@article {Fichtinger2021, title = {Design of an Ultrasound-Navigated Prostate Cancer Biopsy System for Nationwide Implementation in Senegal}, journal = {Journal of Imaging}, volume = {7}, number = {8}, year = {2021}, month = {08/2021}, pages = {154}, abstract = {

This paper presents the design of NaviPBx, an ultrasound-navigated prostate cancer biopsy system. NaviPBx is designed to support an affordable and sustainable national healthcare program in Senegal. It uses spatiotemporal navigation and multiparametric transrectal ultrasound to guide biopsies. NaviPBx integrates concepts and methods that have been independently validated previously in clinical feasibility studies and deploys them together in a practical prostate cancer biopsy system. NaviPBx is based entirely on free open-source software and will be shared as a free open-source program with no restriction on its use. NaviPBx is set to be deployed and sustained nationwide through the Senegalese Military Health Service. This paper reports on the results of the design process of NaviPBx. Our approach concentrates on {\textquotedblleft}frugal technology{\textquotedblright}, intended to be affordable for low{\textendash}middle income (LMIC) countries. Our project promises the wide-scale application of prostate biopsy and will foster time-efficient development and programmatic implementation of ultrasound-guided diagnostic and therapeutic interventions in Senegal and beyond.

}, issn = {2313-433X}, doi = {10.3390/jimaging7080154}, url = {https://www.mdpi.com/2313-433X/7/8/154}, author = {Gabor Fichtinger and Parvin Mousavi and Tamas Ungi and Fenster, Aaron and Purang Abolmaesumi and Gernot Kronreif and Ruiz-Alzola, Juan and Ndoye, Alain and Diao, Babacar and Ron Kikinis} } @conference {CWu2021a, title = {Development of an open-source system for prostate biopsy training in Senegal}, booktitle = {SPIE Medical Imaging 2021: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {11598}, year = {2021}, month = {02/2021}, author = {Wu, Catherine O. and Diao, Babacar and Tamas Ungi and Alireza Sedghi and Ron Kikinis and Parvin Mousavi and Gabor Fichtinger} } @article {Fedorov2020, title = {Quantitative Imaging Informatics for Cancer Research}, journal = {JCO Clinical Cancer Informatics}, volume = {4}, year = {2020}, pages = {444-453.}, doi = {https://doi.org/10. 1200/CCI.19.00165}, author = {Andriy Fedorov and Reinhard Beichel and Jayashree Kalpathy-Cramer and David Clunie and Michael Onken and J{\"o}rg 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} } @article {Lasso2018, title = {Interaction with Volume-Rendered Three-Dimensional Echocardiographic Images in Virtual Reality}, journal = {J Am Soc Echocardiogr}, volume = {31}, number = {10}, year = {2018}, month = {10}, pages = {1158-60{\textendash}}, abstract = {

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).

}, author = {Andras Lasso and HannahH Nam and PatrickV 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} } @article {Herz2017, title = {dcmqi: An Open Source Library for Standardized Communication of Quantitative Image Analysis Results Using DICOM}, journal = {Cancer Research}, volume = {77}, number = {21}, year = {2017}, month = {11/2017}, pages = {e87{\textendash}e90}, abstract = {

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{\textendash}90. {\textcopyright}2017 AACR.

}, issn = {0008-5472}, doi = {10.1158/0008-5472.CAN-17-0336}, url = {http://cancerres.aacrjournals.org/content/77/21/e87}, author = {Christian Herz and Jean-ChristopheC. Fillion-Robin and Michael Onken and J{\"o}rg Riesmeier and Andras Lasso and Csaba Pinter and Gabor Fichtinger and Steve Pieper and Clunie, David and Ron Kikinis and Andriy Fedorov} } @article {Kapur2016, title = {Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience}, journal = {Medical Image Analysis}, volume = {33}, year = {2016}, month = {10/2016}, pages = {176-180}, abstract = {

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{\textemdash}VTK, ITK, CMake, CDash, DCMTK{\textemdash}were 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 ({\textquotedblleft}Open Science{\textquotedblright}); 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.

}, keywords = {3D Slicer, Hackathon, Medical image computing, NA-MIC, Open access, Open science, Open source, Project week, Reproducible research}, doi = {http://doi.org/10.1016/j.media.2016.06.035}, author = {Tina Kapur and Steve Pieper and Andras Lasso and Tamas Ungi and Csaba Pinter and Gabor Fichtinger and Ron Kikinis} } @article {DiMaio2007b, title = {Challenges in image-guided therapy system design}, journal = {Neuroimage}, volume = {37 Suppl 1}, year = {2007}, pages = {S144{\textendash}S151}, publisher = {Brigham, Women{\textquoteright}s Hospital, 75 Francis St , Boston, MA 02115, USA simond@bwh harvard edu}, abstract = {

System development for image-guided therapy (IGT), or image-guided interventions (IGI), continues to be an area of active interest across academic, industry groups This is an emerging field that is growing rapidly: major academic institutions, medical device manufacturers have produced IGT technologies that are in routine clinical use, dozens of high-impact publications are published in well regarded journals each year, and several small companies have successfully commercialized sophisticated IGT systems In meetings between IGT investigators over the last two years, a consensus has emerged that several key areas must be addressed collaboratively by the community to reach the next level of impact, efficiency in IGT research, development to improve patient care These meetings culminated in a two-day workshop that brought together several academic, industrial leaders in the field today The goals of the workshop were to identify gaps in the engineering infrastructure available to IGT researchers, develop the role of research funding agencies, the recently established US-based National Center for Image Guided Therapy (NCIGT), and ultimately to facilitate the transfer of technology among research centers that are sponsored by the National Institutes of Health (NIH) Workshop discussions spanned many of the current challenges in the development, deployment of new IGT systems Key challenges were identified in a number of areas, including: validation standards; workflows, use-cases, and application requirements; component reusability;, device interface standards This report elaborates on these key points, proposes research challenges that are to be addressed by a joint effort between academic, industry, and NIH participants

}, keywords = {adverse effects/instrumentation/trends, Algorithms, Computational Biology, Computer Systems, Computer-Assisted, Humans, instrumentation/trends, Knowledge Bases, Models, National Institutes of Health (U S ), Neurosurgical Procedures, Organizational, Outcome Assessment (Health Care), Reproducibility of Results, Robotics, Software, Surgery, Treatment Outcome, United States}, doi = {10 1016/j neuroimage 2007 04 026}, url = {http://dx doi org/10 1016/j neuroimage 2007 04 026}, author = {Simon DiMaio and Tina Kapur and Kevin Cleary and Stephen Aylward and Peter Kazanzides and Kirby Vosburgh and Randy Ellis and James Duncan and Keyvan Farahani and Heinz Lemke and T. M. Peters and William Bill Lorensen and David Gobbi and John Haller and Laurence Larry Clarke and Stephen Pizer and Russell H. Taylor and Robert L. Galloway, Jr. and Gabor Fichtinger and Nobuhiko Hata and Kimberly Lawson and Clare M Tempany and Ron Kikinis and Ferenc Jolesz} } @article {DiMaio2007a, title = {Robot-assisted needle placement in open MRI: system architecture, integration and validation}, journal = {Journal of Computer Aided Surgery}, volume = {12}, number = {1}, year = {2007}, month = {Jan}, pages = {15{\textendash}24}, publisher = {Brigham, Women{\textquoteright}s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA simond@bwh harvard edu}, abstract = {

In prostate cancer treatment, there is a move toward targeted interventions for biopsy, therapy, which has precipitated the need for precise image-guided methods for needle placement This paper describes an integrated system for planning, performing percutaneous procedures with robotic assistance under MRI guidance A graphical planning interface allows the physician to specify the set of desired needle trajectories, based on anatomical structures, lesions observed in the patient{\textquoteright}s registered pre-operative, pre-procedural MR images, immediately prior to the intervention in an open-bore MRI scanner All image-space coordinates are automatically computed, and are used to position a needle guide by means of an MRI-compatible robotic manipulator, thus avoiding the limitations of the traditional fixed needle template Automatic alignment of real-time intra-operative images aids visualization of the needle as it is manually inserted through the guide Results from in-scanner phantom experiments are provided

}, keywords = {Biopsy, diagnosis, Humans, instrumentation/methods, Magnetic Resonance Imaging, Male, Needle, Neuronavigation, Prostatic Neoplasms, Robotics}, doi = {10 1080/10929080601168254}, url = {http://dx doi org/10 1080/10929080601168254}, author = {Simon DiMaio and Steve Pieper and Kiyoyuki Chinzei and Nobuhiko Hata and Steven Haker and Daniel Kacher and Gabor Fichtinger and Clare M Tempany and Ron Kikinis} } @article {DiMaio2006, title = {Needle artifact localization in 3T MR images}, journal = {Studies in health technology and informatics}, volume = {119}, year = {2006}, pages = {120{\textendash}125}, publisher = {Brigham, Women{\textquoteright}s Hospital, Harvard Medical School, Boston 02115, USA simond@bwh harvard edu}, abstract = {

This work explores an image-based approach for localizing needles during MRI-guided interventions, for the purpose of tracking, navigation Susceptibility artifacts for several needles of varying thickness were imaged, in phantoms, using a 3 tesla MRI system, under a variety of conditions The relationship between the true needle positions, the locations of artifacts within the images, determined both by manual, automatic segmentation methods, have been quantified, are presented here

}, keywords = {Artifacts, Magnetic Resonance Imaging, Needles, United States}, author = {Simon DiMaio and Daniel Kacher and Randy Ellis and Gabor Fichtinger and Nobuhiko Hata and Gary Zientara and Lawrence Panych and Ron Kikinis and Ferenc Jolesz} } @article {DiMaio2006b, title = {Robot-assisted needle placement in open-MRI: system architecture, integration and validation}, journal = {Studies in health technology and informatics}, volume = {119}, year = {2006}, pages = {126{\textendash}131}, publisher = {Brigham, Women{\textquoteright}s Hospital, Harvard Medical School, USA simond@bwh harvard edu}, abstract = {

This work describes an integrated system for planning, performing percutaneous procedures-such as prostate biopsy-with robotic assistance under MRI-guidance The physician interacts with a planning interface in order to specify the set of desired needle trajectories, based on anatomical structures, lesions observed in the patient{\textquoteright}s MR images All image-space coordinates are automatically computed, and used to position a needle guide by means of an MRI-compatible robotic manipulator, thus avoiding the limitations of the traditional fixed needle template Direct control of real-time imaging aids visualization of the needle as it is manually inserted through the guide Results from in-scanner phantom experiments are provided

}, keywords = {Biopsy, Computer Systems, diagnosis, Humans, instrumentation, Magnetic Resonance Imaging, Male, Needle, Prostatic Neoplasms, Robotics}, author = {Simon DiMaio and Steve Pieper and Kiyoyuki Chinzei and Nobuhiko Hata and Emese Balogh and Gabor Fichtinger and Clare M Tempany and Ron Kikinis} } @conference {DiMaio2006a, title = {A System for MRI-guided Prostate Interventions}, booktitle = {Procedings First IEEE/RAS-EMBS International Conference on Biomedical Robotics and Biomechatronics BioRob 2006}, year = {2006}, month = {20{\textendash}22 Feb}, pages = {68{\textendash}73}, doi = {10 1109/BIOROB 2006 1639062}, author = {Simon DiMaio and Gregory Fischer and Maker, S. J. and Nobuhiko Hata and Iulian Iordachita and Clare M Tempany and Ron Kikinis and Gabor Fichtinger} } @conference {Boctor2004a, title = {CISUS: an integrated 3D ultrasound system for IGT using a modular tracking API}, booktitle = {Medical Imaging 2004: Visualization, Image-Guided Procedures, and Display}, volume = {5367}, number = {1}, year = {2004}, pages = {247-256}, publisher = {SPIE}, organization = {SPIE}, doi = {10 1117/12 537776}, url = {http://link aip org/link/?PSI/5367/247/1}, author = {Emad Boctor and Anand Viswanathan and Steve Pieper and Michael Choti and Russell H. Taylor and Ron Kikinis and Gabor Fichtinger}, editor = {Robert L. Galloway, Jr.} } @conference {DiMaio2004, title = {Robot assisted percutaneous intervention in open-MRI}, booktitle = {5th Interventional MRI Symposium}, year = {2004}, author = {Simon DiMaio and Steve Pieper and Kiyoyuki Chinzei and Gabor Fichtinger and Ron Kikinis} }