@article {Fooladgar2022, title = {Uncertainty estimation for margin detection in cancer surgery using mass spectrometry}, journal = {International Journal of Computer Assisted Radiology and Surgery}, year = {2022}, month = {09/2022}, type = {Journal}, doi = {https://doi.org/10.1007/s11548-022-02764-3}, author = {Fahimeh Fooladgar and Amoon Jamzad and Laura Connolly and Alice Santilli and Martin Kaufmann and Kevin Ren and Purang Abolmaesumi and John Rudan and Doug McKay and Gabor Fichtinger and Parvin Mousavi} } @article {Fichtinger2021, title = {Design of an Ultrasound-Navigated Prostate Cancer Biopsy System for Nationwide Implementation in Senegal}, journal = {Journal of Imaging}, volume = {7}, number = {8}, year = {2021}, month = {08/2021}, pages = {154}, abstract = {

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

}, issn = {2313-433X}, doi = {10.3390/jimaging7080154}, url = {https://www.mdpi.com/2313-433X/7/8/154}, author = {Gabor Fichtinger and Parvin Mousavi and Tamas Ungi and Fenster, Aaron and Purang Abolmaesumi and Gernot Kronreif and Ruiz-Alzola, Juan and Ndoye, Alain and Diao, Babacar and Ron Kikinis} } @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} } @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 {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} } @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 {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 {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 {Moult2011a, title = {Automatic C-arm Pose Estimation via 2D/3D Hybrid Registration of a Radiographic Fiducial}, booktitle = {SPIE Medical Imaging}, volume = {7964}, number = {1}, year = {2011}, month = {03/2011}, pages = {79642S}, publisher = {SPIE}, organization = {SPIE}, address = {Lake Buena Vista (Orlando), Florida, USA}, doi = {10.1117/12.877713}, url = {http://link.aip.org/link/?PSI/7964/79642S/1}, author = {Eric Moult and E. Clif Burdette and Danny Y Song and Purang Abolmaesumi and Gabor Fichtinger and Pascal Fallavollita}, editor = {Kenneth H. Wong and David R. Holmes III} } @conference {Khallaghi2011, title = {GPU accelerated registration of a statistical shape model of the lumbar spine to 3D ultrasound images}, booktitle = {SPIE Medical Imaging}, volume = {7964}, number = {1}, year = {2011}, month = {03/2011}, pages = {79642W}, publisher = {SPIE}, organization = {SPIE}, address = {Lake Buena Vista, Florida, USA}, doi = {10.1117/12.878377}, url = {http://link.aip.org/link/?PSI/7964/79642W/1}, author = {Siavash Khallaghi and Purang Abolmaesumi and Ren Hui Gong and Elvis C. S. Chen and Sean Gill and Jonathan Boisvert and David R Pichora and Daniel P. Borschneck and Gabor Fichtinger and Parvin Mousavi} } @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} } @conference {Ghanavati2011, title = {Phantom validation for ultrasound to statistical shape model registration of human pelvis}, booktitle = {SPIE Medical Imaging}, volume = {7964}, number = {1}, year = {2011}, month = {03/2011}, pages = {79642U}, publisher = {SPIE}, organization = {SPIE}, address = {Lake Buena Vista, Florida, USA}, doi = {10.1117/12.876998}, url = {http://link.aip.org/link/?PSI/7964/79642U/1}, author = {Sugantha Ganapathy and Parvin Mousavi and Gabor Fichtinger and Purang Abolmaesumi} } @article {Fallavollita2010e, title = {2D/3D Registration of Ultrasound and Fluoroscopy: is image preprocessing useful?}, year = {2010}, month = {09/2010}, address = {Trondheim, Norway, September 2-4, 2010}, author = {Pascal Fallavollita and Zahra Karim-Aghaloo and E. Clif Burdette and Danny Y Song and Purang Abolmaesumi and Gabor Fichtinger} } @conference {Fallavollita2010d, title = {C-arm Pose Estimation in Prostate Brachytherapy by Registration to Ultrasound}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2010}, year = {2010}, author = {Pascal Fallavollita and E. Clif Burdette and Danny Y Song and Purang Abolmaesumi and Gabor Fichtinger} } @conference {Fallavollita2010a, title = {C-arm tracking by intensity-based registration of a fiducial in prostate brachytherapy}, booktitle = {1st International Conference on Information Processing in Computer-Assisted Interventions}, year = {2010}, month = {2010}, pages = {45-55}, publisher = {Lecture Notes in Computer Science}, organization = {Lecture Notes in Computer Science}, address = {Geneva}, author = {Pascal Fallavollita and E. Clif Burdette and Danny Y Song and Purang Abolmaesumi and Gabor Fichtinger} } @conference {Fallavollita2010b, title = {Localization of brachytherapy seeds in ultrasound by registration to fluoroscopy}, booktitle = {SPIE Medical imaging}, volume = {7625}, year = {2010}, month = {23 February 2010}, pages = {762519-1 - 762519-8}, address = {San Diego}, doi = {10.1117/12.844015}, author = {Pascal Fallavollita and Zahra Karim-Aghaloo and E. Clif Burdette and Danny Y Song and Purang Abolmaesumi and Gabor Fichtinger} } @conference {Ghanavati2010, title = {Multi-Slice to Volume Registration of Ultrasound Data to a Statistical Atlas of Human Pelvis}, booktitle = {SPIE Medical Imaging}, series = {Visualization, Image-Guided Procedures, and Modeling}, volume = {7625}, year = {2010}, month = {23 February 2010}, pages = {76250O-1 {\textendash} 76250O-10}, publisher = {SPIE Digital Library}, organization = {SPIE Digital Library}, address = {San Diego, California, USA}, abstract = {

Identifying the proper orientation of the pelvis is a critical step in accurate placement of the femur prosthesis in the acetabulum in Total Hip Replacement (THR) surgeries. The general approach to localize the orientation of the pelvis coordinate system is to use X-ray fluoroscopy to guide the procedure. An alternative can be employing intra-operative ultrasound (US) imaging with pre-operative CT scan or fluoroscopy imaging. In this paper, we propose to replace the need of pre-operative imaging by using a statistical shape model of the pelvis, constructed from several CT images. We then propose an automatic deformable intensity-based registration of the anatomical atlas to a sparse set of 2D ultrasound images of the pelvis in order to localize its anatomical coordinate system. In this registration technique, we first extract a set of 2D slices from a single instance of the pelvic atlas. Each individual 2D slice is generated based on the location of a corresponding 2D ultrasound image. Next, we create simulated ultrasound images out of the 2D atlas slices and calculate a similarity metric between the simulated images and the actual ultrasound images. The similarity metric guides an optimizer to generate an instance of the atlas that best matches the ultrasound data. We demonstrated the feasibility of our proposed approach on two male human cadaver data. The registration was able to localize a patient-specific pelvic coordinate system with origin translation error of 2 mm and 3.45 mm, and average axes rotation error of 3.5 degrees and 3.9 degrees for the two cadavers, respectively.

}, keywords = {Deformable registration, Freehand ultrasound, Intensity-based registration, Pelvis., Statistical anatomical atlas, Total Hip Replacement}, doi = {10.1117/12.844080}, url = {http://spiedl.aip.org/getabs/servlet/GetabsServlet?prog=normal\&id=PSISDG00762500000176250O000001\&idtype=cvips\&gifs=yes}, author = {Sugantha Ganapathy and Parvin Mousavi and Gabor Fichtinger and Pezhman Foroughi and Purang Abolmaesumi} } @article {Fallavollita2010c, title = {Registration Between Ultrasound and Fluoroscopy or CT in Prostate Brachytherapy}, journal = {Medical Physics}, volume = {37}, year = {2010}, month = {2010}, pages = {2749-2760}, author = {Pascal Fallavollita and Zahra Karim-Aghaloo and E. Clif Burdette and Danny Y Song and Purang Abolmaesumi and Gabor Fichtinger} } @conference {Khallaghi2010, title = {Registration of a Statistical Shape Model of the Lumbar Spine to 3D Ultrasound Images}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2010}, year = {2010}, pages = {68-75}, publisher = {Springer}, organization = {Springer}, address = {Beijing, China}, author = {Siavash Khallaghi and Parvin Mousavi and Ren Hui Gong and Sean Gill and Jonathan Boisvert and Gabor Fichtinger and David R Pichora and Daniel P. Borschneck and Purang Abolmaesumi} } @conference {Gill2009a, title = {Biomechanically Constrained Groupwise US to CT Registration of the Lumbar Spine}, booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI)}, volume = {5761}, year = {2009}, pages = {803-810}, publisher = {Springer}, organization = {Springer}, address = {London, UK}, isbn = {978-3-642-04267-6}, author = {Sean Gill and Parvin Mousavi and Gabor Fichtinger and Purang Abolmaesumi} } @conference {Lang2009, title = {Fusion of electromagnetic tracking with speckle-tracked 3D freehand ultrasound using an unscented Kalman filter}, booktitle = {SPIE Medical Imaging 2009: Ultrasonic Imaging and Signal Processing}, year = {2009}, author = {Andrew Lang and Parvin Mousavi and Gabor Fichtinger and Purang Abolmaesumi} } @conference {Gill2009, title = {Group-wise Registration of Ultrasound to CT Images of Human Vertebrae}, booktitle = {SPIE Medical Imaging 2009: Visualization, Image-Guided Procedures, and Modeling}, volume = {7261}, year = {2009}, pages = {na}, author = {Sean Gill and Parvin Mousavi and Gabor Fichtinger and David R Pichora and Purang Abolmaesumi} } @conference {Karim-Aghaloo2009, title = {Intraoperative localization of brachytherapy implants using intensity-based registration}, booktitle = {SPIE Medical Imaging}, volume = {7261}, year = {2009}, author = {Zahra Karim-Aghaloo and Purang Abolmaesumi and Narges Ahmidi and Thomas K. Chen and David Gobbi and Gabor Fichtinger} } @conference {Aboofazeli2009b, title = {A new scheme for curved needle segmentation in three-dimensional ultrasound images}, booktitle = {Proc. IEEE International Symposium on Biomedical Imaging: From Nano to Macro ISBI {\textquoteright}09}, year = {2009}, pages = {1067{\textendash}1070}, doi = {10.1109/ISBI.2009.5193240}, author = {Mohammad Aboofazeli and Purang Abolmaesumi and Parvin Mousavi and Gabor Fichtinger} } @conference {Aboofazeli2009, title = {Tissue characterization using multiscale products of wavelet transform of ultrasound radio frequency echoes}, booktitle = {Proc. Annual International Conference of the IEEE Engineering in Medicine and Biology Society EMBC 2009}, year = {2009}, pages = {479{\textendash}482}, doi = {10.1109/IEMBS.2009.5335160}, author = {Mohammad Aboofazeli and Purang Abolmaesumi and Gabor Fichtinger and Parvin Mousavi} } @conference {Aboofazeli2008, title = {Automated curved needle segmentation in three-dimensional ultrasound images}, booktitle = {Proceedings of Workshop on Needle Steering: Recent Results and Future Opportunities, a Satellite Workshop of International Conference on Medical Image Computing and Computer Assisted Intervention}, year = {2008}, author = {Mohammad Aboofazeli and Gabor Fichtinger and Purang Abolmaesumi} } @conference {Aboofazeli2008a, title = {Automated curved needle segmentation in three-dimensional ultrasound images}, booktitle = {7th Imaging Symposium of the Imaging Network of Ontario}, year = {2008}, author = {Mohammad Aboofazeli and Gabor Fichtinger and Purang Abolmaesumi} } @conference {Gill2008, title = {Group-wise Ultrasound to CT Registration of the Lumbar Spine}, booktitle = {7th Symposium of the Imaging Network of Ontario, Toronto}, year = {2008}, pages = {73}, author = {Sean Gill and Parvin Mousavi and Gabor Fichtinger and David R Pichora and Purang Abolmaesumi} } @conference {Karim-Aghaloo2008a, title = {Intensity-based registration of prostate brachytherapy implants and ultrasound}, booktitle = {Procedings 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro ISBI 2008}, year = {2008}, month = {14{\textendash}17 May}, pages = {780{\textendash}783}, doi = {10 1109/ISBI 2008 4541112}, author = {Zahra Karim-Aghaloo and Gabor Fichtinger and David Gobbi and E. Clif Burdette and Robert Rohling and Purang Abolmaesumi} } @conference {Karim-Aghaloo2008b, title = {Intra-operative Localization of Brachytherapy Implants Using Intensity-based Registration}, booktitle = {7th Imaging Symposium of the Imaging Network of Ontario}, year = {2008}, author = {Zahra Karim-Aghaloo and Purang Abolmaesumi and Narges Ahmidi and Thomas K. Chen and David Gobbi and Gabor Fichtinger} } @conference {Gill2008a, title = {Intraoperative Prostate Tracking with Slice-to-Volume Registration in MRI}, booktitle = {20th International Conference of the Society for Medical Innovation and Technology}, year = {2008}, month = {08/2008}, pages = {154-158}, publisher = {Society for Medical Innovation and Technology SMIT}, organization = {Society for Medical Innovation and Technology SMIT}, address = {Vienna, Austria, August 28-31, 2008}, isbn = {3-902087-25-0}, author = {Sean Gill and Purang Abolmaesumi and Siddharth Vikal and Parvin Mousavi and Gabor Fichtinger} } @conference {Boisvert2008, title = {An open-source solution for interactive acquisition, processing and transfer of interventional ultrasound images}, booktitle = {Workshop on Systems and Architectures for Computer Assisted Interventions, held in conjunction with the 11th International Conference on Medical Image Computing and Computer Assisted Intervention}, year = {2008}, author = {Jonathan Boisvert and David Gobbi and Siddharth Vikal and Robert Rohling and Gabor Fichtinger and Purang Abolmaesumi} } @article {Hefny2008, title = {Quantification of edematic effects in prostate brachytherapy interventions}, journal = {Medical image computing and computer-assisted intervention (MICCAI)}, volume = {11}, number = {Pt 2}, year = {2008}, pages = {493{\textendash}500}, publisher = {School of Computing, Queen{\textquoteright}s University, Kingston, Ontario, Canada}, abstract = {

We present a quantitative model to analyze the detrimental effects of for edema on the quality of prostate brachytherapy implants We account for both tissue expansion, implant migration by mapping intra-operative ultrasound, post-implant CT We pre-process the ultrasound with a phase congruency filter, and map it to the volume CT using a B-spline deformable mutual information similarity metric To test the method, we implanted a standard training phantom with 48 seeds, imaged the phantom with ultrasound, CT, registered the two for ground truth Edema was simulated by distorting the CT volume by known transformations The objective was to match the distorted implant to the intra-operative ultrasound Performance was measured relative to ground truth We successfully mapped 100\% of deformed seeds to ground truth under edematic expansion up to 40\% of volume growth Seed matching performance was 98\% with random seed migration of 3mm superimposed on 10\% edematic volume growth This method promises to be clinically applicable as the first quantitative analysis tool to measure edematic implant deformations occurring between the operating room, post-operative CT imaging

}, keywords = {adverse effects, adverse effects/instrumentation, Algorithms, Automated, Brachytherapy, complications/radiotherapy, Computer-Assisted, Edema, etiology/radiography, Humans, Male, methods, Pattern Recognition, Prostatic Diseases, Prostatic Neoplasms, Prosthesis Implantation, Radiographic Image Enhancement, Radiographic Image Interpretation, Reproducibility of Results, Sensitivity, Specificity, Tomography, Treatment Outcome, X-Ray Computed}, author = {Mohamed Hefny and Purang Abolmaesumi and Zahra Karim-Aghaloo and David Gobbi and Randy Ellis and Gabor Fichtinger} } @conference {Gobbi2008, title = {Simulink libraries for visual programming of VTK and ITK}, booktitle = {Workshop on Systems and Architectures for Computer Assisted Interventions, held in conjunction with the 11th International Conference on Medical Image Computing and Computer Assisted Intervention}, year = {2008}, author = {David Gobbi and Parvin Mousavi and K Li and Jing Xiang and Adam Campigotto and Gabor Fichtinger and Purang Abolmaesumi} } @conference {Karim-Aghaloo2008, title = {Towards detecting surgical clips in 3D ultrasound for target localization in radiation therapy: a study on tissue phantoms}, booktitle = {International Conference of the IEEE Engineering in Medicine and Biology Society}, volume = {2008}, year = {2008}, pages = {5282{\textendash}5285}, publisher = {Department of Electrical, Computer Engineering, Queens University, Kingston, ON K7L3N6, Canada}, organization = {Department of Electrical, Computer Engineering, Queens University, Kingston, ON K7L3N6, Canada}, abstract = {

A study is performed to measure the visibility of small surgical clips in 3D ultrasound volumes of a phantom as the first step towards using such clips as fiducial markers in radiation therapy Visibility is calculated as the contrast to noise ratio of the echo from the clip to the background The appearance of a resonance tail is also calculated using a moment analysis Contrast is found to be high, mostly independent of material, size of the clip All clips are visible, but the length of the tail is found to be dependent on clip orientation to the ultrasound beam The consistent visibility of the clips suggests they are suitable as fiducial markers in ultrasound, the dependency of the resonance tail on orientation provides an opportunity to distinguish clips from other specular reflectors

}, keywords = {Computer-Assisted, Equipment Design, Equipment Failure Analysis, Humans, Image Enhancement, Imaging, instrumentation, instrumentation/methods, methods, Phantoms, Radiotherapy, Reproducibility of Results, Sensitivity, Specificity, Surgical Instruments, Three-Dimensional, Ultrasonography}, doi = {10 1109/IEMBS 2008 4650406}, url = {http://dx doi org/10 1109/IEMBS 2008 4650406}, author = {Zahra Karim-Aghaloo and Prasad Shrawane and Purang Abolmaesumi and Gabor Fichtinger and Robert Rohling} }