ContraReg: Contrastive Learning of Multi-modality Unsupervised Deformable Image Registration
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ABSTRACT:
SUBMITTER: Dey N
PROVIDER: S-EPMC10415941 | biostudies-literature | 2022 Sep
REPOSITORIES: biostudies-literature
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Project description:Registration is the process of transforming images so they are aligned in the same coordinate space. In the medical field, image registration is often used to align multi-modal or multi-parametric images of the same organ. A uniquely challenging subset of medical image registration is cross-modality registration-the task of aligning images captured with different scanning methodologies. In this study, we present a transformer-based deep learning pipeline for performing cross-modality, radiology-pathology image registration for human prostate samples. While existing solutions for multi-modality prostate image registration focus on the prediction of transform parameters, our pipeline predicts a set of homologous points on the two image modalities. The homologous point registration pipeline achieves better average control point deviation than the current state-of-the-art automatic registration pipeline. It reaches this accuracy without requiring masked MR images which may enable this approach to achieve similar results in other organ systems and for partial tissue samples.
| S-EPMC9748842 | biostudies-literature
Project description:Convolutional neural networks (CNNs) offer a promising means to achieve fast deformable image registration with accuracy comparable to conventional, physics-based methods. A persistent question with CNN methods, however, is whether they will be able to generalize to data outside of the training set. We investigated this question of mismatch between train and test data with respect to first- and second-order image statistics (e.g., spatial resolution, image noise, and power spectrum). A UNet-based architecture was built and trained on simulated CT images for various conditions of image noise (dose), spatial resolution, and deformation magnitude. Target registration error was measured as a function of the difference in statistical properties between the test and training data. Generally, registration error is minimized when the training data exactly match the statistics of the test data; however, networks trained with data exhibiting a diversity in statistical characteristics generalized well across the range of statistical conditions considered. Furthermore, networks trained on simulated image content with first- and second-order statistics selected to match that of real anatomical data were shown to provide reasonable registration performance on real anatomical content, offering potential new means for data augmentation. Characterizing the behavior of a CNN in the presence of statistical mismatch is an important step in understanding how these networks behave when deployed on new, unobserved data. Such characterization can inform decisions on whether retraining is necessary and can guide the data collection and/or augmentation process for training.
| S-EPMC6916745 | biostudies-literature
Project description: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.
| S-EPMC3745275 | biostudies-other
Project description:We present INSPIRE, a top-performing general-purpose method for deformable image registration. INSPIRE brings distance measures which combine intensity and spatial information into an elastic B-splines-based transformation model and incorporates an inverse inconsistency penalization supporting symmetric registration performance. We introduce several theoretical and algorithmic solutions which provide high computational efficiency and thereby applicability of the proposed framework in a wide range of real scenarios. We show that INSPIRE delivers highly accurate, as well as stable and robust registration results. We evaluate the method on a 2D dataset created from retinal images, characterized by presence of networks of thin structures. Here INSPIRE exhibits excellent performance, substantially outperforming the widely used reference methods. We also evaluate INSPIRE on the Fundus Image Registration Dataset (FIRE), which consists of 134 pairs of separately acquired retinal images. INSPIRE exhibits excellent performance on the FIRE dataset, substantially outperforming several domain-specific methods. We also evaluate the method on four benchmark datasets of 3D magnetic resonance images of brains, for a total of 2088 pairwise registrations. A comparison with 17 other state-of-the-art methods reveals that INSPIRE provides the best overall performance. Code is available at github.com/MIDA-group/inspire.
| S-EPMC9983883 | biostudies-literature
Project description:Aim: To assess the ablative margin (AM) after microwave ablation (MWA) for hepatocellular carcinoma (HCC) with a deep learning-based deformable image registration (DIR) technique and analyze the relation between the AM and local tumor progression (LTP). Patients and Methods: From November 2012 to April 2019, 141 consecutive patients with single HCC (diameter ≤ 5 cm) who underwent MWA were reviewed. Baseline characteristics were collected to identify the risk factors for the determination of LTP after MWA. Contrast-enhanced magnetic resonance imaging scans were performed within 1 month before and 3 months after treatment. Complete ablation was confirmed for all lesions. The AM was measured based on the margin size between the tumor region and the deformed ablative region. To correct the misalignment, DIR between images before and after ablation was achieved by an unsupervised landmark-constrained convolutional neural network. The patients were classified into two groups according to their AMs: group A (AM ≤ 5 mm) and group B (AM > 5 mm). The cumulative LTP rates were compared between the two groups using Kaplan-Meier curves and the log-rank test. Multivariate analyses were performed on clinicopathological variables to identify factors affecting LTP. Results: After a median follow-up period of 28.9 months, LTP was found in 19 patients. The mean tumor and ablation zone sizes were 2.3 ± 0.9 cm and 3.8 ± 1.2 cm, respectively. The mean minimum ablation margin was 3.4 ± 0.7 mm (range, 0-16 mm). The DIR technique had higher AUC for 2-year LTP without a significant difference compared with the registration assessment without DL (P = 0.325). The 6-, 12-, and 24-month LTP rates were 9.9, 20.6, and 24.8%, respectively, in group A, and 4.0, 8.4, and 8.4%, respectively, in group B. There were significant differences between the two groups (P = 0.011). Multivariate analysis showed that being >65 years of age (P = 0.032, hazard ratio (HR): 2.463, 95% confidence interval (CI), 1.028-6.152) and AM ≤ 5 mm (P = 0.010, HR: 3.195, 95% CI, 1.324-7.752) were independent risk factors for LTP after MWA. Conclusion: The novel technology of unsupervised landmark-constrained convolutional neural network-based DIR is feasible and useful in evaluating the ablative effect of MWA for HCC.
| S-EPMC7546854 | biostudies-literature
Project description: Not available
| S-EPMC11296048 | biostudies-literature
Project description:Deformable image registration (DIR) is a versatile tool used in many applications in radiotherapy (RT). DIR algorithms have been implemented in many commercial treatment planning systems providing accessible and easy-to-use solutions. However, the geometric uncertainty of DIR can be large and difficult to quantify, resulting in barriers to clinical practice. Currently, there is no agreement in the RT community on how to quantify these uncertainties and determine thresholds that distinguish a good DIR result from a poor one. This review summarises the current literature on sources of DIR uncertainties and their impact on RT applications. Recommendations are provided on how to handle these uncertainties for patient-specific use, commissioning, and research. Recommendations are also provided for developers and vendors to help users to understand DIR uncertainties and make the application of DIR in RT safer and more reliable.
| S-EPMC10725576 | biostudies-literature
Project description:PurposeTo evaluate deep learning (DL)-based deformable image registration (DIR) for dose accumulation during radiotherapy of prostate cancer patients.Methods and materialsData including 341 CBCTs (209 daily, 132 weekly) and 23 planning CTs from 23 patients was retrospectively analyzed. Anatomical deformation during treatment was estimated using free-form deformation (FFD) method from Elastix and DL-based VoxelMorph approaches. The VoxelMorph method was investigated using anatomical scans (VMorph_Sc) or label images (VMorph_Msk), or the combination of both (VMorph_Sc_Msk). Accumulated doses were compared with the planning dose.ResultsThe DSC ranges, averaged for prostate, rectum and bladder, were 0.60-0.71, 0.67-0.79, 0.93-0.98, and 0.89-0.96 for the FFD, VMorph_Sc, VMorph_Msk, and VMorph_Sc_Msk methods, respectively. When including both anatomical and label images, VoxelMorph estimated more complex deformations resulting in heterogeneous determinant of Jacobian and higher percentage of deformation vector field (DVF) folding (up to a mean value of 1.90% in the prostate). Large differences were observed between DL-based methods regarding estimation of the accumulated dose, showing systematic overdosage and underdosage of the bladder and rectum, respectively. The difference between planned mean dose and accumulated mean dose with VMorph_Sc_Msk reached a median value of +6.3 Gy for the bladder and -5.1 Gy for the rectum.ConclusionThe estimation of the deformations using DL-based approach is feasible for male pelvic anatomy but requires the inclusion of anatomical contours to improve organ correspondence. High variability in the estimation of the accumulated dose depending on the deformable strategy suggests further investigation of DL-based techniques before clinical deployment.
| S-EPMC10445205 | biostudies-literature
Project description:Image registration is a key technique in medical image analysis to estimate deformations between image pairs. A good deformation model is important for high-quality estimates. However, most existing approaches use ad-hoc deformation models chosen for mathematical convenience rather than to capture observed data variation. Recent deep learning approaches learn deformation models directly from data. However, they provide limited control over the spatial regularity of transformations. Instead of learning the entire registration approach, we learn a spatially-adaptive regularizer within a registration model. This allows controlling the desired level of regularity and preserving structural properties of a registration model. For example, diffeomorphic transformations can be attained. Our approach is a radical departure from existing deep learning approaches to image registration by embedding a deep learning model in an optimization-based registration algorithm to parameterize and data-adapt the registration model itself. Source code is publicly-available at https://github.com/uncbiag/registration.
| S-EPMC7286567 | biostudies-literature
Project description:While virtual reality (VR) has potential in enhancing cardiovascular diagnosis and treatment, prerequisite labor-intensive image segmentation remains an obstacle for seamlessly simulating 4-dimensional (4-D, 3-D?+?time) imaging data in an immersive, physiological VR environment. We applied deformable image registration (DIR) in conjunction with 3-D reconstruction and VR implementation to recapitulate developmental cardiac contractile function from light-sheet fluorescence microscopy (LSFM). This method addressed inconsistencies that would arise from independent segmentations of time-dependent data, thereby enabling the creation of a VR environment that fluently simulates cardiac morphological changes. By analyzing myocardial deformation at high spatiotemporal resolution, we interfaced quantitative computations with 4-D VR. We demonstrated that our LSFM-captured images, followed by DIR, yielded average dice similarity coefficients of 0.92?±?0.05 (n?=?510) and 0.93?±?0.06 (n?=?240) when compared to ground truth images obtained from Otsu thresholding and manual segmentation, respectively. The resulting VR environment simulates a wide-angle zoomed-in view of motion in live embryonic zebrafish hearts, in which the cardiac chambers are undergoing structural deformation throughout the cardiac cycle. Thus, this technique allows for an interactive micro-scale VR visualization of developmental cardiac morphology to enable high resolution simulation for both basic and clinical science.
| S-EPMC6249076 | biostudies-literature