@article {Yeo2017, title = {3D Segmentation as a Surgical Planning Tool for Residents in Liver Resection Surgery}, year = {In Press}, abstract = {

Introduction: Liver surgery requires identification of tumor(s) in relation to key vessels to preserve healthy tissue, while obtaining negative margins. Current planning is mentally strenuous for residents as it relies on mental 3D reconstruction, anatomical knowledge, spatial sense, and experience. The purpose of this study is to determine if 3D segmentation improves resident ability to devise appropriate liver resection plans.

Methods: Senior general surgery residents were recruited. Pre-operative CT/MR images were selected if they reflected actual surgeries performed. Images were segmented to create interactive 3D models. Residents were asked to devise surgical plans for case-matched 2D and 3D models in an alternating, randomly generated order. Primary outcome was correct preoperative plan based on actual surgery performed. Secondary outcome was time (seconds(s)) to devise plan. Planning data was analyzed using Wilcoxon test, time was analyzed using paired t-test.

Results: All 14 senior residents from our institution participated. The average correct response was 1.7 of 5 (34\%; range 1 to 4) for the 2D group, and 3.1 of 5 (62\%; range 0 to 4) for the 3D group (p\<0.01). The average time to complete each plan was 156{\textpm}107s for the 2D group, and 84{\textpm}73s for the 3D group (p\<0.01).

Conclusions: The results show that 3D segmentation increases accuracy of surgical planning and decreases amount of time required. 3D segmentation is useful as a teaching tool as it reduces cognitive load required to mentally reconstruct 2D images, allowing the resident to focus on surgical planning. It improves understanding of spatial liver anatomy and serves as an adjunct to current 2D planning methods. This has the potential to be developed into a module for teaching liver surgery relevant to a competency-based curriculum.

}, author = {Yeo, Caitlin T and MacDonald, Andrew and Tamas Ungi and Andras Lasso and Diederick Jalink and Gabor Fichtinger and Nanji, Sulaiman} } @article {Brastianos2017a, title = {Electromagnetic Reconstruction of Catheter Paths in Mult-Catheter Interstitial Brachytherapy: A Phantom Model.}, year = {In Press}, author = {Harry Brastianos and Thomas Vaughan and Andras Lasso and Mary Westerland and James Gooding and Gabor Fichtinger and Conrad Falkson} } @conference {connolly2022b, title = {An open-source testbed for developing image-guided robotic tumor-bed inspection}, booktitle = {Imaging Network of Ontario (ImNO) Symposium}, year = {2022}, author = {Laura Connolly and Amoon Jamzad and Arash Nikniazi and Rana Poushimin and Andras Lasso and Kyle R. Sunderland and Tamas Ungi and Jean Michel Nunzi and John Rudan and Gabor Fichtinger and Parvin Mousavi} } @conference {Connolly2021, title = {An open-source platform for cooperative semi-autonomous robotic surgery}, booktitle = {IEEE International Conference on Autonomous Systems}, year = {2021}, month = {10/2021}, publisher = {IEEE}, organization = {IEEE}, address = {Montreal, Quebec}, doi = {https://doi.org/10.1109/ICAS49788.2021.9551149}, author = {Laura Connolly and Anton Degeut and Kyle R. Sunderland and Andras Lasso and Tamas Ungi and John Rudan and Russell H. Taylor and Parvin Mousavi and Gabor Fichtinger} } @article {Connolly2021b, title = {A platform for robot-assisted Intraoperative imaging in breast conserving surgery}, year = {2021}, month = {2021}, publisher = {Imaging Network of Ontario Symposium}, address = {Online}, author = {Laura Connolly and Kyle R. Sunderland and Andras Lasso and Anton Degeut and Tamas Ungi and John Rudan and Russell H. Taylor and Parvin Mousavi and Gabor Fichtinger} } @article {Choi2020, title = {3D Modeling of Surgically Implanted Stent-Based Valves in the Mitral Position in Children}, journal = {The Annals of Thoracic Surgery}, year = {2020}, doi = {10.1016/j.athoracsur.2020.02.020}, url = {https://doi.org/10.1016/j.athoracsur.2020.02.020}, author = {Perry S. Choi and HannahH Nam and Andras Lasso and Christian Herz and Simon Drouin and David M. Harrild and Michael Quartermain and Gabor Fichtinger and Christopher E. Mascio and Sitaram Emani and MatthewA Jolley} } @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 {Gauvin2019, title = {Real-time electromagnetic navigation for breast-conserving surgery using NaviKnife technology: A matched case-control study}, journal = {The Breast Journal}, volume = {26}, number = {3}, year = {2020}, month = {09/2019}, pages = {399-405}, doi = {10.1111/tbj.13480}, author = {Gabrielle Gauvin and Yeo, Caitlin T and Tamas Ungi and Shaila Merchant and Andras Lasso and Doris Jabs and Thomas Vaughan and John Rudan and Ross Walker and Gabor Fichtinger and C. Jay Engel} } @article {Pinter2020, title = {SlicerVR for Medical Intervention Training and Planning in Immersive Virtual Reality}, journal = {IEEE Transactions on Medical Robotics and Bionics}, volume = {2}, number = {2}, year = {2020}, month = {03/2020}, pages = {108-117}, abstract = {

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.

}, doi = {10.1109/TMRB.2020.2983199}, author = {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} } @conference {BarrC2020, title = {Towards portable image guidance and automatic patient registration using an RGB-D camera and video projector}, booktitle = {Medical Imaging 2020: Image-Guided Procedures, Robotic Interventions and Modeling}, volume = {11315}, year = {2020}, publisher = {SPIE}, organization = {SPIE}, address = {Houston, Texas, United States}, doi = {10.1117/12.2549723}, author = {Colton Barr and Andras Lasso and Mark Asselin and Steve Pieper and Faith C. Robertson and William B. Gormley and Gabor Fichtinger} } @conference {Laframboise2019a, title = {Analyzing the curvature of the colon in different patient positions}, booktitle = {SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {10951}, year = {2019}, month = {03/2019}, address = {San Diego, California}, author = {Jacob Laframboise and Tamas Ungi and Andras Lasso and Mark Asselin and M. Holden and Tan, Pearl and Lawrence Hookey and Gabor Fichtinger} } @conference {Choueib2019b, title = {Assessment of immersive medical virtual reality visualization using 3D Slicer}, booktitle = {17th Annual Imaging Network Ontario Symposium (ImNO)}, year = {2019}, month = {03/2019}, address = {London, Ontario}, keywords = {3D Slicer, Planning, SlicerVR, training, Virtual Reality}, author = {Saleh Choueib and Csaba Pinter and Andras Lasso and Jean-ChristopheC. Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and Gabor Fichtinger} } @article {Baum2019b, title = {Assessment of intraoperative neurosurgical planning with the Microsoft HoloLens}, year = {2019}, publisher = {Imaging Network Ontario (ImNO)}, address = {London, Ontario}, author = {Zachary M C Baum and Sarah Ryan and Emily Rae and Andras Lasso and Tamas Ungi and Ron Levy and Gabor Fichtinger} } @article {Baum2020, title = {Augmented reality training platform for neurosurgical burr hole localization}, journal = {Journal of Medical Robotics Research}, volume = {4}, number = {3-4}, year = {2019}, month = {01/2020}, pages = {1942001-1 - 1942001-13}, type = {Special Issue}, abstract = {

Augmented reality (AR) is used in neurosurgery to visualize lesions and plan procedures pre-operatively and intra-operatively, though its use has not been widely adopted in simulation-based neurosurgical training for the same tasks. This work defines metrics to determine performance in drill position and angle identification for neurosurgical training. The metrics were validated intra-operatively and in a simulated training environment, demonstrating that trainees identify drill position and angle faster and more accurately with AR compared to standard techniques. Training using AR and the proposed metrics stands to add value to neurosurgical curricula development.

}, keywords = {augmented reality, competency-based medical education, holography, neurosurgery, surgical planning, visualization}, doi = {https://doi.org/10.1142/S2424905X19420017}, author = {Zachary M C Baum and Andras Lasso and Sarah Ryan and Tamas Ungi and Emily Rae and Boris Zevin and Ron Levy and Gabor Fichtinger} } @conference {Lund2019a, title = {Controlling virtual views in navigated breast conserving surgery}, booktitle = {SPIE Medical Imaging 2019}, year = {2019}, abstract = {

PURPOSE: Lumpectomy is the resection of a tumor in the breast while retaining as much healthy tissue as possible.
Navigated lumpectomy seeks to improve on the traditional technique by employing computer guidance to achieve the
complete excision of the cancer with optimal retention of healthy tissue. Setting up navigation in the OR relies on the
manual interactions of a trained technician to align three-dimensional virtual views to the patient{\textquoteright}s physical position
and maintain their alignment throughout surgery. This work develops automatic alignment tools to improve the
operability of navigation software for lumpectomies.
METHODS: Preset view buttons were developed to refine view setup to a single interaction. These buttons were
tested by measuring the reduction in setup time and the number of manual interactions avoided through their use. An
auto-center feature was created to ensure that three-dimensional models of anatomy and instruments were in the center
of view throughout surgery. Recorded data from 32 lumpectomy cases were replayed and the number of auto-center
view shifts was counted from the first cautery incision until the completion of the excision of cancerous tissue.
RESULTS: View setup can now be performed in a single interaction compared to an average of 13 interactions
(taking 83 seconds) when performed manually. The auto-center feature was activated an average of 33 times in the
cases studied (n=32).
CONCLUSION: The auto-center feature enhances the operability of the surgical navigation system, reducing the
number of manual interactions required by a technician during the surgery. This feature along with preset camera view
options are instrumental in the shift towards a completely surgeon-operable navigated lumpectomy system.

}, author = {Shaun Lund and Thomas Vaughan and Tamas Ungi and Andras Lasso and Mark Asselin and Caitlin Yeo and C. Jay Engel and Gabor Fichtinger} } @article {NGUYEN2019, title = {Dynamic Three-Dimensional Geometry of the Tricuspid Valve Annulus in Hypoplastic Left Heart Syndrome with a Fontan Circulation}, journal = {Journal of the American Society of Echocardiography}, year = {2019}, abstract = {

Background Tricuspid regurgitation (TR) is a significant contributor to morbidity and mortality in patients with hypoplastic left heart syndrome. The goal of this study was to characterize the dynamic annular motion of the tricuspid valve in patients with HLHS with a Fontan circulation and assess the relation to tricuspid valve function. Methods Tricuspid annuli of 48 patients with HLHS with a Fontan circulation were modeled at end-diastole, mid-systole, end-systole, and mid-diastole using transthoracic three-dimensional echocardiography and custom code in 3D Slicer. The angle of the anterior papillary muscle (APM) relative to the annular plane in each systolic phase was also measured. Results Imaging was performed 5.0\ years (interquartile range, 2{\textendash}11\ years) after Fontan operation. The tricuspid annulus varies in shape significantly throughout the cardiac cycle, changing in sphericity (P\ \<\ .001) but not in annular height or bending angle. In univariate modeling, patients with significant TR had larger changes in septolateral diameter, lateral quadrant area, and posterior quadrant area (P\ \<\ .05 for all) as well as lower (more laterally directed) APM angles (P\ \<\ .001) than patients with mild or less TR. In multivariate modeling, a 1\ mm/(body surface area)0.5 increase in the maximum change in septolateral diameter was associated with a 1.7-fold increase in having moderate or greater TR, while a 10{\textdegree} decrease in APM angle at mid-systole was associated with an almost 2.5-fold increase in moderate or greater TR (P\ <=\ .01 for all). Conclusions The tricuspid annulus in patients with HLHS with a Fontan circulation changes in shape significantly throughout the cardiac cycle but remains relatively planar. Increased change in septolateral diameter and decreased APM angle are strongly associated with the presence of TR. These findings may inform annuloplasty methods and subvalvular interventions in these complex patients.

}, keywords = {Congenital heart disease, Echocardiography, Valvular heart disease}, issn = {0894-7317}, doi = {https://doi.org/10.1016/j.echo.2019.01.002}, url = {http://www.sciencedirect.com/science/article/pii/S0894731719300021}, author = {Alexander V. Nguyen and Andras Lasso and HannahH Nam and Jennifer Faerber and Ahmed H. Aly and Alison M. Pouch and Adam B. Scanlan and FrancisX McGowan and Laura Mercer-Rosa and Meryl S. Cohen and John Simpson and Gabor Fichtinger and MatthewA Jolley} } @article {Lasso2019, title = {Enhance medical software applications with immersive virtual reality experience}, year = {2019}, month = {10/2019}, address = {Toronto, ON, Canada}, author = {Andras Lasso and Csaba Pinter and Saleh Choueib and Tamas Ungi and Gabor Fichtinger} } @conference {Choueib2019a, title = {Evaluation of 3D Slicer as a medical virtual reality visualization platform}, booktitle = {SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {10951}, number = {38}, year = {2019}, month = {03/2019}, publisher = {SPIE Medical Imaging}, organization = {SPIE Medical Imaging}, address = {San Diego, California }, keywords = {3D Slicer, Planning, SlicerVR, training, Virtual Reality}, author = {Saleh Choueib and Csaba Pinter and Andras Lasso and Jean-ChristopheC. Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and Gabor Fichtinger} } @conference {Connolly2019a, title = {Mechanically-Controlled Spectroscopic Imaging for Tissue Classification}, booktitle = {SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {10951}, year = {2019}, month = {03/2019}, address = {San Diego, California}, doi = {https://doi.org/10.1117/12.2512481}, author = {Laura Connolly and Tamas Ungi and Andras Lasso and Thomas Vaughan and Mark Asselin and Parvin Mousavi and Scott Yam and Gabor Fichtinger} } @article {House2019a, title = {Monitoring volume changes for breast reconstruction surgery using three dimensional optical surface scanning}, year = {2019}, address = {St. Johns, Newfoundland}, author = {Rachael House and M. Kunz and Chantal Valiquette and Andras Lasso and Tamas Ungi and John Rudan and Glykeria Martou and Gabor Fichtinger} } @conference {Asselin2019a, title = {Navigated real-time molecular analysis in the operating theatre, demonstration of concept}, booktitle = {SPIE Medical Imaging 2019}, year = {2019}, abstract = {

PURPOSE: In the operating theatre surgeons are accustomed to using spatially navigated tools in conjunction with
standard clinical imaging during a procedure. This gives them a good idea where they are in the patients{\textquoteright} anatomy but
doesn{\textquoteright}t provide information about the type of tissue they are dissecting. In this paper we demonstrate an integrated
system consisting of a spatially navigated surgical electrocautery combined with real-time molecular analysis of the
dissected tissue using mass spectrometry.
METHODS: Using the 3D Slicer software package, we have integrated a commercially available neurosurgical
navigation system with an intra-operative mass spectrometer (colloquially referred to as the intelligent knife, or iKnife)
that analyzes the charged ions in the smoke created during cauterization. We demonstrate this system using a simulated
patient comprised of an MRI scan from a brain cancer patient deformably registered to a plastic skull model. On the
skull model we placed porcine and bovine tissues to simulate cancerous and healthy tissue, respectively. We built a
PCA/LDA model to distinguish between these tissue types. The tissue classifications were displayed in a spatially
localized manner in the pre-operative imaging, in both 2D and 3D views.
RESULTS: We have demonstrated the feasibility of performing spatially navigated intra-operative analysis of tissues by
mass spectrometry. We show that machine learning can classify our sample tissues, with an average computed
confidence of 99.37 \% for porcine tissue and 99.36\% for bovine tissue.
CONCLUSION: In this paper we demonstrate a proof of concept system for navigated intra-operative molecular
analysis. This system may enable intra-operative awareness of spatially localized tissue classification during dissection,
information that is especially useful in tumor surgeries where margins may not be visible to the unassisted eye.
Keywords: image guided therapy, intra-operative mass spectrometry, iKnife, 3D Slicer, open-source, rapid evaporative
ionization mass spectrometry (REIMS)

}, author = {Mark Asselin and Martin Kaufmann and Julia Wiercigroch and Tamas Ungi and Andras Lasso and John Rudan and Gabor Fichtinger} } @article {Vaughan2019a, title = {Needle Navigation and Catheter Reconstruction for Breast Brachytherapy Using Open Source Software}, journal = {Acta Polytechnica Hungarica}, volume = {16}, number = {8}, year = {2019}, month = {09/2019}, pages = {99-118}, abstract = {

Abstract: Interstitial breast brachytherapy is a method to deliver radiation therapy directly to the site of cancer. It is a challenging procedure because of issues in localizing the seroma, needles, and catheters within the soft tissue. In this paper we present two open-source technologies based on electromagnetic tracking: a navigation system to help target needles using a tracked needle guide, and software for electromagnetic reconstruction of catheter paths. These technologies were validated phantom studies. We found that the navigation system helped a radiation oncologist to target needles more accurately than under ultrasound guidance (60 needles under each condition, 3.8 vs 3.3 mm placement error, p = 0.04) and that reconstructed catheter paths were accurate within 0.6 mm to those determined on CT scans (144 catheters were compared to the 1.2 mm voxel size of CT scans, p \< 0.001). We conclude that these technologies accurately localize anatomy and instruments in our study.

}, author = {Thomas Vaughan and H Brastianos and Tamas Ungi and Andras Lasso and Conrad Falkson and Gabor Fichtinger} } @article {Pinter2019, title = {Polymorph Segmentation Representation for Medical Image Computing}, journal = {Computer Methods and Programs in Biomedicine}, volume = {171}, year = {2019}, month = {02/2019}, pages = {19-26}, abstract = {

Background and Objective: 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: conversion method selection, data provenance, data consistency, and coherence of in-memory objects. Methods: 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. Results: 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. Conclusions:\  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{\textquoteright}s BSD-style open-source license allows complete freedom of use of the library.

}, keywords = {3D Slicer, DICOM, Open-source, segmentation, Software library, Voxelization}, doi = {https://doi.org/10.1016/j.cmpb.2019.02.011}, author = {Csaba Pinter and Andras Lasso and Gabor Fichtinger} } @article {Laframboise2019b, title = {Quantifying the effect of patient position on the curvature of colons}, year = {2019}, publisher = {Imaging Network Ontario (ImNO)}, address = {London, Ontario}, keywords = {colonoscopy, CT, curvature, curves}, author = {Jacob Laframboise and Tamas Ungi and Andras Lasso and Mark Asselin and M. Holden and Tan, Pearl and Lawrence Hookey and Gabor Fichtinger} } @conference {Perrin2019a, title = {Reproducibility of freehand calibrations for ultrasound-guided needle navigation}, booktitle = {SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {10951}, year = {2019}, address = {San Diego, California}, author = {Sydney Perrin and Zachary M C Baum and Mark Asselin and Underwood, Grace and Saleh Choueib and H. Lia and Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @conference {Pinter2019a, title = {SlicerVR for image-guided therapy planning in immersive virtual reality}, booktitle = {The 12th Hamlyn Symposium on Medical Robotics, 23-26 June 2019, Imperial College, London, UK}, year = {2019}, month = {06/2019}, pages = {91-92}, address = {London, UK}, author = {Csaba Pinter and Andras Lasso and Mark Asselin and Jean-ChristopheC. Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and Gabor Fichtinger} } @conference {Baum2019a, title = {Step-wise identification of ultrasound-visible anatomical landmarks for 3D visualization of scoliotic spine}, booktitle = {SPIE Medical Imaging 2019: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {10951}, year = {2019}, month = {03/2019}, address = {San Diego, California}, author = {Zachary M C Baum and Ben Church and Andras Lasso and Tamas Ungi and Christopher Schlenger and Daniel P. Borschneck and Parvin Mousavi and Gabor Fichtinger} } @article {GarciaMato2018a, title = {3D Gaze tracking for skill assessment in ultrasound-guided needle insertions}, volume = {13}, year = {2018}, month = {06/2018}, pages = {S52-S53}, publisher = {Springer}, address = {Berlin, Germany}, doi = {https://doi.org/10.1007/s11548-018-1766-y}, author = {D. Garc{\'\i}a-Mato and M. Holden and Andras Lasso and A. Szulewski and Javier Pascau and Gabor Fichtinger} } @article {Ilina2018a, title = {3D Surface Scanning for Tumour Localization in Non-Melanoma Skin Cancer}, year = {2018}, month = {03/2018}, address = {Toronto, Canada}, author = {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} } @article {Rae2018b, title = {Accuracy of the Microsoft HoloLens for neurosurgical burr hole placement}, year = {2018}, address = {Toronto, Canada}, author = {Emily Rae and Andras Lasso and M. Holden and Evelyn Morin and Ron Levy and Gabor Fichtinger} } @article {Lia2018b, title = {Basic suturing training using Microsoft HoloLens}, year = {2018}, month = {03/2018}, address = {Toronto, ON}, author = {H. Lia and Paulin, Gregory and Yeo, Caitlin T and Andrews, Jessica and Yi, Nelson and Haq, Hassan and Emmanuel, Steve and Ludig, Kristian and Keri, Zsuzsanna and Andras Lasso and Gabor Fichtinger} } @article {House2018b, title = {Breast volume computation for planning and monitoring fat grafting}, year = {2018}, author = {Rachael House and Andras Lasso and M. Kunz and John Rudan and Glykeria Martou and Gabor Fichtinger} } @article {House2018a, title = {Breast volume measurement using three-dimensional surface scan for fat grafting planning and monitoring}, year = {2018}, author = {Rachael House and Andras Lasso and M. Kunz and John Rudan and Glykeria Martou and Gabor Fichtinger} } @conference {Lia2018a, title = {HoloLens in Suturing Training}, booktitle = {SPIE Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling}, year = {2018}, month = {03/2018}, address = {Houston, Texas}, author = {H. Lia and Paulin, Gregory and Yeo, Caitlin T and Andrews, Jessica and Yi, Nelson and Haq, Hassan and Emmanuel, Steve and Ludig, Kristian and Keri, Zsuzsanna and Andras Lasso and Gabor Fichtinger} } @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} } @conference {Emily2018a, title = {Neurosurgical burr hole placement using the Microsoft HoloLens}, booktitle = {SPIE Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {10576}, year = {2018}, month = {03/2018}, pages = {105760T}, address = {Houston, Texas}, doi = {10.1117/12.2293680}, author = {Emily Rae and Andras Lasso and M. Holden and Evelyn Morin and Ron Levy and Gabor Fichtinger} } @article {Pinter2018a, title = {Real-time transverse process delineation in tracked ultrasound for scoliosis measurement}, year = {2018}, month = {03/2018}, address = {Toronto, Canada}, author = {Csaba Pinter and Bryan Travers and Zachary M C Baum and Tamas Ungi and Andras Lasso and Ben Church and Gabor Fichtinger} } @conference {Pinter2018, title = {Real-time transverse process detection in ultrasound}, booktitle = {SPIE Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling}, year = {2018}, month = {03/2018}, address = {Houston, Texas}, author = {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} } @article {Ilina2018b, title = {Target Definition with 3D Surface Scanning for Orthovoltage Radiation Therapy Planning}, year = {2018}, address = {Berlin, Germany}, author = {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} } @article {doi:10.1002/ccd.27962, title = {Toward predictive modeling of catheter-based pulmonary valve replacement into native right ventricular outflow tracts}, journal = {Catheterization and Cardiovascular Interventions}, year = {2018}, month = {11/2018}, abstract = {

Abstract Background Pulmonary insufficiency is a consequence of transannular patch repair in Tetralogy of Fallot (ToF) leading to late morbidity and mortality. Transcatheter native outflow tract pulmonary valve replacement has become a reality. However, predicting a secure, atraumatic implantation of a catheter-based device remains a significant challenge due to the complex and dynamic nature of the right ventricular outflow tract (RVOT). We sought to quantify the differences in compression and volume for actual implants, and those predicted by pre-implant modeling. Methods We used custom software to interactively place virtual transcatheter pulmonary valves (TPVs) into RVOT models created from pre-implant and post Harmony valve implant CT scans of 5 ovine surgical models of TOF to quantify and visualize device volume and compression. Results Virtual device placement visually mimicked actual device placement and allowed for quantification of device volume and radius. On average, simulated proximal and distal device volumes and compression did not vary statistically throughout the cardiac cycle (P = 0.11) but assessment was limited by small sample size. In comparison to actual implants, there was no significant pairwise difference in the proximal third of the device (P \> 0.80), but the simulated distal device volume was significantly underestimated relative to actual device implant volume (P = 0.06). Conclusions This study demonstrates that pre-implant modeling which assumes a rigid vessel wall may not accurately predict the degree of distal RVOT expansion following actual device placement. We suggest the potential for virtual modeling of TPVR to be a useful adjunct to procedural planning, but further development is needed.

}, keywords = {Magnetic Resonance Imaging, percutaneous pulmonary valve implantation, prosthetic heart valve, tetralogy of Fallot}, doi = {10.1002/ccd.27962}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ccd.27962}, author = {MatthewA Jolley and Andras Lasso and HannahH Nam and Dinh, Patrick V. and Adam B. Scanlan and Alexander V. Nguyen and Anna Ilina and Morray, Brian and Glatz, Andrew C. and FrancisX McGowan and Whitehead, Kevin and Dori, Yoav and Robert C. Gorman and Robert C. Gorman and Gabor Fichtinger and Gillespie, Matthew J.} } @conference {Asselin2018a, title = {Towards webcam-based tracking for interventional navigation}, booktitle = {SPIE Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling}, year = {2018}, month = {03/2018}, address = {Houston, Texas}, author = {Mark Asselin and Andras Lasso and Tamas Ungi and Gabor Fichtinger} } @conference { Asselin2018c, title = {A Training Tool for Ultrasound-Guided Central Line Insertion with Webcam-Based Position Tracking}, booktitle = {Simulation, Image Processing, and Ultrasound Systems for Assisted Diagnosis and Navigation}, year = {2018}, abstract = {

PURPOSE: This paper describes an open-source ultrasound-guided central line insertion training system. Modern clinical guidelines are increasingly recommending ultrasound guidance for this procedure due to the decrease in morbidity it provides. However, there are no adequate low-cost systems for helping new clinicians train their inter-hand coordination for this demanding procedure. METHODS: This paper details a training platform which can be recreated with any standard ultrasound machine using inexpensive components. We describe the hardware, software, and calibration procedures with the intention that a reader can recreate this system themselves. RESULTS: The reproducibility and accuracy of the ultrasound calibration for this system was examined. We found that across the ultrasound image the calibration error was less than 2\ mm. In a small feasibility study, two participants performed 5 needle insertions each with an average of slightly above 2\ mm error. CONCLUSION: We conclude that the accuracy of the system is sufficient for clinician training.

}, doi = {10.1007/978-3-030-01045-4_2}, url = {http://dx.doi.org/10.1007/978-3-030-01045-4_2}, author = {Mark Asselin and Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @article {Baum2018b, title = {Ultrasound-based vertebral landmark localization using deformable spine models}, year = {2018}, publisher = {Imaging Network Ontario (ImNO)}, address = {Toronto, Canada}, author = {Zachary M C Baum and Tamas Ungi and Andras Lasso and Ben Church and Christopher Schlenger and Gabor Fichtinger} } @article {Yeo2017, title = {Utility of 3D Reconstruction of 2D Liver Computed Tomography/Magnetic Resonance Images as a Surgical Planning Tool for Residents in Liver Resection Surgery}, journal = {Journal of Surgical Education}, volume = {75}, number = {3}, year = {2018}, month = {08/2017}, pages = {792-797}, abstract = {

Objective

A fundamental aspect of surgical planning in liver resections is the identification of key vessel tributaries to preserve healthy liver tissue while fully resecting the tumor(s). Current surgical planning relies primarily on the surgeon{\textquoteright}s ability to mentally reconstruct 2D computed tomography/magnetic resonance (CT/MR) images into 3D and plan resection margins. This creates significant cognitive load, especially for trainees, as it relies on image interpretation, anatomical and surgical knowledge, experience, and spatial sense. The purpose of this study is to determine if 3D reconstruction of preoperative CT/MR images will assist resident-level trainees in making appropriate operative plans for liver resection surgery.

Design

Ten preoperative patient CT/MR images were selected. Images were case-matched, 5 to 2D planning and 5 to 3D planning. Images from the 3D group were segmented to create interactive digital models that the resident can manipulate to view the tumor(s) in relation to landmark hepatic structures. Residents were asked to evaluate the images and devise a surgical resection plan for each image. The resident alternated between 2D and 3D planning, in a randomly generated order. The primary outcome was the accuracy of resident{\textquoteright}s plan compared to expert opinion. Time to devise each surgical plan was the secondary outcome. Residents completed a prestudy and poststudy questionnaire regarding their experience with liver surgery and the 3D planning software.

Setting and Participants

Senior level surgical residents from the Queen{\textquoteright}s University General Surgery residency program were recruited to participate.

Results

A total of 14 residents participated in the study. The median correct response rate was 2 of 5 (40\%; range: 0-4) for the 2D group, and 3 of 5 (60\%; range: 1-5) for the 3D group (p \< 0.01). The average time to complete each plan was 156 {\textpm} 107 seconds for the 2D group, and 84 {\textpm} 73 seconds for the 3D group (p \< 0.01). A total 13 of 14 residents found the 3D model easier to use than the 2D. Most residents noticed a difference between the 2 modalities and found that the 3D model improved their confidence with the surgical plan proposed.

Conclusions

The results of this study show that 3D reconstruction for liver surgery planning increases accuracy of resident surgical planning and decreases amount of time required. 3D reconstruction would be a useful model for improving trainee understanding of liver anatomy and surgical resection, and would serve as an adjunct to current 2D planning methods. This has the potential to be developed into a module for teaching liver surgery in a competency-based medical curriculum.

}, doi = {http://dx.doi.org/10.1016/j.jsurg.2017.07.031}, author = {Yeo, Caitlin T and MacDonald, Andrew and Tamas Ungi and Andras Lasso and Diederick Jalink and Boris Zevin and Gabor Fichtinger and Nanji, Sulaiman} } @article {Poulin2017b, title = {Validation of MRI to TRUS registration for HDR prostate brachytherapy}, journal = {Brachytherapy}, volume = {17}, number = {2}, year = {2018}, month = {2018/04}, pages = {283-290}, abstract = {

Purpose: The 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.

Methods and Materials: In this study, fifteen 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. 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 and can compute rigid and deformable transformations.
An extension of 3D Slicer, SlicerRT, allows import 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 identified by an experienced radiation oncologist.

Results: The average time to compute the registration was 35{\textpm}3 seconds.
For the deformable and rigid registration respectively, Dice similarity
coefficients were 0.93{\textpm}0.01 and 0.87{\textpm}0.05 while the 95\% Hausdorff
distance was 2.2{\textpm}0.3 and 4.2{\textpm}1.0 mm. MRI volumes obtained after the rigid
and deformable registration were not statistically different (p\>0.05)
from reference TRUS volumes. For the deformable and rigid registration
respectively, 3D distance error between centroid positions were 0.4{\textpm}0.1
and 2.1{\textpm}1.0 mm while registration errors between common points were
2.3{\textpm}1.1 and 3.5{\textpm}3.2 mm. Deformable registration was found significantly
better (p\<0.05) than rigid registration in all parameters.

Conclusions: An open-source MRI to TRUS registration platform was
validated for integration in the brachytherapy workflow.

}, author = {Eric Poulin and Karim Boudam and Csaba Pinter and Samuel Kadoury and Andras Lasso and Gabor Fichtinger and Cynthia Menard} } @conference {Baum2018a, title = {Visual aid for identifying vertebral landmarks in ultrasound}, booktitle = {SPIE Medical Imaging 2018: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {10576}, year = {2018}, month = {03/2018}, pages = {105760Z}, address = {Houston, Texas}, doi = {10.1117/12.2292820}, author = {Zachary M C Baum and Tamas Ungi and Andras Lasso and Ben Church and Christopher Schlenger and Gabor Fichtinger} } @conference {DGarcia-Mato2017a, title = {3D Gaze Tracking based on Eye and Head Pose Tracking}, booktitle = {Hamlyn Symposium on Medical Robotics}, year = {2017}, address = {London, UK}, author = {D. Garc{\'\i}a-Mato and Andras Lasso and A. Szulewski and J. Pascau and Gabor Fichtinger} } @article {Harish2017b, title = {An application of redundant sensors for intraoperative electromagnetic tracking error monitoring}, year = {2017}, address = {London, ON, Canada}, author = {Vinyas Harish and E Bibic and Andras Lasso and M. Holden and Thomas Vaughan and Zachary M C Baum and Tamas Ungi and Gabor Fichtinger} } @article {Scanlan2017, title = {Comparison of 3D Echocardiogram-Derived 3D Printed Valve Models to Molded Models for Simulated Repair of Pediatric Atrioventricular Valves}, journal = {Pediatric Cardiology}, year = {2017}, month = {Nov}, abstract = {

Mastering the technical skills required to perform pediatric cardiac valve surgery is challenging in part due to limited opportunity for practice. Transformation of 3D echocardiographic (echo) images of congenitally abnormal heart valves to realistic physical models could allow patient-specific simulation of surgical valve repair. We compared materials, processes, and costs for 3D printing and molding of patient-specific models for visualization and surgical simulation of congenitally abnormal heart valves. Pediatric atrioventricular valves (mitral, tricuspid, and common atrioventricular valve) were modeled from transthoracic 3D echo images using semi-automated methods implemented as custom modules in 3D Slicer. Valve models were then both 3D printed in soft materials and molded in silicone using 3D printed {\textquoteleft}{\textquoteleft}negative{\textquoteright}{\textquoteright} molds. Using pre-defined assessment criteria, valve models were evaluated by congenital cardiac surgeons to determine suitability for simulation. Surgeon assessment indicated that the molded valves had superior material properties for the purposes of simulation compared to directly printed valves (p{\th}inspace}\<{\th}inspace}0.01). Patient-specific, 3D echo-derived molded valves are a step toward realistic simulation of complex valve repairs but require more time and labor to create than directly printed models. Patient-specific simulation of valve repair in children using such models may be useful for surgical training and simulation of complex congenital cases.

}, issn = {1432-1971}, doi = {10.1007/s00246-017-1785-4}, url = {https://doi.org/10.1007/s00246-017-1785-4}, author = {Adam B. Scanlan and Alexander V. Nguyen and Anna Ilina and Andras Lasso and Cripe, Linnea and Jegatheeswaran, Anusha and Silvestro, Elizabeth and FrancisX McGowan and Christopher E. Mascio and Fuller, Stephanie and Spray, Thomas L. and Meryl S. Cohen and Gabor Fichtinger and MatthewA Jolley} } @article {Ilina2017b, title = {Creating patient-specific anatomical models from highly elastic materials using 3D-printed molds}, year = {2017}, address = {London, Canada}, keywords = {cardiac, heart, heart valve models, heart valves, molds, pediatric, Phantoms}, author = {Anna Ilina and Andras Lasso and MatthewA Jolley and Brittany Wohler and Alexander V. Nguyen and Adam B. Scanlan and Zachary M C Baum and FrancisX McGowan and Gabor Fichtinger} } @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 {Brastianos2016c, title = {Demonstration of Catheter Insertion Using Electromagnetic Guidance in Breast Brachytherapy}, volume = {Radiother Oncol 123}, year = {2017}, month = {05/2017}, pages = {S91}, author = {Harry Brastianos and Thomas Vaughan and Andras Lasso and Mary Westerland and James Gooding and Tamas Ungi and Gabor Fichtinger and Conrad Falkson} } @article {Vaughan2017b, title = {Electromagnetically-generated catheter paths for breast brachytherapy}, year = {2017}, author = {Thomas Vaughan and Harry Brastianos and Andras Lasso and Tamas Ungi and Conrad Falkson and Gabor Fichtinger} } @article {Baum2017b, title = {Evaluation of a mobile, real-time, tracked augmented reality display for surgical navigation}, year = {2017}, publisher = {Imaging Network Ontario (ImNO)}, address = {London, Canada}, author = {Zachary M C Baum and Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @conference {House2017, title = {Evaluation of the Intel RealSense SR300 camera for image-guided interventions and application in vertebral level localization}, booktitle = {SPIE Medical Imaging }, year = {2017}, author = {Rachael House and Andras Lasso and Vinyas Harish and Zachary M C Baum and Gabor Fichtinger} } @conference {sunderland2017a, title = {Fractional labelmaps for computing accurate dose volume histograms}, booktitle = {SPIE Medical Imaging}, year = {2017}, publisher = {International Society for Optics and Photonics}, organization = {International Society for Optics and Photonics}, abstract = {

PURPOSE: 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.

METHODS: 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.

RESULTS: We found that with manually segmented RANDO{\textregistered} 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\% ΔD, 1\% ΔV) up to 57.46\% higher (average 4.33\%) than DVH from binary labelmaps.

CONCLUSION: Fractional labelmaps promise to be an effective method for structure representation, allowing considerably more information to be stored in the same amount of memory

}, author = {Kyle R. Sunderland and Csaba Pinter and Andras Lasso and Gabor Fichtinger} } @conference {DBLP:conf/fimh/PouchALNSMFGGYJ17, title = {Image Segmentation and Modeling of the Pediatric Tricuspid Valve in Hypoplastic Left Heart Syndrome}, booktitle = {Functional Imaging and Modelling of the Heart - 9th International Conference, {FIMH} 2017, Toronto, ON, Canada, June 11-13, 2017, Proceedings}, year = {2017}, pages = {95{\textendash}105}, doi = {10.1007/978-3-319-59448-4_10}, url = {https://doi.org/10.1007/978-3-319-59448-4_10}, author = {Alison M. Pouch and Ahmed H. Aly and Andras Lasso and Alexander V. Nguyen and Adam B. Scanlan and FrancisX McGowan and Gabor Fichtinger and Robert C. Gorman and Robert C. Gorman and Paul A. Yushkevich and MatthewA Jolley} } @article {Moult2017, title = {Improved temporal calibration of tracked ultrasound: an open-source solution}, journal = {Journal of Medical Robotics Research}, volume = {2}, number = {04}, year = {2017}, month = {07/2017}, pages = {1750008}, abstract = {

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).

}, author = {Eric Moult and Andras Lasso and Tamas Ungi and Csaba Pinter and Mattea Welch and Gabor Fichtinger} } @conference {Kamali2017a, title = {Localization of the transverse processes in ultrasound for spinal curvature measurement}, booktitle = {SPIE Medical Imaging}, volume = {10135}, year = {2017}, month = {02/2017}, pages = {101350I-101350I-7}, abstract = {

PURPOSE: In scoliosis monitoring, tracked ultrasound has been explored as a safer imaging alternative to traditional radiography. The use of ultrasound in spinal curvature measurement requires identification of vertebral landmarks such as transverse processes, but as bones have reduced visibility in ultrasound imaging, skeletal landmarks are typically segmented manually, which is an exceedingly laborious and long process. We propose an automatic algorithm to segment and localize the surface of bony areas in the transverse process for scoliosis in ultrasound.METHODS: The algorithm uses cascade of filters to remove low intensity pixels, smooth the image and detect bony edges. By applying first differentiation, candidate bony areas are classified. The average intensity under each area has a correlation with the possibility of a shadow, and areas with strong shadow are kept for bone segmentation. The segmented images are used to reconstruct a 3-D volume to represent the whole spinal structure around the transverse processes. RESULTS: A comparison between the manual ground truth segmentation and the automatic algorithm in 50 images showed 0.17 mm average difference. The time to process all 1,938 images was about 37 Sec. (0.0191 Sec. / Image), including reading the original sequence file.CONCLUSION: Initial experiments showed the algorithm to be sufficiently accurate and fast for segmentation transverse processes in ultrasound for spinal curvature measurement. An extensive evaluation of the method is currently underway on images from a larger patient cohort and using multiple observers in producing ground truth segmentation.

}, doi = {10.1117/12.2256007}, url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=2615387}, author = {Shahrokh Kamali and Tamas Ungi and Andras Lasso and Christina Yan and Lougheed, Matthew and Gabor Fichtinger} } @conference {Harish2017a, title = {Monitoring electromagnetic tracking error using redundant sensors}, booktitle = {SPIE Medical Imaging 2017}, year = {2017}, publisher = {SPIE Society for Optics and Photonics}, organization = {SPIE Society for Optics and Photonics}, address = {Orlando, FL, USA}, abstract = {

PURPOSE: The intraoperative measurement of tracking error is crucial to ensure the reliability of electromagnetically navigated procedures. For intraoperative use, methods need to be quick to set up, easy to interpret, and not interfere with the ongoing procedure. Our goal was to evaluate the feasibility of using redundant electromagnetic sensors to alert users to tracking error in a navigated intervention setup. METHODS: Electromagnetic sensors were fixed to a rigid frame around a region of interest and on surgical tools. A software module was designed to detect tracking error by comparing real-time measurements of the differences between inter-sensor distances and angles to baseline measurements. Once these measurements were collected, a linear support vector machine-based classifier was used to predict tracking errors from redundant sensor readings. RESULTS: Measuring the deviation in the reported inter-sensor distance and angle between the needle and cautery served as a valid indicator for electromagnetic tracking error. The highest classification accuracy, 86\%, was achieved based on readings from the cautery when the two sensors on the cautery were close together. The specificity of this classifier was 93\% and the sensitivity was 82\%. CONCLUSION: Placing redundant electromagnetic sensors in a workspace seems to be feasible for the intraoperative detection of electromagnetic tracking error in controlled environments. Further testing should be performed to optimize the measurement error threshold used for classification in the support vector machine, and improve the sensitivity of our method before application in real procedures.\ 

}, author = {Vinyas Harish and Eden Bibic and Andras Lasso and M. Holden and Thomas Vaughan and Zachary M C Baum and Tamas Ungi and Gabor Fichtinger} } @conference {Ilina2017a, title = {Patient-specific pediatric silicone heart valve models based on 3D ultrasound}, booktitle = {SPIE Medical Imaging 2017}, volume = {10135}, year = {2017}, month = {03/2017}, publisher = {SPIE Medical Imaging}, organization = {SPIE Medical Imaging}, address = {Orlando, FL, United States, Feb. 16, 2017}, abstract = {

PURPOSE: Patient-specific heart and valve models have shown promise as training and planning tools for heart surgery, but physically realistic valve models remain elusive. Available proprietary, simulation-focused heart valve models are generic adult mitral valves and do not allow for patient-specific modeling as may be needed for rare diseases such as congenitally abnormal valves. We propose creating silicone valve models from a 3D-printed plastic mold as a solution that can be adapted to any individual patient and heart valve at a fraction of the cost of direct 3D-printing using soft materials.

METHODS: Leaflets of a pediatric mitral valve, a tricuspid valve in a patient with hypoplastic left heart syndrome, and a complete atrioventricular canal valve were segmented from ultrasound images. A custom software was developed to automatically generate molds for each valve based on the segmentation. These molds were 3D-printed and used to make silicone valve models. The models were designed with cylindrical rims of different sizes surrounding the leaflets, to show the outline of the valve and add rigidity. Pediatric cardiac surgeons practiced suturing on the models and evaluated them for use as surgical planning and training tools.

RESULTS: Five out of six surgeons reported that the valve models would be very useful as training tools for cardiac surgery. In this first iteration of valve models, leaflets were felt to be unrealistically thick or stiff compared to real pediatric leaflets. A thin tube rim was preferred for valve flexibility.

CONCLUSION: The valve models were well received and considered to be valuable and accessible tools for heart valve surgery training. Further improvements will be made based on surgeons{\textquoteright} feedback.

Keywords: surgery, training, heart valve models, pediatric, patient-specific, 3D-printing, congenital heart disease, mitral valve, tricuspid valve, complete atrioventricular canal defect, ultrasound

}, author = {Anna Ilina and Andras Lasso and MatthewA Jolley and Brittany Wohler and Alexander V. Nguyen and Adam B. Scanlan and Zachary M C Baum and FrancisX McGowan and Gabor Fichtinger} } @article {Bibic2017a, title = {PLUS Model Catalog: A library of 3D-printable models}, year = {2017}, publisher = {Imaging Network Ontario (ImNO)}, address = {London, Canada}, author = {Eden Bibic and Zachary M C Baum and Vinyas Harish and Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @article {Yan2017b, title = {Quantification of tumor localization needle displacement prior to tumor excision in navigated lumpectomy}, year = {2017}, author = {Christina Yan and Tamas Ungi and Gabrielle Gauvin and Doris Jabs and Andras Lasso and C. Jay Engel and John Rudan and Gabor Fichtinger} } @article {Brastianos2017b, title = {Real Time Electomagnetic Reconstruction of Catheter Paths in Multi-Catheter Interstitial Brachytherapy: A Phantom Model}, volume = {Int J Radiat Oncol Biol Phys 99}, year = {2017}, month = {10/2017}, pages = {E642}, author = {Harry Brastianos and Thomas Vaughan and Andras Lasso and Mary Westerland and James Gooding and Gabor Fichtinger and Conrad Falkson} } @article {Baum2017c, title = {Real-Time, Tracked, Mobile Augmented Reality Display for Surgical Navigation: Usability Study on Simulated Patients}, year = {2017}, publisher = {National Center for Image Guided Therapy}, address = {Bethesda, USA}, author = {Zachary M C Baum and Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @article {Church2017b, title = {Scoliosis visualization using transverse process landmarks}, year = {2017}, keywords = {scoliosis, Spine, Ultrasound, visualization}, author = {Ben Church}, editor = {Andras Lasso and Christopher Schlenger and Daniel P. Borschneck and Parvin Mousavi and Gabor Fichtinger and Tamas Ungi} } @conference {Underwood2017, title = {Skull registration for prone patient position using tracked ultrasound}, booktitle = {SPIE Medical Imaging 2017}, year = {2017}, author = {Underwood, Grace and Tamas Ungi and Zachary M C Baum and Andras Lasso and Gernot Kronreif and Gabor Fichtinger} } @conference {Yan2017a, title = {Study into the displacement of tumor localization needle during navigated breast cancer surgery}, booktitle = {SPIE Medical Imaging}, year = {2017}, publisher = {SPIE}, organization = {SPIE}, address = {Orlando, Florida, USA}, author = {Christina Yan and Tamas Ungi and Gabrielle Gauvin and Doris Jabs and Andras Lasso and C. Jay Engel and John Rudan and Gabor Fichtinger} } @conference {Baum2017a, title = {Usability of a real-time tracked augmented reality display system in musculoskeletal injections}, booktitle = {SPIE Medical Imaging 2017: Image-Guided Procedures, Robotic Interventions, and Modeling}, year = {2017}, month = {03/2017}, doi = {10.1117/12.2255897}, author = {Zachary M C Baum and Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @article {House2017b, title = {Validation of breast volume measurement using 3D surface scanner}, year = {2017}, month = {02/2017}, author = {Rachael House and Andras Lasso and Glykeria Martou and Gabor Fichtinger} } @conference {Poulin2017, title = {Validation Of MRI To US Registration For Focal Hdr Prostate Brachytherapy Treatment}, booktitle = {Annual Scientific Meeting of the American Brachytherapy Society}, volume = {16}, number = {3}, year = {2017}, pages = {S56-S57}, publisher = {Elsevier}, organization = {Elsevier}, address = {Boston, MA, USA}, keywords = {Brachytherapy, contour propagation, MRI, Ultrasound}, issn = {1538-4721}, doi = {http://dx.doi.org/10.1016/j.brachy.2017.04.093}, url = {http://www.brachyjournal.com/article/S1538-4721(17)30154-X/fulltext}, author = {Eric Poulin}, editor = {Karim Boudam and Csaba Pinter and Samuel Kadoury and Andras Lasso and Gabor Fichtinger and Cynthia Menard} } @article {Vaughan2017a, title = {Virtual views controlled by surgical tools for computer assisted interventions}, year = {2017}, author = {Thomas Vaughan and Tamas Ungi and Andras Lasso and Gabrielle Gauvin and C. Jay Engel and John Rudan and Gabor Fichtinger} } @conference {Church2017, title = {Visualization of scoliotic spine using ultrasound-accessible skeletal landmarks}, booktitle = {SPIE Medical Imaging 2017}, year = {2017}, keywords = {scoliosis, Spine, Ultrasound, visualization}, author = {Ben Church and Andras Lasso and Christopher Schlenger and Daniel P. Borschneck and Parvin Mousavi and Gabor Fichtinger and Tamas Ungi} } @conference {Heffernan2016, title = {Accuracy of lesion boundary tracking in navigated breast tumor excision}, booktitle = {SPIE Medical Imaging 2016}, volume = {9786}, year = {2016}, month = {03/2016}, pages = {97860Y-1-6}, address = {San Diego, CA, USA}, doi = {10.1117/12.2217017}, url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=2505913\&resultClick=1}, author = {Emily Heffernan and Tamas Ungi and Thomas Vaughan and Padina Pezeshki and Andras Lasso and Gabrielle Gauvin and John Rudan and C. Jay Engel and Evelyn Morin and Gabor Fichtinger} } @article {Sunderland2016b, title = {Analysis of dose volume histogram deviations using different voxelization parameters}, year = {2016}, address = {Toronto, Canada}, author = {Kyle R. Sunderland and Csaba Pinter and Andras Lasso and Gabor Fichtinger} } @article {Gauvin2016a, title = {Breast-Conserving Surgery using NaviKnife Technology: Pilot Study on Non-Palpable Tumors}, year = {2016}, month = {08/2016}, author = {Gabrielle Gauvin and Tamas Ungi and Andras Lasso and Yeo, Caitlin T and Gabor Fichtinger and Doris Jabs and Ross Walker and Shaila Merchant and John Rudan and C. Jay Engel} } @article {Vaughan2016a, title = {Catheter targeting under electromagnetic guidance in breast brachytherapy {\textendash} a demonstration of concept}, volume = {Int J CARS}, number = {Suppl 1}, year = {2016}, month = {05/2016}, pages = {S60-62}, keywords = {Brachytherapy, breast}, author = {Thomas Vaughan and Harry Brastianos and Andras Lasso and Mary Westerland and Tamas Ungi and Conrad Falkson and Gabor Fichtinger} } @article {Pinter2016, title = {Dynamic management of segmented structures in 3D Slicer}, year = {2016}, month = {03/2016}, author = {Csaba Pinter and Andras Lasso and Gabor Fichtinger} } @conference {sunderland2016a, title = {Effects of voxelization on dose volume histogram accuracy}, booktitle = {SPIE Medical Imaging}, year = {2016}, pages = {97862O{\textendash}97862O}, publisher = {International Society for Optics and Photonics}, organization = {International Society for Optics and Photonics}, abstract = {

PURPOSE: 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.

METHODS: 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.

RESULTS: 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.

CONCLUSION: 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.\ 

}, author = {Kyle R. Sunderland and Csaba Pinter and Andras Lasso and Gabor Fichtinger} } @article {Brastianos2016a, title = {Electromagnetic tracking for catheter insertion guidance for HDR breast brachytherapy: demonstration of concept in phantoms}, volume = {Radiother Oncol 120}, year = {2016}, month = {09/2016}, pages = {S73-S74}, address = {Banff, AB, Canada}, author = {H Brastianos and Thomas Vaughan and Andras Lasso and M Westerland and James Gooding and Gabor Fichtinger and Conrad Falkson} } @article {Brastianos2016b, title = {Electromagnetic tracking for catheter insertion guidance for HDR breast brachytherapy: a phantom experiment}, volume = {Int J Radiat Oncol Biol Phys 96}, year = {2016}, month = {09/2016}, pages = {E643}, address = {Boston, MA, USA}, author = {H Brastianos and Thomas Vaughan and Andras Lasso and M Westerland and James Gooding and Gabor Fichtinger and Conrad Falkson} } @article {Vaughan2016b, title = {Electromagnetically-guided catheter insertions in breast phantoms for brachytherapy}, year = {2016}, month = {Submitted}, keywords = {Brachytherapy, breast}, author = {Thomas Vaughan and Harry Brastianos and Andras Lasso and Mary Westerland and Tamas Ungi and Conrad Falkson and Gabor Fichtinger} } @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} } @conference {Ungi2016c, title = {Intraoperative user interface for navigated breast tumor surgery}, booktitle = {Computer Assisted Radiology and Surgery, 30th International Congress}, volume = {11}, year = {2016}, month = {05/2016}, pages = {S108-9}, publisher = {Springer}, organization = {Springer}, address = {Heidelberg, Germany}, doi = {10.1007/s11548-016-1412-5}, author = {Tamas Ungi and Thomas Vaughan and Gabrielle Gauvin and Padina Pezeshki and Andras Lasso and C. Jay Engel and John Rudan and Gabor Fichtinger} } @conference {doi:10.1117/12.2217189, title = {Investigation of permanent magnets in low-cost position tracking}, booktitle = {Proc. SPIE}, year = {2016}, pages = {97862F-97862F-9}, abstract = {

PURPOSE: Low cost portable ultrasound systems could see improved utility if similarly low cost portable trackers were developed. Permanent magnet based tracking systems potentially offer adequate tracking accuracy in a small workspace suitable for ultrasound image reconstruction. In this study the use of simple permanent magnet tracking techniques is investigated to determine feasibility for use in an ultrasound tracking system. METHODS: Permanent magnet tracking requires finding a position input into a field model which minimizes the error between the measured field, and the field expected from the model. A simulator was developed in MATLAB to determine the effect of sources of error in permanent magnet tracking systems. Insights from the simulations were used to develop a calibration and tracking experiment to determine the accuracy of a simple and low cost permanent magnet tracking system. RESULTS: Simulation and experimental results show permanent magnet based tracking to be highly sensitive to errors in sensor measurements, calibration and experimental setup. The reduction in field strength of permanent magnets lowers with the cube of distance, which leads to very poor signal-to-noise ratios at distances above 20 cm. Small errors in experimental setup also led to high tracking error. CONCLUSION: Permanent magnet tracking was found to be less accurate than is clinically useful, and highly sensitive to errors in sensors and experimental setup. Sensor and calibration limitations make simple permanent magnet tracking systems a poor choice given the present state of sensor technology.

}, doi = {10.1117/12.2217189}, url = {http://dx.doi.org/10.1117/12.2217189}, author = {Anderson, Ryan and Andras Lasso and Keyvan Hashtrudi-Zaad and Gabor Fichtinger} } @conference {Harish2016a, title = {Measurement of electromagnetic tracking error in a navigated breast surgery setup}, booktitle = {SPIE Medical Imaging 2016}, volume = {9786}, year = {2016}, publisher = {SPIE Medical Imaging}, organization = {SPIE Medical Imaging}, address = {San Diego, CA, United States, Feb. 29, 2016}, abstract = {

The measurement of tracking error is crucial to ensure the safety and feasibility of electromagnetically tracked, image-guided procedures. Measurement should occur in a clinical environment because electromagnetic field distortion depends on positioning relative to the field generator and metal objects. However, we could not find an accessible and open-source system for calibration, error measurement, and visualization. We developed such a system and tested it in a navigated breast surgery setup.A pointer tool was designed for concurrent electromagnetic and optical tracking. Software modules were developed for automatic calibration of the measurement system, real-time error visualization, and analysis. The system was taken to an operating room to test for field distortion in a navigated breast surgery setup. Positional and rotational electromagnetic tracking errors were then calculated using optical tracking as a ground truth. Our system is quick to set up and can be rapidly deployed. The process from calibration to visualization also only takes a few minutes. Field distortion was measured in the presence of various surgical equipment. Positional and rotational error in a clean field was approximately 0.90 mm and 0.31{\textdegree}. The presence of a surgical table, an electrosurgical cautery, and anesthesia machine increased the error by up to a few tenths of a millimetre and tenth of a degree.In a navigated breast surgery setup, measurement and visualization of tracking error defines a safe working area in the presence of surgical equipment. Our system is available as an extension for the open-source 3D Slicer platform.

}, author = {Vinyas Harish and A Baksh and Tamas Ungi and Andras Lasso and Zachary M C Baum and G Gauvin and C. Jay Engel and John Rudan and Gabor Fichtinger} } @article {Harish2016c, title = {Monitoring electromagnetic tracking error in computer-navigated breast cancer surgery}, year = {2016}, publisher = {Imaging Network Ontario (ImNO)}, address = {Toronto, Canada}, keywords = {Breast cancer, EM Tracking, Lumpectomy}, author = {Vinyas Harish and A Baksh and Tamas Ungi and Andras Lasso and Zachary M C Baum and G Gauvin and C. Jay Engel and John Rudan and Gabor Fichtinger} } @article {Ungi2016a, title = {Open-source platforms for navigated image-guided interventions}, journal = {Medical Image Analysis}, volume = {33}, year = {2016}, month = {10/2016}, pages = {181-6}, abstract = {

Navigation technology is changing the clinical standards in medical interventions by making existing procedures more accurate, and new procedures possible. Navigation is based on preoperative or intraoperative imaging combined with 3-dimensional position tracking of interventional tools registered to the images. Research of navigation technology in medical interventions requires significant engineering efforts. The difficulty of developing such complex systems has been limiting the clinical translation of new methods and ideas. A key to the future success of this field is to provide researchers with platforms that allow rapid implementation of applications with minimal resources spent on reimplementing existing system features. A number of platforms have been already developed that can share data in real time through standard interfaces. Complete navigation systems can be built using these platforms using a layered software architecture. In this paper, we review the most popular platforms, and show an effective way to take advantage of them through an example surgical navigation application.

}, doi = {10.1016/j.media.2016.06.011}, author = {Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @article {Baum2016b, title = {Real-time self-calibration of a handheld augmented reality overlay system}, year = {2016}, publisher = {Imaging Network Ontario (ImNO)}, address = {Toronto, Canada}, author = {Zachary M C Baum and Andras Lasso and Tamas Ungi and Gabor Fichtinger} } @conference {Baum2016a, title = {Real-time self-calibration of a tracked augmented reality display}, booktitle = {SPIE Medical Imaging 2016}, volume = {9786}, year = {2016}, publisher = {SPIE Medical Imaging}, organization = {SPIE Medical Imaging}, address = {San Diego, CA, United States, Feb. 29, 2016}, abstract = {

PURPOSE: Augmented reality systems have been proposed for image-guided needle interventions but they have not become widely used in clinical practice due to restrictions such as limited portability, low display refresh rates, and tedious calibration procedures. We propose a handheld tablet-based self-calibrating image overlay system.

METHODS: A modular handheld augmented reality viewbox was constructed from a tablet computer and a semi-transparent mirror. A consistent and precise self-calibration method, without the use of any temporary markers, was designed to achieve an accurate calibration of the system. Markers attached to the viewbox and patient are simultaneously tracked using an optical pose tracker to report the position of the patient with respect to a displayed image plane that is visualized in real-time. The software was built using the open-source 3D Slicer application platform{\textquoteright}s SlicerIGT extension and the PLUS toolkit.

RESULTS: The accuracy of the image overlay with image-guided needle interventions yielded a mean absolute position error of 0.99 mm (95th percentile 1.93 mm) in-plane of the overlay and a mean absolute position error of 0.61 mm (95th percentile 1.19 mm) out-of-plane. This accuracy is clinically acceptable for tool guidance during various procedures, such as musculoskeletal injections.

CONCLUSION: A self-calibration method was developed and evaluated for a tracked augmented reality display. The results show potential for the use of handheld image overlays in clinical studies with image-guided needle interventions.\ 

}, author = {Zachary M C Baum and Andras Lasso and Tamas Ungi and Gabor Fichtinger} } @conference {Gauvin2016a, title = {Safety and Feasibility Study for Real-Time Electromagnetic Navigation in Breast-Conserving Surgery}, booktitle = {Computer Assisted Radiology and Surgery, 30th International Congress}, volume = {11}, year = {2016}, month = {05/2016}, pages = {S106-7}, publisher = {Springer}, organization = {Springer}, address = {Heidelberg, Germany}, doi = {10.1007/s11548-016-1412-5}, author = {Gabrielle Gauvin and Tamas Ungi and Andras Lasso and Ross Walker and John Rudan and Gabor Fichtinger and C. Jay Engel} } @conference {Carter2016a, title = {Visual feedback mounted on surgical tool: proof of concept}, booktitle = {SPIE Medical Imaging 2016}, volume = {9786}, year = {2016}, month = {In Press}, address = {San Diego, CA, USA}, author = {Kaci Carter and Thomas Vaughan and M. Holden and Gabrielle Gauvin and Padina Pezeshki and Andras Lasso and Tamas Ungi and Evelyn Morin and John Rudan and C. Jay Engel and Gabor Fichtinger} } @conference {Schumacher2015, title = {3D-printed surface mould applicator for high-dose-rate brachytherapy}, booktitle = {SPIE Medical Imaging 2015}, volume = {9415}, year = {2015}, abstract = {

ABSTRACT

PURPOSE: In contemporary high-dose-rate brachytherapy treatment of superficial tumors, catheters are placed in a wax mould. The creation of current wax models is a difficult and time consuming proces.The irradiation plan can only be computed post-construction and requires a second CT scan. In case no satisfactory dose plan can be created, the mould is discarded and the process is repeated. The objective of this work was to develop an automated method to replace suboptimal wax moulding. METHODS: We developed a method to design and manufacture moulds that guarantee to yield satisfactory dosimetry. A 3D-printed mould with channels for the catheters designed from the patient{\textquoteright}s CT and mounted on a patient-specific thermoplastic mesh mask. The mould planner was implemented as an open-source module in the 3D Slicer platform. RESULTS: Series of test moulds were created to accommodate standard brachytherapy catheters of 1.70mm diameter. A calibration object was used to conclude that tunnels with a diameter of 2.25mm, minimum 12mm radius of curvature, and 1.0mm open channel gave the best fit for this printer/catheter combination. Moulds were created from the CT scan of thermoplastic mesh masks of actual patients. The patient-specific moulds have been visually verified to fit on the thermoplastic meshes. CONCLUSION: The masks were visually shown to fit onto the thermoplastic meshes, next the resulting dosimetry will have to be compared with treatment plans and dosimetry achieved with conventional wax moulds in order to validate our 3D printed moulds.

}, author = {Mark Schumacher and Andras Lasso and Ian Cumming and Adam Rankin and Conrad Falkson and John Schreiner and C.P. Joshi and Gabor Fichtinger} } @article {Ungi2015c, title = {Clinical Translation of Real Time Cautery Navigation for Breast Surgery}, year = {2015}, month = {06/2015}, pages = {19-20}, isbn = {978-0-9563776-6-1}, author = {Tamas Ungi and Gabrielle Gauvin and Andras Lasso and Yeo, Caitlin T and John Rudan and C. Jay Engel and Gabor Fichtinger} } @article {Alexander2015a, title = {Cross-Validation of 3D Gamma Comparison Tools}, volume = {42}, number = {15}, year = {2015}, month = {06/2015}, pages = {3385-3385}, publisher = {Medical Physics}, doi = {10.1118/1.4924592}, author = {Kevin Alexander and Christopher Jechel and Csaba Pinter and Greg Salomons and Andras Lasso and Gabor Fichtinger and L. John Schreiner} } @article {Carter2015b, title = {Current sensing for navigated electrosurgery }, year = {2015}, month = {03/2015}, pages = {37}, author = {Kaci Carter and Andras Lasso and Tamas Ungi and Evelyn Morin and Gabor Fichtinger} } @article {AbouSeido2015, title = {Data Management Workflow And Architecture For Simulation-Based Medical Training}, volume = {10}, year = {2015}, month = {06/2015}, pages = {s78}, keywords = {AbouSeido2015}, doi = {10.1007/s11548-015-1213-2}, author = {Nisrin Abou-Seido and Tamas Ungi and Andras Lasso and McGraw, Robert C and Gabor Fichtinger} } @article {Vaughan2015, title = {Hole filling with oriented sticks in ultrasound volume reconstruction}, journal = {J. Med. Imag.}, volume = {2}, number = {3}, year = {2015}, author = {Thomas Vaughan and Andras Lasso and Tamas Ungi and Gabor Fichtinger} } @conference {King2015, title = {An Immersive Virtual Reality Environment for Diagnostic Imaging}, booktitle = {Int Conf Med Image Comput Comput Assist Interv. MICCAI 2015}, year = {2015}, month = {10/2015}, abstract = {

Advancements in and adoption of consumer virtual reality are currently being propelled by numerous upcoming devices such as the Oculus Rift. Although applications are currently growing around the entertainment field, widespread adoption of virtual reality devices opens up the potential for other applications that may have been unfeasible with past implementations of virtual reality. A virtual reality environment may provide an equal or larger viewing volume than what is provided with the use of multiple conventional displays while remaining comparatively cheaper and more portable. A virtual reality application for the viewing of multiple image slices was designed using: the Oculus Rift head-mounted display, Unity, 3D Slicer, and a gamepad controller. A web server acquires data from volumes loaded within 3D Slicer and forwards it to a Unity application that proceeds to render a scene for the Oculus Rift head- mounted display. Users may interact with the images adjusting windowing and leveling using the handheld gamepad controller. Multiple images could also be brought closer to the user for detailed inspection. Application usage was demonstrated with the simultaneous visualization of concurrent slices of a serial CT scan of a patient with a lung nodule. The tasks of identifying the lesion and determining the malignancy status by monitoring the growth of the lesion over time were performed successfully. Also demonstrated was the studying of multiple- sclerosis lesion evolution by visualization of a large time-series MRI dataset. A virtual reality environment for the purpose of aiding diagnostic radiology has been created and demonstrated with potential use cases.

}, author = {Franklin King and Jagadeesan Jayender and Steve Pieper and Tina Kapur and Andras Lasso and Gabor Fichtinger} } @conference {Harish2015, title = {Intraoperative visualization and assessment of electromagnetic tracking error}, booktitle = {SPIE Medical Imaging 2015}, volume = {9415}, year = {2015}, pages = {94152H-94152H-6}, address = {Orlando,FL, United States, Feb. 23, 2015}, abstract = {

Electromagnetic tracking allows for increased flexibility in designing image-guided interventions, however it is well understood that electromagnetic tracking is prone to error. Visualization and assessment of the tracking error should take place in the operating room with minimal interference with the clinical procedure. The goal was to achieve this ideal in an open-source software implementation in a plug and play manner, without requiring programming from the user. We use optical tracking as a ground truth. An electromagnetic sensor and optical markers are mounted onto a stylus device, pivot calibrated for both trackers. Electromagnetic tracking error is defined as difference of tool tip position between electromagnetic and optical readings. Multiple measurements are interpolated into the thin-plate B-spline transform visualized in real time using 3D Slicer. All tracked devices are used in a plug and play manner through the open-source SlicerIGT and PLUS extensions of the 3D Slicer platform. Tracking error was measured multiple times to assess reproducibility of the method, both with and without placing ferromagnetic objects in the workspace. Results from exhaustive grid sampling and freehand sampling were similar, indicating that a quick freehand sampling is sufficient to detect unexpected or excessive field distortion in the operating room. The software is available as a plug-in for the 3D Slicer platforms. Results demonstrate potential for visualizing electromagnetic tracking error in real time for intraoperative environments in feasibility clinical trials in image-guided interventions.

}, doi = {10.1117/12.2082330}, url = {http://dx.doi.org/10.1117/12.2082330}, author = {Vinyas Harish and Tamas Ungi and Andras Lasso and MacDonald, Andrew and Nanji, Sulaiman and Gabor Fichtinger} } @conference {Meyer2015, title = {Live ultrasound volume reconstruction using scout scanning}, booktitle = {SPIE Medical Imaging 2015}, volume = {9415}, year = {2015}, pages = {94152A-94152A-9}, abstract = {

Ultrasound-guided interventions often necessitate scanning of deep-seated anatomical structures that may be hard to visualize. Visualization can be improved using reconstructed 3D ultrasound volumes. High-resolution 3D reconstruction of a large area during clinical interventions is challenging if the region of interest is unknown. We propose a two-stage scanning method allowing the user to perform quick low-resolution scouting followed by high-resolution live volume reconstruction. Scout scanning is accomplished by stacking 2D tracked ultrasound images into a low-resolution volume. Then, within a region of interest defined in the scout scan, live volume reconstruction can be performed by continuous scanning until sufficient image density is achieved. We implemented the workflow as a module of the open-source 3D Slicer application, within the SlicerIGT extension and building on the PLUS toolkit. Scout scanning is performed in a few seconds using 3 mm spacing to allow region of interest definition. Live reconstruction parameters are set to provide good image quality (0.5 mm spacing, hole filling enabled) and feedback is given during live scanning by regularly updated display of the reconstructed volume. Use of scout scanning may allow the physician to identify anatomical structures. Subsequent live volume reconstruction in a region of interest may assist in procedures such as targeting needle interventions or estimating brain shift during surgery.

}, doi = {10.1117/12.2081488}, url = {http://dx.doi.org/10.1117/12.2081488}, author = {Meyer, Amelie and Andras Lasso and Tamas Ungi and Gabor Fichtinger} } @article {Ungi2015b, title = {Navigated breast tumor excision using electromagnetically tracked ultrasound and surgical instruments}, journal = {IEEE Transactions on Biomedical Engineering}, year = {2015}, month = {08/2015 }, abstract = {

OBJECTIVE:

Lumpectomy, breast conserving tumor excision, is the standard surgical treatment in early stage breast cancer. A common problem with lumpectomy is that the tumor may not be completely excised, and additional surgery becomes necessary. We investigated if a surgical navigation system using intraoperative ultrasound improves the outcomes of lumpectomy, and if such a system can be implemented in the clinical environment.

METHODS:

Position sensors were applied on the tumor localization needle, the ultrasound probe, and the cautery, and three-dimensional navigation views were generated using real time tracking information. The system was tested against standard wire-localization procedures on phantom breast models by eight surgical residents. Clinical safety and feasibility was tested in six palpable tumor patients undergoing lumpectomy by two experienced surgical oncologists.

RESULTS:

Navigation resulted in significantly less tissue excised compared to control procedures (10.3 {\textpm} 4.4 vs. 18.6 {\textpm} 8.7 g, p = 0.01) and lower number of tumorpositive margins (1/8 vs. 4/8) in the phantom experiments. Excision-tumor distance was also more consistently outside the tumor margins with navigation in phantoms. The navigation system has been successfully integrated in an operating room, and user experience was rated positively by surgical oncologists.

CONCLUSION:

Electromagnetic navigation may improve the outcomes of lumpectomy by making the tumor excision more accurate.

SIGNIFICANCE:

Breast cancer is the most common cancer in women, and lumpectomy is its first choice treatment. Therefore, improvement of lumpectomy outcomes have a significant impact on a large patient population.

}, issn = {0018-9294}, doi = {10.1109/TBME.2015.2466591}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26302503}, author = {Tamas Ungi and Gabrielle Gauvin and Andras Lasso and Yeo, Caitlin T and Padina Pezeshki and Thomas Vaughan and Kaci Carter and John Rudan and C. Jay Engel and Gabor Fichtinger} } @article {raey, title = {Open-source image registration for MRI-TRUS fusion-guided prostate interventions}, journal = {International Journal of Computer Assisted Radiology and Surgery}, volume = {10}, number = {6}, year = {2015}, pages = {925-934}, keywords = {Image registration, Image-guided interventions, Magnetic Resonance Imaging, prostate cancer, Targeted biopsy, Ultrasound}, issn = {1861-6410}, doi = {10.1007/s11548-015-1180-7}, url = {http://dx.doi.org/10.1007/s11548-015-1180-7}, author = {Andriy Fedorov and Siavash Khallaghi and Sanchez, C. Antonio and Andras Lasso and Fels, Sidney and Kemal Tuncali and Sugar, Emily Neubauer and Tina Kapur and Zhang, Chenxi and William Wells and Paul Nguyen and Purang Abolmaesumi and Clare M Tempany} } @conference {Pinter2015, title = {Performing radiation therapy research using the open-source SlicerRT toolkit}, booktitle = {World Congress on Medical Physics and Biomedical Engineering}, year = {2015}, month = {07/2015}, publisher = {Springer}, organization = {Springer}, address = {Toronto}, abstract = {

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.

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{\textquoteright} 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.

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.

}, doi = {10.1007/978-3-319-19387-8_152}, author = {Csaba Pinter and Andras Lasso and An Wang and Gregory C Sharp and Kevin Alexander and David Jaffray and Gabor Fichtinger} } @conference {Hess2015, title = {Quantification of intraventricular blood clot in MR-guided focused ultrasound surgery}, booktitle = {SPIE Medical Imaging 2015}, volume = {9415}, year = {2015}, month = {02/2015}, pages = {94152J-94152J-9}, abstract = {

Intraventricular hemorrhage (IVH) affects nearly 15\% of preterm infants. It can lead to ventricular dilation and cognitive impairment. To ablate IVH clots, MR-guided focused ultrasound surgery (MRgFUS) is investigated. This procedure requires accurate, fast and consistent quantification of ventricle and clot volumes. We developed a semi-autonomous segmentation (SAS) algorithm for measuring changes in the ventricle and clot volumes. Images are normalized, and then ventricle and clot masks are registered to the images. Voxels of the registered masks and voxels obtained by thresholding the normalized images are used as seed points for competitive region growing, which provides the final segmentation. The user selects the areas of interest for correspondence after thresholding and these selections are the final seeds for region growing. SAS was evaluated on an IVH porcine model. SAS was compared to ground truth manual segmentation (MS) for accuracy, efficiency, and consistency. Accuracy was determined by comparing clot and ventricle volumes produced by SAS and MS, and comparing contours by calculating 95\% Hausdorff distances between the two labels. In Two-One-Sided Test, SAS and MS were found to be significantly equivalent (p \< 0.01). SAS on average was found to be 15 times faster than MS (p \< 0.01). Consistency was determined by repeated segmentation of the same image by both SAS and manual methods, SAS being significantly more consistent than MS (p \< 0.05). SAS is a viable method to quantify the IVH clot and the lateral brain ventricles and it is serving in a large-scale porcine study of MRgFUS treatment of IVH clot lysis.

}, doi = {10.1117/12.2081330}, url = {http://dx.doi.org/10.1117/12.2081330}, author = {Hess, Margaret A. and Thomas Looi and Andras Lasso and Gabor Fichtinger and James Drake} } @conference {Hess2014a, title = {Quantification of intraventricular blood clot in MR-guided focused ultrasound surgery}, booktitle = {SPIE Medical Imaging 2015: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {9415}, year = {2015}, month = {03/2015}, pages = {94152J1-94152J9}, address = {Orlando, Florida}, abstract = {

Purpose: Intraventricular hemorrhage (IVH) affects nearly 15\% of preterm infants. It can lead to ventricular dilation and cognitive impairment. To ablate IVH clots, MR-guided focused ultrasound surgery (MRgFUS) is investigated. This procedure requires accurate, fast and consistent quantification of ventricle and clot volumes.
Methods: We developed a semi-autonomous segmentation (SAS) algorithm for measuring changes in the ventricle and clot volumes. Images are normalized, and then ventricle and clot masks are registered to the images. Voxels of the registered masks and voxels obtained by thresholding the normalized images are used as seed points for competitive region growing, which provides the final segmentation. The user selects the areas of interest for correspondence after thresholding and these selections are the final seeds for region growing. SAS was evaluated on an IVH porcine model. Results: SAS was compared to ground truth manual segmentation (MS) for accuracy, efficiency, and consistency. Accuracy was determined by comparing clot and ventricle volumes produced by SAS and MS, and comparing contours by calculating 95\% Hausdorff distances between the two labels. In Two-One-Sided Test, SAS and MS were found to be significantly equivalent (p \< 0.01). SAS on average was found to be 15 times faster than MS (p \< 0.01). Consistency was determined by repeated segmentation of the same image by both SAS and manual methods, SAS being significantly more consistent than MS (p \< 0.05).

Conclusion: SAS is a viable method to quantify the IVH clot and the lateral brain ventricles and it is serving in a large- scale porcine study of MRgFUS treatment of IVH clot lysis.\ 

}, doi = {10.1117/12.2081330}, url = {http://proceedings.spiedigitallibrary.org/proceeding.aspx?articleid=2210357}, author = {Maggie Hess and James Drake}, editor = {Thomas Looi and Andras Lasso and Gabor Fichtinger} } @article {Soehl2015a, title = {Scalable Ultrasound Calibration Phantoms Made From LEGO{\textregistered} Bricks}, volume = {10}, year = {2015}, month = {06/2015}, pages = {S218-S219}, address = {Barcelona, Spain}, doi = {10.1007/s11548-015-1213-2}, author = {Marie Soehl and M. Holden and Andras Lasso and Gabor Fichtinger} } @article {Brudfors2015, title = {Towards real-time, tracker-less 3D ultrasound guidance for spine anaesthesia.}, journal = {Int J Comput Assist Radiol Surg}, year = {2015}, month = {04/2015}, abstract = {

Epidural needle insertions and facet joint injections play an important role in spine anaesthesia. The main challenge of safe needle insertion is the deep location of the target, resulting in a narrow and small insertion channel close to sensitive anatomy. Recent approaches utilizing ultrasound (US) as a low-cost and widely available guiding modality are promising but have yet to become routinely used in clinical practice due to the difficulty in interpreting US images, their limited view of the internal anatomy of the spine, and/or inclusion of cost-intensive tracking hardware which impacts the clinical workflow.We propose a novel guidance system for spine anaesthesia. An efficient implementation allows us to continuously align and overlay a statistical model of the lumbar spine on the live 3D US stream without making use of additional tracking hardware. The system is evaluated in vivo on 12 volunteers.The in vivo study showed that the anatomical features of the epidural space and the facet joints could be continuously located, at a volume rate of 0.5\ Hz, within an accuracy of 3 and 7\ mm, respectively.A novel guidance system for spine anaesthesia has been presented which augments a live 3D US stream with detailed anatomical information of the spine. Results from an in vivo study indicate that the proposed system has potential for assisting the physician in quickly finding the target structure and planning a safe insertion trajectory in the spine.

}, doi = {10.1007/s11548-015-1206-1}, url = {http://dx.doi.org/10.1007/s11548-015-1206-1}, author = {Brudfors, Mikael and Seitel, Alexander and Rasoulian, Abtin and Andras Lasso and Lessoway, Victoria A. and Osborn, Jill and Maki, Atsuto and Robert Rohling and Purang Abolmaesumi} } @article {Carter2015a, title = {Visual feedback mounted on surgical tool}, year = {2015}, month = {03/2015}, pages = {36}, author = {Kaci Carter and Andras Lasso and Tamas Ungi and Evelyn Morin and Gabor Fichtinger} } @article {Cumming2014, title = {3D Printed Patient-Specific Surface Mould Applicators for Brachytherapy Treatment of Superficial Lesions}, volume = {41 (abstract in Medical Physics)}, number = {222}, year = {2014}, month = {06/2014}, abstract = {

Purpose:
Evaluate the feasibility of constructing 3D-printed patient-specific surface mould applicators for HDR brachytherapy treatment of superficial lesions.

Methods:
We propose using computer-aided design software to create 3D printed surface mould applicators for brachytherapy. A mould generation module was developed in the open-source 3D Slicer (www.slicer.org) medical image analysis platform. The system extracts the skin surface from CT images, and generates smooth catheter paths over the region of interest based on user-defined start and end points at a specified stand-off distance from the skin surface. The catheter paths are radially extended to create catheter channels that are sufficiently wide to ensure smooth insertion of catheters for a safe source travel. An outer mould surface is generated to encompass the channels. The mould is also equipped with fiducial markers to ensure its reproducible placement.

A surface mould applicator with eight parallel catheter channels of 4mm diameters was fabricated for the nose region of a head phantom; flexible plastic catheters of 2mm diameter were threaded through these channels maintaining 10mm catheter separations and a 5mm stand-off distance from the skin surface. The apparatus yielded 3mm thickness of mould material between channels and the skin. The mould design was exported as a stereolithography file to a Dimension SST1200es 3D printer and printed using ABS Plus plastic material.

Results:
The applicator closely matched its design and was found to be sufficiently rigid without deformation during repeated application on the head phantom. Catheters were easily threaded into channels carved along catheter paths. Further tests are required to evaluate feasibility of channel diameters smaller than 4mm.

Conclusion:
Construction of 3D-printed mould applicators show promise for use in patient specific brachytherapy of superficial lesions. Further evaluation of 3D printing techniques and materials is required for constructing sufficiently thin, rigid and durable surface moulds suitable for clinical deployment.

}, doi = {http://dx.doi.org/10.1118/1.4888333}, author = {Ian Cumming and C.P. Joshi and Andras Lasso and Adam Rankin and Conrad Falkson and John Schreiner and Gabor Fichtinger} } @article {Xu2014a, title = {Accuracy analysis in MRI-guided robotic prostate biopsy}, year = {2014}, month = {03/2014}, pages = {43}, url = {http://www.imno.ca/sites/default/files/2014Proceedings.pdf}, author = {Xu, Helen and Andras Lasso and Peter Guion and Axel Krieger and Aradhana Kaushal and A.K. Singh and P.A. Pinto and Jonathan Coleman and R.L. Grubb III and Jean-Baptiste Lattouf and Cynthia Menard and L.L. Whitcomb and Gabor Fichtinger} } @conference {Cifuentes2014a, title = {Customized deformable image registration using open-source software SlicerRT}, booktitle = {American Association Physicists in Medicine (AAPM)}, volume = {41 (abstract in Medical Physics)}, year = {2014}, month = {06/2014}, address = {Austin, TX}, abstract = {
Purpose:

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.

Methods:

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.

Results:

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.

Conclusion:

Based phantom validation, SlicerRT is capable of achieving comparable DIR accuracy to commercial programs such as MIM and VEL.

}, doi = {http://dx.doi.org/10.1118/1.4888094}, author = {J Cifuentes and N Kirby and Andras Lasso and L Chin and Csaba Pinter and J Pouliot and Gabor Fichtinger and J Pignol} } @conference {Anand2014b, title = {Design and Development of a Mobile Image Overlay System for Image-Guided Needle Interventions}, booktitle = {36th Annual International Conference of IEEE EMBS}, year = {2014}, month = {Accepted}, publisher = {IEEE EMBS}, organization = {IEEE EMBS}, address = {Chicago, IL, USA}, author = {Manjunath Anand and Franklin King and Tamas Ungi and Andras Lasso and John Rudan and Jagadeesan Jayender and Jan Fritz and John A Carrino and Ferenc Jolesz and Gabor Fichtinger} } @conference {Walsh2014, title = {Design of a tracked ultrasound calibration phantom made of LEGO bricks}, booktitle = {SPIE Medical ImagingMedical Imaging 2014: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {9036}, year = {2014}, month = {03/2014}, pages = {90362C}, publisher = {SPIE}, organization = {SPIE}, address = {San Diego, California, USA}, doi = {10.1117/12.2043533}, author = {Ryan Walsh and Marie Soehl and Adam Rankin and Andras Lasso and Gabor Fichtinger} } @article {Anand2014a, title = {Design of mobile image overlay system for image-guided interventions}, year = {2014}, month = {03/2014}, publisher = {ImNO}, address = {Toronto, Canada. March 24-25}, author = {Manjunath Anand and Franklin King and Tamas Ungi and Andras Lasso and John Rudan and Jagadeesan Jayender and Jan Fritz and Ferenc Jolesz and John A Carrino and Gabor Fichtinger} } @conference {Kotwicz2014, title = {Feasibility of a touch-free user interface for ultrasound snapshot-guided nephrostomy}, booktitle = {SPIE Medical Imaging 2014: Image-Guided Procedures, Robotic Interventions, and Modeling}, volume = {9036}, year = {2014}, month = {03/2014}, pages = {90362F}, publisher = {SPIE}, organization = {SPIE}, address = {San Diego, California, USA}, doi = {10.1117/12.2043564}, author = {Simon Kotwicz Herniczek and Andras Lasso and Tamas Ungi and Gabor Fichtinger} } @article {Pinter2014, title = {Improvements in SlicerRT, the radiation therapy research toolkit for 3D Slicer}, year = {2014}, month = {03/2014}, pages = {79}, address = {Toronto, ON, Canada, March 24-25, 2014}, url = {http://www.imno.ca/sites/default/files/2014Proceedings.pdf}, author = {Csaba Pinter and Andras Lasso and An Wang and Gregory C Sharp and David Jaffray and Gabor Fichtinger} } @article {Cifuentes2014, title = {Integration of SlicerRT into the clinical adaptive radiation therapy workflow: deformable image registration algorithm optimization and validation}, year = {2014}, month = {03/2014}, pages = {66}, url = {http://www.imno.ca/sites/default/files/2014Proceedings.pdf}, author = {J Cifuentes and Eric Vorauer and Peggy Le and Daniel Glick and Jonathan Livergant and Csaba Pinter and Andras Lasso and Gabor Fichtinger and Lee Chin} } @article {Glick2014, title = {Interfraction Variation in Dose and Position During the Treatment of Pancreatic Cancer Using Tomotherapy}, year = {2014}, month = {03/2014}, pages = {70}, url = {http://www.imno.ca/sites/default/files/2014Proceedings.pdf}, author = {Daniel Glick and Eric Vorauer and J Cifuentes and Frances Tonolete and Csaba Pinter and Gabor Fichtinger and Andras Lasso and Lee Chin and Hans Chung} } @article {Xu2014c, title = {Multi-slice-to-volume registration for MRI-guided transperineal prostate biopsy}, journal = {International Journal of Computer Assisted Radiology and Surgery}, volume = {10}, number = {5}, year = {2014}, month = {09/2014}, pages = {563-572}, issn = {1861-6410}, doi = {10.1007/s11548-014-1108-7}, author = {Xu, Helen and Andras Lasso and Andriy Fedorov and Kemal Tuncali and Clare M Tempany and Gabor Fichtinger} } @article {Lasso2014a, title = {PLUS: Open-source toolkit for ultrasound-guided intervention systems}, journal = {IEEE Transactions on Biomedical Engineering}, volume = {61}, number = {10}, year = {2014}, month = {10/2014}, pages = {2527-2537}, issn = {0018-9294}, doi = {10.1109/TBME.2014.2322864}, author = {Andras Lasso and Tamas Heffter and Adam Rankin and Csaba Pinter and Tamas Ungi and Gabor Fichtinger} } @article {Anderson2014, title = {Proposed Feasibility Analysis of Low Cost Inertial Freehand Ultrasound Position Tracking}, year = {2014}, address = {Toronto, Ontario}, author = {Anderson, Ryan and Andras Lasso and Keyvan Hashtrudi-Zaad and Gabor Fichtinger} } @article {Lasso2014b, title = {Running Matlab functions in 3D Slicer using MatlabBridge}, year = {2014}, month = {03/2014}, pages = {78}, address = {Toronto, ON, Canada, March 24-25, 2014}, url = {http://www.imno.ca/sites/default/files/2014Proceedings.pdf}, author = {Andras Lasso and Kevin Alexander and Christopher Jechel and Kevin Wang and John Schreiner and Gabor Fichtinger} } @article {Ungi2014a, title = {Spinal curvature measurement by tracked ultrasound snapshots}, journal = {Ultrasound in Medicine and Biology}, volume = {40}, year = {2014}, month = {02/2014}, pages = {447-54}, author = {Tamas Ungi and Franklin King and Michael Kempston and Keri, Zsuzsanna and Andras Lasso and Parvin Mousavi and John Rudan and Daniel P. Borschneck and Gabor Fichtinger} } @article {Xu2014b, title = {Target Localization in MRI-guided Transperineal Prostate Biopsy using Multi-Slice-to-Volume Registration}, year = {2014}, month = {03/2014}, pages = {44}, url = {http://www.imno.ca/sites/default/files/2014Proceedings.pdf}, author = {Xu, Helen and Andras Lasso and Andriy Fedorov and Clare M Tempany and Gabor Fichtinger} } @article {King2014b, title = {A tool for intraoperative visualization of image registration results}, year = {2014}, month = {03/2014}, publisher = {ImNO}, address = {Toronto, Canada, March 24-25}, author = {Franklin King and Andras Lasso and Csaba Pinter and Gabor Fichtinger} } @conference {King2014a, title = {A tool for intraoperative visualization of registration results}, booktitle = {SPIE Medical Imaging 2014}, volume = {9036}, year = {2014}, month = {03/2014}, pages = {90362A}, publisher = {SPIE}, organization = {SPIE}, address = {San Diego, California, USA}, doi = {10.1117/12.2043496}, author = {Franklin King and Andras Lasso and Csaba Pinter and Gabor Fichtinger} } @conference {Soehl2014, title = {Tracked ultrasound calibration studies with a phantom made of LEGO(r) bricks}, booktitle = {SPIE Medical Imaging 2014}, volume = {9036}, year = {2014}, month = {03/2014}, pages = {90362R}, address = {San Diego, United States, March 12, 2014}, doi = {10.1117/12.2044121}, author = {Marie Soehl and Ryan Walsh and Adam Rankin and Andras Lasso and Gabor Fichtinger} } @article {Soehl2014a, title = {Tracked ultrasound calibration studies with a phantom made of LEGO{\textregistered} bricks}, year = {2014}, address = {Toronto, Canada, March 24-25, 2014}, author = {Marie Soehl and Ryan Walsh and Adam Rankin and Andras Lasso and Gabor Fichtinger} } @inbook {Ungi2014c, title = {Tracked Ultrasound in Navigated Spine Interventions}, booktitle = {Spinal Imaging and Image Analysis}, year = {2014}, month = {12/2014}, pages = {469-94}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, chapter = {15}, address = {Cham, Switzerland}, abstract = {

Ultrasound is an increasingly popular imaging modality in image-guided interventions, due to its safety, accessibility, and low cost. But ultrasound imaging\ has a steep learning curve, and requires significant coordination skills from the operator. It is difficult to interpret cross-sectional anatomy in arbitrary angles, and\ even more challenging to orient a needle with respect to the ultrasound plane. Position tracking technology is a promising augmentation method to ultrasound\ imaging. Both the ultrasound transducer and the needle can be tracked, enabling computer-assisted navigation applications in ultrasound-guided spinal interventions.\ Furthermore, the patient can also be tracked, which enables fusion of other imaging modalities with ultrasound. In this chapter, we first present the technical\ background of tracked ultrasound. We will review how to build research systems from commercially available components and open-source software. Then we will\ review some spine-related applications of tracked ultrasound modality, including procedural skills training, needle navigation for anesthesia, surgical navigation, and\ other potential applications.

}, doi = {10.1007/978-3-319-12508-4_15}, url = {http://link.springer.com/chapter/10.1007/978-3-319-12508-4_15}, author = {Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @article {Xu2013b, title = {Accuracy analysis in MRI-guided robotic prostate biopsy}, journal = {International Journal of Computer Assisted Radiology and Surgery}, volume = {8}, number = {6}, year = {2013}, month = {03/2013}, pages = {937-944}, doi = {10.1007/s11548-013-0831-9}, author = {Xu, Helen and Andras Lasso and Peter Guion and Axel Krieger and Aradhana Kaushal and Anurag K. Singh and P.A. Pinto and Jonathan Coleman and R.L. Grubb III and Jean-Baptiste Lattouf and Cynthia Menard and Whitcomb, Louis L. and Gabor Fichtinger} } @article {Xu2013, title = {Accuracy analysis in MRI-guided robotic prostate biopsy}, volume = {8}, number = {1}, year = {2013}, pages = {211}, publisher = {Springer}, address = {Heidelberg, Germany, June 26-29}, author = {Xu, Helen and Andras Lasso and Peter Guion and Axel Krieger and Aradhana Kaushal and Anurag K. Singh and P.A. Pinto and Jonathan Coleman and R.L. Grubb III and Jean-Baptiste Lattouf and Cynthia Menard and Whitcomb, Louis L. and Gabor Fichtinger} } @article {Wolff2013b, title = {C-arm angle measurement with accelerometer for brachytherapy: an accuracy study}, journal = {International Journal of Computer Assisted Radiology and Surgery}, year = {2013}, month = {07/2013}, issn = {1861-6429}, doi = {10.1007/s11548-013-0918-3}, author = {Wolff, Thomas and Andras Lasso and Eblenkamp, Markus and Wintermantel, Erich and Gabor Fichtinger} } @article {Wolff2013, title = {C-arm angle measurement with accelerometer for brachytherapy{\textemdash}an accuracy study}, volume = {8}, year = {2013}, pages = {183-184}, author = {Wolff, Thomas and Andras Lasso and Eblenkamp, Markus and Wintermantel, Erich and Gabor Fichtinger} } @article {Carbajal2013c, title = {Improving N-Wire Phantom-based Freehand Ultrasound Calibration}, journal = {IJCARS}, volume = {8}, year = {2013}, month = {11/2013}, pages = {1063-1072}, abstract = {

Purpose: Freehand tracked ultrasound imaging is an inexpensive non-invasive technique used in several guided interventions. This technique requires spatial calibration between the tracker and the ultrasound image plane. Several calibration devices (a.k.a. phantoms) use N-wires that are convenient for automatic procedures since the segmentation of fiducials in the images and the localization of the middle wires in space are straightforward and can be performed in real time. The procedures reported in literature consider only the spatial position of the middle wire. We investigate if better results can be achieved if the information of all the wires is equally taken into account. We also evaluated the precision and accuracy of the implemented methods to allow comparison with other methods. Methods: We consider a cost function based on the in-plane errors between the intersection of all the wires with the image plane and their respective segmented points in the image. This cost function is minimized iteratively starting from a seed computed with a closed-form solution based on the middle wires. Results: Mean calibration precision achieved with the N-wire phantom was about 0.5 mm using a shallow probe and mean accuracy was around 1.4 mm with all implemented methods. Precision was about 2.0 mm using a deep probe. Conclusions: Precision and accuracy achieved with the N-wire phantom and a shallow probe are at least comparable to that obtained with other methods traditionally considered more precise. Calibration using N-wires can be done more consistently if the parameters are optimized with the proposed 2D cost function.

}, doi = {10.1007/s11548-013-0904-9}, author = {Guillermo Carbajal and Andras Lasso and {\'A}lvaro G{\'o}mez and Gabor Fichtinger} } @article {Carbajal2013a, title = {Improving N-Wire Phantom-based Freehand Ultrasound Calibration}, year = {2013}, month = {02/2013}, address = {Toronto, Canada, February 4th-5th 2013}, author = {Guillermo Carbajal and Andras Lasso and {\'A}lvaro G{\'o}mez and Gabor Fichtinger} } @conference {Carbajal2013b, title = {Improving N-Wire Phantom-based Freehand Ultrasound Calibration}, booktitle = {CARS 2013}, year = {2013}, author = {Guillermo Carbajal and Andras Lasso and {\'A}lvaro G{\'o}mez and Gabor Fichtinger} } @article {Chin2013, title = {Integration of SlicerRT into the Radiation Therapy Clinical Workflow}, year = {2013}, month = {02/2013}, author = {Lee Chin and Matt Wronski and Jonathan Livergant and Andrew Agbanti and Darren Yohan and Judith Balogh and Andras Lasso and Gabor Fichtinger} } @article {Livergant2013, title = {Investigation of daily deformable image registration for adaptive radiation therapy in head and neck cancer}, year = {2013}, address = {Montreal, QC}, author = {Jonathan Livergant and Eric Vorauer and Andrew Agbanti and Andras Lasso and Csaba Pinter and Gabor Fichtinger and Lee Chin} } @article {Anand2013a, title = {Mobile Image Overlay System for Image Guided Interventions}, year = {2013}, month = {03/2013}, address = {Washington DC, USA, March 21-23, 2013.}, keywords = {image guided interventions, mobile image overlay, needle placement interventions, percutaneous interventions, static image overlay}, author = {Manjunath Anand and Tamas Ungi and Andras Lasso and Paweena U-Thainual and Jagadeesan Jayender and Jan Fritz and John A Carrino and Ferenc Jolesz and Gabor Fichtinger} } @article {Anand2013c, title = {MOBILE IMAGE OVERLAY SYSTEM (MIOS) FOR IMAGE GUIDED INTERVENTIONS}, year = {2013}, month = {06/2013}, address = {Faculty of Health Sciences, Queen{\textquoteright}s University}, author = {Manjunath Anand and Tamas Ungi and Andras Lasso and Paweena U-Thainual and Jagadeesan Jayender and Jan Fritz and John A Carrino and Ferenc Jolesz and Gabor Fichtinger} } @article {Bartha2013a, title = {Open Source Ultrasound Simulation Using Surface Meshes}, year = {2013}, month = {02/2013}, address = {Toronto, Canada, February 4th-5th}, keywords = {PLUS toolkit, surface mesh, training, ultrasound simulation}, author = {Laura Bartha and Andras Lasso and Csaba Pinter and Tamas Ungi and Gabor Fichtinger} } @conference {Bartha2013c, title = {Open-Source Surface Mesh-Based Ultrasound Simulator}, booktitle = {CARS 2013}, volume = {8}, year = {2013}, month = {06/2013}, pages = {156}, author = {Laura Bartha and Andras Lasso and Csaba Pinter and Tamas Ungi and Gabor Fichtinger} } @article {Bartha2013b, title = {Open-source surface mesh-based ultrasound-guided spinal intervention simulator}, journal = {International Journal of Computer Assisted Radiology and Surgery}, volume = {8}, year = {2013}, month = {06/2013}, pages = {1043-51}, doi = {10.1007/s11548-013-0901-z}, author = {Laura Bartha and Andras Lasso and Csaba Pinter and Tamas Ungi and Keri, Zsuzsanna and Gabor Fichtinger} } @article {Ungi2013b, title = {Perk Tutor: Open-source platform for ultrasound-guided needle intervention training}, year = {2013}, month = {02/2013}, address = {Toronto, ON, Canada}, author = {Tamas Ungi and Eric Moult and Andras Lasso and McGraw, Robert C and Gabor Fichtinger} } @article {Bartha2013, title = {The Perk Tutor Training Platform Integrated with Simulated Ultrasound}, year = {2013}, month = {03/2013}, author = {Laura Bartha and Andras Lasso and Csaba Pinter and Tamas Ungi and Gabor Fichtinger} } @article {Lasso2013a, title = {Prototyping Clinical Applications with the Public Library for Ultrasound (PLUS) Toolkit and 3D Slicer}, volume = {6}, year = {2013}, month = {03/2013}, pages = {34}, address = {Crystal City, VA, USA}, url = {http://www.ncigt.org/publications/item/view/2334}, author = {Andras Lasso and Tamas Ungi and Csaba Pinter and Tamas Heffter and Adam Rankin and Gabor Fichtinger} } @article {Ungi2013c, title = {Prototyping image-guided therapy applications using the SlicerIGT platform}, volume = {6}, year = {2013}, month = {03/2013}, pages = {61}, address = {Crystal City, VA, USA}, url = {http://www.spl.harvard.edu/publications/item/view/2334}, author = {Tamas Ungi and Junichi Tokuda and Adam Rankin and Andras Lasso and Gabor Fichtinger} } @article {Ungi2013a, title = {SlicerIGT: Open-source platform for image-guided needle interventions}, year = {2013}, month = {02/2013}, address = {Toronto, ON, Canada}, author = {Tamas Ungi and Andras Lasso and Csaba Pinter and Adam Rankin and Gabor Fichtinger} } @article {Pinter2013a, title = {SlicerRT {\textendash} Radiation therapy research toolkit for 3D Slicer}, year = {2013}, month = {02/2013}, address = {Toronto, ON, Canada}, author = {Csaba Pinter and Andras Lasso and An Wang and David Jaffray and Gabor Fichtinger} } @article {Pinter2013b, title = {SlicerRT sets new standard for radiation therapy research tools}, journal = {ECR Today 2013}, year = {2013}, month = {03/2013}, pages = {19}, edition = {Technology Focus}, author = {Csaba Pinter and Andras Lasso and An Wang and David Jaffray and Gabor Fichtinger} } @article {Moult2013b, title = {Temporal calibration of tracked ultrasound}, year = {2013}, month = {02/2013}, address = {Toronto, ON, Canada}, author = {Eric Moult and Tamas Ungi and Csaba Pinter and Mattea Welch and Andras Lasso and Gabor Fichtinger} } @article {Fedorov2013, title = {Towards Open Source Infrastructure for Joint MRI/TRUS Guided Prostate Interventions}, volume = {6}, year = {2013}, month = {03/2013}, pages = {67}, address = {Crystal City, VA, USA}, url = {http://www.spl.harvard.edu/publications/item/view/2334}, author = {Andriy Fedorov and Andras Lasso and Mehdi Moradi and Sang-Eun Song and Emily Neubauer and Robert Owen and Tina Kapur and William Wells and Paul Nguyen and Gabor Fichtinger and Clare M Tempany} } @article {Imani2013, title = {Ultrasound-guided Characterization of Interstitial Ablated Tissue Using RF Time Series: Feasibility Study.}, journal = {IEEE transactions on bio-medical engineering}, year = {2013}, month = {01/2013}, abstract = {

This paper presents the results of a feasibility study to demonstrate the application of ultrasound RF time series imaging to accurately differentiate ablated and non-ablated tissue. Methods: For 12 ex vivo and two in situ tissue samples, RF ultrasound signals are acquired prior to, and following, high intensity ultrasound ablation. Spatial and temporal features of these signals are used to characterize ablated and non-ablated tissue in a supervised-learning framework. Results: In crossvalidation evaluation, a subset of four features extracted from RF time series produce a classification accuracy of 84.5\%, and an area under ROC curve of 0.91 for ex vivo data, and an accuracy of 85\% for in situ data. Conclusion: Ultrasound RF time series is a promising approach for characterizing ablated tissue.

}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23335657}, author = {F Imani and Purang Abolmaesumi and Wu, M. and Andras Lasso and E. Clif Burdette and Ghoshal, G and Tamas Heffter and Williams, E and Neubauer, P and Gabor Fichtinger and Parvin Mousavi} } @conference {Anand2013b, title = {Workspace Analysis and Calibration Method for Mobile Image Overlay System used for Image-Guided Interventions}, booktitle = {The Hamlyn Symposium on Medical Robotics - 2013}, year = {2013}, month = {06/2013}, author = {Manjunath Anand and Tamas Ungi and Andras Lasso and Paweena U-Thainual and Jagadeesan Jayender and Jan Fritz and John A Carrino and Ferenc Jolesz and Gabor Fichtinger} } @conference {Pinter2012c, title = {Application of the SlicerRT toolkit for image-guided radiation therapy research}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI 2012) - Image-Guidance and Multimodal Dose Planning in Radiation Therapy}, year = {2012}, month = {10/2012}, address = {Nice, France}, author = {Csaba Pinter and Andras Lasso and An Wang and David Jaffray and Gabor Fichtinger} } @article {MPeikari2012, title = {Characterization of ultrasound elevation beamwidth artifacts for prostate brachytherapy needle insertion}, journal = {Medical Physics}, volume = {39}, year = {2012}, month = {01/2012}, pages = {246-256}, abstract = {

Purpose: Ultrasound elevation beamwidth leads to image artefacts and uncertainties in localizing objects (such as a surgical needle) in ultrasound images. We examined the clinical significance of errors caused by elevation beamwidth artefacts and imaging parameters in needle insertion procedures. Method: Beveled prostate brachytherapy needles were inserted through all holes of a grid template under real-time transrectal ultrasound (TRUS) guidance. The needle tip position as indicated by the TRUS image was compared to their observed physical location. A new device was developed to measure the ultrasound elevation beamwidth. Result: Imaging parameters of the TRUS scanner have direct impact on the localization error ranging from 0.5 mm upto 4 mm. The smallest localization error was observed laterally close to the center of the grid template, and axially within the beam{\textquoteright}s focal zone. Largest localization error occurs laterally around both sides of the grid template, and axially within the beam{\textquoteright}s far field. we also found that the localization errors vary with both lateral and elevation offsets. Conclusion: We found properly adjusting the TRUS imaging settings to lower the ultrasound gain and power effectively minimized the appearance of elevation beamwidth artefacts and in turn reduced the localization errors of the needle tip.

}, keywords = {Brachytherapy, localization error, main lobe, side lobe, ultrasound imaging}, issn = {0094-2405}, doi = {10.1118/1.3669488}, url = {http://online.medphys.org/resource/1/mphya6/v39/i1/p246_s1}, author = {Mohammad Peikari and Thomas K. Chen and Andras Lasso and Tamas Heffter and E. Clif Burdette and Gabor Fichtinger} } @conference {Lasso2012d, title = {Implementation of the PLUS open-source toolkit for translational research of ultrasound-guided intervention systems}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI 2012) - Systems and Architectures for Computer Assisted Interventions}, year = {2012}, month = {10/2012}, pages = {1-12}, publisher = {The MIDAS Journal}, organization = {The MIDAS Journal}, address = {Nice, France}, url = {http://hdl.handle.net/10380/3367}, author = {Andras Lasso and Tamas Heffter and Csaba Pinter and Tamas Ungi and Gabor Fichtinger} } @article {Tokuda2012, title = {In-bore Setup and Software for 3T MRI-guided Transperineal Prostate Biopsy}, journal = {Physics in Medicine and Biology}, year = {2012}, month = {09/2012}, author = {Junichi Tokuda and Kemal Tuncali and Iulian Iordachita and Sam Sang-Eun Song and Andriy Fedorov and Sota Oguro and Andras Lasso and Fiona M. Fennessy and Clare M Tempany and Nobuhiko Hata} } @article {Lasso2012e, title = {Multi-slice-to-volume registration for reducing targeting error during MRI-guided transrectal prostate biopsy}, year = {2012}, month = {09/2012}, address = {Boston, MA, USA}, author = {Andras Lasso and Andriy Fedorov and Janice Fairhurst and Junichi Tokuda and Kemal Tuncali and Robert Mulkern and Nobuhiko Hata and Clare M Tempany and Gabor Fichtinger} } @conference {Ungi2012d, title = {Open-source training platform for ultrasound-guided needle insertions}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI 2012) - Systems and Architectures for Computer Assisted Interventions}, year = {2012}, month = {10/2012}, address = {Nice, France}, author = {Tamas Ungi and Andras Lasso and Gabor Fichtinger} } @article {Ungi2012c, title = {Perk Tutor: An open-source training platform for ultrasound-guided needle insertions}, journal = {IEEE Trans Biomed Eng}, volume = {59}, year = {2012}, month = {12/2012}, pages = {3475-3481}, issn = {0018-9294}, doi = {10.1109/TBME.2012.2219307}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6304910}, author = {Tamas Ungi and Sargent, D. and Eric Moult and Andras Lasso and Csaba Pinter and McGraw, Robert C and Gabor Fichtinger} } @article {Lasso2012b, title = {Planning and Targeting System for MRI-guided Robotic Interventions}, year = {2012}, month = {02/2012}, address = {Toronto, ON, Canada}, author = {Andras Lasso and Junichi Tokuda and Andriy Fedorov and Siddharth Vikal and Hadi Tadayyon and Aradhana Kaushal and Peter Guion and Gabor Fichtinger} } @article {Lasso2012a, title = {PLUS: An open-source toolkit for ultrasound-guided intervention systems development}, year = {2012}, month = {02/2012}, address = {Toronto, ON, Canada}, author = {Andras Lasso and Tamas Heffter and Csaba Pinter and Tamas Ungi and Thomas K. Chen and Alexis Boucharin and Gabor Fichtinger} } @article {Lasso2012c, title = {Real-time data acquisition for cardiovascular research}, year = {2012}, month = {06/2012}, address = {Toronto, ON, Canada}, author = {Andras Lasso and Gabor Fichtinger} } @article {Pinter2012b, title = {SlicerRT - Radiation therapy research toolkit for 3D Slicer}, volume = {39}, year = {2012}, month = {10/2012}, pages = {6332/7}, abstract = {

Purpose: Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing. Methods: SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications. Results: Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases.

}, keywords = {3D Slicer, DICOM-RT, dose comparison, dose volume histogram, Radiation therapy}, doi = {http://dx.doi.org/10.1118/1.4754659}, author = {Csaba Pinter and Andras Lasso and An Wang and David Jaffray and Gabor Fichtinger} } @article {Pinter2012a, title = {SlicerRT {\textendash} Radiotherapy toolkit for 3D Slicer}, year = {2012}, month = {02/2012}, address = {Toronto, ON, Canada}, keywords = {Radiotherapy}, author = {Csaba Pinter and Andras Lasso and An Wang and Gabor Fichtinger} } @article {Ungi2012b, title = {Spinal Needle Navigation by Tracked Ultrasound Snapshots}, journal = {IEEE Trans Biomed Eng}, volume = {59}, year = {2012}, month = {10/2012}, pages = {2766-2772}, author = {Tamas Ungi and Purang Abolmaesumi and Rayhan Jalal and Mattea Welch and Irene Ayukawa and Simrin Nagpal and Andras Lasso and Melanie Jaeger and Daniel P. Borschneck and Gabor Fichtinger and Parvin Mousavi} } @article {Vaughan2012, title = {Ultrasound Volume Reconstruction: Open-Source Implementation with Hole Filling Functionality}, year = {2012}, month = {09/2012}, address = {Boston, MA}, author = {Thomas Vaughan and Andras Lasso and Gabor Fichtinger} } @article {Imani2012, title = {Ultrasound-guided Characterization of ablated Tissue Using RF Time Series}, year = {2012}, month = {06/2012}, address = {Rosslyn, VA, USA}, author = {F Imani and Mohammad Daoud and Andras Lasso and E. Clif Burdette and Gabor Fichtinger and Purang Abolmaesumi and Parvin Mousavi} } @article {Ungi2012a, title = {Ultrasound-guided spinal needle placement on open source platform}, year = {2012}, month = {02/2012}, address = {Toronto, ON, Canada}, author = {Tamas Ungi and Andras Lasso and Mattea Welch and Rayhan Jalal and Simrin Nagpal and Melanie Jaeger and Daniel P. Borschneck and Parvin Mousavi and Gabor Fichtinger} } @article {Tuncali2011, title = {3T MRI-guided Transperineal Targeted Prostate Biopsy: Clinical Feasibility, Safety, and Early Results}, volume = {19}, year = {2011}, pages = {53}, author = {Kemal Tuncali and Junichi Tokuda and Iulian Iordachita and Sam Sang-Eun Song and Andriy Fedorov and Sota Oguro and Andras Lasso and Fiona M. Fennessy and Yi Tang and Clare M Tempany and Nobuhiko Hata} } @conference {Ungi2011a, title = {Augmented reality training to improve needle-based percutaneous interventions}, booktitle = {ImNO2011 - Imaging Network Ontario Symposium}, year = {2011}, month = {01/2011}, address = {Toronto, ON, Canada, Jan 31-Feb 1}, author = {Tamas Ungi and Paweena U-Thainual and Andras Lasso and Yeo, Caitlin T and McGraw, Robert C and Gabor Fichtinger} } @article {Chen2011, title = {Automated Intraoperative Calibration for Prostate Cancer Brachytherapy}, journal = {Medical Physics}, volume = {38}, year = {2011}, month = {11/2011}, pages = {6285-6299}, doi = {10.1118/1.3651690}, author = {Thomas K. Chen and Tamas Heffter and Andras Lasso and Csaba Pinter and Purang Abolmaesumi and E. Clif Burdette and Gabor Fichtinger} } @conference {Bartha2011a, title = {Automatic fiducial localization in ultrasound images for a thermal ablation validation platform}, booktitle = {SPIE Medical Imaging}, volume = {7964}, number = {1}, year = {2011}, month = {03/2011}, pages = {796421}, publisher = {SPIE}, organization = {SPIE}, address = {Lake Buena Vista (Orlando), Florida, USA}, doi = {10.1117/12.878568}, url = {http://link.aip.org/link/?PSI/7964/796421/1}, author = {Laura Bartha and Andras Lasso and Thomas K. Chen and Gabor Fichtinger} } @article {Yeo2011, title = {The Effect of Augmented Reality Training on Percutaneous Needle Placement in Spinal Facet Joint Injections}, journal = {IEEE Transactions on Biomedical Engineering}, volume = {58}, year = {2011}, month = {07/2011}, pages = {2031-7}, keywords = {augmented reality, surgical training}, issn = {0018-9294}, doi = {10.1109/TBME.2011.2132131}, url = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5739103\&tag=1}, author = {Yeo, Caitlin T and Tamas Ungi and Paweena U-Thainual and Andras Lasso and McGraw, Robert C and Gabor Fichtinger} } @conference {MPeikari2011, title = {Effects of Ultrasound Section-Thickness on Brachytherapy Needle Tip Localization Error}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011)}, year = {2011}, address = {Toronto, ON, Canada}, author = {Mohammad Peikari and Thomas K. Chen and Andras Lasso and Tamas Heffter and Gabor Fichtinger} } @conference {HPeikari2011a, title = {Improved validation platform for ultrasound-based monitoring of thermal ablation}, booktitle = {SPIE Medical Imaging}, volume = {7964}, number = {1}, year = {2011}, pages = {79641H}, publisher = {SPIE}, organization = {SPIE}, address = {Lake Buena Vista (Orlando), Florida, USA}, doi = {10.1117/12.878333}, url = {http://link.aip.org/link/?PSI/7964/79641H/1}, author = {Hamed Peikari and Andras Lasso and Gabor Fichtinger} } @conference {Imani2011, title = {Monitoring of Tissue Ablation Using Time Series of Ultrasound RF data}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI 2011)}, year = {2011}, month = {09/2011}, pages = {379-386}, address = {Toronto, ON, Canada}, author = {F Imani and Wu, M. and Andras Lasso and E. Clif Burdette and Mohammad Daoud and Gabor Fichtinger and Purang Abolmaesumi and Parvin Mousavi} } @article {Lasso2011b, title = {Multi-slice-to-volume registration for reducing targeting error during MRI-guided transrectal biopsy}, volume = {4}, year = {2011}, month = {10/2011}, pages = {31}, address = {Arlington VA, October 12-13, 2011}, author = {Andras Lasso and Hadi Tadayyon and Aradhana Kaushal and Peter Guion and Gabor Fichtinger} } @article {Ungi2011c, title = {Perk Station image overlay improves training of facet joint injections}, volume = {4}, year = {2011}, month = {10/2011}, pages = {118}, address = {Arlington VA, October 12-13, 2011}, author = {Tamas Ungi and Paweena U-Thainual and Yeo, Caitlin T and Andras Lasso and McGraw, Robert C and Gabor Fichtinger} } @article {Lasso2011c, title = {PLUS: An open-source toolkit for developing ultrasound-guided intervention systems}, volume = {4}, year = {2011}, month = {10/2011}, pages = {103}, address = {Arlington VA, October 12-13, 2011}, author = {Andras Lasso and Tamas Heffter and Csaba Pinter and Tamas Ungi and Thomas K. Chen and Alexis Boucharin and Gabor Fichtinger} } @article {Tokuda2011, title = {Preliminary Accuracy Evaluation of 3T MRI-guided Transperineal Prostate Biopsy with Grid Template}, volume = {19}, year = {2011}, pages = {3761}, author = {Junichi Tokuda and Kemal Tuncali and Iulian Iordachita and Sam Sang-Eun Song and Andriy Fedorov and Sota Oguro and Andras Lasso and Fiona M. Fennessy and Yi Tang and Clare M Tempany and Nobuhiko Hata} } @article {Lasso2011a, title = {System design of adaptive image-guided percutaneous needle intervention software using open source components}, year = {2011}, pages = {45}, address = {Toronto, ON, Canada, Jan 31-Feb 1}, author = {Andras Lasso and Gabor Fichtinger} } @article {Tadayyon2011, title = {Target Motion Tracking in MRI-guided Transrectal Robotic Prostate Biopsy}, journal = {IEEE Transactions on Biomedical Engineering}, volume = {58}, year = {2011}, month = {08/2011}, pages = {3135-42}, issn = {0018-9294}, doi = {10.1109/TBME.2011.2163633}, author = {Hadi Tadayyon and Andras Lasso and Aradhana Kaushal and Peter Guion and Gabor Fichtinger} } @conference {Xu2010, title = {Accuracy validation for MRI-guided robotic prostate biopsy}, booktitle = {Medical Imaging 2010: Visualization, Image-Guided Procedures, and Modeling}, year = {2010}, pages = {762517 - 762517-8}, publisher = {SPIE}, organization = {SPIE}, address = {San Diego, California, USA}, doi = {10.1117/12.844251}, author = {Xu, Helen and Andras Lasso and Siddharth Vikal and Peter Guion and Axel Krieger and Aradhana Kaushal and Whitcomb, Louis L. and Gabor Fichtinger} } @conference {Xu2010b, title = {Clinical Accuracy of Robot-Assisted Prostate Biopsy in Closed MRI Scanner}, booktitle = {The Hamlyn Symposium on Medical Robotics}, year = {2010}, address = {The Royal Society, London, UK, 25 May 2010}, url = {http://www.hamlyn-robotics.org/}, author = {Xu, Helen and Andras Lasso and Siddharth Vikal and Peter Guion and Axel Krieger and Aradhana Kaushal and Whitcomb, Louis L. and Gabor Fichtinger} } @article {Hall2010a, title = {Compilation of a pathological validation database for ultrasound monitoring of tumour ablation}, year = {2010}, month = {09/2010}, address = {Trondheim, Norway, September 2-4, 2010}, author = {Jena Hall and Andras Lasso and Hamed Peikari and Alexandra M. Pompeu-Robinson and Gabor Fichtinger} } @conference {Lasso2010a, title = {Gynecology brachytherapy applicator pose reconstruction in MR images}, booktitle = {CARS 2010 - Proceedings of the 24th International Congress and Exhibition, Geneva. Switzerland, June 23-26, 2010}, series = {International Journal of Computer Assisted Radiology and Surgery}, volume = {5}, year = {2010}, month = {06/2010}, pages = {S324-S325}, publisher = {Springer}, organization = {Springer}, address = {Geneva, Switzerland}, doi = {10.1007/s11548-010-0471-2}, url = {http://www.springerlink.com/content/v7633809m2877373/?p=3a8265d1f57d493d9ef4ad82a8d9b18e\&pi=43}, author = {Andras Lasso and Marton Kelemen and Tamas Haidegger and Christian Kirisits and Gabor Fichtinger} } @conference {Tadayyon2010a, title = {MRI-Guided prostate motion tracking by means of multislice-to-volume registration}, booktitle = {SPIE Medical Imaging}, year = {2010}, month = {02/2010}, keywords = {Biopsy, motion tracking, MRI, slice-to-volume registation}, doi = {10.1117/12.844454}, author = {Hadi Tadayyon and Gabor Fichtinger and Andras Lasso and Siddharth Vikal and Sean Gill} } @conference {Xu2010c, title = {MRI-Guided Robotic Prostate Biopsy: A Clinical Accuracy Validation}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI 2010)}, year = {2010}, pages = {383-391}, publisher = {Springer}, organization = {Springer}, address = {Beijing, China}, isbn = {978-3-642-15710-3}, doi = {http://dx.doi.org/10.1007/978-3-642-15711-0_48}, author = {Xu, Helen and Andras Lasso and Siddharth Vikal and Peter Guion and Axel Krieger and Aradhana Kaushal and Whitcomb, Louis L. and Gabor Fichtinger} } @conference {Xu2010d, title = {MRI-Guided Transrectal Robotic Prostate Biopsy Validation}, booktitle = {The American Association of Physicists in Medicine (AAPM) Annual Meeting 2010, July 18-22}, volume = {37, 3128 (2010)}, year = {2010}, pages = {3128-3129}, address = {Philadelphia, Pennsylvania}, doi = {10.1118/1.3468153}, url = {http://dx.doi.org/10.1118/1.3468153}, author = {Xu, Helen and Andras Lasso and Siddharth Vikal and Peter Guion and Axel Krieger and Aradhana Kaushal and Whitcomb, Louis L. and Gabor Fichtinger} } @conference {Tadayyon2010b, title = {Target Motion Compensation in MRI-guided Prostate Biopsy with Static Images}, booktitle = {EMBC2010 - 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society}, year = {2010}, pages = {5416-5419}, publisher = {Crown}, organization = {Crown}, address = {Buenos Aires, Argentina}, author = {Hadi Tadayyon and Andras Lasso and Sean Gill and Aradhana Kaushal and Peter Guion and Gabor Fichtinger} } @conference {Lasso2010b, title = {Targeting Error Simulator for Image-guided Prostate Needle Placement}, booktitle = {EMBC2010 - 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society}, year = {2010}, pages = {5424-5427}, address = {Buenos Aires, Argentina}, author = {Andras Lasso and Shachar Avni and Gabor Fichtinger} } @conference {Pompeu-Robinson2010, title = {Validation platform for ultrasound-based monitoring of thermal ablation}, booktitle = {SPIE - Medical Imaging}, year = {2010}, address = {San Diego}, abstract = {

PURPOSE: A ground-truth validation platform was developed to provide spatial correlation between ultrasound (US), temperature measurements and histopathology images to validate US based thermal ablation monitoring methods. METHOD: The test-bed apparatus consists of a container box with integrated fiducial lines. Tissue samples are suspended within the box using agar gel as the fixation medium. Following US imaging, the gel block is sliced and pathology images are acquired. Interactive software segments the fiducials as well as structures of interest in the pathology and US images. The software reconstructs the regions in 3D space and performs analysis and comparison of the features identified from both imaging modalities. RESULTS: The apparatus and software were constructed to meet technical requirements. Tissue samples were contoured, reconstructed and registered in the common coordinate system of fiducials. There was agreement between the sample shapes, but systematic shift of several millimeters was found between histopathology and US. This indicates that during pathology slicing shear forces tend to dislocate the fiducial lines. Softer fiducial lines and harder gel material can eliminate this problem. CONCLUSION: Viability of concept was presented. Despite our straightforward approach, further experimental work is required to optimize all materials and customize software.

}, doi = {10.1117/12.844053}, author = {Alexandra M. Pompeu-Robinson and James Gray and Joshua Marble and Hamed Peikari and Jena Hall and Paweena U-Thainual and Mohammad Aboofazeli and Andras Lasso and Gabor Fichtinger} } @conference {Lasso2009, title = {A generic computer assisted intervention plug-in module for 3D Slicer with multiple device support}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI)}, year = {2009}, month = {2009}, address = {London, UK}, abstract = {

Various frameworks and toolkits have been proposed for rapid development of computer assisted intervention (CAI) software. In this paper, we investigate how the open-source 3D Slicer application framework can be used for this purpose. We defined general requirements for CAI software to be able to evaluate and enhance 3D Slicer for interventional applications in general, and not just for a specific system. 3D Slicer is found to be an appropriate basis for CAI software, as its built-in functions fulfill many requirements and missing functionalities can be conveniently added. We describe the implementation of a CAI software based on extending core 3D Slicer functions. Three enhancements are described in detail: the management of workflow, DICOM image transfer, and multiple views. The resulting software fulfills general CAI requirements and supports two different MRI-guided prostate biopsy systems (each with a different imaging mode, robotic manipulator and calibration method), thereby demonstrating the usability of our software for implementing CAI applications in general.

}, url = {http://www.insight-journal.org/browse/journal/47}, author = {Andras Lasso and Junichi Tokuda and Siddharth Vikal and Clare M Tempany and Nobuhiko Hata and Gabor Fichtinger} }