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Ariyurek C, Koçanaoğulları A, Afacan O, Kurugol S. Motion-compensated image reconstruction for improved kidney function assessment using dynamic contrast-enhanced MRI. NMR Biomed 2024; 37:e5116. [PMID: 38359842 DOI: 10.1002/nbm.5116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/08/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024]
Abstract
Accurately measuring renal function is crucial for pediatric patients with kidney conditions. Traditional methods have limitations, but dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) provides a safe and efficient approach for detailed anatomical evaluation and renal function assessment. However, motion artifacts during DCE-MRI can degrade image quality and introduce misalignments, leading to unreliable results. This study introduces a motion-compensated reconstruction technique for DCE-MRI data acquired using golden-angle radial sampling. Our proposed method achieves three key objectives: (1) identifying and removing corrupted data (outliers) using a Gaussian process model fitting with a k -space center navigator, (2) efficiently clustering the data into motion phases and performing interphase registration, and (3) utilizing a novel formulation of motion-compensated radial reconstruction. We applied the proposed motion correction (MoCo) method to DCE-MRI data affected by varying degrees of motion, including both respiratory and bulk motion. We compared the outcomes with those obtained from the conventional radial reconstruction. Our evaluation encompassed assessing the quality of images, concentration curves, and tracer kinetic model fitting, and estimating renal function. The proposed MoCo reconstruction improved the temporal signal-to-noise ratio for all subjects, with a 21.8% increase on average, while total variation values of the aorta, right, and left kidney concentration were improved for each subject, with 32.5%, 41.3%, and 42.9% increases on average, respectively. Furthermore, evaluation of tracer kinetic model fitting indicated that the median standard deviation of the estimated filtration rate (σ F T ), mean normalized root-mean-squared error (nRMSE), and chi-square goodness-of-fit of tracer kinetic model fit were decreased from 0.10 to 0.04, 0.27 to 0.24, and, 0.43 to 0.27, respectively. The proposed MoCo technique enabled more reliable renal function assessment and improved image quality for detailed anatomical evaluation in the case of bulk and respiratory motion during the acquisition of DCE-MRI.
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Affiliation(s)
- Cemre Ariyurek
- Quantitative Intelligent Imaging Lab (QUIN), Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Aziz Koçanaoğulları
- Quantitative Intelligent Imaging Lab (QUIN), Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Onur Afacan
- Quantitative Intelligent Imaging Lab (QUIN), Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Sila Kurugol
- Quantitative Intelligent Imaging Lab (QUIN), Department of Radiology, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Merton R, Bosshardt D, Strijkers GJ, Nederveen AJ, Schrauben EM, van Ooij P. Reproducibility of 3D thoracic aortic displacement from 3D cine balanced SSFP at 3 T without contrast enhancement. Magn Reson Med 2024; 91:466-480. [PMID: 37831612 DOI: 10.1002/mrm.29856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 10/15/2023]
Abstract
PURPOSE Aortic motion has direct impact on the mechanical stresses acting on the aorta. In aortic disease, increased stiffness of the aorta may lead to decreased aortic motion over time, which could be a predictor for aortic dissection or rupture. This study investigates the reproducibility of obtaining 3D displacement and diameter maps quantified using accelerated 3D cine MRI at 3 T. METHODS A noncontrast-enhanced, free-breathing 3D cine sequence based on balanced SSFP and pseudo-spiral undersampling with high spatial isotropic resolution was developed (spatial/temporal resolution [1.6 mm]3 /67 ms). The thoracic aorta of 14 healthy volunteers was prospectively scanned three times at 3 T: twice on the same day and a third time 2 weeks later. Aortic displacement was calculated using iterative closest point nonrigid registration of manual segmentations of the 3D aorta at end-systole and mid-diastole. Interexamination and interobserver regional analysis of mean displacement for five regions of interest was performed using Bland-Altman analysis. Additionally, a complementary voxel-by-voxel analysis was done, allowing a more local inspection of the method. RESULTS No significant differences were found in mean and maximum displacement for any of the regions of interest for the interexamination and interobserver analysis. The maximum displacement measured in the lower half of the ascending aorta was 11.0 ± 3.4 mm (range: 3.0-17.5 mm) for the first scan. The smallest detectable change in mean displacement in the lower half of the ascending aorta was 3 mm. CONCLUSION Detailed 3D cine balanced SSFP at 3 T allows for reproducible quantification of systolic-diastolic mean aortic displacement within acceptable limits.
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Affiliation(s)
- Renske Merton
- Radiology and Nuclear Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Daan Bosshardt
- Radiology and Nuclear Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Gustav J Strijkers
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
- Biomedical Physics and Engineering, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Movement Sciences, Amsterdam, the Netherlands
| | - Aart J Nederveen
- Radiology and Nuclear Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
- Amsterdam Movement Sciences, Amsterdam, the Netherlands
| | - Eric M Schrauben
- Radiology and Nuclear Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
| | - Pim van Ooij
- Radiology and Nuclear Medicine, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands
- Amsterdam Cardiovascular Sciences, Amsterdam, the Netherlands
- Amsterdam Movement Sciences, Amsterdam, the Netherlands
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Karmakar A, Olender ML, Marlevi D, Shlofmitz E, Shlofmitz RA, Edelman ER, Nezami FR. Framework for lumen-based nonrigid tomographic coregistration of intravascular images. J Med Imaging (Bellingham) 2022; 9:044006. [PMID: 36043032 PMCID: PMC9402451 DOI: 10.1117/1.jmi.9.4.044006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 08/09/2022] [Indexed: 08/25/2023] Open
Abstract
Purpose: Modern medical imaging enables clinicians to effectively diagnose, monitor, and treat diseases. However, clinical decision-making often relies on combined evaluation of either longitudinal or disparate image sets, necessitating coregistration of multiple acquisitions. Promising coregistration techniques have been proposed; however, available methods predominantly rely on time-consuming manual alignments or nontrivial feature extraction with limited clinical applicability. Addressing these issues, we present a fully automated, robust, nonrigid registration method, allowing for coregistering of multimodal tomographic vascular image datasets using luminal annotation as the sole alignment feature. Approach: Registration is carried out by the use of the registration metrics defined exclusively for lumens shapes. The framework is primarily broken down into two sequential parts: longitudinal and rotational registration. Both techniques are inherently nonrigid in nature to compensate for motion and acquisition artifacts in tomographic images. Results: Performance was evaluated across multimodal intravascular datasets, as well as in longitudinal cases assessing pre-/postinterventional coronary images. Low registration error in both datasets highlights method utility, with longitudinal registration errors-evaluated throughout the paired tomographic sequences-of 0.29 ± 0.14 mm ( < 2 longitudinal image frames) and 0.18 ± 0.16 mm ( < 1 frame) for multimodal and interventional datasets, respectively. Angular registration for the interventional dataset rendered errors of 7.7 ° ± 6.7 ° , and 29.1 ° ± 23.2 ° for the multimodal set. Conclusions: Satisfactory results across datasets, along with additional attributes such as the ability to avoid longitudinal over-fitting and correct nonlinear catheter rotation during nonrigid rotational registration, highlight the potential wide-ranging applicability of our presented coregistration method.
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Affiliation(s)
- Abhishek Karmakar
- Cornell University, Department of Biomedical Engineering, Ithaca, New York, United States
| | - Max L. Olender
- Massachusetts Institute of Technology, Institute for Medical Engineering and Science, Cambridge, Massachusetts, United States
| | - David Marlevi
- Massachusetts Institute of Technology, Institute for Medical Engineering and Science, Cambridge, Massachusetts, United States
| | - Evan Shlofmitz
- St. Francis Hospital, Department of Cardiology, Roslyn, New York, United States
| | | | - Elazer R. Edelman
- Massachusetts Institute of Technology, Institute for Medical Engineering and Science, Cambridge, Massachusetts, United States
| | - Farhad R. Nezami
- Brigham and Women’s Hospital, Harvard Medical School, Division of Thoracic and Cardiac Surgery, Boston, Massachusetts, United States
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Hwang SI, Ahn H, Lee HJ, Hong SK, Byun SS, Lee S, Choe G, Park JS, Son Y. Comparison of Accuracies between Real-Time Nonrigid and Rigid Registration in the MRI-US Fusion Biopsy of the Prostate. Diagnostics (Basel) 2021; 11:1481. [PMID: 34441415 DOI: 10.3390/diagnostics11081481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 11/17/2022] Open
Abstract
Magnetic resonance imaging (MRI) is increasingly important in the detection and localization of prostate cancer. Regarding suspicious lesions on MRI, a targeted biopsy using MRI fused with ultrasound (US) is widely used. To achieve a successful targeted biopsy, a precise registration between MRI and US is essential. The purpose of our study was to show any decrease in errors using a real-time nonrigid registration technique for prostate biopsy. Nineteen patients with suspected prostate cancer were prospectively enrolled in this study. Registration accuracy was calculated by the measuring distance of corresponding points by rigid and nonrigid registration between MRI and US, and compared for rigid and nonrigid registration methods. Overall cancer detection rates were also evaluated by patient and by core. Prostate volume was measured automatically from MRI and manually from US, and compared to each other. Mean distances between the corresponding points in MRI and US were 5.32 ± 2.61 mm for rigid registration and 2.11 ± 1.37 mm for nonrigid registration (p < 0.05). Cancer was diagnosed in 11 of 19 patients (57.9%), and in 67 of 266 biopsy cores (25.2%). There was no significant difference in prostate-volume measurement between the automatic and manual methods (p = 0.89). In conclusion, nonrigid registration reduces targeting errors.
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Zhang C, Feng J, Yankovich AB, Kvit A, Berkels B, Voyles PM. Optimizing Nonrigid Registration for Scanning Transmission Electron Microscopy Image Series. Microsc Microanal 2021; 27:90-98. [PMID: 33222719 DOI: 10.1017/s1431927620024708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Achieving sub-picometer precision measurements of atomic column positions in high-resolution scanning transmission electron microscope images using nonrigid registration (NRR) and averaging of image series requires careful optimization of experimental conditions and the parameters of the registration algorithm. On experimental data from SrTiO3 [100], sub-pm precision requires alignment of the sample to the zone axis to within 1 mrad tilt and sample drift of less than 1 nm/min. At fixed total electron dose for the series, precision in the fast scan direction improves with shorter pixel dwell time to the limit of our microscope hardware, but the best precision along the slow scan direction occurs at 6 μs/px dwell time. Within the NRR algorithm, the “smoothness factor” that penalizes large estimated shifts is the most important parameter for sub-pm precision, but in general, the precision of NRR images is robust over a wide range of parameters.
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Affiliation(s)
- Chenyu Zhang
- Department of Materials Science and Engineering, University of Wisconsin - Madison, 1509 University Avenue, Madison, WI53706, USA
| | - Jie Feng
- Department of Materials Science and Engineering, University of Wisconsin - Madison, 1509 University Avenue, Madison, WI53706, USA
| | - Andrew B Yankovich
- Department of Materials Science and Engineering, University of Wisconsin - Madison, 1509 University Avenue, Madison, WI53706, USA
| | - Alexander Kvit
- Department of Materials Science and Engineering, University of Wisconsin - Madison, 1509 University Avenue, Madison, WI53706, USA
| | - Benjamin Berkels
- Aachen Institute for Advanced Study in Computational Engineering Science, RWTH Aachen University, Schinkelstr. 2, 52056Aachen, Germany
| | - Paul M Voyles
- Department of Materials Science and Engineering, University of Wisconsin - Madison, 1509 University Avenue, Madison, WI53706, USA
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Yang T, Tang Q, Li L, Song J, Zhu C, Tang L. Nonrigid registration of medical image based on adaptive local structure tensor and normalized mutual information. J Appl Clin Med Phys 2019; 20:99-110. [PMID: 31124248 PMCID: PMC6560247 DOI: 10.1002/acm2.12612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/24/2019] [Accepted: 04/24/2019] [Indexed: 11/07/2022] Open
Abstract
Nonrigid registration of medical images is especially critical in clinical treatment. Mutual information is a popular similarity measure for medical image registration; however, only the intensity statistical characteristics of the global consistency of image are considered in MI, and the spatial information is ignored. In this paper, a novel intensity-based similarity measure combining normalized mutual information with spatial information for nonrigid medical image registration is proposed. The different parameters of Gaussian filtering are defined according to the regional variance, the adaptive Gaussian filtering is introduced into the local structure tensor. Then, the obtained adaptive local structure tensor is used to extract the spatial information and define the weighting function. Finally, normalized mutual information is distributed to each pixel, and the discrete normalized mutual information is multiplied with a weighting term to obtain a new measure. The novel measure fully considers the spatial information of the image neighborhood, gives the location of the strong spatial information a larger weight, and the registration of the strong gradient regions has a priority over the small gradient regions. The simulated brain image with single-modality and multimodality are used for registration validation experiments. The results show that the new similarity measure improves the registration accuracy and robustness compared with the classical registration algorithm, reduces the risk of falling into local extremes during the registration process.
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Affiliation(s)
- Tiejun Yang
- College of Informational Science and EngineeringHenan University of TechnologyHigh‐Tech ZoneZhengzhou CityChina
| | - Qi Tang
- College of Informational Science and EngineeringHenan University of TechnologyHigh‐Tech ZoneZhengzhou CityChina
| | - Lei Li
- College of Informational Science and EngineeringHenan University of TechnologyHigh‐Tech ZoneZhengzhou CityChina
| | - Jikun Song
- College of Informational Science and EngineeringHenan University of TechnologyHigh‐Tech ZoneZhengzhou CityChina
| | - Chunhua Zhu
- College of Informational Science and EngineeringHenan University of TechnologyHigh‐Tech ZoneZhengzhou CityChina
| | - Lu Tang
- College of Informational Science and EngineeringHenan University of TechnologyHigh‐Tech ZoneZhengzhou CityChina
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Li D, Zhong W, Deh KM, Nguyen TD, Prince MR, Wang Y, Spincemaille P. Discontinuity Preserving Liver MR Registration with 3D Active Contour Motion Segmentation. IEEE Trans Biomed Eng 2018; 66:10.1109/TBME.2018.2880733. [PMID: 30418878 PMCID: PMC6565504 DOI: 10.1109/tbme.2018.2880733] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVE The sliding motion of the liver during respiration violates the homogeneous motion smoothness assumption in conventional non-rigid image registration and commonly results in compromised registration accuracy. This paper presents a novel approach, registration with 3D active contour motion segmentation (RAMS), to improve registration accuracy with discontinuity-aware motion regularization. METHODS A Markov random field-based discrete optimization with dense displacement sampling and self-similarity context metric is used for registration, while a graph cuts-based 3D active contour approach is applied to segment the sliding interface. In the first registration pass, a mask-free L1 regularization on an image-derived minimum spanning tree is performed to allow motion discontinuity. Based on the motion field estimates, a coarse segmentation finds the motion boundaries. Next, based on MR signal intensity, a fine segmentation aligns the motion boundaries with anatomical boundaries. In the second registration pass, smoothness constraints across the segmented sliding interface are removed by masked regularization on a minimum spanning forest and masked interpolation of the motion field. RESULTS For in vivo breath-hold abdominal MRI data, the motion masks calculated by RAMS are highly consistent with manual segmentations in terms of Dice similarity and bidirectional local distance measure. These automatically obtained masks are shown to substantially improve registration accuracy for both the proposed discrete registration as well as conventional continuous non-rigid algorithms. CONCLUSION/SIGNIFICANCE The presented results demonstrated the feasibility of automated segmentation of the respiratory sliding motion interface in liver MR images and the effectiveness of using the derived motion masks to preserve motion discontinuity.
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Affiliation(s)
- Dongxiao Li
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China
| | - Wenxiong Zhong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China
| | - Kofi M. Deh
- Department of Radiology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Thanh D. Nguyen
- Department of Radiology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Martin R. Prince
- Department of Radiology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Yi Wang
- Department of Radiology, Weill Cornell Medical College, New York, NY 10021, USA., Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Pascal Spincemaille
- Department of Radiology, Weill Cornell Medical College, New York, NY 10021, USA
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Lu Y, Zhao S, Younes N, Hahn JK. Accurate nonrigid 3D human body surface reconstruction using commodity depth sensors. Comput Animat Virtual Worlds 2018; 29:e1807. [PMID: 31156352 PMCID: PMC6541015 DOI: 10.1002/cav.1807] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 02/27/2018] [Indexed: 06/09/2023]
Abstract
In the last decade, 3D modeling techniques enjoyed a booming development in both hardware and software. High-end hardware generates high fidelity results, but the cost is prohibitive, whereas consumer-level devices generate plausible results for entertainment purposes but are not appropriate for medical uses. We present a cost-effective and easy-to-use 3D body reconstruction system using consumer-grade depth sensors, which provides reconstructed body shapes with a high degree of accuracy and reliability appropriate for medical applications. Our surface registration framework integrates the articulated motion assumption, global loop closure constraint, and a general as-rigid-as-possible deformation model. To enhance the reconstruction quality, we propose a novel approach to accurately infer skeletal joints from anatomical data using multimodality registration. We further propose a supervised predictive model to infer the skeletal joints for arbitrary subjects independent from anatomical data reference. A rigorous validation test has been conducted on real subjects to evaluate the reconstruction accuracy and repeatability. Our system has the potential to make accurate body surface scanning systems readily available for medical professionals and the general public. The system can be used to obtain additional health data derived from 3D body shapes, such as the percentage of body fat.
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Affiliation(s)
- Yao Lu
- Department of Computer Science, School of Engineering and Applied Science, Institute for Computer Graphics, The George Washington University, 800 22nd Street NW Suite 3400, Washington, DC 20052, USA
| | - Shang Zhao
- Department of Computer Science, School of Engineering and Applied Science, Institute for Computer Graphics, The George Washington University, 800 22nd Street NW Suite 3400, Washington, DC 20052, USA
| | - Naji Younes
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, The George Washington University, 800 22nd Street NW Suite 7680, Washington, DC 20052, USA
| | - James K. Hahn
- Department of Computer Science, School of Engineering and Applied Science, and Department of Pediatrics, School of Medicine and Health Sciences, Institute for Computer Graphics, The George Washington University, 800 22nd Street NW Suite 5830, Washington, DC 20052, USA
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El-Rewaidy H, Nezafat M, Jang J, Nakamori S, Fahmy AS, Nezafat R. Nonrigid active shape model-based registration framework for motion correction of cardiac T 1 mapping. Magn Reson Med 2018; 80:780-791. [PMID: 29314198 PMCID: PMC5941305 DOI: 10.1002/mrm.27068] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 12/08/2017] [Accepted: 12/11/2017] [Indexed: 01/23/2023]
Abstract
PURPOSE Accurate reconstruction of myocardial T1 maps from a series of T1 -weighted images consists of cardiac motions induced from breathing and diaphragmatic drifts. We propose and evaluate a new framework based on active shape models to correct for motion in myocardial T1 maps. METHODS Multiple appearance models were built at different inversion time intervals to model the blood-myocardium contrast and brightness changes during the longitudinal relaxation. Myocardial inner and outer borders were automatically segmented using the built models, and the extracted contours were used to register the T1 -weighted images. Data acquired from 210 patients using a free-breathing acquisition protocol were used to train and evaluate the proposed framework. Two independent readers evaluated the quality of the T1 maps before and after correction using a four-point score. The mean absolute distance and Dice index were used to validate the registration process. RESULTS The testing data set from 180 patients at 5 short axial slices showed a significant decrease of mean absolute distance (from 3.3 ± 1.6 to 2.3 ± 0.8 mm, P < 0.001) and increase of Dice (from 0.89 ± 0.08 to 0.94 ± 0.4%, P < 0.001) before and after correction, respectively. The T1 map quality improved in 70 ± 0.3% of the motion-affected maps after correction. Motion-corrupted segments of the myocardium reduced from 21.8 to 8.5% (P < 0.001) after correction. CONCLUSION The proposed method for nonrigid registration of T1 -weighted images allows T1 measurements in more myocardial segments by reducing motion-induced T1 estimation errors in myocardial segments. Magn Reson Med 80:780-791, 2018. © 2018 International Society for Magnetic Resonance in Medicine.
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Affiliation(s)
- Hossam El-Rewaidy
- Department of Medicine (Cardiovascular Division), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Maryam Nezafat
- Department of Medicine (Cardiovascular Division), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
- Division of Imaging Sciences & Biomedical Engineering, King’s College London, London, UK
| | - Jihye Jang
- Department of Medicine (Cardiovascular Division), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
- Department of Computer Science, Technical University of Munich, Munich, Germany
| | - Shiro Nakamori
- Department of Medicine (Cardiovascular Division), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Ahmed S. Fahmy
- Department of Medicine (Cardiovascular Division), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
- Systems and Biomedical Engineering, Cairo University, Giza, Egypt
| | - Reza Nezafat
- Department of Medicine (Cardiovascular Division), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
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Fu T, Li Q, Liu D, Ai D, Song H, Liang P, Wang Y, Yang J. Local incompressible registration for liver ablation surgery assessment. Med Phys 2017; 44:5873-5888. [PMID: 28857194 DOI: 10.1002/mp.12535] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE In liver microwave ablation (MWA) surgery, the ablation area covers the tumor to generate tissue necrosis and treat the cancer. As the liver deforms during the operation, deviation between the target area determined during preoperative planning and the resultant ablation area is inevitable. Therefore, an accurate assessment of tumor coverage is crucial for treatment. Through registration between the pre- and postoperative livers, the ablation area is warped on the preoperative liver for the computation of tumor coverage. However, large deformations between the pre- and postoperative livers are caused by multiple factors, and these diverse deformations make registration a challenging task. The purpose of this paper was to develop an automatic method that can accurately register post- to preoperative livers. METHODS In the proposed method, nonrigid deformations caused by respiratory movement and edema are separately considered and estimated by the local incompressible model in the registration of livers. The pre- and postoperative livers are first aligned by a rigid registration based on a convex hull. In the nonrigid registrations, local incompressible constraints are then set on the liver and the ablation area to estimate the deformations caused by respiratory movement and edema, respectively. The concatenation of the rigid and nonrigid deformations is used to warp the ablation area on the preoperative liver. RESULTS The proposed method was evaluated using clinical CT datasets from 20 patients. The Dice similarity coefficient (DSC) between the preoperative and warped postoperative livers is 94.35%, the mean surface distance (MSD) between the livers is 1.65 mm, the mean Hausdorff distance (HDD) between the livers is 3.36 mm, and the mean corresponding distance (MCD) between the corresponding landmarks is 1.70 mm. Compared with five other state-of-the-art methods, the proposed method achieves automatic ablation assessment with highly accurate registration. CONCLUSIONS The proposed method achieves a high accuracy for registering the livers. The sizes and positions of the ablation area and tumor are accurately compared for the assessment of ablation surgery.
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Affiliation(s)
- Tianyu Fu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.,Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Qin Li
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Dingkun Liu
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Danni Ai
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Hong Song
- School of Software, Beijing Institute of Technology, Beijing, 100081, China
| | - Ping Liang
- Department of Interventional Ultrasonics, General Hospital of Chinese PLA, Beijing, 100853, China
| | - Yongtian Wang
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Electronics, Beijing Institute of Technology, Beijing, 100081, China
| | - Jian Yang
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Electronics, Beijing Institute of Technology, Beijing, 100081, China
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Cibis M, Bustamante M, Eriksson J, Carlhäll CJ, Ebbers T. Creating hemodynamic atlases of cardiac 4D flow MRI. J Magn Reson Imaging 2017; 46:1389-1399. [PMID: 28295788 PMCID: PMC5655727 DOI: 10.1002/jmri.25691] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/14/2017] [Indexed: 01/22/2023] Open
Abstract
Purpose Hemodynamic atlases can add to the pathophysiological understanding of cardiac diseases. This study proposes a method to create hemodynamic atlases using 4D Flow magnetic resonance imaging (MRI). The method is demonstrated for kinetic energy (KE) and helicity density (Hd). Materials and Methods Thirteen healthy subjects underwent 4D Flow MRI at 3T. Phase‐contrast magnetic resonance cardioangiographies (PC‐MRCAs) and an average heart were created and segmented. The PC‐MRCAs, KE, and Hd were nonrigidly registered to the average heart to create atlases. The method was compared with 1) rigid, 2) affine registration of the PC‐MRCAs, and 3) affine registration of segmentations. The peak and mean KE and Hd before and after registration were calculated to evaluate interpolation error due to nonrigid registration. Results The segmentations deformed using nonrigid registration overlapped (median: 92.3%) more than rigid (23.1%, P < 0.001), and affine registration of PC‐MRCAs (38.5%, P < 0.001) and affine registration of segmentations (61.5%, P < 0.001). The peak KE was 4.9 mJ using the proposed method and affine registration of segmentations (P = 0.91), 3.5 mJ using rigid registration (P < 0.001), and 4.2 mJ using affine registration of the PC‐MRCAs (P < 0.001). The mean KE was 1.1 mJ using the proposed method, 0.8 mJ using rigid registration (P < 0.001), 0.9 mJ using affine registration of the PC‐MRCAs (P < 0.001), and 1.0 mJ using affine registration of segmentations (P = 0.028). The interpolation error was 5.2 ± 2.6% at mid‐systole, 2.8 ± 3.8% at early diastole for peak KE; 9.6 ± 9.3% at mid‐systole, 4.0 ± 4.6% at early diastole, and 4.9 ± 4.6% at late diastole for peak Hd. The mean KE and Hd were not affected by interpolation. Conclusion Hemodynamic atlases can be obtained with minimal user interaction using nonrigid registration of 4D Flow MRI. Level of Evidence: 2 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2017;46:1389–1399.
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Affiliation(s)
- Merih Cibis
- Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden.,Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Mariana Bustamante
- Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden.,Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
| | - Jonatan Eriksson
- Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Carl-Johan Carlhäll
- Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden.,Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden.,Division of Clinical Physiology, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Tino Ebbers
- Division of Cardiovascular Medicine, Department of Medical and Health Sciences, Linköping University, Linköping, Sweden.,Center for Medical Image Science and Visualization (CMIV), Linköping University, Linköping, Sweden
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Kalantari F, Wang J. Attenuation correction in 4D-PET using a single-phase attenuation map and rigidity-adaptive deformable registration. Med Phys 2017; 44:522-532. [PMID: 27987223 DOI: 10.1002/mp.12063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/03/2016] [Accepted: 12/05/2016] [Indexed: 11/11/2022] Open
Abstract
PURPOSE Four-dimensional positron emission tomography (4D-PET) imaging is a potential solution to the respiratory motion effect in the thoracic region. Computed tomography (CT)-based attenuation correction (AC) is an essential step toward quantitative imaging for PET. However, due to the temporal difference between 4D-PET and a single attenuation map from CT, typically available in routine clinical scanning, motion artifacts are observed in the attenuation-corrected PET images, leading to errors in tumor shape and uptake. We introduced a practical method to align single-phase CT with all other 4D-PET phases for AC. METHODS A penalized non-rigid Demons registration between individual 4D-PET frames without AC provides the motion vectors to be used for warping single-phase attenuation map. The non-rigid Demons registration was used to derive deformation vector fields (DVFs) between PET matched with the CT phase and other 4D-PET images. While attenuated PET images provide useful data for organ borders such as those of the lung and the liver, tumors cannot be distinguished from the background due to loss of contrast. To preserve the tumor shape in different phases, an ROI-covering tumor was excluded from nonrigid transformation. Instead the mean DVF of the central region of the tumor was assigned to all voxels in the ROI. This process mimics a rigid transformation of the tumor along with a nonrigid transformation of other organs. A 4D-XCAT phantom with spherical lung tumors, with diameters ranging from 10 to 40 mm, was used to evaluate the algorithm. The performance of the proposed hybrid method for attenuation map estimation was compared to (a) the Demons nonrigid registration only and (b) a single attenuation map based on quantitative parameters in individual PET frames. RESULTS Motion-related artifacts were significantly reduced in the attenuation-corrected 4D-PET images. When a single attenuation map was used for all individual PET frames, the normalized root-mean-square error (NRMSE) values in tumor region were 49.3% (STD: 8.3%), 50.5% (STD: 9.3%), 51.8% (STD: 10.8%) and 51.5% (STD: 12.1%) for 10-mm, 20-mm, 30-mm, and 40-mm tumors, respectively. These errors were reduced to 11.9% (STD: 2.9%), 13.6% (STD: 3.9%), 13.8% (STD: 4.8%), and 16.7% (STD: 9.3%) by our proposed method for deforming the attenuation map. The relative errors in total lesion glycolysis (TLG) values were -0.25% (STD: 2.87%) and 3.19% (STD: 2.35%) for 30-mm and 40-mm tumors, respectively, in proposed method. The corresponding values for Demons method were 25.22% (STD: 14.79%) and 18.42% (STD: 7.06%). Our proposed hybrid method outperforms the Demons method especially for larger tumors. For tumors smaller than 20 mm, nonrigid transformation could also provide quantitative results. CONCLUSION Although non-AC 4D-PET frames include insignificant anatomical information, they are still useful to estimate the DVFs to align the attenuation map for accurate AC. The proposed hybrid method can recover the AC-related artifacts and provide quantitative AC-PET images.
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Affiliation(s)
- Faraz Kalantari
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, 75235-8808, USA
| | - Jing Wang
- Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, TX, 75235-8808, USA
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13
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Hötte GJ, Schaafsma PJ, Botha CP, Wielopolski PA, Simonsz HJ. Visualization of Sliding and Deformation of Orbital Fat During Eye Rotation. Transl Vis Sci Technol 2016; 5:9. [PMID: 27540495 PMCID: PMC4981490 DOI: 10.1167/tvst.5.4.9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 05/30/2016] [Indexed: 11/24/2022] Open
Abstract
Purpose Little is known about the way orbital fat slides and/or deforms during eye movements. We compared two deformation algorithms from a sequence of MRI volumes to visualize this complex behavior. Methods Time-dependent deformation data were derived from motion-MRI volumes using Lucas and Kanade Optical Flow (LK3D) and nonrigid registration (B-splines) deformation algorithms. We compared how these two algorithms performed regarding sliding and deformation in three critical areas: the sclera-fat interface, how the optic nerve moves through the fat, and how the fat is squeezed out under the tendon of a relaxing rectus muscle. The efficacy was validated using identified tissue markers such as the lens and blood vessels in the fat. Results Fat immediately behind the eye followed eye rotation by approximately one-half. This was best visualized using the B-splines technique as it showed less ripping of tissue and less distortion. Orbital fat flowed around the optic nerve during eye rotation. In this case, LK3D provided better visualization as it allowed orbital fat tissue to split. The resolution was insufficient to visualize fat being squeezed out between tendon and sclera. Conclusion B-splines performs better in tracking structures such as the lens, while LK3D allows fat tissue to split as should happen as the optic nerve slides through the fat. Orbital fat follows eye rotation by one-half and flows around the optic nerve during eye rotation. Translational Relevance Visualizing orbital fat deformation and sliding offers the opportunity to accurately locate a region of cicatrization and permit an individualized surgical plan.
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Affiliation(s)
- Gijsbert J Hötte
- Department of Ophthalmology Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter J Schaafsma
- Department of Mediamatics, Technical University Delft, Delft, the Netherlands
| | - Charl P Botha
- Department of Mediamatics, Technical University Delft, Delft, the Netherlands ; Department of Radiology, Laboratory for Clinical and Experimental Image Processing, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Huibert J Simonsz
- Department of Ophthalmology Erasmus Medical Center, Rotterdam, the Netherlands
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Onofrey JA, Staib LH, Sarkar S, Venkataraman R, Papademetris X. LEARNING NONRIGID DEFORMATIONS FOR CONSTRAINED POINT-BASED REGISTRATION FOR IMAGE-GUIDED MR-TRUS PROSTATE INTERVENTION. Proc IEEE Int Symp Biomed Imaging 2015; 2015:1592-1595. [PMID: 26405508 DOI: 10.1109/isbi.2015.7164184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This paper presents and validates a low-dimensional nonrigid registration method for fusing magnetic resonance imaging (MRI) and trans-rectal ultrasound (TRUS) in image-guided prostate biopsy. Prostate cancer is one of the most prevalent forms of cancer and the second leading cause of cancer-related death in men in the United States. Conventional clinical practice uses TRUS to guide prostate biopsies when there is a suspicion of cancer. Pre-procedural MRI information can reveal lesions and may be fused with intra-procedure TRUS imaging to provide patient-specific, localization of lesions for targeting. The state-of-the-art MRI-TRUS nonrigid image fusion process relies upon semi-automated segmentation of the prostate in both the MRI and TRUS images. In this paper, we develop a fast, automated nonrigid registration approach to MRI-TRUS fusion based on a statistical deformation model of intra-procedural deformations derived from a clinical sample.
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Affiliation(s)
- John A Onofrey
- Department of Diagnostic Radiology, Yale University, New Haven, CT, USA
| | - Lawrence H Staib
- Department of Diagnostic Radiology, Yale University, New Haven, CT, USA ; Department of Biomedical Engineering, Yale University, New Haven, CT, USA ; Department of Electrical Engineering, Yale University, New Haven, CT, USA
| | | | | | - Xenophon Papademetris
- Department of Diagnostic Radiology, Yale University, New Haven, CT, USA ; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
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15
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Gass T, Székely G, Goksel O. Consistency-based rectification of nonrigid registrations. J Med Imaging (Bellingham) 2015; 2:014005. [PMID: 26158083 DOI: 10.1117/1.jmi.2.1.014005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 03/03/2015] [Indexed: 11/14/2022] Open
Abstract
We present a technique to rectify nonrigid registrations by improving their group-wise consistency, which is a widely used unsupervised measure to assess pair-wise registration quality. While pair-wise registration methods cannot guarantee any group-wise consistency, group-wise approaches typically enforce perfect consistency by registering all images to a common reference. However, errors in individual registrations to the reference then propagate, distorting the mean and accumulating in the pair-wise registrations inferred via the reference. Furthermore, the assumption that perfect correspondences exist is not always true, e.g., for interpatient registration. The proposed consistency-based registration rectification (CBRR) method addresses these issues by minimizing the group-wise inconsistency of all pair-wise registrations using a regularized least-squares algorithm. The regularization controls the adherence to the original registration, which is additionally weighted by the local postregistration similarity. This allows CBRR to adaptively improve consistency while locally preserving accurate pair-wise registrations. We show that the resulting registrations are not only more consistent, but also have lower average transformation error when compared to known transformations in simulated data. On clinical data, we show improvements of up to 50% target registration error in breathing motion estimation from four-dimensional MRI and improvements in atlas-based segmentation quality of up to 65% in terms of mean surface distance in three-dimensional (3-D) CT. Such improvement was observed consistently using different registration algorithms, dimensionality (two-dimensional/3-D), and modalities (MRI/CT).
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Affiliation(s)
- Tobias Gass
- ETH Zurich , Department of Information Technology and Electrical Engineering, Computer Vision Lab, Sternwartstr.7, Zurich 8092, Switzerland
| | - Gábor Székely
- ETH Zurich , Department of Information Technology and Electrical Engineering, Computer Vision Lab, Sternwartstr.7, Zurich 8092, Switzerland
| | - Orcun Goksel
- ETH Zurich , Department of Information Technology and Electrical Engineering, Computer Vision Lab, Sternwartstr.7, Zurich 8092, Switzerland
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Sun Y, Qiu W, Yuan J, Romagnoli C, Fenster A. Three-dimensional nonrigid landmark-based magnetic resonance to transrectal ultrasound registration for image-guided prostate biopsy. J Med Imaging (Bellingham) 2015; 2:025002. [PMID: 26158111 DOI: 10.1117/1.jmi.2.2.025002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/27/2015] [Indexed: 12/13/2022] Open
Abstract
Registration of three-dimensional (3-D) magnetic resonance (MR) to 3-D transrectal ultrasound (TRUS) prostate images is an important step in the planning and guidance of 3-D TRUS guided prostate biopsy. In order to accurately and efficiently perform the registration, a nonrigid landmark-based registration method is required to account for the different deformations of the prostate when using these two modalities. We describe a nonrigid landmark-based method for registration of 3-D TRUS to MR prostate images. The landmark-based registration method first makes use of an initial rigid registration of 3-D MR to 3-D TRUS images using six manually placed approximately corresponding landmarks in each image. Following manual initialization, the two prostate surfaces are segmented from 3-D MR and TRUS images and then nonrigidly registered using the following steps: (1) rotationally reslicing corresponding segmented prostate surfaces from both 3-D MR and TRUS images around a specified axis, (2) an approach to find point correspondences on the surfaces of the segmented surfaces, and (3) deformation of the surface of the prostate in the MR image to match the surface of the prostate in the 3-D TRUS image and the interior using a thin-plate spline algorithm. The registration accuracy was evaluated using 17 patient prostate MR and 3-D TRUS images by measuring the target registration error (TRE). Experimental results showed that the proposed method yielded an overall mean TRE of [Formula: see text] for the rigid registration and [Formula: see text] for the nonrigid registration, which is favorably comparable to a clinical requirement for an error of less than 2.5 mm. A landmark-based nonrigid 3-D MR-TRUS registration approach is proposed, which takes into account the correspondences on the prostate surface, inside the prostate, as well as the centroid of the prostate. Experimental results indicate that the proposed method yields clinically sufficient accuracy.
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Affiliation(s)
- Yue Sun
- University of Western Ontario , Imaging Research Laboratories, Robarts Research Institute, London, Ontario N6A 5K8, Canada
| | - Wu Qiu
- University of Western Ontario , Imaging Research Laboratories, Robarts Research Institute, London, Ontario N6A 5K8, Canada
| | - Jing Yuan
- University of Western Ontario , Imaging Research Laboratories, Robarts Research Institute, London, Ontario N6A 5K8, Canada
| | - Cesare Romagnoli
- University of Western Ontario , Department of Medical Imaging, London, Ontario N6A 5K8, Canada
| | - Aaron Fenster
- University of Western Ontario , Imaging Research Laboratories, Robarts Research Institute, London, Ontario N6A 5K8, Canada ; University of Western Ontario , Department of Medical Imaging, London, Ontario N6A 5K8, Canada ; University of Western Ontario , Department of Medical Biophysics, London, Ontario N6A 5K8, Canada
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Rabbani H, Allingham MJ, Mettu PS, Cousins SW, Farsiu S. Fully automatic segmentation of fluorescein leakage in subjects with diabetic macular edema. Invest Ophthalmol Vis Sci 2015; 56:1482-92. [PMID: 25634978 DOI: 10.1167/iovs.14-15457] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To create and validate software to automatically segment leakage area in real-world clinical fluorescein angiography (FA) images of subjects with diabetic macular edema (DME). METHODS Fluorescein angiography images obtained from 24 eyes of 24 subjects with DME were retrospectively analyzed. Both video and still-frame images were obtained using a Heidelberg Spectralis 6-mode HRA/OCT unit. We aligned early and late FA frames in the video by a two-step nonrigid registration method. To remove background artifacts, we subtracted early and late FA frames. Finally, after postprocessing steps, including detection and inpainting of the vessels, a robust active contour method was utilized to obtain leakage area in a 1500-μm-radius circular region centered at the fovea. Images were captured at different fields of view (FOVs) and were often contaminated with outliers, as is the case in real-world clinical imaging. Our algorithm was applied to these images with no manual input. Separately, all images were manually segmented by two retina specialists. The sensitivity, specificity, and accuracy of manual interobserver, manual intraobserver, and automatic methods were calculated. RESULTS The mean accuracy was 0.86 ± 0.08 for automatic versus manual, 0.83 ± 0.16 for manual interobserver, and 0.90 ± 0.08 for manual intraobserver segmentation methods. CONCLUSIONS Our fully automated algorithm can reproducibly and accurately quantify the area of leakage of clinical-grade FA video and is congruent with expert manual segmentation. The performance was reliable for different DME subtypes. This approach has the potential to reduce time and labor costs and may yield objective and reproducible quantitative measurements of DME imaging biomarkers.
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Affiliation(s)
- Hossein Rabbani
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States Medical Image and Signal Processing Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Michael J Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Priyatham S Mettu
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Scott W Cousins
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Sina Farsiu
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States Department of Biomedical Engineering, Duke University, Durham, North Carolina, United States
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Cazoulat G, Simon A, Dumenil A, Gnep K, De Crevoisier R, Acosta-Tamayo O, Haigron P. Surface-constrained nonrigid registration for dose monitoring in prostate cancer radiotherapy. IEEE Trans Med Imaging 2014; 33:1464-1474. [PMID: 24710827 PMCID: PMC5325876 DOI: 10.1109/tmi.2014.2314574] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper addresses the issue of cumulative dose estimation from cone beam computed tomography (CBCT) images in prostate cancer radiotherapy. It focuses on the dose received by the surfaces of the main organs at risk, namely the bladder and rectum. We have proposed both a surface-constrained dose accumulation approach and its extensive evaluation. Our approach relied on the nonrigid registration (NRR) of daily acquired CBCT images on the planning CT image. This proposed NRR method was based on a Demons-like algorithm, implemented in combination with mutual information metric. It allowed for different levels of geometrical constraints to be considered, ensuring a better point to point correspondence, especially when large deformations occurred, or in high dose gradient areas. The three following implementations: 1) full iconic NRR; 2) iconic NRR constrained with landmarks (LCNRR); 3) NRR constrained with full delineation of organs (DBNRR). To obtain reference data, we designed a numerical phantom based on finite-element modeling and image simulation. The methods were assessed on both the numerical phantom and real patient data in order to quantify uncertainties in terms of dose accumulation. The LCNRR method appeared to constitute a good compromise for dose monitoring in clinical practice.
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Affiliation(s)
- Guillaume Cazoulat
- LTSI, Laboratoire Traitement du Signal et de l'Image
Institut National de la Santé et de la Recherche Médicale - U1099Université de Rennes 1 - Campus Universitaire de Beaulieu - Bât 22 - 35042 Rennes
| | - Antoine Simon
- LTSI, Laboratoire Traitement du Signal et de l'Image
Institut National de la Santé et de la Recherche Médicale - U1099Université de Rennes 1 - Campus Universitaire de Beaulieu - Bât 22 - 35042 Rennes
| | - Aurelien Dumenil
- LTSI, Laboratoire Traitement du Signal et de l'Image
Institut National de la Santé et de la Recherche Médicale - U1099Université de Rennes 1 - Campus Universitaire de Beaulieu - Bât 22 - 35042 Rennes
| | - Khemara Gnep
- Centre Eugène Marquis
CRLCC Eugène Marquis - Avenue Bataille Flandres-Dunkerque 35042 RENNES CEDEX
| | - Renaud De Crevoisier
- LTSI, Laboratoire Traitement du Signal et de l'Image
Institut National de la Santé et de la Recherche Médicale - U1099Université de Rennes 1 - Campus Universitaire de Beaulieu - Bât 22 - 35042 Rennes
- Centre Eugène Marquis
CRLCC Eugène Marquis - Avenue Bataille Flandres-Dunkerque 35042 RENNES CEDEX
| | - Oascar Acosta-Tamayo
- LTSI, Laboratoire Traitement du Signal et de l'Image
Institut National de la Santé et de la Recherche Médicale - U1099Université de Rennes 1 - Campus Universitaire de Beaulieu - Bât 22 - 35042 Rennes
| | - Pascal Haigron
- LTSI, Laboratoire Traitement du Signal et de l'Image
Institut National de la Santé et de la Recherche Médicale - U1099Université de Rennes 1 - Campus Universitaire de Beaulieu - Bât 22 - 35042 Rennes
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Garlapati RR, Roy A, Joldes GR, Wittek A, Mostayed A, Doyle B, Warfield SK, Kikinis R, Knuckey N, Bunt S, Miller K. More accurate neuronavigation data provided by biomechanical modeling instead of rigid registration. J Neurosurg 2014; 120:1477-83. [PMID: 24460486 DOI: 10.3171/2013.12.jns131165] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
It is possible to improve neuronavigation during image-guided surgery by warping the high-quality preoperative brain images so that they correspond with the current intraoperative configuration of the brain. In this paper, the accuracy of registration results obtained using comprehensive biomechanical models is compared with the accuracy of rigid registration, the technology currently available to patients. This comparison allows investigation into whether biomechanical modeling provides good-quality image data for neuronavigation for a larger proportion of patients than rigid registration. Preoperative images for 33 neurosurgery cases were warped onto their respective intraoperative configurations using both the biomechanics-based method and rigid registration. The Hausdorff distance-based evaluation process, which measures the difference between images, was used to quantify the performance of both registration methods. A statistical test for difference in proportions was conducted to evaluate the null hypothesis that the proportion of patients for whom improved neuronavigation can be achieved is the same for rigid and biomechanics-based registration. The null hypothesis was confidently rejected (p < 10(-4)). Even the modified hypothesis that fewer than 25% of patients would benefit from the use of biomechanics-based registration was rejected at a significance level of 5% (p = 0.02). The biomechanics-based method proved particularly effective in cases demonstrating large craniotomy-induced brain deformations. The outcome of this analysis suggests that nonlinear biomechanics-based methods are beneficial to a large proportion of patients and can be considered for use in the operating theater as a possible means of improving neuronavigation and surgical outcomes.
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Abstract
With the advent of in vivo laser scanning fluorescence microscopy techniques, time-series and three-dimensional volumes of living tissue and vessels at micron scales can be acquired to firmly analyze vessel architecture and blood flow. Analysis of a large number of image stacks to extract architecture and track blood flow manually is cumbersome and prone to observer bias. Thus, an automated framework to accomplish these analytical tasks is imperative. The first initiative toward such a framework is to compensate for motion artifacts manifest in these microscopy images. Motion artifacts in in vivo microscopy images are caused by respiratory motion, heart beats, and other motions from the specimen. Consequently, the amount of motion present in these images can be large and hinders further analysis of these images. In this article, an algorithmic framework for the correction of time-series images is presented. The automated algorithm is comprised of a rigid and a nonrigid registration step based on shape contexts. The framework performs considerably well on time-series image sequences of the islets of Langerhans and provides for the pivotal step of motion correction in the further automatic analysis of microscopy images.
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Affiliation(s)
- Ankur N. Kumar
- Department of Electrical Engineering, 367 Jacobs Hall, Vanderbilt University, Nashville, TN 37212, USA
| | - Kurt W. Short
- Department of Molecular Physiology & Biophysics, 747 Light Hall, Vanderbilt University, Nashville, TN 37232, USA
| | - David W. Piston
- Department of Molecular Physiology & Biophysics, 747 Light Hall, Vanderbilt University, Nashville, TN 37232, USA
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Onofrey JA, Staib LH, Papademetris X. FAST NONRIGID IMAGE REGISTRATION USING STATISTICAL DEFORMATION MODELS LEARNED FROM RICHLY-ANNOTATED DATA. Proc IEEE Int Symp Biomed Imaging 2013:580-583. [PMID: 25000401 DOI: 10.1109/isbi.2013.6556541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Nonrigid image registrations require a large number of degrees of freedom (DoFs) to capture intersubject anatomical variations. With such high DoFs and lack of anatomical correspondences, algorithms may not converge to the globally optimal solution. In this work, we propose a fast, two-step nonrigid registration procedure with low DoFs to accurately register brain images. Our method makes use of a statistical deformation model based upon a principal component analysis of deformations learned from a manually-segmented dataset to perform an initial registration. We then follow with a low DoF nonrigid transformation to complete the registration. Our results show the same registration accuracy in terms of volume of interest overlap as high DoF transformations, but with a 96% reduction in DoF and 98% decrease in computation time.
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Affiliation(s)
- John A Onofrey
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Lawrence H Staib
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA ; Department of Diagnostic Radiology, Yale University, New Haven, CT, USA ; Department of Electrical Engineering, Yale University, New Haven, CT, USA
| | - Xenophon Papademetris
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA ; Department of Diagnostic Radiology, Yale University, New Haven, CT, USA
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Fripp J, Crozier S, Warfield SK, Ourselin S. Automatic segmentation and quantitative analysis of the articular cartilages from magnetic resonance images of the knee. IEEE Trans Med Imaging 2010; 29:55-64. [PMID: 19520633 PMCID: PMC3717377 DOI: 10.1109/tmi.2009.2024743] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this paper, we present a segmentation scheme that automatically and accurately segments all the cartilages from magnetic resonance (MR) images of nonpathological knees. Our scheme involves the automatic segmentation of the bones using a three-dimensional active shape model, the extraction of the expected bone-cartilage interface (BCI), and cartilage segmentation from the BCI using a deformable model that utilizes localization, patient specific tissue estimation and a model of the thickness variation. The accuracy of this scheme was experimentally validated using leave one out experiments on a database of fat suppressed spoiled gradient recall MR images. The scheme was compared to three state of the art approaches, tissue classification, a modified semi-automatic watershed algorithm and nonrigid registration (B-spline based free form deformation). Our scheme obtained an average Dice similarity coefficient (DSC) of (0.83, 0.83, 0.85) for the (patellar, tibial, femoral) cartilages, while (0.82, 0.81, 0.86) was obtained with a tissue classifier and (0.73, 0.79, 0.76) was obtained with nonrigid registration. The average DSC obtained for all the cartilages using a semi-automatic watershed algorithm (0.90) was slightly higher than our approach (0.89), however unlike this approach we segment each cartilage as a separate object. The effectiveness of our approach for quantitative analysis was evaluated using volume and thickness measures with a median volume difference error of (5.92, 4.65, 5.69) and absolute Laplacian thickness difference of (0.13, 0.24, 0.12) mm.
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Affiliation(s)
- Jurgen Fripp
- CSIRO, ICTC, The Australian e-Health Research Centre-BioMedIA, Royal Brisbane and Women's Hospital, 4029 Herston, Qld., Australia.
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Sdika M, Pelletier D. Nonrigid registration of multiple sclerosis brain images using lesion inpainting for morphometry or lesion mapping. Hum Brain Mapp 2009; 30:1060-7. [PMID: 18412131 PMCID: PMC6870756 DOI: 10.1002/hbm.20566] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Revised: 01/14/2008] [Accepted: 02/19/2008] [Indexed: 11/09/2022] Open
Abstract
Morphometric studies of medical images often include a nonrigid registration step from a subject to a common reference. The presence of white matter multiple sclerosis lesions will distort and bias the output of the registration. In this article, we present a method to remove this bias by filling such lesions to make the brain look like a healthy brain before the registration. We finally propose a dedicated method to fill the lesions and present numerical results showing that our method outperforms current state of the art method.
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Affiliation(s)
- Michaël Sdika
- Department of Neurology, University of California, San Francisco, 94107 San Francisco, California
| | - Daniel Pelletier
- Department of Neurology, University of California, San Francisco, 94107 San Francisco, California
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24
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Gu Z, Qin B. Nonrigid Registration of Brain Tumor Resection MR Images Based on Joint Saliency Map and Keypoint Clustering. Sensors (Basel) 2009; 9:10270-90. [PMID: 22303173 DOI: 10.3390/s91210270] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/01/2009] [Accepted: 12/09/2009] [Indexed: 11/25/2022]
Abstract
This paper proposes a novel global-to-local nonrigid brain MR image registration to compensate for the brain shift and the unmatchable outliers caused by the tumor resection. The mutual information between the corresponding salient structures, which are enhanced by the joint saliency map (JSM), is maximized to achieve a global rigid registration of the two images. Being detected and clustered at the paired contiguous matching areas in the globally registered images, the paired pools of DoG keypoints in combination with the JSM provide a useful cluster-to-cluster correspondence to guide the local control-point correspondence detection and the outlier keypoint rejection. Lastly, a quasi-inverse consistent deformation is smoothly approximated to locally register brain images through the mapping the clustered control points by compact support radial basis functions. The 2D implementation of the method can model the brain shift in brain tumor resection MR images, though the theory holds for the 3D case.
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25
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Chaudhari AJ, Joshi AA, Bowen SL, Leahy RM, Cherry SR, Badawi RD. Crystal identification in positron emission tomography using nonrigid registration to a Fourier-based template. Phys Med Biol 2008; 53:5011-27. [PMID: 18723924 PMCID: PMC2748910 DOI: 10.1088/0031-9155/53/18/011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Modern positron emission tomography (PET) detectors are typically made from 2D modular arrays of scintillation crystals. Their characteristic flood field response (or flood histogram) must be segmented in order to correctly determine the crystal of annihilation photon interaction in the system. Crystal identification information thus generated is also needed for accurate system modeling as well as for detailed detector characterization and performance studies. In this paper, we present a semi-automatic general purpose template-guided scheme for the segmentation of flood histograms. We first generate a template image that exploits the spatial frequency information in the given flood histogram using Fourier-space analysis. This template image is a lower order approximation of the flood histogram, and can be segmented with horizontal and vertical lines drawn midway between adjacent peaks in the histogram. The template is then registered to the given flood histogram by a diffeomorphic polynomial-based warping scheme that is capable of iteratively minimizing intensity differences. The displacement field thus calculated is applied to the segmentation of the template resulting in a segmentation of the given flood histogram. We evaluate our segmentation scheme for a photomultiplier tube based PET detector, a detector with readout by a position-sensitive avalanche photodiode (PSAPD) and a detector consisting of a stack of photomultiplier tubes and scintillator arrays. Further, we quantitatively compare the performance of the proposed method to that of a manual segmentation scheme using reconstructed images of a line-source phantom. We also present an adaptive method for distortion reduction in flood histograms obtained for PET detectors that use PSAPDs.
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Affiliation(s)
- Abhijit J. Chaudhari
- Department of Biomedical Engineering, University of California-Davis, Davis, CA 95616
| | - Anand A. Joshi
- Signal and Image Processing Institute, University of Southern California, Los Angeles, CA 90089
| | - Spencer L. Bowen
- Department of Biomedical Engineering, University of California-Davis, Davis, CA 95616
| | - Richard M. Leahy
- Signal and Image Processing Institute, University of Southern California, Los Angeles, CA 90089
| | - Simon R. Cherry
- Department of Biomedical Engineering, University of California-Davis, Davis, CA 95616
| | - Ramsey D. Badawi
- Department of Radiology, UC Davis Medical Center, Sacramento, CA 95817
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