volume\">vol. 33, <\/span><span class=\"tp_pub_additional_pages\">pp. 176-180, <\/span><span class=\"tp_pub_additional_year\">2016<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_164\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('164','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_164\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('164','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_164\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('164','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_164\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Kapur2016,<br \/>\r\ntitle = {Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience},<br \/>\r\nauthor = {Tina Kapur and Steve Pieper and Andras Lasso and Tamas Ungi and Csaba Pinter and Gabor Fichtinger and Ron Kikinis},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Kapur2016.pdf},<br \/>\r\ndoi = {http:\/\/doi.org\/10.1016\/j.media.2016.06.035},<br \/>\r\nyear  = {2016},<br \/>\r\ndate = {2016-10-01},<br \/>\r\nurldate = {2016-10-01},<br \/>\r\njournal = {Medical Image Analysis},<br \/>\r\nvolume = {33},<br \/>\r\npages = {176-180},<br \/>\r\nabstract = {&lt;p&gt;&lt;span style=\"color:rgb(46, 46, 46); font-family:arial,helvetica,lucida sans unicode,microsoft sans serif,segoe ui symbol,stixgeneral,cambria math,arial unicode ms,sans-serif; font-size:16px\"&gt;The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools\u2014VTK, ITK, CMake, CDash, DCMTK\u2014were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science (\u201cOpen Science\u201d); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.&lt;\/span&gt;&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('164','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_164\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;&lt;span style=&quot;color:rgb(46, 46, 46); font-family:arial,helvetica,lucida sans unicode,microsoft sans serif,segoe ui symbol,stixgeneral,cambria math,arial unicode ms,sans-serif; font-size:16px&quot;&gt;The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools\u2014VTK, ITK, CMake, CDash, DCMTK\u2014were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science (\u201cOpen Science\u201d); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision.&lt;\/span&gt;&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('164','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_164\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Kapur2016.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Kapur2016.[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Kapur2016.[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/http:\/\/doi.org\/10.1016\/j.media.2016.06.035\" title=\"Follow DOI:http:\/\/doi.org\/10.1016\/j.media.2016.06.035\" target=\"_blank\">doi:http:\/\/doi.org\/10.1016\/j.media.2016.06.035<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('164','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Alexander, Kevin;  Robinson, Alec;  Pinter, Csaba;  Fichtinger, Gabor;  Schreiner, John<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/IC3DDose016-Alexander-FilmSlicelet.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/IC3DDose016-Alexander-FilmSlicelet.pdf\" target=\"blank\">Development of 3D Slicer Based Film Dosimetry Analysis<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">IC3DDose (9th International Conference on 3D Radiation Dosimetry), <\/span><span class=\"tp_pub_additional_volume\">vol. 847, <\/span><span class=\"tp_pub_additional_organization\">IOP Science <\/span><span class=\"tp_pub_additional_publisher\">IOP Science, <\/span><span class=\"tp_pub_additional_address\">Houston, TX, USA, <\/span><span class=\"tp_pub_additional_year\">2016<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_157\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('157','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_157\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('157','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_157\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('157','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_157\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Alexander2016,<br \/>\r\ntitle = {Development of 3D Slicer Based Film Dosimetry Analysis},<br \/>\r\nauthor = {Kevin Alexander and Alec Robinson and Csaba Pinter and Gabor Fichtinger and John Schreiner},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/IC3DDose016-Alexander-FilmSlicelet.pdf},<br \/>\r\nyear  = {2016},<br \/>\r\ndate = {2016-10-01},<br \/>\r\nurldate = {2016-10-01},<br \/>\r\nbooktitle = {IC3DDose (9th International Conference on 3D Radiation Dosimetry)},<br \/>\r\nvolume = {847},<br \/>\r\npublisher = {IOP Science},<br \/>\r\naddress = {Houston, TX, USA},<br \/>\r\norganization = {IOP Science},<br \/>\r\nabstract = {&lt;p&gt;Radiochromic film dosimetry has been widely adopted in the clinic as it is a convenient option for dose measurement and verification. Film dosimetry analysis is typically performed using expensive commercial software, or custom made scripts in Matlab. However, common clinical film analysis software is not transparent regarding what corrections\/optimizations are running behind the scenes. An extension to the open-source medical imaging platform 3D Slicer has been designed and implemented in our centre for film dosimetry analysis. This extension enables importing treatment planning system dose and film imaging data, film calibration, registration, and comparison of 2D dose distributions, enabling greater accessibility to film analysis and higher reliability.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('157','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_157\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;Radiochromic film dosimetry has been widely adopted in the clinic as it is a convenient option for dose measurement and verification. Film dosimetry analysis is typically performed using expensive commercial software, or custom made scripts in Matlab. However, common clinical film analysis software is not transparent regarding what corrections\/optimizations are running behind the scenes. An extension to the open-source medical imaging platform 3D Slicer has been designed and implemented in our centre for film dosimetry analysis. This extension enables importing treatment planning system dose and film imaging data, film calibration, registration, and comparison of 2D dose distributions, enabling greater accessibility to film analysis and higher reliability.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('157','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_157\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/IC3DDose016-Alexander-FilmSlicelet.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/IC3DDose01[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/IC3DDose01[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('157','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Lasso, Andras;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter_ImNO2016_Segmentations_v03.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter_ImNO2016_Segmentations_v03.pdf\" target=\"blank\">Dynamic management of segmented structures in 3D Slicer<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">Imaging Network Ontario Symposium (ImNO 2016), <\/span><span class=\"tp_pub_additional_year\">2016<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_158\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('158','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_158\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('158','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_158\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Pinter2016,<br \/>\r\ntitle = {Dynamic management of segmented structures in 3D Slicer},<br \/>\r\nauthor = {Csaba Pinter and Andras Lasso and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter_ImNO2016_Segmentations_v03.pdf},<br \/>\r\nyear  = {2016},<br \/>\r\ndate = {2016-03-01},<br \/>\r\nurldate = {2016-03-01},<br \/>\r\nbooktitle = {Imaging Network Ontario Symposium (ImNO 2016)},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('158','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_158\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter_ImNO2016_Segmentations_v03.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter_ImN[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter_ImN[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('158','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Sunderland, Kyle R.;  Pinter, Csaba;  Lasso, Andras;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/sunderland2016a_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/sunderland2016a_0.pdf\" target=\"blank\">Effects of voxelization on dose volume histogram accuracy<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">SPIE Medical Imaging, <\/span><span class=\"tp_pub_additional_organization\">International Society for Optics and Photonics <\/span><span class=\"tp_pub_additional_publisher\">International Society for Optics and Photonics, <\/span><span class=\"tp_pub_additional_year\">2016<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_159\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('159','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_159\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('159','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_159\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('159','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_159\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{sunderland2016a,<br \/>\r\ntitle = {Effects of voxelization on dose volume histogram accuracy},<br \/>\r\nauthor = {Kyle R. Sunderland and Csaba Pinter and Andras Lasso and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/sunderland2016a_0.pdf},<br \/>\r\nyear  = {2016},<br \/>\r\ndate = {2016-01-01},<br \/>\r\nurldate = {2016-01-01},<br \/>\r\nbooktitle = {SPIE Medical Imaging},<br \/>\r\npages = {97862O\u201397862O},<br \/>\r\npublisher = {International Society for Optics and Photonics},<br \/>\r\norganization = {International Society for Optics and Photonics},<br \/>\r\nabstract = {&lt;p&gt;&lt;strong&gt;PURPOSE:&lt;\/strong&gt; In radiotherapy treatment planning systems, structures of interest such as targets and organs at risk are stored as 2D contours on evenly spaced planes. In order to be used in various algorithms, contours must be converted into binary labelmap volumes using voxelization. The voxelization process results in lost information, which has little effect on the volume of large structures, but has significant impact on small structures, which contain few voxels. Volume differences for segmented structures affects metrics such as dose volume histograms (DVH), which are used for treatment planning. Our goal is to evaluate the impact of voxelization on segmented structures, as well as how factors like voxel size affects metrics, such as DVH.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;METHODS:&lt;\/strong&gt; We create a series of implicit functions, which represent simulated structures. These structures are sampled at varying resolutions, and compared to labelmaps with high sub-millimeter resolutions. We generate DVH and evaluate voxelization error for the same structures at different resolutions by calculating the agreement acceptance percentage between the DVH.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;RESULTS:&lt;\/strong&gt; We implemented tools for analysis as modules in the SlicerRT toolkit based on the 3D Slicer platform. We found that there were large DVH variation from the baseline for small structures or for structures located in regions with a high dose gradient, potentially leading to the creation of suboptimal treatment plans.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;CONCLUSION:&lt;\/strong&gt; This work demonstrates that labelmap and dose volume voxel size is an important factor in DVH accuracy, which must be accounted for in order to ensure the development of accurate treatment plans. &lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('159','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_159\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;&lt;strong&gt;PURPOSE:&lt;\/strong&gt; In radiotherapy treatment planning systems, structures of interest such as targets and organs at risk are stored as 2D contours on evenly spaced planes. In order to be used in various algorithms, contours must be converted into binary labelmap volumes using voxelization. The voxelization process results in lost information, which has little effect on the volume of large structures, but has significant impact on small structures, which contain few voxels. Volume differences for segmented structures affects metrics such as dose volume histograms (DVH), which are used for treatment planning. Our goal is to evaluate the impact of voxelization on segmented structures, as well as how factors like voxel size affects metrics, such as DVH.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;METHODS:&lt;\/strong&gt; We create a series of implicit functions, which represent simulated structures. These structures are sampled at varying resolutions, and compared to labelmaps with high sub-millimeter resolutions. We generate DVH and evaluate voxelization error for the same structures at different resolutions by calculating the agreement acceptance percentage between the DVH.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;RESULTS:&lt;\/strong&gt; We implemented tools for analysis as modules in the SlicerRT toolkit based on the 3D Slicer platform. We found that there were large DVH variation from the baseline for small structures or for structures located in regions with a high dose gradient, potentially leading to the creation of suboptimal treatment plans.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;&lt;strong&gt;CONCLUSION:&lt;\/strong&gt; This work demonstrates that labelmap and dose volume voxel size is an important factor in DVH accuracy, which must be accounted for in order to ensure the development of accurate treatment plans.&amp;nbsp;&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('159','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_159\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/sunderland2016a_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/sunderland[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/sunderland[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('159','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Sunderland, Kyle R.;  Pinter, Csaba;  Lasso, Andras;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2016b.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2016b.pdf\" target=\"blank\">Analysis of dose volume histogram deviations using different voxelization parameters<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">14th Annual Imaging Network Ontario Symposium (ImNO), <\/span><span class=\"tp_pub_additional_address\">Toronto, Canada, <\/span><span class=\"tp_pub_additional_year\">2016<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_149\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('149','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_149\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('149','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_149\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Sunderland2016b,<br \/>\r\ntitle = {Analysis of dose volume histogram deviations using different voxelization parameters},<br \/>\r\nauthor = {Kyle R. Sunderland and Csaba Pinter and Andras Lasso and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2016b.pdf},<br \/>\r\nyear  = {2016},<br \/>\r\ndate = {2016-01-01},<br \/>\r\nurldate = {2016-01-01},<br \/>\r\nbooktitle = {14th Annual Imaging Network Ontario Symposium (ImNO)},<br \/>\r\naddress = {Toronto, Canada},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('149','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_149\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2016b.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('149','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Andrea, Jennifer;  Pinter, Csaba;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1007\/978-3-319-19387-8_105\" title=\"Measuring radiation treatment plan similarity in the cloud\" target=\"blank\">Measuring radiation treatment plan similarity in the cloud<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">World Congress on Medical Physics and Biomedical Engineering, <\/span><span class=\"tp_pub_additional_volume\">vol. 51, <\/span><span class=\"tp_pub_additional_organization\">Springer <\/span><span class=\"tp_pub_additional_publisher\">Springer, <\/span><span class=\"tp_pub_additional_address\">Toronto, Canada, <\/span><span class=\"tp_pub_additional_year\">2015<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 1680-0737<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_195\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('195','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_195\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('195','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_195\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Andrea2015b,<br \/>\r\ntitle = {Measuring radiation treatment plan similarity in the cloud},<br \/>\r\nauthor = {Jennifer Andrea and Csaba Pinter and Gabor Fichtinger},<br \/>\r\nurl = {http:\/\/link.springer.com\/book\/10.1007\/978-3-319-19387-8<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015b_0.pdf},<br \/>\r\ndoi = {10.1007\/978-3-319-19387-8_105},<br \/>\r\nissn = {1680-0737},<br \/>\r\nyear  = {2015},<br \/>\r\ndate = {2015-07-01},<br \/>\r\nurldate = {2015-07-01},<br \/>\r\nbooktitle = {World Congress on Medical Physics and Biomedical Engineering},<br \/>\r\nvolume = {51},<br \/>\r\npages = {432-435},<br \/>\r\npublisher = {Springer},<br \/>\r\naddress = {Toronto, Canada},<br \/>\r\norganization = {Springer},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('195','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_195\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/link.springer.com\/book\/10.1007\/978-3-319-19387-8\" title=\"http:\/\/link.springer.com\/book\/10.1007\/978-3-319-19387-8\" target=\"_blank\">http:\/\/link.springer.com\/book\/10.1007\/978-3-319-19387-8<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015b_0.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1007\/978-3-319-19387-8_105\" title=\"Follow DOI:10.1007\/978-3-319-19387-8_105\" target=\"_blank\">doi:10.1007\/978-3-319-19387-8_105<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('195','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Pinter, Csaba;  Lasso, Andras;  Wang, An;  Sharp, Gregory C;  Alexander, Kevin;  Jaffray, David;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1007\/978-3-319-19387-8_152\" title=\"Performing radiation therapy research using the open-source SlicerRT toolkit\" target=\"blank\">Performing radiation therapy research using the open-source SlicerRT toolkit<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">World Congress on Medical Physics and Biomedical Engineering, <\/span><span class=\"tp_pub_additional_organization\">Springer <\/span><span class=\"tp_pub_additional_publisher\">Springer, <\/span><span class=\"tp_pub_additional_address\">Toronto, <\/span><span class=\"tp_pub_additional_year\">2015<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_200\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('200','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_200\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('200','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_200\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('200','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_200\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Pinter2015,<br \/>\r\ntitle = {Performing radiation therapy research using the open-source SlicerRT toolkit},<br \/>\r\nauthor = {Csaba Pinter and Andras Lasso and An Wang and Gregory C Sharp and Kevin Alexander and David Jaffray and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2015.pdf},<br \/>\r\ndoi = {10.1007\/978-3-319-19387-8_152},<br \/>\r\nyear  = {2015},<br \/>\r\ndate = {2015-07-01},<br \/>\r\nurldate = {2015-07-01},<br \/>\r\nbooktitle = {World Congress on Medical Physics and Biomedical Engineering},<br \/>\r\npublisher = {Springer},<br \/>\r\naddress = {Toronto},<br \/>\r\norganization = {Springer},<br \/>\r\nabstract = {&lt;p&gt;Radiation therapy (RT) is a common treatment option for a wide variety of cancer types. Despite significant improvements in this technique over the past years, software tools for research in RT are limited to either expensive, closed, proprietary applications or heterogeneous sets of open-source software packages with limited scope, reliability, and user support. Our SlicerRT toolkit aspires to overcome these limitations by providing an extensive set of RT research tools leveraging the advanced visualization and image analysis features of its base platform 3D Slicer.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;The SlicerRT toolkit comprises of a set of 3D Slicer extensions: SlicerRT core, Matlab Bridge, Multi-dimensional Data, and Gel Dosimetry. The SlicerRT core extension contains 26 modules, many of which provide common RT tools used in most RT research scenarios. Matlab Bridge provides a convenient way for connecting the researchers\u2019 existing MATLAB algorithms to the SlicerRT ecosystem. Multi-dimensional Data offers a feature set for handling multi-dimensional datasets, such as longitudinal studies or 4D data. Finally, Gel Dosimetry facilitates gel dosimetry analysis workflows through a streamlined, workflow-based end-user application. It serves as an example and proof of concept for such applications implementing advanced clinical or research workflows.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;Using these open-source software tools makes it possible to conduct cutting edge RT research without parallel development efforts. It acts as a medium into which researchers can integrate their methods into, and which they can use to perform comparative validation, develop novel RT techniques, or transition advanced methods into routine clinical practice.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('200','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_200\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;Radiation therapy (RT) is a common treatment option for a wide variety of cancer types. Despite significant improvements in this technique over the past years, software tools for research in RT are limited to either expensive, closed, proprietary applications or heterogeneous sets of open-source software packages with limited scope, reliability, and user support. Our SlicerRT toolkit aspires to overcome these limitations by providing an extensive set of RT research tools leveraging the advanced visualization and image analysis features of its base platform 3D Slicer.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;The SlicerRT toolkit comprises of a set of 3D Slicer extensions: SlicerRT core, Matlab Bridge, Multi-dimensional Data, and Gel Dosimetry. The SlicerRT core extension contains 26 modules, many of which provide common RT tools used in most RT research scenarios. Matlab Bridge provides a convenient way for connecting the researchers\u2019 existing MATLAB algorithms to the SlicerRT ecosystem. Multi-dimensional Data offers a feature set for handling multi-dimensional datasets, such as longitudinal studies or 4D data. Finally, Gel Dosimetry facilitates gel dosimetry analysis workflows through a streamlined, workflow-based end-user application. It serves as an example and proof of concept for such applications implementing advanced clinical or research workflows.&lt;\/p&gt; <br \/>\r\n&lt;p&gt;Using these open-source software tools makes it possible to conduct cutting edge RT research without parallel development efforts. It acts as a medium into which researchers can integrate their methods into, and which they can use to perform comparative validation, develop novel RT techniques, or transition advanced methods into routine clinical practice.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('200','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_200\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2015.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2015[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Pinter2015[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1007\/978-3-319-19387-8_152\" title=\"Follow DOI:10.1007\/978-3-319-19387-8_152\" target=\"_blank\">doi:10.1007\/978-3-319-19387-8_152<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('200','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Alexander, Kevin;  Pinter, Csaba;  Andrea, Jennifer;  Fichtinger, Gabor;  Schreiner, John<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1007\/978-3-319-19387-8_128\" title=\"3D Slicer Gel Dosimetry Analysis: Validation of the Calibration Process\" target=\"blank\">3D Slicer Gel Dosimetry Analysis: Validation of the Calibration Process<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">World Congress on Medical Physics and Biomedical Engineering, June 7-12, 2015, Toronto, Canada, <\/span><span class=\"tp_pub_additional_volume\">vol. 51, <\/span><span class=\"tp_pub_additional_organization\">Springer International Publishing <\/span><span class=\"tp_pub_additional_publisher\">Springer International Publishing, <\/span><span class=\"tp_pub_additional_year\">2015<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_179\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('179','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_179\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('179','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_179\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('179','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_179\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Alexander2015,<br \/>\r\ntitle = {3D Slicer Gel Dosimetry Analysis: Validation of the Calibration Process},<br \/>\r\nauthor = {Kevin Alexander and Csaba Pinter and Jennifer Andrea and Gabor Fichtinger and John Schreiner},<br \/>\r\nurl = {http:\/\/link.springer.com\/chapter\/10.1007%2F978-3-319-19387-8_128<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2015.pdf},<br \/>\r\ndoi = {10.1007\/978-3-319-19387-8_128},<br \/>\r\nyear  = {2015},<br \/>\r\ndate = {2015-06-01},<br \/>\r\nurldate = {2015-06-01},<br \/>\r\nbooktitle = {World Congress on Medical Physics and Biomedical Engineering, June 7-12, 2015, Toronto, Canada},<br \/>\r\nvolume = {51},<br \/>\r\npages = {521-524},<br \/>\r\npublisher = {Springer International Publishing},<br \/>\r\norganization = {Springer International Publishing},<br \/>\r\nabstract = {&lt;p&gt;An extension tailored to dose data processing and analysis has been developed in the open source imaging application 3D Slicer to aid in routine clinical use of gel dosim-etry. This extension allows for registration, calibration, and comparison of 3D gel dosimeter data (imaged using an optical CT scanner) to treatment planning data. In this work, we present the accuracy and reproducibility of the gel dosimeter calibration component of the 3D Slicer extension. We examine the consistency of the calibration curves for a range of electron beam irradiations, and the inter-user variability of the gel dosimeter calibration process.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('179','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_179\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;An extension tailored to dose data processing and analysis has been developed in the open source imaging application 3D Slicer to aid in routine clinical use of gel dosim-etry. This extension allows for registration, calibration, and comparison of 3D gel dosimeter data (imaged using an optical CT scanner) to treatment planning data. In this work, we present the accuracy and reproducibility of the gel dosimeter calibration component of the 3D Slicer extension. We examine the consistency of the calibration curves for a range of electron beam irradiations, and the inter-user variability of the gel dosimeter calibration process.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('179','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_179\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/link.springer.com\/chapter\/10.1007%2F978-3-319-19387-8_128\" title=\"http:\/\/link.springer.com\/chapter\/10.1007%2F978-3-319-19387-8_128\" target=\"_blank\">http:\/\/link.springer.com\/chapter\/10.1007%2F978-3-319-19387-8_128<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2015.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1007\/978-3-319-19387-8_128\" title=\"Follow DOI:10.1007\/978-3-319-19387-8_128\" target=\"_blank\">doi:10.1007\/978-3-319-19387-8_128<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('179','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Alexander, Kevin;  Jechel, Christopher;  Pinter, Csaba;  Salomons, Greg;  Lasso, Andras;  Fichtinger, Gabor;  Schreiner, L. John<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1118\/1.4924592\" title=\"Cross-Validation of 3D Gamma Comparison Tools\" target=\"blank\">Cross-Validation of 3D Gamma Comparison Tools<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_volume\">vol. 42, <\/span><span class=\"tp_pub_additional_number\">no. 15, <\/span><span class=\"tp_pub_additional_publisher\">Medical Physics, <\/span><span class=\"tp_pub_additional_year\">2015<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_185\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('185','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_185\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('185','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_185\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Alexander2015a,<br \/>\r\ntitle = {Cross-Validation of 3D Gamma Comparison Tools},<br \/>\r\nauthor = {Kevin Alexander and Christopher Jechel and Csaba Pinter and Greg Salomons and Andras Lasso and Gabor Fichtinger and L. John Schreiner},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2015_AAPM_Gamma.pdf},<br \/>\r\ndoi = {10.1118\/1.4924592},<br \/>\r\nyear  = {2015},<br \/>\r\ndate = {2015-06-01},<br \/>\r\nurldate = {2015-06-01},<br \/>\r\nvolume = {42},<br \/>\r\nnumber = {15},<br \/>\r\npages = {3385-3385},<br \/>\r\npublisher = {Medical Physics},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('185','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_185\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2015_AAPM_Gamma.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Alexander2[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1118\/1.4924592\" title=\"Follow DOI:10.1118\/1.4924592\" target=\"_blank\">doi:10.1118\/1.4924592<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('185','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Andrea, Jennifer;  Pinter, Csaba;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"http:\/\/www.imno.ca\/sites\/default\/files\/IMNO-Conference-Program-Final.pdf\" title=\"http:\/\/www.imno.ca\/sites\/default\/files\/IMNO-Conference-Program-Final.pdf\" target=\"blank\">Cloud computing of anatomical similarity<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">13th Imaging Network Ontario Symposium (ImNO 2015), <\/span><span class=\"tp_pub_additional_address\">London, Canada, <\/span><span class=\"tp_pub_additional_year\">2015<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_183\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('183','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_183\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('183','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_183\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Andrea2015a,<br \/>\r\ntitle = {Cloud computing of anatomical similarity},<br \/>\r\nauthor = {Jennifer Andrea and Csaba Pinter and Gabor Fichtinger},<br \/>\r\nurl = {http:\/\/www.imno.ca\/sites\/default\/files\/IMNO-Conference-Program-Final.pdf<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015a-poster.pptx<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015a-poster.pptx},<br \/>\r\nyear  = {2015},<br \/>\r\ndate = {2015-03-01},<br \/>\r\nurldate = {2015-03-01},<br \/>\r\nbooktitle = {13th Imaging Network Ontario Symposium (ImNO 2015)},<br \/>\r\npages = {35},<br \/>\r\naddress = {London, Canada},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('183','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_183\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/www.imno.ca\/sites\/default\/files\/IMNO-Conference-Program-Final.pdf\" title=\"http:\/\/www.imno.ca\/sites\/default\/files\/IMNO-Conference-Program-Final.pdf\" target=\"_blank\">http:\/\/www.imno.ca\/sites\/default\/files\/IMNO-Conference-Program-Final.pdf<\/a><\/li><li><i class=\"fas fa-file-powerpoint\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015a-poster.pptx\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015[...]<\/a><\/li><li><i class=\"fas fa-file-powerpoint\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015a-poster.pptx\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Andrea2015[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('183','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Sunderland, Kyle R.;  Woo, Boyeong;  Pinter, Csaba;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1117\/12.2081436\" title=\"Reconstruction of surfaces from planar contours through contour interpolation\" target=\"blank\">Reconstruction of surfaces from planar contours through contour interpolation<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">SPIE Medical Imaging 2015, <\/span><span class=\"tp_pub_additional_volume\">vol. 9415, <\/span><span class=\"tp_pub_additional_year\">2015<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_205\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('205','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_205\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('205','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_205\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('205','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_205\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Sunderland2015,<br \/>\r\ntitle = {Reconstruction of surfaces from planar contours through contour interpolation},<br \/>\r\nauthor = {Kyle R. Sunderland and Boyeong Woo and Csaba Pinter and Gabor Fichtinger},<br \/>\r\nurl = {http:\/\/dx.doi.org\/10.1117\/12.2081436<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2015-manuscript.pdf<br \/>\r\nhttps:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2015-poster.pdf},<br \/>\r\ndoi = {10.1117\/12.2081436},<br \/>\r\nyear  = {2015},<br \/>\r\ndate = {2015-01-01},<br \/>\r\nurldate = {2015-01-01},<br \/>\r\nbooktitle = {SPIE Medical Imaging 2015},<br \/>\r\nvolume = {9415},<br \/>\r\npages = {94151R-94151R-8},<br \/>\r\nabstract = {&lt;p&gt;Segmented structures such as targets or organs at risk are typically stored as 2D contours contained on evenly spaced cross sectional images (slices). Contour interpolation algorithms are implemented in radiation oncology treatment planning software to turn 2D contours into a 3D surface, however the results differ between algorithms, causing discrepancies in analysis. Our goal was to create an accurate and consistent contour interpolation algorithm that can handle issues such as keyhole contours, rapid changes, and branching. This was primarily motivated by radiation therapy research using the open source SlicerRT extension for the 3D Slicer platform. The implemented algorithm triangulates the mesh by minimizing the length of edges spanning the contours with dynamic programming. The first step in the algorithm is removing keyholes from contours. Correspondence is then found between contour layers and branching patterns are determined. The final step is triangulating the contours and sealing the external contours. The algorithm was tested on contours segmented on computed tomography (CT) images. Some cases such as inner contours, rapid changes in contour size, and branching were handled well by the algorithm when encountered individually. There were some special cases in which the simultaneous occurrence of several of these problems in the same location could cause the algorithm to produce suboptimal mesh. An open source contour interpolation algorithm was implemented in SlicerRT for reconstructing surfaces from planar contours. The implemented algorithm was able to generate qualitatively good 3D mesh from the set of 2D contours for most tested structures.&lt;\/p&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('205','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_205\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;p&gt;Segmented structures such as targets or organs at risk are typically stored as 2D contours contained on evenly spaced cross sectional images (slices). Contour interpolation algorithms are implemented in radiation oncology treatment planning software to turn 2D contours into a 3D surface, however the results differ between algorithms, causing discrepancies in analysis. Our goal was to create an accurate and consistent contour interpolation algorithm that can handle issues such as keyhole contours, rapid changes, and branching. This was primarily motivated by radiation therapy research using the open source SlicerRT extension for the 3D Slicer platform. The implemented algorithm triangulates the mesh by minimizing the length of edges spanning the contours with dynamic programming. The first step in the algorithm is removing keyholes from contours. Correspondence is then found between contour layers and branching patterns are determined. The final step is triangulating the contours and sealing the external contours. The algorithm was tested on contours segmented on computed tomography (CT) images. Some cases such as inner contours, rapid changes in contour size, and branching were handled well by the algorithm when encountered individually. There were some special cases in which the simultaneous occurrence of several of these problems in the same location could cause the algorithm to produce suboptimal mesh. An open source contour interpolation algorithm was implemented in SlicerRT for reconstructing surfaces from planar contours. The implemented algorithm was able to generate qualitatively good 3D mesh from the set of 2D contours for most tested structures.&lt;\/p&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('205','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_205\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"http:\/\/dx.doi.org\/10.1117\/12.2081436\" title=\"http:\/\/dx.doi.org\/10.1117\/12.2081436\" target=\"_blank\">http:\/\/dx.doi.org\/10.1117\/12.2081436<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2015-manuscript.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland[...]<\/a><\/li><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland2015-poster.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Sunderland[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1117\/12.2081436\" title=\"Follow DOI:10.1117\/12.2081436\" target=\"_blank\">doi:10.1117\/12.2081436<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('205','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Alexander, Kevin M;  Pinter, Csaba;  Andrea, Jennifer;  Fichtinger, Gabor;  Schreiner, L John<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19387-8_128\" title=\"https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19387-8_128\" target=\"blank\">3D slicer gel dosimetry analysis: validation of the calibration process<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_pages\">pp. 521-524, <\/span><span class=\"tp_pub_additional_year\">2015<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_873\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('873','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_873\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('873','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_873\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('873','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_873\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{fichtinger2015e,<br \/>\r\ntitle = {3D slicer gel dosimetry analysis: validation of the calibration process},<br \/>\r\nauthor = {Kevin M Alexander and Csaba Pinter and Jennifer Andrea and Gabor Fichtinger and L John Schreiner},<br \/>\r\nurl = {https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19387-8_128},<br \/>\r\nyear  = {2015},<br \/>\r\ndate = {2015-01-01},<br \/>\r\npages = {521-524},<br \/>\r\npublisher = {Springer International Publishing},<br \/>\r\nabstract = {An extension tailored to dose data processing and analysis has been developed in the open source imaging application 3D Slicer to aid in routine clinical use of gel dosimetry. This extension allows for registration, calibration, and comparison of 3D gel dosimeter data (imaged using an optical CT scanner) to treatment planning data. In this work, we present the accuracy and reproducibility of the gel dosimeter calibration component of the 3D Slicer extension. We examine the consistency of the calibration curves for a range of electron beam irradiations, and the inter-user variability of the gel dosimeter calibration process.},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('873','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_873\" style=\"display:none;\"><div class=\"tp_abstract_entry\">An extension tailored to dose data processing and analysis has been developed in the open source imaging application 3D Slicer to aid in routine clinical use of gel dosimetry. This extension allows for registration, calibration, and comparison of 3D gel dosimeter data (imaged using an optical CT scanner) to treatment planning data. In this work, we present the accuracy and reproducibility of the gel dosimeter calibration component of the 3D Slicer extension. We examine the consistency of the calibration curves for a range of electron beam irradiations, and the inter-user variability of the gel dosimeter calibration process.<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('873','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_873\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-globe\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19387-8_128\" title=\"https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19387-8_128\" target=\"_blank\">https:\/\/link.springer.com\/chapter\/10.1007\/978-3-319-19387-8_128<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('873','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_article\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Lasso, Andras;  Heffter, Tamas;  Rankin, Adam;  Pinter, Csaba;  Ungi, Tamas;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/10.1109\/TBME.2014.2322864\" title=\"PLUS: Open-source toolkit for ultrasound-guided intervention systems\" target=\"blank\">PLUS: Open-source toolkit for ultrasound-guided intervention systems<\/a> <span class=\"tp_pub_type tp_  article\">Journal Article<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_in\">In: <\/span><span class=\"tp_pub_additional_journal\">IEEE Transactions on Biomedical Engineering, <\/span><span class=\"tp_pub_additional_volume\">vol. 61, <\/span><span class=\"tp_pub_additional_number\">no. 10, <\/span><span class=\"tp_pub_additional_pages\">pp. 2527-2537, <\/span><span class=\"tp_pub_additional_year\">2014<\/span>, <span class=\"tp_pub_additional_issn\">ISSN: 0018-9294<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_240\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('240','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_240\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('240','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_240\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@article{Lasso2014a,<br \/>\r\ntitle = {PLUS: Open-source toolkit for ultrasound-guided intervention systems},<br \/>\r\nauthor = {Andras Lasso and Tamas Heffter and Adam Rankin and Csaba Pinter and Tamas Ungi and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2014a-manuscript.pdf},<br \/>\r\ndoi = {10.1109\/TBME.2014.2322864},<br \/>\r\nissn = {0018-9294},<br \/>\r\nyear  = {2014},<br \/>\r\ndate = {2014-10-01},<br \/>\r\nurldate = {2014-10-01},<br \/>\r\njournal = {IEEE Transactions on Biomedical Engineering},<br \/>\r\nvolume = {61},<br \/>\r\nnumber = {10},<br \/>\r\npages = {2527-2537},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {article}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('240','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_240\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2014a-manuscript.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2014a[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/Lasso2014a[...]<\/a><\/li><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/10.1109\/TBME.2014.2322864\" title=\"Follow DOI:10.1109\/TBME.2014.2322864\" target=\"_blank\">doi:10.1109\/TBME.2014.2322864<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('240','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> Cifuentes, J;  Kirby, N;  Lasso, Andras;  Chin, Lee;  Pinter, Csaba;  Pouliot, J;  Fichtinger, Gabor;  Pignol, J<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/dx.doi.org\/http:\/\/dx.doi.org\/10.1118\/1.4888094\" title=\"Customized deformable image registration using open-source software SlicerRT\" target=\"blank\">Customized deformable image registration using open-source software SlicerRT<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">American Association Physicists in Medicine (AAPM), <\/span><span class=\"tp_pub_additional_volume\">vol. 41 (abstract in Medical Physics), <\/span><span class=\"tp_pub_additional_address\">Austin, TX, <\/span><span class=\"tp_pub_additional_year\">2014<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_abstract_link\"><a id=\"tp_abstract_sh_215\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('215','tp_abstract')\" title=\"Show abstract\" style=\"cursor:pointer;\">Abstract<\/a><\/span> | <span class=\"tp_resource_link\"><a id=\"tp_links_sh_215\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('215','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_215\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('215','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_215\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{Cifuentes2014a,<br \/>\r\ntitle = {Customized deformable image registration using open-source software SlicerRT},<br \/>\r\nauthor = {J Cifuentes and N Kirby and Andras Lasso and Lee Chin and Csaba Pinter and J Pouliot and Gabor Fichtinger and J Pignol},<br \/>\r\ndoi = {http:\/\/dx.doi.org\/10.1118\/1.4888094},<br \/>\r\nyear  = {2014},<br \/>\r\ndate = {2014-06-01},<br \/>\r\nurldate = {2014-06-01},<br \/>\r\nbooktitle = {American Association Physicists in Medicine (AAPM)},<br \/>\r\nvolume = {41 (abstract in Medical Physics)},<br \/>\r\naddress = {Austin, TX},<br \/>\r\nabstract = {&lt;div&gt;Purpose: <br \/>\r\n&lt;p&gt;SlicerRT is a flexible platform that allows the user to incorporate the necessaryimages registration and processing tools to improve clinical workflow. This work validates the accuracy and the versatility of the deformable image registrationalgorithm of the free open-source software SlicerRT using a deformable physical pelvic phantom versus available commercial image fusion algorithms.&lt;\/p&gt; <br \/>\r\n&lt;\/div&gt; <br \/>\r\n&lt;div&gt;Methods: <br \/>\r\n&lt;p&gt;Optical camera images of nonradiopaque markers implanted in an anatomical pelvic phantom were used to measure the ground-truth deformation and evaluate the theoretical deformations for several DIR algorithms. To perform the registration, full and empty bladder computed tomography (CT) images of the phantom were obtained and used as fixed and moving images, respectively. The DIR module, found in SlicerRT, used a B-spline deformable image registration with multiple optimization parameters that allowed customization of the registration including a regularization term that controlled the amount of local voxel displacement. The virtual deformation field at the center of the phantom was obtained and compared to the experimental ground-truth values. The parameters of SlicerRT were then varied to improve spatial accuracy. To quantify imagesimilarity, the mean absolute difference (MAD) parameter using Hounsfield units was calculated. In addition, the Dice coefficient of the contoured rectum was evaluated to validate the strength of the algorithm to transfer anatomical contours.&lt;\/p&gt; <br \/>\r\n&lt;\/div&gt; <br \/>\r\n&lt;div&gt;Results: <br \/>\r\n&lt;p&gt;Overall, SlicerRT achieved one of the lowest MAD values across the algorithm spectrum, but slightly smaller mean spatial errors in comparison to MIM software(MIM). On the other hand, SlicerRT created higher mean spatial errors than Velocity Medical Solutions (VEL), although obtaining an improvement on the DICE to 0.91. The large spatial errors were attributed to the poor contrast in the prostate bladder interface of the phantom.&lt;\/p&gt; <br \/>\r\n&lt;\/div&gt; <br \/>\r\n&lt;div&gt;Conclusion: <br \/>\r\n&lt;p&gt;Based phantom validation, SlicerRT is capable of achieving comparable DIR accuracy to commercial programs such as MIM and VEL.&lt;\/p&gt; <br \/>\r\n&lt;\/div&gt;},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('215','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_abstract\" id=\"tp_abstract_215\" style=\"display:none;\"><div class=\"tp_abstract_entry\">&lt;div&gt;Purpose: <br \/>\r\n&lt;p&gt;SlicerRT is a flexible platform that allows the user to incorporate the necessaryimages registration&amp;nbsp;and processing tools to improve clinical workflow. This work validates the accuracy and the versatility of the deformable&amp;nbsp;image registrationalgorithm of the free open-source&amp;nbsp;software&amp;nbsp;SlicerRT using a deformable physical pelvic phantom versus available commercial&amp;nbsp;image&amp;nbsp;fusion algorithms.&lt;\/p&gt; <br \/>\r\n&lt;\/div&gt; <br \/>\r\n&lt;div&gt;Methods: <br \/>\r\n&lt;p&gt;Optical&amp;nbsp;camera&amp;nbsp;images&amp;nbsp;of nonradiopaque markers implanted in an anatomical pelvic phantom were used to measure the ground-truth deformation and evaluate the theoretical deformations for several DIR algorithms. To perform the registration, full and empty bladder&amp;nbsp;computed tomography&amp;nbsp;(CT)&amp;nbsp;images&amp;nbsp;of the phantom were obtained and used as fixed and moving&amp;nbsp;images,&amp;nbsp;respectively. The DIR module, found in SlicerRT, used a B-spline deformable&amp;nbsp;image registration&amp;nbsp;with multiple optimization parameters that allowed customization of the registration including a regularization term that controlled the amount of local voxel displacement. The virtual deformation field at the center of the phantom was obtained and compared to the experimental ground-truth values. The parameters of SlicerRT were then varied to improve spatial accuracy. To quantify&amp;nbsp;imagesimilarity, the mean absolute difference (MAD) parameter using Hounsfield units was calculated. In addition, the Dice coefficient of the contoured rectum was evaluated to validate the strength of the algorithm to transfer anatomical contours.&lt;\/p&gt; <br \/>\r\n&lt;\/div&gt; <br \/>\r\n&lt;div&gt;Results: <br \/>\r\n&lt;p&gt;Overall, SlicerRT achieved one of the lowest MAD values across the algorithm spectrum, but slightly smaller mean spatial errors in comparison to MIM&amp;nbsp;software(MIM). On the other hand, SlicerRT created higher mean spatial errors than Velocity Medical Solutions (VEL), although obtaining an improvement on the DICE to 0.91. The large spatial errors were attributed to the poor contrast in the prostate bladder interface of the phantom.&lt;\/p&gt; <br \/>\r\n&lt;\/div&gt; <br \/>\r\n&lt;div&gt;Conclusion: <br \/>\r\n&lt;p&gt;Based phantom validation, SlicerRT is capable of achieving comparable DIR accuracy to commercial programs such as MIM and VEL.&lt;\/p&gt; <br \/>\r\n&lt;\/div&gt;<\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('215','tp_abstract')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_215\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"ai ai-doi\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/dx.doi.org\/http:\/\/dx.doi.org\/10.1118\/1.4888094\" title=\"Follow DOI:http:\/\/dx.doi.org\/10.1118\/1.4888094\" target=\"_blank\">doi:http:\/\/dx.doi.org\/10.1118\/1.4888094<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('215','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><div class=\"tp_publication tp_publication_conference\"><div class=\"tp_pub_info\"><p class=\"tp_pub_author\"> King, Franklin;  Lasso, Andras;  Pinter, Csaba;  Fichtinger, Gabor<\/p><p class=\"tp_pub_title\"><a class=\"tp_title_link\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/King2014b-poster.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/King2014b-poster.pdf\" target=\"blank\">A tool for intraoperative visualization of image registration results<\/a> <span class=\"tp_pub_type tp_  conference\">Conference<\/span> <\/p><p class=\"tp_pub_additional\"><span class=\"tp_pub_additional_booktitle\">Imaging Network Ontario 2014, <\/span><span class=\"tp_pub_additional_publisher\">ImNO, <\/span><span class=\"tp_pub_additional_address\">Toronto, Canada, March 24-25, <\/span><span class=\"tp_pub_additional_year\">2014<\/span>.<\/p><p class=\"tp_pub_menu\"><span class=\"tp_resource_link\"><a id=\"tp_links_sh_250\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('250','tp_links')\" title=\"Show links and resources\" style=\"cursor:pointer;\">Links<\/a><\/span> | <span class=\"tp_bibtex_link\"><a id=\"tp_bibtex_sh_250\" class=\"tp_show\" onclick=\"teachpress_pub_showhide('250','tp_bibtex')\" title=\"Show BibTeX entry\" style=\"cursor:pointer;\">BibTeX<\/a><\/span><\/p><div class=\"tp_bibtex\" id=\"tp_bibtex_250\" style=\"display:none;\"><div class=\"tp_bibtex_entry\"><pre>@conference{King2014b,<br \/>\r\ntitle = {A tool for intraoperative visualization of image registration results},<br \/>\r\nauthor = {Franklin King and Andras Lasso and Csaba Pinter and Gabor Fichtinger},<br \/>\r\nurl = {https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/King2014b-poster.pdf},<br \/>\r\nyear  = {2014},<br \/>\r\ndate = {2014-03-01},<br \/>\r\nurldate = {2014-03-01},<br \/>\r\nbooktitle = {Imaging Network Ontario 2014},<br \/>\r\npublisher = {ImNO},<br \/>\r\naddress = {Toronto, Canada, March 24-25},<br \/>\r\nkeywords = {},<br \/>\r\npubstate = {published},<br \/>\r\ntppubtype = {conference}<br \/>\r\n}<br \/>\r\n<\/pre><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('250','tp_bibtex')\">Close<\/a><\/p><\/div><div class=\"tp_links\" id=\"tp_links_250\" style=\"display:none;\"><div class=\"tp_links_entry\"><ul class=\"tp_pub_list\"><li><i class=\"fas fa-file-pdf\"><\/i><a class=\"tp_pub_list\" href=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/King2014b-poster.pdf\" title=\"https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/King2014b-[...]\" target=\"_blank\">https:\/\/labs.cs.queensu.ca\/perklab\/wp-content\/uploads\/sites\/3\/2024\/02\/King2014b-[...]<\/a><\/li><\/ul><\/div><p class=\"tp_close_menu\"><a class=\"tp_close\" onclick=\"teachpress_pub_showhide('250','tp_links')\">Close<\/a><\/p><\/div><\/div><\/div><\/div><div class=\"tablenav\"><div class=\"tablenav-pages\"><span class=\"displaying-num\">83 entries<\/span> <a class=\"page-numbers button disabled\">&laquo;<\/a> <a class=\"page-numbers button disabled\">&lsaquo;<\/a> 1 of 2 <a href=\"https:\/\/labs.cs.queensu.ca\/perklab\/members\/csaba-pinter\/?limit=2&amp;tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=&amp;tsr=#tppubs\" title=\"next page\" class=\"page-numbers button\">&rsaquo;<\/a> <a href=\"https:\/\/labs.cs.queensu.ca\/perklab\/members\/csaba-pinter\/?limit=2&amp;tgid=&amp;yr=&amp;type=&amp;usr=&amp;auth=&amp;tsr=#tppubs\" title=\"last page\" class=\"page-numbers button\">&raquo;<\/a> 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