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Heo JU, Zhou F, Jones R, Zheng J, Song X, Qian P, Baydoun A, Traughber MS, Kuo JW, Helo RA, Thompson C, Avril N, DeVincent D, Hunt H, Gupta A, Faraji N, Kharouta MZ, Kardan A, Bitonte D, Langmack CB, Nelson A, Kruzer A, Yao M, Dorth J, Nakayama J, Waggoner SE, Biswas T, Harris E, Sandstrom S, Traughber BJ, Muzic RF. Abdominopelvic MR to CT registration using a synthetic CT intermediate. J Appl Clin Med Phys 2022; 23:e13731. [PMID: 35920116 PMCID: PMC9512351 DOI: 10.1002/acm2.13731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 11/21/2022] Open
Abstract
Accurate coregistration of computed tomography (CT) and magnetic resonance (MR) imaging can provide clinically relevant and complementary information and can serve to facilitate multiple clinical tasks including surgical and radiation treatment planning, and generating a virtual Positron Emission Tomography (PET)/MR for the sites that do not have a PET/MR system available. Despite the long‐standing interest in multimodality co‐registration, a robust, routine clinical solution remains an unmet need. Part of the challenge may be the use of mutual information (MI) maximization and local phase difference (LPD) as similarity metrics, which have limited robustness, efficiency, and are difficult to optimize. Accordingly, we propose registering MR to CT by mapping the MR to a synthetic CT intermediate (sCT) and further using it in a sCT‐CT deformable image registration (DIR) that minimizes the sum of squared differences. The resultant deformation field of a sCT‐CT DIR is applied to the MRI to register it with the CT. Twenty‐five sets of abdominopelvic imaging data are used for evaluation. The proposed method is compared to standard MI‐ and LPD‐based methods, and the multimodality DIR provided by a state of the art, commercially available FDA‐cleared clinical software package. The results are compared using global similarity metrics, Modified Hausdorff Distance, and Dice Similarity Index on six structures. Further, four physicians visually assessed and scored registered images for their registration accuracy. As evident from both quantitative and qualitative evaluation, the proposed method achieved registration accuracy superior to LPD‐ and MI‐based methods and can refine the results of the commercial package DIR when using its results as a starting point. Supported by these, this manuscript concludes the proposed registration method is more robust, accurate, and efficient than the MI‐ and LPD‐based methods.
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Affiliation(s)
- Jin Uk Heo
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Feifei Zhou
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robert Jones
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Jiamin Zheng
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, Jiangsu, China
| | - Xin Song
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, Jiangsu, China
| | - Pengjiang Qian
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, Jiangsu, China
| | - Atallah Baydoun
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Internal Medicine, Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, USA
| | - Melanie S Traughber
- Department of Radiation Oncology, Penn State University, Hershey, Pennsylvania, USA
| | - Jung-Wen Kuo
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rose Al Helo
- Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Cheryl Thompson
- Department of Public Health Sciences, Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - Norbert Avril
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Daniel DeVincent
- Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Harold Hunt
- Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Amit Gupta
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Navid Faraji
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Michael Z Kharouta
- Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Arash Kardan
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - David Bitonte
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Christian B Langmack
- Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | | | | | - Min Yao
- Department of Radiation Oncology, Penn State University, Hershey, Pennsylvania, USA
| | - Jennifer Dorth
- Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Radiation Oncology, Case Western Reserve University, Cleveland, Ohio, USA
| | - John Nakayama
- Department of Obstetrics and Gynecology, Allegheny Health Network, Pittsburgh, Pennsylvania, USA
| | - Steven E Waggoner
- Department of Obstetrics and Gynecology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tithi Biswas
- Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Radiation Oncology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Eleanor Harris
- Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA.,Department of Radiation Oncology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Susan Sandstrom
- Department of Radiation Oncology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Bryan J Traughber
- Department of Radiation Oncology, Penn State University, Hershey, Pennsylvania, USA
| | - Raymond F Muzic
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA.,Department of Radiology, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
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Hussein M, Akintonde A, McClelland J, Speight R, Clark CH. Clinical use, challenges, and barriers to implementation of deformable image registration in radiotherapy - the need for guidance and QA tools. Br J Radiol 2021; 94:20210001. [PMID: 33882253 PMCID: PMC8173691 DOI: 10.1259/bjr.20210001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/06/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE The aim of this study was to evaluate the current status of the clinical use of deformable image registration (DIR) in radiotherapy and to gain an understanding of the challenges faced by centres in clinical implementation of DIR, including commissioning and quality assurance (QA), and to determine the barriers faced. The goal was to inform whether additional guidance and QA tools were needed. METHODS A survey focussed on clinical use, metrics used, how centres would like to use DIR in the future and challenges faced, was designed and sent to 71 radiotherapy centres in the UK. Data were gathered specifically on which centres we using DIR clinically, which applications were being used, what commissioning and QA tests were performed, and what barriers were preventing the integration of DIR into the clinical workflow. Centres that did not use DIR clinically were encouraged to fill in the survey and were asked if they have any future plans and in what timescale. RESULTS 51 out of 71 (70%) radiotherapy centres responded. 47 centres reported access to a commercial software that could perform DIR. 20 centres already used DIR clinically, and 22 centres had plans to implement an application of DIR within 3 years of the survey. The most common clinical application of DIR was to propagate contours from one scan to another (19 centres). In each of the applications, the types of commissioning and QA tests performed varied depending on the type of application and between centres. Some of the key barriers were determining when a DIR was satisfactory including which metrics to use, and lack of resources. CONCLUSION The survey results highlighted that there is a need for additional guidelines, training, better tools for commissioning DIR software and for the QA of registration results, which should include developing or recommending which quantitative metrics to use. ADVANCES IN KNOWLEDGE This survey has given a useful picture of the clinical use and lack of use of DIR in UK radiotherapy centres. The survey provided useful insight into how centres commission and QA DIR applications, especially the variability among centres. It was also possible to highlight key barriers to implementation and determine factors that may help overcome this which include the need for additional guidance specific to different applications, better tools and metrics.
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Affiliation(s)
- Mohammad Hussein
- Metrology for Medical Physics Centre, National Physical Laboratory, Teddington, UK
| | - Adeyemi Akintonde
- Centre for Medical Image Computing, University College London, London, UK
| | - Jamie McClelland
- Centre for Medical Image Computing, University College London, London, UK
| | - Richard Speight
- Leeds Cancer Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
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Accurate validation of ultrasound imaging of prostate cancer: a review of challenges in registration of imaging and histopathology. J Ultrasound 2018; 21:197-207. [PMID: 30062440 PMCID: PMC6113189 DOI: 10.1007/s40477-018-0311-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/11/2018] [Indexed: 01/20/2023] Open
Abstract
As the development of modalities for prostate cancer (PCa) imaging advances, the challenge of accurate registration between images and histopathologic ground truth becomes more pressing. Localization of PCa, rather than detection, requires a pixel-to-pixel validation of imaging based on histopathology after radical prostatectomy. Such a registration procedure is challenging for ultrasound modalities; not only the deformations of the prostate after resection have to be taken into account, but also the deformation due to the employed transrectal probe and the mismatch in orientation between imaging planes and pathology slices. In this work, we review the latest techniques to facilitate accurate validation of PCa localization in ultrasound imaging studies and extrapolate a general strategy for implementation of a registration procedure.
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Abstract
Multi-parametric magnetic resonance imaging (mp-MRI) has an increasingly important role in the diagnosis of prostate cancer. Due to the large amount of data and variations in mp-MRI, tumor detection can be affected by multiple factors, such as the observer's clinical experience, image quality, and appearance of the lesions. In order to improve the quantitative assessment of the disease and reduce the reporting time, various computer-aided diagnosis (CAD) systems have been designed to help radiologists identify lesions. This manuscript presents an overview of the literature regarding prostate CAD using mp-MRI, while focusing on the studies of the most recent five years. Current prostate CAD technologies and their utilization are discussed in this review.
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Ferrante E, Paragios N. Slice-to-volume medical image registration: A survey. Med Image Anal 2017; 39:101-123. [DOI: 10.1016/j.media.2017.04.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 04/08/2017] [Accepted: 04/27/2017] [Indexed: 11/25/2022]
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Qin X, Wang S, Shen M, Zhang X, Lerakis S, Wagner MB, Fei B. Register cardiac fiber orientations from 3D DTI volume to 2D ultrasound image of rat hearts. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9415. [PMID: 26855466 DOI: 10.1117/12.2082317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Two-dimensional (2D) ultrasound or echocardiography is one of the most widely used examinations for the diagnosis of cardiac diseases. However, it only supplies the geometric and structural information of the myocardium. In order to supply more detailed microstructure information of the myocardium, this paper proposes a registration method to map cardiac fiber orientations from three-dimensional (3D) magnetic resonance diffusion tensor imaging (MR-DTI) volume to the 2D ultrasound image. It utilizes a 2D/3D intensity based registration procedure including rigid, log-demons, and affine transformations to search the best similar slice from the template volume. After registration, the cardiac fiber orientations are mapped to the 2D ultrasound image via fiber relocations and reorientations. This method was validated by six images of rat hearts ex vivo. The evaluation results indicated that the final Dice similarity coefficient (DSC) achieved more than 90% after geometric registrations; and the inclination angle errors (IAE) between the mapped fiber orientations and the gold standards were less than 15 degree. This method may provide a practical tool for cardiologists to examine cardiac fiber orientations on ultrasound images and have the potential to supply additional information for diagnosis of cardiac diseases.
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Affiliation(s)
- Xulei Qin
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA
| | - Silun Wang
- Yerkes National Primate Research Center, Emory University, Atlanta, GA
| | - Ming Shen
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA
| | - Xiaodong Zhang
- Yerkes National Primate Research Center, Emory University, Atlanta, GA
| | - Stamatios Lerakis
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA; Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA
| | - Mary B Wagner
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Baowei Fei
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA; Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA
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Qin X, Wang S, Shen M, Zhang X, Lerakis S, Wagner MB, Fei B. 3D in vivo imaging of rat hearts by high frequency ultrasound and its application in myofiber orientation wrapping. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2015; 9419. [PMID: 26412926 DOI: 10.1117/12.2082326] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Cardiac ultrasound plays an important role in the imaging of hearts in basic cardiovascular research and clinical examinations. 3D ultrasound imaging can provide the geometry or motion information of the heart. Especially, the wrapping of cardiac fiber orientations to the ultrasound volume could supply useful information on the stress distributions and electric action spreading. However, how to acquire 3D ultrasound volumes of the heart of small animals in vivo for cardiac fiber wrapping is still a challenging problem. In this study, we provide an approach to acquire 3D ultrasound volumes of the rat hearts in vivo. The comparison between both in vivo and ex vivo geometries indicated 90.1% Dice similarity. In this preliminary study, the evaluations of the cardiac fiber orientation wrapping errors were 24.7° for the acute angle error and were 22.4° for the inclination angle error. This 3D ultrasound imaging and fiber orientation estimation technique have potential applications in cardiac imaging.
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Affiliation(s)
- Xulei Qin
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA
| | - Silun Wang
- Yerkes National Primate Research Center, Emory University, Atlanta, GA
| | - Ming Shen
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA
| | - Xiaodong Zhang
- Yerkes National Primate Research Center, Emory University, Atlanta, GA
| | - Stamatios Lerakis
- Division of Cardiology, Department of Medicine, Emory University, Atlanta, GA ; Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA
| | - Mary B Wagner
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Baowei Fei
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA ; Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA
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Qin X, Lu G, Sechopoulos I, Fei B. Breast Tissue Classification in Digital Tomosynthesis Images Based on Global Gradient Minimization and Texture Features. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 9034:90341V. [PMID: 25426271 PMCID: PMC4241347 DOI: 10.1117/12.2043828] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Digital breast tomosynthesis (DBT) is a pseudo-three-dimensional x-ray imaging modality proposed to decrease the effect of tissue superposition present in mammography, potentially resulting in an increase in clinical performance for the detection and diagnosis of breast cancer. Tissue classification in DBT images can be useful in risk assessment, computer-aided detection and radiation dosimetry, among other aspects. However, classifying breast tissue in DBT is a challenging problem because DBT images include complicated structures, image noise, and out-of-plane artifacts due to limited angular tomographic sampling. In this project, we propose an automatic method to classify fatty and glandular tissue in DBT images. First, the DBT images are pre-processed to enhance the tissue structures and to decrease image noise and artifacts. Second, a global smooth filter based on L0 gradient minimization is applied to eliminate detailed structures and enhance large-scale ones. Third, the similar structure regions are extracted and labeled by fuzzy C-means (FCM) classification. At the same time, the texture features are also calculated. Finally, each region is classified into different tissue types based on both intensity and texture features. The proposed method is validated using five patient DBT images using manual segmentation as the gold standard. The Dice scores and the confusion matrix are utilized to evaluate the classified results. The evaluation results demonstrated the feasibility of the proposed method for classifying breast glandular and fat tissue on DBT images.
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Affiliation(s)
- Xulei Qin
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA
| | - Guolan Lu
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA
| | - Ioannis Sechopoulos
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA
- Winship Cancer Institute, Emory University, Atlanta, GA
| | - Baowei Fei
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA
- Department of Mathematics & Computer Science, Emory University, Atlanta, GA
- Winship Cancer Institute, Emory University, Atlanta, GA
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Lu G, Halig L, Wang D, Chen ZG, Fei B. Hyperspectral Imaging for Cancer Surgical Margin Delineation: Registration of Hyperspectral and Histological Images. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 9036:90360S. [PMID: 25328640 PMCID: PMC4201054 DOI: 10.1117/12.2043805] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
The determination of tumor margins during surgical resection remains a challenging task. A complete removal of malignant tissue and conservation of healthy tissue is important for the preservation of organ function, patient satisfaction, and quality of life. Visual inspection and palpation is not sufficient for discriminating between malignant and normal tissue types. Hyperspectral imaging (HSI) technology has the potential to noninvasively delineate surgical tumor margin and can be used as an intra-operative visual aid tool. Since histological images provide the ground truth of cancer margins, it is necessary to warp the cancer regions in ex vivo histological images back to in vivo hyperspectral images in order to validate the tumor margins detected by HSI and to optimize the imaging parameters. In this paper, principal component analysis (PCA) is utilized to extract the principle component bands of the HSI images, which is then used to register HSI images with the corresponding histological image. Affine registration is chosen to model the global transformation. A B-spline free form deformation (FFD) method is used to model the local non-rigid deformation. Registration experiment was performed on animal hyperspectral and histological images. Experimental results from animals demonstrated the feasibility of the hyperspectral imaging method for cancer margin detection.
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Affiliation(s)
- Guolan Lu
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia
Institute of Technology and Emory University, Atlanta, GA
| | - Luma Halig
- Department of Hematology and Medical Oncology, Emory University,
Atlanta, GA
| | - Dongsheng Wang
- Department of Hematology and Medical Oncology, Emory University,
Atlanta, GA
| | - Zhuo Georgia Chen
- Department of Hematology and Medical Oncology, Emory University,
Atlanta, GA
| | - Baowei Fei
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia
Institute of Technology and Emory University, Atlanta, GA
- Department of Radiology and Imaging Sciences, Emory University,
Atlanta, GA
- Department of Mathematics & Computer Science, Emory University,
Atlanta, GA
- Winship Cancer Institute of Emory University, Atlanta, GA
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Qin X, Wang S, Shen M, Zhang X, Wagner MB, Fei B. Mapping Cardiac Fiber Orientations from High-Resolution DTI to High-Frequency 3D Ultrasound. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 9036:90361O. [PMID: 25328641 DOI: 10.1117/12.2043821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The orientation of cardiac fibers affects the anatomical, mechanical, and electrophysiological properties of the heart. Although echocardiography is the most common imaging modality in clinical cardiac examination, it can only provide the cardiac geometry or motion information without cardiac fiber orientations. If the patient's cardiac fiber orientations can be mapped to his/her echocardiography images in clinical examinations, it may provide quantitative measures for diagnosis, personalized modeling, and image-guided cardiac therapies. Therefore, this project addresses the feasibility of mapping personalized cardiac fiber orientations to three-dimensional (3D) ultrasound image volumes. First, the geometry of the heart extracted from the MRI is translated to 3D ultrasound by rigid and deformable registration. Deformation fields between both geometries from MRI and ultrasound are obtained after registration. Three different deformable registration methods were utilized for the MRI-ultrasound registration. Finally, the cardiac fiber orientations imaged by DTI are mapped to ultrasound volumes based on the extracted deformation fields. Moreover, this study also demonstrated the ability to simulate electricity activations during the cardiac resynchronization therapy (CRT) process. The proposed method has been validated in two rat hearts and three canine hearts. After MRI/ultrasound image registration, the Dice similarity scores were more than 90% and the corresponding target errors were less than 0.25 mm. This proposed approach can provide cardiac fiber orientations to ultrasound images and can have a variety of potential applications in cardiac imaging.
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Affiliation(s)
- Xulei Qin
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA
| | - Silun Wang
- Yerkes National Primate Research Center, Emory University, Atlanta, GA
| | - Ming Shen
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Xiaodong Zhang
- Yerkes National Primate Research Center, Emory University, Atlanta, GA
| | - Mary B Wagner
- Department of Pediatrics, Emory University, Atlanta, GA
| | - Baowei Fei
- Department of Radiology and Imaging Sciences, Emory University, Atlanta, GA ; Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA
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Fei B, Yang X, Nye JA, Aarsvold JN, Raghunath N, Cervo M, Stark R, Meltzer CC, Votaw JR. MR∕PET quantification tools: registration, segmentation, classification, and MR-based attenuation correction. Med Phys 2012; 39:6443-54. [PMID: 23039679 DOI: 10.1118/1.4754796] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Combined MR∕PET is a relatively new, hybrid imaging modality. A human MR∕PET prototype system consisting of a Siemens 3T Trio MR and brain PET insert was installed and tested at our institution. Its present design does not offer measured attenuation correction (AC) using traditional transmission imaging. This study is the development of quantification tools including MR-based AC for quantification in combined MR∕PET for brain imaging. METHODS The developed quantification tools include image registration, segmentation, classification, and MR-based AC. These components were integrated into a single scheme for processing MR∕PET data. The segmentation method is multiscale and based on the Radon transform of brain MR images. It was developed to segment the skull on T1-weighted MR images. A modified fuzzy C-means classification scheme was developed to classify brain tissue into gray matter, white matter, and cerebrospinal fluid. Classified tissue is assigned an attenuation coefficient so that AC factors can be generated. PET emission data are then reconstructed using a three-dimensional ordered sets expectation maximization method with the MR-based AC map. Ten subjects had separate MR and PET scans. The PET with [(11)C]PIB was acquired using a high-resolution research tomography (HRRT) PET. MR-based AC was compared with transmission (TX)-based AC on the HRRT. Seventeen volumes of interest were drawn manually on each subject image to compare the PET activities between the MR-based and TX-based AC methods. RESULTS For skull segmentation, the overlap ratio between our segmented results and the ground truth is 85.2 ± 2.6%. Attenuation correction results from the ten subjects show that the difference between the MR and TX-based methods was <6.5%. CONCLUSIONS MR-based AC compared favorably with conventional transmission-based AC. Quantitative tools including registration, segmentation, classification, and MR-based AC have been developed for use in combined MR∕PET.
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Affiliation(s)
- Baowei Fei
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, USA.
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Pursley J, Risholm P, Fedorov A, Tuncali K, Fennessy FM, Wells WM, Tempany CM, Cormack RA. A Bayesian nonrigid registration method to enhance intraoperative target definition in image-guided prostate procedures through uncertainty characterization. Med Phys 2012; 39:6858-67. [PMID: 23127078 PMCID: PMC3494726 DOI: 10.1118/1.4760992] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 09/28/2012] [Accepted: 10/02/2012] [Indexed: 11/07/2022] Open
Abstract
PURPOSE This study introduces a probabilistic nonrigid registration method for use in image-guided prostate brachytherapy. Intraoperative imaging for prostate procedures, usually transrectal ultrasound (TRUS), is typically inferior to diagnostic-quality imaging of the pelvis such as endorectal magnetic resonance imaging (MRI). MR images contain superior detail of the prostate boundaries and provide substructure features not otherwise visible. Previous efforts to register diagnostic prostate images with the intraoperative coordinate system have been deterministic and did not offer a measure of the registration uncertainty. The authors developed a Bayesian registration method to estimate the posterior distribution on deformations and provide a case-specific measure of the associated registration uncertainty. METHODS The authors adapted a biomechanical-based probabilistic nonrigid method to register diagnostic to intraoperative images by aligning a physician's segmentations of the prostate in the two images. The posterior distribution was characterized with a Markov Chain Monte Carlo method; the maximum a posteriori deformation and the associated uncertainty were estimated from the collection of deformation samples drawn from the posterior distribution. The authors validated the registration method using a dataset created from ten patients with MRI-guided prostate biopsies who had both diagnostic and intraprocedural 3 Tesla MRI scans. The accuracy and precision of the estimated posterior distribution on deformations were evaluated from two predictive distance distributions: between the deformed central zone-peripheral zone (CZ-PZ) interface and the physician-labeled interface, and based on physician-defined landmarks. Geometric margins on the registration of the prostate's peripheral zone were determined from the posterior predictive distance to the CZ-PZ interface separately for the base, mid-gland, and apical regions of the prostate. RESULTS The authors observed variation in the shape and volume of the segmented prostate in diagnostic and intraprocedural images. The probabilistic method allowed us to convey registration results in terms of posterior distributions, with the dispersion providing a patient-specific estimate of the registration uncertainty. The median of the predictive distance distribution between the deformed prostate boundary and the segmented boundary was ≤3 mm (95th percentiles within ±4 mm) for all ten patients. The accuracy and precision of the internal deformation was evaluated by comparing the posterior predictive distance distribution for the CZ-PZ interface for each patient, with the median distance ranging from -0.6 to 2.4 mm. Posterior predictive distances between naturally occurring landmarks showed registration errors of ≤5 mm in any direction. The uncertainty was not a global measure, but instead was local and varied throughout the registration region. Registration uncertainties were largest in the apical region of the prostate. CONCLUSIONS Using a Bayesian nonrigid registration method, the authors determined the posterior distribution on deformations between diagnostic and intraprocedural MR images and quantified the uncertainty in the registration results. The feasibility of this approach was tested and results were positive. The probabilistic framework allows us to evaluate both patient-specific and location-specific estimates of the uncertainty in the registration result. Although the framework was tested on MR-guided procedures, the preliminary results suggest that it may be applied to TRUS-guided procedures as well, where the addition of diagnostic MR information may have a larger impact on target definition and clinical guidance.
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Affiliation(s)
- Jennifer Pursley
- Department of Radiation Oncology, Harvard Medical School, Boston, MA 02115, USA.
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Fei B, Flask C, Wang H, Pi A, Wilson D, Shillingford J, Murcia N, Weimbs T, Duerk J. Image Segmentation, Registration and Visualization of Serial MR Images for Therapeutic Assessment of Polycystic Kidney Disease in Transgenic Mice. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2012; 2006:467-9. [PMID: 17282217 DOI: 10.1109/iembs.2005.1616448] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In vivo small animal imaging provides a powerful tool for the study of a variety of diseases. Magnetic resonance imaging (MRI) has become an established technology for the assessment of therapies. In this study, we used high-resolution MRI to evaluate polycystic kidney disease (PKD) in transgenic mice. We used a customized mouse coil to acquire serial MR images from both wide-type and transgenic PKD mice immediately prior to, and 2-week and 4-week after therapy. We developed image segmentation, registration and visualization methods for this novel imaging application. We measured the kidney volumes for each mouse to assess the efficacy of the therapy. The segmentation results show that the kidney volumes are consistent, which are 348.7 ± 19.7 mm<sup>3</sup>for wild-type mice and 756.3 ± 44.1 mm<sup>3</sup>for transgenic mice, respectively. The image analysis methods provide a useful tool for this new application.
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Affiliation(s)
- Baowei Fei
- Department of Radiology, Case Western Reserve University & University Hospitals of Cleveland, USA
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15
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Shi Y, Liao S, Shen D. Learning statistical correlation for fast prostate registration in image-guided radiotherapy. Med Phys 2012; 38:5980-91. [PMID: 22047362 DOI: 10.1118/1.3641645] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
PURPOSE In adaptive radiation therapy of prostate cancer, fast and accurate registration between the planning image and treatment images of the patient is of essential importance. With the authors' recently developed deformable surface model, prostate boundaries in each treatment image can be rapidly segmented and their correspondences (or relative deformations) to the prostate boundaries in the planning image are also established automatically. However, the dense correspondences on the nonboundary regions, which are important especially for transforming the treatment plan designed in the planning image space to each treatment image space, are remained unresolved. This paper presents a novel approach to learn the statistical correlation between deformations of prostate boundary and nonboundary regions, for rapidly estimating deformations of the nonboundary regions when given the deformations of the prostate boundary at a new treatment image. METHODS The main contributions of the proposed method lie in the following aspects. First, the statistical deformation correlation will be learned from both current patient and other training patients, and further updated adaptively during the radiotherapy. Specifically, in the initial treatment stage when the number of treatment images collected from the current patient is small, the statistical deformation correlation is mainly learned from other training patients. As more treatment images are collected from the current patient, the patient-specific information will play a more important role in learning patient-specific statistical deformation correlation to effectively reflect prostate deformation of the current patient during the treatment. Eventually, only the patient-specific statistical deformation correlation is used to estimate dense correspondences when a sufficient number of treatment images have been acquired from the current patient. Second, the statistical deformation correlation will be learned by using a multiple linear regression (MLR) model, i.e., ridge regression (RR) model, which has the best prediction accuracy than other MLR models such as canonical correlation analysis (CCA) and principal component regression (PCR). RESULTS To demonstrate the performance of the proposed method, we first evaluate its registration accuracy by comparing the deformation field predicted by our method with the deformation field estimated by the thin plate spline (TPS) based correspondence interpolation method on 306 serial prostate CT images of 24 patients. The average predictive error on the voxels around 5 mm of prostate boundary is 0.38 mm for our method of RR-based correlation model. Also, the corresponding maximum error is 2.89 mm. We then compare the speed for deformation interpolation by different methods. When considering the larger region of interest (ROI) with the size of 512 × 512 × 61, our method takes 24.41 seconds to interpolate the dense deformation field while TPS method needs 6.7 minutes; when considering a small ROI (surrounding prostate) with size of 112 × 110 × 93, our method takes 1.80 seconds, while TPS method needs 25 seconds. CONCLUSIONS Experimental results show that the proposed method can achieve much faster registration speed yet with comparable registration accuracy, compared to the TPS-based correspondence (or deformation) interpolation approach.
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Affiliation(s)
- Yonghong Shi
- Fudan University, Shanghai Medical College, Shanghai, Taiwan.
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Risholm P, Fedorov A, Pursley J, Tuncali K, Cormack R, Wells WM. PROBABILISTIC NON-RIGID REGISTRATION OF PROSTATE IMAGES: MODELING AND QUANTIFYING UNCERTAINTY. PROCEEDINGS. IEEE INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING 2011; 2011:553-556. [PMID: 22288004 DOI: 10.1109/isbi.2011.5872467] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Registration of pre- to intra-procedural prostate images needs to handle the large changes in position and shape of the prostate caused by varying rectal filling and patient positioning. We describe a probabilistic method for non-rigid registration of prostate images which can quantify the most probable deformation as well as the uncertainty of the estimated deformation. The method is based on a biomechanical Finite Element model which treats the prostate as an elastic material. We use a Markov Chain Monte Carlo sampler to draw deformation configurations from the posterior distribution. In practice, we simultaneously estimate the boundary conditions (surface displacements) and the internal deformations of our biomechanical model. The proposed method was validated on a clinical MRI dataset with registration results comparable to previously published methods, but with the added benefit of also providing uncertainty estimates which may be important to take into account during prostate biopsy and brachytherapy procedures.
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Affiliation(s)
- Petter Risholm
- Brigham and Women's Hospital, Harvard Medical School, Boston, USA
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Chen X, Gilkeson RC, Fei B. Automatic 3D-to-2D registration for CT and dual-energy digital radiography for calcification detection. Med Phys 2008; 34:4934-43. [PMID: 18196818 DOI: 10.1118/1.2805994] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We are investigating three-dimensional (3D) to two-dimensional (2D) registration methods for computed tomography (CT) and dual-energy digital radiography (DEDR). CT is an established tool for the detection of cardiac calcification. DEDR could be a cost-effective alternative screening tool. In order to utilize CT as the "gold standard" to evaluate the capability of DEDR images for the detection and localization of calcium, we developed an automatic, intensity-based 3D-to-2D registration method for 3D CT volumes and 2D DEDR images. To generate digitally reconstructed radiography (DRR) from the CT volumes, we developed several projection algorithms using the fast shear-warp method. In particular, we created a Gaussian-weighted projection for this application. We used normalized mutual information (NMI) as the similarity measurement. Simulated projection images from CT values were fused with the corresponding DEDR images to evaluate the localization of cardiac calcification. The registration method was evaluated by digital phantoms, physical phantoms, and clinical data sets. The results from the digital phantoms show that the success rate is 100% with a translation difference of less than 0.8 mm and a rotation difference of less than 0.2 degrees. For physical phantom images, the registration accuracy is 0.43 +/- 0.24 mm. Color overlay and 3D visualization of clinical images show that the two images registered well. The NMI values between the DRR and DEDR images improved from 0.21 +/- 0.03 before registration to 0.25 +/- 0.03 after registration. Registration errors measured from anatomic markers decreased from 27.6 +/- 13.6 mm before registration to 2.5 +/- 0.5 mm after registration. Our results show that the automatic 3D-to-2D registration is accurate and robust. This technique can provide a useful tool for correlating DEDR with CT images for screening coronary artery calcification.
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Affiliation(s)
- Xiang Chen
- Department of Radiology, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Fei B, Chen X, Wang H, Sabol JM, DuPont E, Gilkeson RC. Automatic registration of CT volumes and dual-energy digital radiography for detection of cardiac and lung diseases. CONFERENCE PROCEEDINGS : ... ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL CONFERENCE 2008; 2006:1976-9. [PMID: 17945687 DOI: 10.1109/iembs.2006.259888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We are investigating image processing and analysis techniques to improve the ability of dual-energy digital radiography (DR) for the detection of cardiac calcification. Computed tomography (CT) is an established tool for the diagnosis of coronary artery diseases. Dual-energy digital radiography could be a cost-effective alternative. In this study, we use three-dimensional (3D) CT images as the "gold standard" to evaluate the DR X-ray images for calcification detection. To this purpose, we developed an automatic registration method for 3D CT volumes and two-dimensional (2D) X-ray images. We call this 3D-to-2D registration. We first use a 3D CT image volume to simulate X-ray projection images and then register them with X-ray images. The registered CT projection images are then used to aid the interpretation dual-energy X-ray images for the detection of cardiac calcification. We acquired both CT and X-ray images from patients with coronary artery diseases. Experimental results show that the 3D-to-2D registration is accurate and useful for this new application.
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Affiliation(s)
- Baowei Fei
- Dept. of Radiol. & Biomed. Eng., Case Western Reserve Univ., Cleveland, OH 44106, USA.
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Abstract
In this article the current issues of diagnosis and detection of prostate cancer are reviewed. The limitations for current techniques are highlighted and some possible solutions with MR imaging and MR-guided biopsy approaches are reviewed. There are several different biopsy approaches under investigation. These include transperineal open magnet approaches to closed-bore 1.5T transrectal biopsies. The imaging, image processing, and tracking methods are also discussed. In the arena of therapy, MR guidance has been used in conjunction with radiation methods, either brachytherapy or external delivery. The principles of the radiation treatment, the toxicities, and use of images are outlined. The future role of imaging and image-guided interventions lie with providing a noninvasive surrogate for cancer surveillance or monitoring treatment response. The shift to minimally invasive focal therapies has already begun and will be very exciting when MR-guided focused ultrasound surgery reaches its full potential.
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Affiliation(s)
- Clare Tempany
- Department of Radiology, Brigham & Women's Hospital, Boston, MA 02115, USA.
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Birkfellner W, Figl M, Kettenbach J, Hummel J, Homolka P, Schernthaner R, Nau T, Bergmann H. Rigid 2D/3D slice-to-volume registration and its application on fluoroscopic CT images. Med Phys 2007; 34:246-55. [PMID: 17278510 DOI: 10.1118/1.2401661] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Registration of single slices from FluoroCT, CineMR, or interventional magnetic resonance imaging to three dimensional (3D) volumes is a special aspect of the two-dimensional (2D)/3D registration problem. Rather than digitally rendered radiographs (DRR), single 2D slice images obtained during interventional procedures are compared to oblique reformatted slices from a high resolution 3D scan. Due to the lack of perspective information and the different imaging geometry, convergence behavior differs significantly from 2D/3D registration applications comparing DRR images with conventional x-ray images. We have implemented a number of merit functions and local and global optimization algorithms for slice-to-volume registration of computed tomography (CT) and FluoroCT images. These methods were tested on phantom images derived from clinical scans for liver biopsies. Our results indicate that good registration accuracy in the range of 0.50 and 1.0 mm is achievable using simple cross correlation and repeated application of local optimization algorithms. Typically, a registration took approximately 1 min on a standard personal computer. Other merit functions such as pattern intensity or normalized mutual information did not perform as well as cross correlation in this initial evaluation. Furthermore, it appears as if the use of global optimization algorithms such as simulated annealing does not improve reliability or accuracy of the registration process. These findings were also confirmed in a preliminary registration study on five clinical scans. These experiments have, however, shown that a strict breath-hold protocol is inevitable when using rigid registration techniques for lesion localization in image-guided biopsy retrieval. Finally, further possible applications of slice-to-volume registration are discussed.
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Affiliation(s)
- Wolfgang Birkfellner
- Center for Biomedical Engineering and Physics, Medical University Vienna, Vienna A-1090, Austria.
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Hawkes DJ, Barratt D, Blackall JM, Chan C, Edwards PJ, Rhode K, Penney GP, McClelland J, Hill DLG. Tissue deformation and shape models in image-guided interventions: a discussion paper. Med Image Anal 2004; 9:163-75. [PMID: 15721231 DOI: 10.1016/j.media.2004.11.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
This paper promotes the concept of active models in image-guided interventions. We outline the limitations of the rigid body assumption in image-guided interventions and describe how intraoperative imaging provides a rich source of information on spatial location of anatomical structures and therapy devices, allowing a preoperative plan to be updated during an intervention. Soft tissue deformation and variation from an atlas to a particular individual can both be determined using non-rigid registration. Established methods using free-form deformations have a very large number of degrees of freedom. Three examples of deformable models--motion models, biomechanical models and statistical shape models--are used to illustrate how prior information can be used to restrict the number of degrees of freedom of the registration algorithm and thus provide active models for image-guided interventions. We provide preliminary results from applications for each type of model.
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Affiliation(s)
- D J Hawkes
- Division of Imaging Sciences, GKT School of Medicine, King's College London, UK.
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Fei B, Lee Z, Duerk JL, Wilson DL. Image Registration for Interventional MRI Guided Procedures: Interpolation Methods, Similarity Measurements, and Applications to the Prostate. ACTA ACUST UNITED AC 2003. [DOI: 10.1007/978-3-540-39701-4_34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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