Mutual-information-based registration of medical images: a survey
28 Jul 2003-IEEE Transactions on Medical Imaging (Institute of Electrical and Electronics Engineers)-Vol. 22, Iss: 8, pp 986-1004
TL;DR: An overview is presented of the medical image processing literature on mutual-information-based registration, an introduction for those new to the field, an overview for those working in the field and a reference for those searching for literature on a specific application.
Abstract: An overview is presented of the medical image processing literature on mutual-information-based registration. The aim of the survey is threefold: an introduction for those new to the field, an overview for those working in the field, and a reference for those searching for literature on a specific application. Methods are classified according to the different aspects of mutual-information-based registration. The main division is in aspects of the methodology and of the application. The part on methodology describes choices made on facets such as preprocessing of images, gray value interpolation, optimization, adaptations to the mutual information measure, and different types of geometrical transformations. The part on applications is a reference of the literature available on different modalities, on interpatient registration and on different anatomical objects. Comparison studies including mutual information are also considered. The paper starts with a description of entropy and mutual information and it closes with a discussion on past achievements and some future challenges.
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TL;DR: The software consists of a collection of algorithms that are commonly used to solve medical image registration problems, and allows the user to quickly configure, test, and compare different registration methods for a specific application.
Abstract: Medical image registration is an important task in medical image processing. It refers to the process of aligning data sets, possibly from different modalities (e.g., magnetic resonance and computed tomography), different time points (e.g., follow-up scans), and/or different subjects (in case of population studies). A large number of methods for image registration are described in the literature. Unfortunately, there is not one method that works for all applications. We have therefore developed elastix, a publicly available computer program for intensity-based medical image registration. The software consists of a collection of algorithms that are commonly used to solve medical image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. The command-line interface enables automated processing of large numbers of data sets, by means of scripting. The usage of elastix for comparing different registration methods is illustrated with three example experiments, in which individual components of the registration method are varied.
3,444 citations
Cites background from "Mutual-information-based registrati..."
...tion (MI) [26], [44]–[46], and normalized mutual information...
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TL;DR: A broad survey of the recent advances in convolutional neural networks can be found in this article, where the authors discuss the improvements of CNN on different aspects, namely, layer design, activation function, loss function, regularization, optimization and fast computation.
3,125 citations
TL;DR: This paper attempts to give an overview of deformable registration methods, putting emphasis on the most recent advances in the domain, and provides an extensive account of registration techniques in a systematic manner.
Abstract: Deformable image registration is a fundamental task in medical image processing. Among its most important applications, one may cite: 1) multi-modality fusion, where information acquired by different imaging devices or protocols is fused to facilitate diagnosis and treatment planning; 2) longitudinal studies, where temporal structural or anatomical changes are investigated; and 3) population modeling and statistical atlases used to study normal anatomical variability. In this paper, we attempt to give an overview of deformable registration methods, putting emphasis on the most recent advances in the domain. Additional emphasis has been given to techniques applied to medical images. In order to study image registration methods in depth, their main components are identified and studied independently. The most recent techniques are presented in a systematic fashion. The contribution of this paper is to provide an extensive account of registration techniques in a systematic manner.
1,434 citations
Cites background from "Mutual-information-based registrati..."
...For a survey on MI-based registration methods, the interested reader is referred to [259]....
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Posted Content•
TL;DR: This paper details the improvements of CNN on different aspects, including layer design, activation function, loss function, regularization, optimization and fast computation, and introduces various applications of convolutional neural networks in computer vision, speech and natural language processing.
Abstract: In the last few years, deep learning has led to very good performance on a variety of problems, such as visual recognition, speech recognition and natural language processing. Among different types of deep neural networks, convolutional neural networks have been most extensively studied. Leveraging on the rapid growth in the amount of the annotated data and the great improvements in the strengths of graphics processor units, the research on convolutional neural networks has been emerged swiftly and achieved state-of-the-art results on various tasks. In this paper, we provide a broad survey of the recent advances in convolutional neural networks. We detailize the improvements of CNN on different aspects, including layer design, activation function, loss function, regularization, optimization and fast computation. Besides, we also introduce various applications of convolutional neural networks in computer vision, speech and natural language processing.
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TL;DR: A review of recent advances in medical imaging using the adversarial training scheme with the hope of benefiting researchers interested in this technique.
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Cites background from "Mutual-information-based registrati..."
...(2018a) LPIPS Learned perceptual image patch similarity M16 Pluim et al. (2003) Mutual information Commonly used in cross modality registration in evaluating the alignment of two images...
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...D39 Prentasic et al. (2013) DRiDB Diabetic Retinopathy Detection Eye Fundus Imaging D40 Kälviäinen and Uusitalo (2007) DIARETDB1 Diabetic Retinopathy Detection Eye Fundus Imaging...
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References
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TL;DR: This final installment of the paper considers the case where the signals or the messages or both are continuously variable, in contrast with the discrete nature assumed until now.
Abstract: In this final installment of the paper we consider the case where the signals or the messages or both are continuously variable, in contrast with the discrete nature assumed until now. To a considerable extent the continuous case can be obtained through a limiting process from the discrete case by dividing the continuum of messages and signals into a large but finite number of small regions and calculating the various parameters involved on a discrete basis. As the size of the regions is decreased these parameters in general approach as limits the proper values for the continuous case. There are, however, a few new effects that appear and also a general change of emphasis in the direction of specialization of the general results to particular cases.
65,425 citations
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01 Jan 1991TL;DR: The author examines the role of entropy, inequality, and randomness in the design of codes and the construction of codes in the rapidly changing environment.
Abstract: Preface to the Second Edition. Preface to the First Edition. Acknowledgments for the Second Edition. Acknowledgments for the First Edition. 1. Introduction and Preview. 1.1 Preview of the Book. 2. Entropy, Relative Entropy, and Mutual Information. 2.1 Entropy. 2.2 Joint Entropy and Conditional Entropy. 2.3 Relative Entropy and Mutual Information. 2.4 Relationship Between Entropy and Mutual Information. 2.5 Chain Rules for Entropy, Relative Entropy, and Mutual Information. 2.6 Jensen's Inequality and Its Consequences. 2.7 Log Sum Inequality and Its Applications. 2.8 Data-Processing Inequality. 2.9 Sufficient Statistics. 2.10 Fano's Inequality. Summary. Problems. Historical Notes. 3. Asymptotic Equipartition Property. 3.1 Asymptotic Equipartition Property Theorem. 3.2 Consequences of the AEP: Data Compression. 3.3 High-Probability Sets and the Typical Set. Summary. Problems. Historical Notes. 4. Entropy Rates of a Stochastic Process. 4.1 Markov Chains. 4.2 Entropy Rate. 4.3 Example: Entropy Rate of a Random Walk on a Weighted Graph. 4.4 Second Law of Thermodynamics. 4.5 Functions of Markov Chains. Summary. Problems. Historical Notes. 5. Data Compression. 5.1 Examples of Codes. 5.2 Kraft Inequality. 5.3 Optimal Codes. 5.4 Bounds on the Optimal Code Length. 5.5 Kraft Inequality for Uniquely Decodable Codes. 5.6 Huffman Codes. 5.7 Some Comments on Huffman Codes. 5.8 Optimality of Huffman Codes. 5.9 Shannon-Fano-Elias Coding. 5.10 Competitive Optimality of the Shannon Code. 5.11 Generation of Discrete Distributions from Fair Coins. Summary. Problems. Historical Notes. 6. Gambling and Data Compression. 6.1 The Horse Race. 6.2 Gambling and Side Information. 6.3 Dependent Horse Races and Entropy Rate. 6.4 The Entropy of English. 6.5 Data Compression and Gambling. 6.6 Gambling Estimate of the Entropy of English. Summary. Problems. Historical Notes. 7. Channel Capacity. 7.1 Examples of Channel Capacity. 7.2 Symmetric Channels. 7.3 Properties of Channel Capacity. 7.4 Preview of the Channel Coding Theorem. 7.5 Definitions. 7.6 Jointly Typical Sequences. 7.7 Channel Coding Theorem. 7.8 Zero-Error Codes. 7.9 Fano's Inequality and the Converse to the Coding Theorem. 7.10 Equality in the Converse to the Channel Coding Theorem. 7.11 Hamming Codes. 7.12 Feedback Capacity. 7.13 Source-Channel Separation Theorem. Summary. Problems. Historical Notes. 8. Differential Entropy. 8.1 Definitions. 8.2 AEP for Continuous Random Variables. 8.3 Relation of Differential Entropy to Discrete Entropy. 8.4 Joint and Conditional Differential Entropy. 8.5 Relative Entropy and Mutual Information. 8.6 Properties of Differential Entropy, Relative Entropy, and Mutual Information. Summary. Problems. Historical Notes. 9. Gaussian Channel. 9.1 Gaussian Channel: Definitions. 9.2 Converse to the Coding Theorem for Gaussian Channels. 9.3 Bandlimited Channels. 9.4 Parallel Gaussian Channels. 9.5 Channels with Colored Gaussian Noise. 9.6 Gaussian Channels with Feedback. Summary. Problems. Historical Notes. 10. Rate Distortion Theory. 10.1 Quantization. 10.2 Definitions. 10.3 Calculation of the Rate Distortion Function. 10.4 Converse to the Rate Distortion Theorem. 10.5 Achievability of the Rate Distortion Function. 10.6 Strongly Typical Sequences and Rate Distortion. 10.7 Characterization of the Rate Distortion Function. 10.8 Computation of Channel Capacity and the Rate Distortion Function. Summary. Problems. Historical Notes. 11. Information Theory and Statistics. 11.1 Method of Types. 11.2 Law of Large Numbers. 11.3 Universal Source Coding. 11.4 Large Deviation Theory. 11.5 Examples of Sanov's Theorem. 11.6 Conditional Limit Theorem. 11.7 Hypothesis Testing. 11.8 Chernoff-Stein Lemma. 11.9 Chernoff Information. 11.10 Fisher Information and the Cram-er-Rao Inequality. Summary. Problems. Historical Notes. 12. Maximum Entropy. 12.1 Maximum Entropy Distributions. 12.2 Examples. 12.3 Anomalous Maximum Entropy Problem. 12.4 Spectrum Estimation. 12.5 Entropy Rates of a Gaussian Process. 12.6 Burg's Maximum Entropy Theorem. Summary. Problems. Historical Notes. 13. Universal Source Coding. 13.1 Universal Codes and Channel Capacity. 13.2 Universal Coding for Binary Sequences. 13.3 Arithmetic Coding. 13.4 Lempel-Ziv Coding. 13.5 Optimality of Lempel-Ziv Algorithms. Compression. Summary. Problems. Historical Notes. 14. Kolmogorov Complexity. 14.1 Models of Computation. 14.2 Kolmogorov Complexity: Definitions and Examples. 14.3 Kolmogorov Complexity and Entropy. 14.4 Kolmogorov Complexity of Integers. 14.5 Algorithmically Random and Incompressible Sequences. 14.6 Universal Probability. 14.7 Kolmogorov complexity. 14.9 Universal Gambling. 14.10 Occam's Razor. 14.11 Kolmogorov Complexity and Universal Probability. 14.12 Kolmogorov Sufficient Statistic. 14.13 Minimum Description Length Principle. Summary. Problems. Historical Notes. 15. Network Information Theory. 15.1 Gaussian Multiple-User Channels. 15.2 Jointly Typical Sequences. 15.3 Multiple-Access Channel. 15.4 Encoding of Correlated Sources. 15.5 Duality Between Slepian-Wolf Encoding and Multiple-Access Channels. 15.6 Broadcast Channel. 15.7 Relay Channel. 15.8 Source Coding with Side Information. 15.9 Rate Distortion with Side Information. 15.10 General Multiterminal Networks. Summary. Problems. Historical Notes. 16. Information Theory and Portfolio Theory. 16.1 The Stock Market: Some Definitions. 16.2 Kuhn-Tucker Characterization of the Log-Optimal Portfolio. 16.3 Asymptotic Optimality of the Log-Optimal Portfolio. 16.4 Side Information and the Growth Rate. 16.5 Investment in Stationary Markets. 16.6 Competitive Optimality of the Log-Optimal Portfolio. 16.7 Universal Portfolios. 16.8 Shannon-McMillan-Breiman Theorem (General AEP). Summary. Problems. Historical Notes. 17. Inequalities in Information Theory. 17.1 Basic Inequalities of Information Theory. 17.2 Differential Entropy. 17.3 Bounds on Entropy and Relative Entropy. 17.4 Inequalities for Types. 17.5 Combinatorial Bounds on Entropy. 17.6 Entropy Rates of Subsets. 17.7 Entropy and Fisher Information. 17.8 Entropy Power Inequality and Brunn-Minkowski Inequality. 17.9 Inequalities for Determinants. 17.10 Inequalities for Ratios of Determinants. Summary. Problems. Historical Notes. Bibliography. List of Symbols. Index.
45,034 citations
"Mutual-information-based registrati..." refers background in this paper
...In addition, the classesimage dimensionalityand number of imagesare defined....
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01 Jan 1994
TL;DR: The Diskette v 2.06, 3.5''[1.44M] for IBM PC, PS/2 and compatibles [DOS] Reference Record created on 2004-09-07, modified on 2016-08-08.
Abstract: Note: Includes bibliographical references, 3 appendixes and 2 indexes.- Diskette v 2.06, 3.5''[1.44M] for IBM PC, PS/2 and compatibles [DOS] Reference Record created on 2004-09-07, modified on 2016-08-08
19,881 citations
TL;DR: It is demonstrated that the use of local optimisation methods together with the standard multi-resolution approach is not sufficient to reliably find the global minimum, so a global optimisation method is proposed that is specifically tailored to this form of registration.
6,413 citations
"Mutual-information-based registrati..." refers background or methods in this paper
...To conclude, we present a list of papers that we did not consider true comparison studies, but that do contain comparisons between mutual information and other measures [12], [29], [44], [46], [51]–[53], [64], [69], [89], [91], [93], [95], [102], [103], [107], [127], [128], [130], [152], [156]....
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...the degrees of freedom of the rigid transformation with a scaling factor for each image dimension [25], [32], [58], [105], [106] and, additionally, a shearing in each dimension [13], [28], [38], [99], [107], [108]....
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...[46] P. M. Hayton, M. Brady, S. M. Smith, and N. Moore, “A non-rigid registration algorithm for dynamic breast MR images,”Artif....
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...[14], [24], [26]–[30], [32], [35]–[37], [41]–[44], [47], [49]–[53], [57], [64], [67], [69]–[71], [76], [80], [84], [86], [88], [92]–[94], [97]–[101], [104], [107] [108], [111], [115]–[117] [123], [125], [126], [135], [136], [140]–[142], [150], [160], [162]....
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...Jenkinson and Smith [107] propose an optimization routine that extends Powell’s method with initialization and a multistart technique....
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TL;DR: The results clearly indicate that the proposed nonrigid registration algorithm is much better able to recover the motion and deformation of the breast than rigid or affine registration algorithms.
Abstract: In this paper the authors present a new approach for the nonrigid registration of contrast-enhanced breast MRI. A hierarchical transformation model of the motion of the breast has been developed. The global motion of the breast is modeled by an affine transformation while the local breast motion is described by a free-form deformation (FFD) based on B-splines. Normalized mutual information is used as a voxel-based similarity measure which is insensitive to intensity changes as a result of the contrast enhancement. Registration is achieved by minimizing a cost function, which represents a combination of the cost associated with the smoothness of the transformation and the cost associated with the image similarity. The algorithm has been applied to the fully automated registration of three-dimensional (3-D) breast MRI in volunteers and patients. In particular, the authors have compared the results of the proposed nonrigid registration algorithm to those obtained using rigid and affine registration techniques. The results clearly indicate that the nonrigid registration algorithm is much better able to recover the motion and deformation of the breast than rigid or affine registration algorithms.
5,490 citations
"Mutual-information-based registrati..." refers background in this paper
...apply to the deformation grid of curved registration methods [29], [30], [36], [37], [46], [60], [64], [65], [72], [74]–[76], [82], [94], [121], [122], [125]....
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...MR: Registration of MR images has been described in many publications [21], [51], [52], [149], often for curved transformations [26], [27], [29], [36], [37], [46], [62], [64], [72], [74], [77], [80], [94], [111], [114], [117], [120], [121], [123], [124]....
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...Methods that do require function derivatives (whether mathematically derived or numerically estimated) are gradient ascent [36], [37], [45], [72]–[74], [99], [100], [121], [127], [140]–[142], quasi-Newton methods [122], [141] and the...
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...[47], [51], [52], [57], [58], [66], [72], [74], [77], [88], [91], [101], [106], [107], [112], [116], [120], [121], [125], [126], [134]–[136]....
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...for various imaging modalities, in particular, MR [46], [62], [74], [77], [114], [149], X-ray [95] and ultrasound [39], [113]....
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