Andras Lasso

@article{bumm2024,

title = {Artificial intelligence (AI)-assisted chest computer tomography (CT) insights: a study on intensive care unit (ICU) admittance trends in 78 coronavirus disease 2019 (COVID-19 …},

author = {Rudolf Bumm and Paolo Zaffino and Andras Lasso and Raúl San José Estépar and Steven Pieper and Jakob Wasserthal and Maria Francesca Spadea and Tsogyal Latshang and Nadine Kawel-Boehm and Adrian Wäckerlin and Raphael Werner and Gabriela Hässig and Markus Furrer and Ron Kikinis},

year  = {2024},

date = {2024-01-01},

journal = {Journal of Thoracic Disease},

volume = {16},

number = {2},

publisher = {AME Publishing Company},

abstract = {Background: The global coronavirus disease 2019 (COVID-19) pandemic has posed substantial challenges for healthcare systems, notably the increased demand for chest computed tomography (CT) scans, which lack automated analysis. Our study addresses this by utilizing artificial intelligence-supported automated computer analysis to investigate lung involvement distribution and extent in COVID-19 patients. Additionally, we explore the association between lung involvement and intensive care unit (ICU) admission, while also comparing computer analysis performance with expert radiologists’ assessments.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{herz2024,

title = {Open-source graphical user interface for the creation of synthetic skeletons for medical image analysis},

author = {Christian Herz and Nicolas Vergnet and Sijie Tian and Abdullah H Aly and Matthew A Jolley and Nathanael Tran and Gabriel Arenas and Andras Lasso and Nadav Schwartz and Kathleen E O’Neill and Paul A Yushkevich and Alison M Pouch},

year  = {2024},

date = {2024-01-01},

journal = {Journal of Medical Imaging},

volume = {11},

number = {3},

pages = {036001-036001},

publisher = {Society of Photo-Optical Instrumentation Engineers},

abstract = {Purpose 

Deformable medial modeling is an inverse skeletonization approach to representing anatomy in medical images, which can be used for statistical shape analysis and assessment of patient-specific anatomical features such as locally varying thickness. It involves deforming a pre-defined synthetic skeleton, or template, to anatomical structures of the same class. The lack of software for creating such skeletons has been a limitation to more widespread use of deformable medial modeling. Therefore, the objective of this work is to present an open-source user interface (UI) for the creation of synthetic skeletons for a range of medial modeling applications in medical imaging. 

Approach 

A UI for interactive design of synthetic skeletons was implemented in 3D Slicer, an open-source medical image analysis application. The steps in synthetic skeleton design include importation and skeletonization of a 3D …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2024f,

title = {Using NURBS for virtual resections in liver surgery planning: a comparative usability study},

author = {Gabriella d'Albenzio and Rebecca Hisey and Dilakshan Srikanthan and Tamas Ungi and Andras Lasso and Davit Aghayan and Gabor Fichtinger and Rafael Palomar},

url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/12927/129270Z/Using-NURBS-for-virtual-resections-in-liver-surgery-planning/10.1117/12.3006486.short},

year  = {2024},

date = {2024-01-01},

volume = {12927},

pages = {235-241},

publisher = {SPIE},

abstract = {PURPOSE 

Accurate preoperative planning is crucial for liver resection surgery due to the complex anatomical structures and variations among patients. The need of virtual resections utilizing deformable surfaces presents a promising approach for effective liver surgery planning. However, the range of available surface definitions poses the question of which definition is most appropriate. 

METHODS 

The study compares the use of NURBS and B´ezier surfaces for the definition of virtual resections through a usability study, where 25 participants (19 biomedical researchers and 6 liver surgeons) completed tasks using varying numbers of control points driving surface deformations and different surface types. Specifically, participants aim to perform virtual liver resections using 16 and 9 control points for NURBS and B´ezier surfaces. The goal is to assess whether they can attain an optimal resection plan, effectively …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2024,

title = {Preoperative CT and survival data for patients undergoing resection of colorectal liver metastases},

author = {Amber L Simpson and Jacob Peoples and John M Creasy and Gabor Fichtinger and Natalie Gangai and Krishna N Keshavamurthy and Andras Lasso and Jinru Shia and Michael I D’Angelica and Richard KG Do},

url = {https://www.nature.com/articles/s41597-024-02981-2},

year  = {2024},

date = {2024-01-01},

journal = {Scientific Data},

volume = {11},

issue = {1},

pages = {172},

publisher = {Nature Publishing Group UK},

abstract = {The liver is a common site for the development of metastases in colorectal cancer. Treatment selection for patients with colorectal liver metastases (CRLM) is difficult; although hepatic resection will cure a minority of CRLM patients, recurrence is common. Reliable preoperative prediction of recurrence could therefore be a valuable tool for physicians in selecting the best candidates for hepatic resection in the treatment of CRLM. It has been hypothesized that evidence for recurrence could be found via quantitative image analysis on preoperative CT imaging of the future liver remnant before resection. To investigate this hypothesis, we have collected preoperative hepatic CT scans, clinicopathologic data, and recurrence/survival data, from a large, single-institution series of patients (n = 197) who underwent hepatic resection of CRLM. For each patient, we also created segmentations of the liver, vessels, tumors, and …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2024b,

title = {Euclidean and shape-based analysis of the dynamic mitral annulus in children using a novel open-source framework},

author = {Silvani Amin and Hannah Dewey and Andras Lasso and Patricia Sabin and Ye Han and Jared Vicory and Beatriz Paniagua and Christian Herz and Hannah Nam and Alana Cianciulli and Maura Flynn and Devin W Laurence and David Harrild and Gabor Fichtinger and Meryl S Cohen and Matthew A Jolley},

url = {https://www.sciencedirect.com/science/article/pii/S0894731723005941},

year  = {2024},

date = {2024-01-01},

journal = {Journal of the American Society of Echocardiography},

volume = {37},

issue = {2},

pages = {259-267},

publisher = {Mosby},

abstract = {Background 

The dynamic shape of the normal adult mitral annulus has been shown to be important to mitral valve function. However, annular dynamics of the healthy mitral valve in children have yet to be explored. The aim of this study was to model and quantify the shape and major modes of variation of pediatric mitral valve annuli in four phases of the cardiac cycle using transthoracic echocardiography. 

Methods 

The mitral valve annuli of 100 children and young adults with normal findings on three-dimensional echocardiography were modeled in four different cardiac phases using the SlicerHeart extension for 3D Slicer. Annular metrics were quantified using SlicerHeart, and optimal normalization to body surface area was explored. Mean annular shapes and the principal components of variation were computed using custom code implemented in a new SlicerHeart module (Annulus Shape Analyzer). Shape was …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2023c,

title = {Modeling of the tricuspid valve and right ventricle in hypoplastic left heart syndrome with a Fontan circulation},

author = {Hannah H Nam and Maura Flynn and Andras Lasso and Christian Herz and Patricia Sabin and Yan Wang and Alana Cianciulli and Chad Vigil and Jing Huang and Jared Vicory and Beatriz Paniagua and David Allemang and David J Goldberg and Mohammed Nuri and Meryl S Cohen and Gabor Fichtinger and Matthew A Jolley},

url = {https://www.ahajournals.org/doi/abs/10.1161/CIRCIMAGING.122.014671},

year  = {2023},

date = {2023-01-01},

journal = {Circulation: Cardiovascular Imaging},

volume = {16},

issue = {3},

pages = {e014671},

publisher = {Lippincott Williams & Wilkins},

abstract = {Background 

In hypoplastic left heart syndrome, tricuspid regurgitation (TR) is associated with circulatory failure and death. We hypothesized that the tricuspid valve (TV) structure of patients with hypoplastic left heart syndrome with a Fontan circulation and moderate or greater TR differs from those with mild or less TR, and that right ventricle volume is associated with TV structure and dysfunction. 

Methods 

TV of 100 patients with hypoplastic left heart syndrome and a Fontan circulation were modeled using transthoracic 3-dimensional echocardiograms and custom software in SlicerHeart. Associations of TV structure to TR grade and right ventricle function and volume were investigated. Shape parameterization and analysis was used to calculate the mean shape of the TV leaflets, their principal modes of variation, and to characterize associations of TV leaflet shape to TR. 

Results 

In univariate modeling, patients with …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2022c,

title = {SlicerHeart: An open-source computing platform for cardiac image analysis and modeling},

author = {Andras Lasso and Christian Herz and Hannah Nam and Alana Cianciulli and Steve Pieper and Simon Drouin and Csaba Pinter and Samuelle St-Onge and Chad Vigil and Stephen Ching and Kyle Sunderland and Gabor Fichtinger and Ron Kikinis and Matthew A Jolley},

url = {https://www.frontiersin.org/articles/10.3389/fcvm.2022.886549/full},

year  = {2022},

date = {2022-01-01},

volume = {9},

pages = {886549},

publisher = {Frontiers},

abstract = {Cardiovascular disease is a significant cause of morbidity and mortality in the developed world. 3D imaging of the heart’s structure is critical to the understanding and treatment of cardiovascular disease. However, open-source tools for image analysis of cardiac images, particularly 3D echocardiographic (3DE) data, are limited. We describe the rationale, development, implementation, and application of SlicerHeart, a cardiac-focused toolkit for image analysis built upon 3D Slicer, an open-source image computing platform. We designed and implemented multiple Python scripted modules within 3D Slicer to import, register, and view 3DE data, including new code to volume render and crop 3DE. In addition, we developed dedicated workflows for the modeling and quantitative analysis of multi-modality image-derived heart models, including heart valves. Finally, we created and integrated new functionality to facilitate the planning of cardiac interventions and surgery. We demonstrate application of SlicerHeart to a diverse range of cardiovascular modeling and simulation including volume rendering of 3DE images, mitral valve modeling, transcatheter device modeling, and planning of complex surgical intervention such as cardiac baffle creation. SlicerHeart is an evolving open-source image processing platform based on 3D Slicer initiated to support the investigation and treatment of congenital heart disease. The technology in SlicerHeart provides a robust foundation for 3D image-based investigation in cardiovascular medicine.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2022g,

title = {Dynamic annular modeling of the unrepaired complete atrioventricular canal annulus},

author = {Hannah H Nam and Patrick V Dinh and Andras Lasso and Christian Herz and Jing Huang and Adriana Posada and Ahmed H Aly and Alison M Pouch and Saleha Kabir and John Simpson and Andrew C Glatz and David M Harrild and Gerald Marx and Gabor Fichtinger and Meryl S Cohen and Matthew A Jolley},

url = {https://www.sciencedirect.com/science/article/pii/S0003497520321585},

year  = {2022},

date = {2022-01-01},

journal = {The Annals of thoracic surgery},

volume = {113},

issue = {2},

pages = {654-662},

publisher = {Elsevier},

abstract = {Background 

Repair of complete atrioventricular canal (CAVC) is often complicated by atrioventricular valve regurgitation, particularly of the left-sided valve. Understanding the 3-dimensional (3D) structure of the atrioventricular canal annulus before repair may help to inform optimized repair. However, the 3D shape and movement of the CAVC annulus has been neither quantified nor rigorously compared with a normal mitral valve annulus. 

Methods 

The complete annuli of 43 patients with CAVC were modeled in 4 cardiac phases using transthoracic 3D echocardiograms and custom code. The annular structure was compared with the annuli of 20 normal pediatric mitral valves using 3D metrics and statistical shape analysis (Procrustes analysis). 

Results 

The unrepaired CAVC annulus varied in shape significantly throughout the cardiac cycle. Procrustes analysis visually demonstrated that the average normalized CAVC …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2021d,

title = {An open-source platform for cooperative, semi-autonomous robotic surgery},

author = {Laura Connolly and Anton Deguet and Kyle Sunderland and Andras Lasso and Tamas Ungi and John F Rudan and Russell H Taylor and Parvin Mousavi and Gabor Fichtinger},

url = {https://ieeexplore.ieee.org/abstract/document/9551149/},

year  = {2021},

date = {2021-01-01},

pages = {1-5},

publisher = {IEEE},

abstract = {Introduction 

In this paper, we present and assess a proof of concept platform for semi-autonomous, cooperative robotic surgery. The platform is easily reproducible thanks to simple hardware components and open-source software. Moreover, the design accommodates open, soft tissue surgeries that recent advancements in surgical robotics do not generally focus on. 

Methods 

The system is made up of an inexpensive robotic manipulator, a navigation system and a software interface. Accuracy measurement is performed on a rigid phantom that mimics the conditions of breast conserving surgery (BCS) as an example of a surgical use case. 

Results 

The average target registration error (TRE) and fiducial registration error (FRE) of the system is within 1 mm. This indicates that the navigation system is sufficient for certain surgical applications such as BCS. The platform can also be easily replicated and used in a lab or …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2021g,

title = {Simulation of delivery of clip-based therapies within multimodality images to facilitate preprocedural planning},

author = {Alana Cianciulli and Andras Lasso and Csaba Pinter and Stephen Ching and Reena M Ghosh and Tiffany Chen and Christian Herz and Chad Vigil and Simon Drouin and Lindsay S Rogers and Michael D Quartermain and David M Biko and Kevin K Whitehead and Gabor Fichtinger and Matthew J Gillespie and Matthew A Jolley},

url = {https://www.onlinejase.com/article/S0894-7317(21)00588-5/abstract},

year  = {2021},

date = {2021-01-01},

journal = {Journal of the American Society of Echocardiography},

volume = {34},

issue = {10},

pages = {1111-1114},

publisher = {Elsevier},

abstract = {Brief Research Communications 1111 repair (TEER) has emerged as a therapeutic option for the treatment of severe mitral regurgitation and tricuspid regurgitation and avoids the morbidity and mortality associated with open heart surgery. 1, 2 One challenge to the successful application of this therapy is delivering the clip to a precise location within the constraints of the unique anatomy and resulting geometry of an individual patient. Threedimensional echocardiography (3DE) is typically used to plan and execute TEER using catheter delivery systems designed to access a specific anatomic location (mitral valve, tricuspid valve) via a known path. These systems are then empirically validated and iteratively improved via large clinical trials and clinical practice. However, there has been little work on modeling the catheter path and approach to deliver the clip to the desired location in atypical or surgically altered …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2021j,

title = {Open-source tool kit for interactive planning of transcatheter mitral valve replacement using multimodality imaging},

author = {Christian Herz and Alana Cianciulli and Stephen Ching and Chad Vigil and Andras Lasso and Hannah H Nam and Simon Drouin and David M Biko and Matthew Gillespie and Gabor Fichtinger and Matthew A Jolley},

url = {https://www.onlinejase.com/article/S0894-7317(21)00180-2/abstract},

year  = {2021},

date = {2021-01-01},

journal = {Journal of the American Society of Echocardiography},

volume = {34},

issue = {8},

pages = {917-920},

publisher = {Elsevier},

abstract = {Brief Research Communications 917 outflow tract (LVOT) obstruction or perivalvar leak. 2 However, the complexity of cardiac anatomy can make two-dimensional and even three-dimensional (3D) derived linear measurements difficult to translate into improved appropriate device selection, which in turn has led to exploration of CT-derived virtual and 3D printing-based modeling. 3, 4 While CT-based structural modeling software is now commercially available, and there is mitral annular modeling available in commercial 3DE-based platforms, to our knowledge there is no configurable modeling platform of 3DE modeling that allows the insertion of a library of existing and customizable virtual devices into 3DE images to see how devices would actually fit. In order to potentially inform patient candidacy, appropriate device selection, and the design of new devices for transcatheter mitral valve (TMV) therapies, we created …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gauvin2019,

title = {Real-time electromagnetic navigation for breast-conserving surgery using NaviKnife technology: A matched case-control study},

author = {Gabrielle Gauvin and Caitlin T Yeo 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},

doi = {10.1111/tbj.13480},

year  = {2020},

date = {2020-09-01},

urldate = {2020-09-01},

journal = {The Breast Journal},

volume = {26},

number = {3},

pages = {399-405},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pinter2020,

title = {SlicerVR for Medical Intervention Training and Planning in Immersive Virtual Reality},

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},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/03/Pinter2020a_0.pdf},

doi = {10.1109/TMRB.2020.2983199},

year  = {2020},

date = {2020-03-01},

urldate = {2020-03-01},

journal = {IEEE Transactions on Medical Robotics and Bionics},

volume = {2},

number = {2},

pages = {108-117},

abstract = {<p>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.</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020e,

title = {Simulation of transcatheter atrial and ventricular septal defect device closure within three-dimensional echocardiography–derived heart models on screen and in virtual reality},

author = {Hannah H Nam and Christian Herz and Andras Lasso and Simon Drouin and Adriana Posada and Brian Morray and Michael L O'Byrne and Beatriz Paniagua and Denise Joffe and Burkhard Mackensen and Lindsay Rogers and Gabor Fichtinger and Matthew A Jolley},

url = {https://www.onlinejase.com/article/S0894-7317(20)30033-X/abstract},

year  = {2020},

date = {2020-01-01},

journal = {Journal of the American Society of Echocardiography},

volume = {33},

issue = {5},

pages = {641-644. e2},

publisher = {Elsevier},

abstract = {Appropriate matching of the device to the defect is crucial to successfully close the defect and to prevent complications such as device embolization, erosion, and obstruction of structures near the device. Two-dimensional (2D) echocardiographic and three-dimensional (3D) echocardiographic data are used to inform this process but typically require multiple measurements in different imaging planes. The complexity of cardiac anatomy can make 2D-and even 3D-derived linear measurements difficult to translate into improved contextualization of relevant patient anatomy and appropriate device selection. To inform patient selection and appropriate device selection for ASD and VSD closure, we created a modeling and visualization system to insert virtual device models into both segmented and volumerendered 3D echocardiographic images of patients with ASDs and VSDs using custom code in 3D Slicer. 2, 3 First …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020j,

title = {Electromagnetic (EM) catheter path tracking in ultrasound-guided brachytherapy of the breast},

author = {Natasja NY Janssen and Harry Brastianos and Aquila Akingbade and Tim Olding and Thomas Vaughan and Tamas Ungi and Andras Lasso and Chandra Joshi and Martin Korzeniowski and Conrad Falkson and Gabor Fichtinger},

url = {https://link.springer.com/article/10.1007/s11548-020-02233-9},

year  = {2020},

date = {2020-01-01},

journal = {International journal of computer assisted radiology and surgery},

volume = {15},

pages = {1645-1652},

publisher = {Springer International Publishing},

abstract = {Purpose 

To evaluate a novel navigation system for breast brachytherapy, based on ultrasound (US)-guided catheter needle implantations followed by electromagnetic (EM) tracking of catheter paths. 

Methods 

Breast phantoms were produced, containing US–visible tumors. Ultrasound was used to localize the tumor pose and volume within the phantom, followed by planning an optimal catheter pattern through the tumor using navigation software. An electromagnetic (EM)-tracked catheter needle was used to insert the catheters in the desired pattern. The inserted catheters were visualized on a post-implant CT, serving as ground truth. Electromagnetic (EM) tracking and reconstruction of the inserted catheter paths were performed by pulling a flexible EM guidewire through each catheter, performed in two clinical brachytherapy suites. The accuracy of EM catheter tracking was evaluated by calculating the Hausdorff …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Fedorov2020,

title = {Quantitative Imaging Informatics for Cancer Research},

author = {Andriy Fedorov and Reinhard Beichel and Jayashree Kalpathy-Cramer and David Clunie and Michael Onken and Jörg 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},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Fedorov2020.pdf},

doi = {https://doi.org/10. 1200/CCI.19.00165},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {JCO Clinical Cancer Informatics},

volume = {4},

pages = {444-453.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020f,

title = {Three-dimensional modeling of surgically implanted stent-based valves in the mitral position in children},

author = {Perry S Choi and Hannah H 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 Matthew A Jolley},

url = {https://www.sciencedirect.com/science/article/pii/S0003497520303908},

year  = {2020},

date = {2020-01-01},

journal = {The Annals of thoracic surgery},

volume = {110},

issue = {2},

pages = {670-675},

publisher = {Elsevier},

abstract = {Purpose 

In children with a mitral annulus too small to accommodate traditional prostheses, surgical implantation of stent-based valves is a promising option. However no reliable preoperative methods exist to guide patient selection, device sizing, and positioning. We describe a novel methodology to visualize and quantify device fit in 3-dimensional echocardiogram (3DE)-derived heart models. 

Description 

Heart models were created from existing preoperative 3DEs using custom software. Valve models were virtually implanted into the models, and both device fit and left ventricular outflow tract (LVOT) area were quantified. 

Evaluation 

The 3DEs of 3 patients who underwent Melody valve placement in the mitral position were retrospectively modeled: 1 with LVOT obstruction, 1 with perivalvar leak, and 1 without complications. In all cases 2-dimensional measurements underestimated 3D annular dimensions, and the …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020h,

title = {External tracking devices and tracked tool calibration},

author = {Elvis CS Chen and Andras Lasso and Gabor Fichtinger},

url = {https://www.sciencedirect.com/science/article/pii/B9780128161760000363},

year  = {2020},

date = {2020-01-01},

pages = {777-794},

publisher = {Academic Press},

abstract = {Spatial measure device, i.e. tracking system, is the enabling technology for any surgical navigation system. The primary function of a tracking system is to infer the pose (orientation and position) of surgical instrument intraoperatively in real time. The secondary function is patient registration: locations of anatomical landmarks can be inferred by the use of a tracked and calibrated surgical instrument. Because the tracking system can only track its pose sensor directly, a pose sensor must be integrated into the surgical instrument; the geometry of the instrument must be related to its pose sensor via a spatial calibration process. This chapter provides a short overview on the principle tracking technology, error propagation, and specifics of surgical instrument calibration.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Choi2020,

title = {3D Modeling of Surgically Implanted Stent-Based Valves in the Mitral Position in Children},

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},

url = {https://doi.org/10.1016/j.athoracsur.2020.02.020

},

doi = {10.1016/j.athoracsur.2020.02.020},

year  = {2020},

date = {2020-01-01},

urldate = {2020-01-01},

journal = {The Annals of Thoracic Surgery},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020c,

title = {Real‐time electromagnetic navigation for breast‐conserving surgery using NaviKnife technology: A matched case‐control study},

author = {Gabrielle Gauvin and Caitlin T Yeo and Tamas Ungi and Shaila Merchant and Andras Lasso and Doris Jabs and Thomas Vaughan and John F Rudan and Ross Walker and Gabor Fichtinger and Cecil Jay Engel},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tbj.13480},

year  = {2020},

date = {2020-01-01},

journal = {The breast journal},

volume = {26},

issue = {3},

pages = {399-405},

abstract = {Breast‐conserving surgery (BCS) is a mainstay in breast cancer treatment. For nonpalpable breast cancers, current strategies have limited accuracy, contributing to high positive margin rates. We developed NaviKnife, a surgical navigation system based on real‐time electromagnetic (EM) tracking. The goal of this study was to confirm the feasibility of intraoperative EM navigation in patients with nonpalpable breast cancer and to assess the potential value of surgical navigation. We recruited 40 patients with ultrasound visible, single, nonpalpable lesions, undergoing BCS. Feasibility was assessed by equipment functionality and sterility, acceptable duration of the operation, and surgeon feedback. Secondary outcomes included specimen volume, positive margin rate, and reoperation outcomes. Study patients were compared to a control group by a matched case‐control analysis. There was no equipment failure or …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020,

title = {SlicerVR for medical intervention training and planning in immersive virtual reality},

author = {Csaba Pinter and Andras Lasso and Saleh Choueib and Mark Asselin and Jean-Christophe Fillion-Robin and Jean-Baptiste Vimort and Ken Martin and Matthew A Jolley and Gabor Fichtinger},

url = {https://ieeexplore.ieee.org/abstract/document/9047949/},

year  = {2020},

date = {2020-01-01},

journal = {IEEE transactions on medical robotics and bionics},

volume = {2},

issue = {2},

pages = {108-117},

publisher = {IEEE},

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 …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020l,

title = {Simulation of Transcatheter Atrial and Ventricular Septal Defect Device Closure Within 3D Echo Derived Heart Models On Screen and in Virtual Reality},

author = {Hannah H Nam and Christian Herz and Andras Lasso and Simon Drouin and Adriana Posada and Brian Morray and Michael L O’Byrne and Beatriz Paniagua and Denise Joffe and Burkhard Mackensen and Lindsay Rogers and Gabor Fichtinger and Matthew A Jolley},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8083019/},

year  = {2020},

date = {2020-01-01},

journal = {Journal of the American Society of Echocardiography: official publication of the American Society of Echocardiography},

volume = {33},

issue = {5},

pages = {641},

publisher = {NIH Public Access},

abstract = {Transcatheter device closures of atrial septal defects (ASD) and ventricular septal defects (VSD) have many advantages over surgical repair. Percutaneous intervention avoids the morbidity and mortality associated with open heart surgery, and is associated with a shorter hospital stay, lower risk of complications, and lower procedural costs.[1] Appropriate matching of the device to the defect is crucial to successfully close the defect and to prevent complications such as device embolization, erosion, and obstruction of structures near the device. Two-dimensional (2D) echocardiographic and three-dimensional (3D) echocardiographic (3DE) data are used to inform this process, but typically require multiple measurements in different imaging planes. The complexity of cardiac anatomy can make 2D and even 3D derived linear measurements difficult to translate into improved contextualization of relevant patient anatomy …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020o,

title = {Robotic tissue scanning with biophotonic probe},

author = {Lauren Yates and Laura Connolly and Amoon Jamzad and Mark Asselin and Rachel Rubino and Scott Yam and Tamas Ungi and Andras Lasso and Christopher Nicol and Parvin Mousavi and Gabor Fichtinger},

url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/11315/1131519/Robotic-tissue-scanning-with-biophotonic-probe/10.1117/12.2549635.short},

year  = {2020},

date = {2020-01-01},

volume = {11315},

pages = {330-335},

publisher = {SPIE},

abstract = {PURPOSE 

Raman spectroscopy is an optical imaging technique used to characterize tissue via molecular analysis. The use of Raman spectroscopy for real-time intraoperative tissue classification requires fast analysis with minimal human intervention. In order to have accurate predictions and classifications, a large and reliable database of tissue classifications with spectra results is required. We have developed a system that can be used to generate an efficient scanning path for robotic scanning of tissues using Raman spectroscopy. 

METHODS 

A camera mounted to a robotic controller is used to take an image of a tissue slide. The corners of the tissue slides within the sample image are identified, and the size of the slide is calculated. The image is cropped to fit the size of the slide and the image is manipulated to identify the tissue contour. A grid set to fit around the size of the tissue is calculated and a grid …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2020t,

title = {91: Use of Electromagnetic Tracking Technology to Reconstruct Catheter Paths in Breast Brachytherapy-A Pilot Study},

author = {Harry Brastianos and Natasja Janssen and Aquila Akingbade and Tim Olding and Thomas Vaughan and Tamas Ungi and Andras Lasso and Mary Westerland and Chandra Joshi and Martin Korzeniowski and Gabor Fichtinger and Conrad Falkson},

url = {https://scholar.google.com/scholar?cluster=9660613250415496944&hl=en&oi=scholarr},

year  = {2020},

date = {2020-01-01},

journal = {Radiotherapy and Oncology},

volume = {150},

pages = {S41},

publisher = {Elsevier},

abstract = {Conclusions: The combined modality treatment factors and outcomes are comparable to the results of ASCENDE-RT and remain an effective treatment option for IR and HR prostate cancer. Higher GGG, HRF, PPC are potentially associated with worse outcomes. People who had early relapse had worse OS as demonstrated by ASCENDE-RT.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vaughan2019a,

title = {Needle Navigation and Catheter Reconstruction for Breast Brachytherapy Using Open Source Software},

author = {Thomas Vaughan and H Brastianos and Tamas Ungi and Andras Lasso and Conrad Falkson and Gabor Fichtinger},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Vaughan2019a_0.pdf},

year  = {2019},

date = {2019-09-01},

urldate = {2019-09-01},

journal = {Acta Polytechnica Hungarica},

volume = {16},

number = {8},

pages = {99-118},

abstract = {<p>\emph{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},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pinter2019,

title = {Polymorph Segmentation Representation for Medical Image Computing},

author = {Csaba Pinter and Andras Lasso and Gabor Fichtinger},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Pinter2019_Manuscript.pdf},

doi = {https://doi.org/10.1016/j.cmpb.2019.02.011},

year  = {2019},

date = {2019-02-01},

urldate = {2019-02-01},

journal = {Computer Methods and Programs in Biomedicine},

volume = {171},

pages = {19-26},

abstract = {<p><strong>Background and Objective: </strong>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: <a name="OLE_LINK3"></a><a name="OLE_LINK2">conversion </a>method selection, data provenance, data consistency, and coherence of in-memory objects. <strong>Methods:</strong> 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. <strong>Results: </strong>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. <strong>Conclusions:</strong>  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’s BSD-style open-source license allows complete freedom of use of the library.</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2019e,

title = {Toward predictive modeling of catheter‐based pulmonary valve replacement into native right ventricular outflow tracts},

author = {Matthew A Jolley and Andras Lasso and Hannah H Nam and Patrick V Dinh and Adam B Scanlan and Alex V Nguyen and Anna Ilina and Brian Morray and Andrew C Glatz and Francis X McGowan and Kevin Whitehead and Yoav Dori and Joseph H Gorman III and Robert C Gorman and Gabor Fichtinger and Matthew J Gillespie},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ccd.27962},

year  = {2019},

date = {2019-01-01},

journal = {Catheterization and Cardiovascular Interventions},

volume = {93},

issue = {3},

pages = {E143-E152},

publisher = {John Wiley & Sons, Inc.},

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 …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{NGUYEN2019,

title = {Dynamic Three-Dimensional Geometry of the Tricuspid Valve Annulus in Hypoplastic Left Heart Syndrome with a Fontan Circulation},

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},

url = {http://www.sciencedirect.com/science/article/pii/S0894731719300021

},

doi = {https://doi.org/10.1016/j.echo.2019.01.002},

issn = {0894-7317},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Journal of the American Society of Echocardiography},

abstract = {<p>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, 2–11 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° 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.</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2019f,

title = {Evaluation of 3D slicer as a medical virtual reality visualization platform},

author = {Saleh Choueib and Csaba Pinter and Andras Lasso and Jean-Christophe Fillion-Robin and Jean-Batiste Vimort and Ken Martin and Gabor Fichtinger},

url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10951/1095113/Evaluation-of-3D-slicer-as-a-medical-virtual-reality-visualization/10.1117/12.2513053.short},

year  = {2019},

date = {2019-01-01},

volume = {10951},

pages = {279-286},

publisher = {SPIE},

abstract = {PURPOSE 

There is a lack of open-source or free virtual reality (VR) software that can be utilized for research by medical professionals and researchers. We propose the design and implementation of such software. We also aim to assess the feasibility of using VR as a modality for navigating 3D visualizations of medical scenes. 

METHODS 

To achieve our goal, we added VR capabilities to the open-source medical image analysis and visualization platform, 3D Slicer. We designed the VR extension by basing the software architecture on VTK’s vtkRenderingOpenVR software module. We extended this module by adding features such as full interactivity between 3D Slicer and the VR extension during VR use, variable volume rendering quality based on user headset motion etc. Furthermore, the VR extension was tested in a feasibility study in which participants were asked to complete specific tasks using bot the …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2019c,

title = {Dynamic three-dimensional geometry of the tricuspid valve annulus in hypoplastic left heart syndrome with a Fontan circulation},

author = {Alex V Nguyen and Andras Lasso and Hannah H Nam and Jennifer Faerber and Ahmed H Aly and Alison M Pouch and Adam B Scanlan and Francis X McGowan and Laura Mercer-Rosa and Meryl S Cohen and John Simpson and Gabor Fichtinger and Matthew A Jolley},

url = {https://www.sciencedirect.com/science/article/pii/S0894731719300021},

year  = {2019},

date = {2019-01-01},

journal = {Journal of the American Society of Echocardiography},

volume = {32},

issue = {5},

pages = {655-666. e13},

publisher = {Mosby},

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, 2–11 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 …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2019h,

title = {Navigated real-time molecular analysis in the operating theatre: demonstration of concept},

author = {Mark Asselin and Martin Kaufmann and Julia Wiercigroch and Tamas Ungi and Andras Lasso and John Rudan and Gabor Fichtinger},

url = {https://www.spiedigitallibrary.org/conference-proceedings-of-spie/10951/109512C/Navigated-real-time-molecular-analysis-in-the-operating-theatre/10.1117/12.2512586.short},

year  = {2019},

date = {2019-01-01},

volume = {10951},

pages = {618-624},

publisher = {SPIE},

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’ anatomy but doesn’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 …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Baum2020,

title = {Augmented reality training platform for neurosurgical burr hole localization},

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},

url = {https://labs.cs.queensu.ca/perklab/wp-content/uploads/sites/3/2024/02/Baum2020a.pdf},

doi = {https://doi.org/10.1142/S2424905X19420017},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Journal of Medical Robotics Research},

volume = {4},

number = {3-4},

pages = {1942001-1 - 1942001-13},

abstract = {<p>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.</p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fichtinger2019b,

title = {Polymorph segmentation representation for medical image computing},

author = {Csaba Pinter and Andras Lasso and Gabor Fichtinger},

url = {https://www.sciencedirect.com/science/article/pii/S0169260718313038},

year  = {2019},

date = {2019-01-01},

journal = {Computer methods and programs in biomedicine},

volume = {171},

pages = {19-26},

publisher = {Elsevier},

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 …},

keywords = {},

pubstate = {published},

tppubtype = {article}

}