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Deformable current-prior registration of DCE breast MR images on multi-site data
Abstract
Recent studies indicate that malignant breast lesions can be predicted from structural changes in prior exams of preventive breast MRI examinations. Due to non-rigid deformation between studies, spatial correspondences between structures in two consecutive studies are lost. Thus, deformable image registration can contribute to predicting individual cancer risks. This study evaluates a registration approach based on a novel breast mask segmentation and non-linear image registration based on data from 5 different sites. The landmark error (mean ± standard deviation [1st quartile, 3rd quartile]), annotated by three radiologists, is 2.9 ± 2.8 [1.3, 3.2] mm when leaving out two outlier cases from the evaluation for which the registration failed completely. We assess the inter-observer variabilities of keypoint errors and find an error of 3.6 ± 4.7 [1.6, 4.0] mm, 4.4 ± 4.9 [1.8, 4.8] mm, and 3.8 ± 4.0 [1.7, 4.1] mm when comparing each radiologist to the mean keypoints of the other two radiologists. Our study shows that the current state of the art in registration is well suited to recover spatial correspondences of structures in cancerous and non-cancerous cases, despite the high level of difficulty of this task.
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Background
Patient motion can degrade image quality of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) due to subtraction artifacts. By objectively and subjectively assessing the impact of principal component analysis (PCA)-based registration on pretreatment DCE-MRIs of breast cancer patients, we aim to validate four-dimensional registration for DCE breast MRI.
Results
After applying a four-dimensional, PCA-based registration algorithm to 154 pretreatment DCE-MRIs of histopathologically well-described breast cancer patients, we quantitatively determined image quality in unregistered and registered images. For subjective assessment, we ranked motion severity in a clinical reading setting according to four motion categories (0: no motion, 1: mild motion, 2: moderate motion, 3: severe motion with nondiagnostic image quality). The median of images with either moderate or severe motion (median category 2, IQR 0) was reassigned to motion category 1 (IQR 0) after registration. Motion category and motion reduction by registration were correlated (Spearman’s rho: 0.83, p < 0.001). For objective assessment, we performed perfusion model fitting using the extended Tofts model and calculated its volume transfer coefficient K trans as surrogate parameter for motion artifacts. Mean K trans decreased from 0.103 (± 0.077) before registration to 0.097 (± 0.070) after registration ( p < 0.001). Uncertainty in perfusion quantification was reduced by 7.4% after registration (± 15.5, p < 0.001).
Conclusions
Four-dimensional, PCA-based image registration improves image quality of breast DCE-MRI by correcting for motion artifacts in subtraction images and reduces uncertainty in quantitative perfusion modeling. The improvement is most pronounced when moderate-to-severe motion artifacts are present.
Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https:// learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods.
Purpose
Image registration plays a vital role in spatially aligning multiple MRI scans for better longitudinal assessment of tumor morphological features. The objective was to evaluate the effect of registration accuracy of six established deformable registration methods(ANTs, DRAMMS, ART, NiftyReg, SSD-FFD, and NMI-FFD) on the predictive value of extracted radiomic features when modeling recurrence-free-survival(RFS) for women after neoadjuvant chemotherapy(NAC) for locally advanced breast cancer.
Methods
130 women had DCE-MRI scans available from the first two visits in the ISPY1/ACRIN-6657 cohort. We calculated the transformation field from each of the different deformable registration methods, and used it to compute voxel-wise parametric-response-maps(PRM) for established four kinetic features.104-radiomic features were computed from each PRM map to characterize intra-tumor heterogeneity. We evaluated performance for RFS using Cox-regression, C-statistic, and Kaplan-Meier(KM) plots.
Results
A baseline model(F1:Age, Race, and Hormone-receptor-status) had a 0.54 C-statistic, and model F2(baseline + functional-tumor-volume at early treatment visit(FTV2)) had 0.63. The F2+ANTs had the highest C-statistic(0.72) with the smallest landmark differences(5.40±4.40mm) as compared to other models. The KM curve for model F2 gave p=0.004 for separation between women above and below the median hazard compared to the model F1(p=0.31). A models augmented with radiomic features, also achieved significant KM curve separation(p<0.001) except the F2+ART model.
Conclusion
Incorporating image registration in quantifying changes in tumor heterogeneity during NAC can improve prediction of RFS. Radiomic features of PRM maps derived from warping the DCE-MRI kinetic maps using ANTs registration method further improved the early prediction of RFS as compared to other methods.
MRI screening of high-risk patients for breast cancer provides very high sensitivity, but with a high recall rate and negative biopsies. Comparing the current exam to prior exams reduces the number of follow-up procedures requested by radiologists. Such comparison, however, can be challenging due to the highly deformable nature of breast tissues. Automated co-registration of multiple scans has the potential to aid diagnosis by providing 3D images for side-by-side comparison and also for use in CAD systems. Although many deformable registration techniques exist, they generally have a large number of parameters that need to be optimized and validated for each new application. Here, we propose a framework for such optimization and also identify the optimal input parameter set for registration of 3D T1-weighted MRI of breast using Elastix, a widely used and freely available registration tool. A numerical simulation study was first conducted to model the breast tissue and its deformation through finite element (FE) modeling. This model generated the ground truth for evaluating the registration accuracy by providing the deformation of each voxel in the breast volume. An exhaustive search was performed over various values of 7 registration parameters (4050 different combinations of parameters were assessed) and the optimum parameter set was determined. This study showed that there was a large variation in the registration accuracy of different parameter sets ranging from 0.29 mm to 2.50 mm in median registration error and 3.71 mm to 8.90 mm in 95 percentile of the registration error. Mean registration errors of 0.32 mm, 0.29 mm, and 0.30 mm and 95 percentile errors of 3.71 mm, 5.02 mm, and 4.70 mm were obtained by the three best parameter sets. The optimal parameter set was applied to consecutive breast MRI scans of 13 patients. A radiologist identified 113 landmark pairs (~ 11 per patient) which were used to assess registration accuracy. The results demonstrated that using the optimal registration parameter set, a registration accuracy (in mm) of 3.4 [1.8 6.8] was achieved.
In breast cancer screening for high-risk women, follow-up magnetic resonance images (MRI) are acquired with a time interval ranging from several months up to a few years. Prior MRI studies may provide additional clinical value when examining the current one and thus have the potential to increase sensitivity and specificity of screening. To build a spatial correlation between suspicious findings in both current and prior studies, a reliable alignment method between follow-up studies is desirable. However, long time interval, different scanners and imaging protocols, and varying breast compression can result in a large deformation, which challenges the registration process.
In this work, we present a fast and robust spatial alignment framework, which combines automated breast segmentation and current-prior registration techniques in a multi-level fashion. First, fully automatic breast segmentation is applied to extract the breast masks that are used to obtain an initial affine transform. Then, a non-rigid registration algorithm using normalized gradient fields as similarity measure together with curvature regularization is applied. A total of 29 subjects and 58 breast MR images were collected for performance assessment. To evaluate the global registration accuracy, the volume overlap and boundary surface distance metrics are calculated, resulting in an average Dice Similarity Coefficient (DSC) of 0.96 and root mean square distance (RMSD) of 1.64 mm. In addition, to measure local registration accuracy, for each subject a radiologist annotated 10 pairs of markers in the current and prior studies representing corresponding anatomical locations. The average distance error of marker pairs dropped from 67.37 mm to 10.86 mm after applying registration.
Welcome to the proceedings of the 4th Workshop on Biomedical Image R- istration (WBIR). Previous WBIRs took place in Bled, Slovenia (1999), at the UniversityofPennsylvania,USA(2003)andinUtrecht,TheNetherlands(2006). This year, WBIR was hosted by the Institute Mathematics and Image Proce- ing and the Fraunhofer Project Group on Image Registration and it was held in Lub ¨ eck, Germany. It provided the opportunity to bring together researchers from all over the world to discuss some of the most recent advances in image registration and its applications. We had an excellent collection of papers that were reviewed by at least three reviewers each from a 35-member Program Committee assembled from a wor- wide community of registration experts. This year 17 papers were accepted for oral presentation, while another 7 papers were accepted as poster papers. We believe all of the conference papers were of excellent quality. Registration is a fundamental task in image processing used to match two or more pictures taken, for example, at di?erent times, from di?erent sensors, or from di?erent viewpoints. Establishing the correspondence of structures within medical images is fundamental to diagnosis, treatment planning, and surgical guidance. The conference papers address state-of-the-art techniques for prov- ing reliable and e?cient registration techniques, thereby imposing relationships between speci?c application areas and appropriate registration schemes. We are grateful to all those who contributed to the success of WBIR 2010.
In den letzten Jahren hat sich der Workshop "Bildverarbeitung für die Medizin" durch erfolgreiche Veranstaltungen etabliert. Ziel ist auch 2011 wieder die Darstellung aktueller Forschungsergebnisse und die Vertiefung der Gespräche zwischen Wissenschaftlern, Industrie und Anwendern. Die Beiträge dieses Bandes - einige davon in englischer Sprache - behandeln alle Bereiche der medizinischen Bildverarbeitung, insbesondere Molekulare Bildgebung, Visualisierung und Animation, Patientenindividuelle Simulation und Planung, Computerunterstützte Diagnose, Biomechanische Modellierung, Bildverarbeitung in der Telemedizin, Bildgestützte Roboter, Chirurgische Simulatoren und viele mehr.
A particular problem in image registration arises for multimodal images taken from different imaging devices and/or modalities. Starting in 1995, mutual information has shown to be a very successful distance measure for multi-modal image registration. However, mutual information has also a number of well-known drawbacks. Its main disadvantage is that it is known to be highly non-convex and has typically many local maxima. This observation motivate us to seek a different image similarity measure which is better suited for optimization but as well capable to handle multi-modal images. In this work we investigate an alternative distance measure which is based on normalized gradients and compare its performance to Mutual Information. We call the new distance measure Normalized Gradient Fields (NGF).
This book really shows how registration works: the flip-book appearing at the top right corners shows a registration of a human knee from bent to straight position (keeping bones rigid). Of course, the book also provides insight into concepts and practical tools. The presented framework exploits techniques from various fields such as image processing, numerical linear algebra, and optimization. Therefore, a brief overview of some preliminary literature in those fields is presented in the introduction (references [1–51]), and registration-specific literature is assembled at the end of the book (references [52–212]). Examples and results are based on the FAIR software, a package written in MATLAB. The FAIR software, as well as a PDF version of this entire book, can be freely downloaded from www.siam.org/books/fa06.
This book would not have been possible without the help of Bernd Fischer, Eldad Haber, Claudia Kremling, Jim Nagy, and the Safir Research Group from Lübeck: Sven Barendt, Björn Beuthin, Konstantin Ens, Stefan Heldmann, Sven Kabus, Janine Olesch, Nils Papenberg, Hanno Schumacher, and Stefan Wirtz. I'm also indebted to Sahar Alipour, Reza Heydarian, Raya Horesh, Ramin Mafi, and Bahram Marami Dizaji for improving the manuscript.
A fully automated, non-rigid image registration algorithm is presented. The deformation field is found by minimizing a suitable measure subject to a curvature based constraint. It is a well-known fact that non-rigid image registration techniques may converge poorly if the initial position is not sufficiently near to the solution. A common approach to address this problem is to perform a time consuming rigid pre-registration step. In this paper we show that the new curvature registration not only produces accurate and smooth solutions but also allows for an automatic rigid alignment. Thus, in contrast to other popular registration schemes, the new method no longer requires a pre-registration step. Furthermore, we present an implementation of the new scheme based on the numerical solution of the underlying Euler-Lagrange equations. The real discrete cosine transform is the backbone of our implementation and leads to a stable and fast O(N log N) algorithm, where N denotes the number of voxels. Finally, we report on some numerical test runs.
Breast cancer is the most common type of cancer in women worldwide. Image registration lays an important role in breast cancer detection. This paper gives an overview of the current state-of-the-art in the breast image registration techniques. For the intra-modality registration techniques, X-ray, MRI, and ultrasound are the primary focuses of interest. Inter-modality techniques will cover the combination of different modalities. Validation of breast registration methods is also discussed. © International Federation for Medical and Biological Engineering 2006.