Nonrigid registration of 3-D free-hand ultrasound images of the breast

Three-dimensional (3-D) ultrasound imaging of the breast enables better assessment of diseases than conventional two-dimensional (2-D) imaging. Free-hand techniques are often used for generating 3-D data from a sequence of 2-D slice images. However, the breast deforms substantially during scanning because it is composed primarily of soft tissue. This often causes tissue mis-registration in spatial compounding of multiple scan sweeps. To overcome this problem, in this paper, instead of introducing additional constraints on scanning conditions, we use image processing techniques. We present a fully automatic algorithm for 3-D nonlinear registration of free-hand ultrasound data. It uses a block matching scheme and local statistics to estimate local tissue deformation. A Bayesian regularization method is applied to the sample displacement field. The final deformation field is obtained by fitting a B-spline approximating mesh to the sample displacement field. Registration accuracy is evaluated using phantom data and similar registration errors are achieved with (0.19 mm) and without (0.16 mm) gaps in the data. Experimental results show that registration is crucial in spatial compounding of different sweeps. The execution time of the method on moderate hardware is sufficiently fast for fairly large research studies.     

Estimating 3-D respiratory motion from orbiting views by tomographic image registration

Respiratory motion remains a significant source of errors in treatment planning for the thorax and upper abdomen. Recently, we proposed a method to estimate two-dimensional (2-D) object motion from a sequence of slowly rotating X-ray projection views, which we called deformation from orbiting views (DOVs). In this method, we model the motion as a time varying deformation of a static prior of the anatomy. We then optimize the parameters of the motion model by maximizing the similarity between the modeled and actual projection views. This paper extends the method to full three-dimensional (3-D) motion and cone-beam projection views. We address several practical issues for using a cone-beam computed tomography (CBCT) scanner that is integrated in a radiotherapy system, such as the effects of Compton scatter and the limited gantry rotation for one breathing cycle. We also present simulation and phantom results to illustrate the performance of this method.     

3-D reconstruction of microcalcification clusters using stereo imaging: algorithm and mammographic unit calibration

The three-dimensional (3-D) shape of microcalcification clusters is an important indicator in early breast cancer detection. In fact, there is a relationship between the cluster topology and the type of lesion (malignant or benign). This paper presents a 3-D reconstruction method for such clusters using two 2-D views acquired during standard mammographic examinations. For this purpose, the mammographic unit was modeled using a camera with virtual optics. This model was used to calibrate the acquisition unit and then to reconstruct the clusters in the 3-D space after microcalcification segmentation and matching. The proposed model is hardware independent since it is suitable for digital mammographic units with different geometries and with various physical acquisition principles. Three-dimensional reconstruction results are presented here to prove the validity of the method. Tests were first performed using a phantom with a well-known geometry. The latter contained X-ray opaque glass balls representing microcalcifications. The positions of these balls were reconstructed with a 16.25-microm mean accuracy. This very high inherent algorithm accuracy is more than enough for a precise 3-D cluster representation. Further validation tests were carried out using a second phantom including a spherical cluster. This phantom was built with materials simulating the behavior of both mammary tissue and microcalcifications toward Xrays. The reconstructed shape was effectively spherical. Finally, reconstructions were carried out for real clusters and their results are also presented.     

Markerless real-time 3-D target region tracking by motion backprojection from projection images

Accurate and fast localization of a predefined target region inside the patient is an important component of many image-guided therapy procedures. This problem is commonly solved by registration of intraoperative 2-D projection images to 3-D preoperative images. If the patient is not fixed during the intervention, the 2-D image acquisition is repeated several times during the procedure, and the registration problem can be cast instead as a 3-D tracking problem. To solve the 3-D problem, we propose in this paper to apply 2-D region tracking to first recover the components of the transformation that are in-plane to the projections. The 2-D motion estimates of all projections are backprojected into 3-D space, where they are then combined into a consistent estimate of the 3-D motion. We compare this method to intensity-based 2-D to 3-D registration and a combination of 2-D motion backprojection followed by a 2-D to 3-D registration stage. Using clinical data with a fiducial marker-based gold-standard transformation, we show that our method is capable of accurately tracking vertebral targets in 3-D from 2-D motion measured in X-ray projection images. Using a standard tracking algorithm (hyperplane tracking), tracking is achieved at video frame rates but fails relatively often (32% of all frames tracked with target registration error (TRE) better than 1.2 mm, 82% of all frames tracked with TRE better than 2.4 mm). With intensity-based 2-D to 2-D image registration using normalized mutual information (NMI) and pattern intensity (PI), accuracy and robustness are substantially improved. NMI tracked 82% of all frames in our data with TRE better than 1.2 mm and 96% of all frames with TRE better than 2.4 mm. This comes at the cost of a reduced frame rate, 1.7 s average processing time per frame and projection device. Results using PI were slightly more accurate, but required on average 5.4 s time per frame. These results are still substantially faster than 2-D to 3-D registration. We conclude that motion backprojection from 2-D motion tracking is an accurate and efficient method for tracking 3-D target motion, but tracking 2-D motion accurately and robustly remains a challenge.     

3-D/2-D registration of CT and MR to X-ray images

A crucial part of image-guided therapy is registration of preoperative and intraoperative images, by which the precise position and orientation of the patient's anatomy is determined in three dimensions. This paper presents a novel approach to register three-dimensional (3-D) computed tomography (CT) or magnetic resonance (MR) images to one or more two-dimensional (2-D) X-ray images. The registration is based solely on the information present in 2-D and 3-D images. It does not require fiducial markers, intraoperative X-ray image segmentation, or timely construction of digitally reconstructed radiographs. The originality of the approach is in using normals to bone surfaces, preoperatively defined in 3-D MR or CT data, and gradients of intraoperative X-ray images at locations defined by the X-ray source and 3-D surface points. The registration is concerned with finding the rigid transformation of a CT or MR volume, which provides the best match between surface normals and back projected gradients, considering their amplitudes and orientations. We have thoroughly validated our registration method by using MR, CT, and X-ray images of a cadaveric lumbar spine phantom for which "gold standard" registration was established by means of fiducial markers, and its accuracy assessed by target registration error. Volumes of interest, containing single vertebrae L1-L5, were registered to different pairs of X-ray images from different starting positions, chosen randomly and uniformly around the "gold standard" position. CT/X-ray (MR/ X-ray) registration, which is fast, was successful in more than 91% (82% except for L1) of trials if started from the "gold standard" translated or rotated for less than 6 mm or 17 degrees (3 mm or 8.6 degrees), respectively. Root-mean-square target registration errors were below 0.5 mm for the CT to X-ray registration and below 1.4 mm for MR to X-ray registration.     

A "twisting and bending" model-based nonrigid image registration technique for 3-D ultrasound carotid images

Atherosclerosis at the carotid bifurcation resulting in cerebral emboli is a major cause of ischemic stroke. Most strokes associated with carotid atherosclerosis can be prevented by lifestyle/dietary changes and pharmacological treatments if identified early by monitoring carotid plaque changes. Registration of 3-D ultrasound (US) images of carotid plaque obtained at different time points is essential for sensitive monitoring of plaque changes in volume and surface morphology. This registration technique should be nonrigid, since different head positions during image acquisition sessions cause relative bending and torsion in the neck, producing nonlinear deformations between the images. We modeled the movement of the neck using a “twisting and bending” model with only six parameters for nonrigid registration. We evaluated the algorithm using 3-D US carotid images acquired at two different head positions to simulate images acquired at different times. We calculated the mean registration error (MRE) between the segmented vessel surfaces in the target image and the registered image using a distance-based error metric after applying our “twisting and bending” model-based nonrigid registration algorithm. We achieved an average registration error of $0.80 pm 0.26$ mm using our nonrigid registration technique, which was a significant improvement in registration accuracy over rigid registration, even with reduced degrees-of-freedom compared to the other nonrigid registration algorithms.      

A comparison of similarity measures for use in 2-D-3-D medicalimage registration

A comparison of six similarity measures for use in intensity-based two-dimensional-three-dimensional (2-D-3-D) image registration is presented. The accuracy of the similarity measures are compared to a “gold-standard” registration which has been accurately calculated using fiducial markers. The similarity measures are used to register a computed tomography (CT) scan of a spine phantom to a fluoroscopy image of the phantom. The registration is carried out within a region-of-interest in the fluoroscopy image which is user defined to contain a single vertebra. Many of the problems involved in this type of registration are caused by features which were not modeled by a phantom image alone. More realistic “gold-standard” data sets were simulated using the phantom image with clinical image features overlaid. Results show that the introduction of soft-tissue structures and interventional instruments into the phantom image can have a large effect on the performance of some similarity measures previously applied to 2-D-3-D image registration. Two measures were able to register accurately and robustly even when soft-tissue structures and interventional instruments were present as differences between the images. These measures were pattern intensity and gradient difference. Their registration accuracy, for all the rigid-body parameters except for the source to film translation, was within a root-mean-square (rms) error of 0.53 mm or degrees to the “gold-standard” values. No failures occurred while registering using these measures     

3-D/2-D registration by integrating 2-D information in 3-D

In image-guided therapy, high-quality preoperative images serve for planning and simulation, and intraoperatively as "background", onto which models of surgical instruments or radiation beams are projected. The link between a preoperative image and intraoperative physical space of the patient is established by image-to-patient registration. In this paper, we present a novel 3-D/2-D registration method. First, a 3-D image is reconstructed from a few 2-D X-ray images and next, the preoperative 3-D image is brought into the best possible spatial correspondence with the reconstructed image by optimizing a similarity measure (SM). Because the quality of the reconstructed image is generally low, we introduce a novel SM, which is able to cope with low image quality as well as with different imaging modalities. The novel 3-D/2-D registration method has been evaluated and compared to the gradient-based method (GBM) using standardized evaluation methodology and publicly available 3-D computed tomography (CT), 3-D rotational X-ray (3DRX), and magnetic resonance (MR) and 2-D X-ray images of two spine phantoms, for which gold standard registrations were known. For each of the 3DRX, CT, or MR images and each set of X-ray images, 1600 registrations were performed from starting positions, defined as the mean target registration error (mTRE), randomly generated and uniformly distributed in the interval of 0-20 mm around the gold standard. The capture range was defined as the distance from gold standard for which the final TRE was less than 2 mm in at least 95% of all cases. In terms of success rate, as the function of initial misalignment and capture range the proposed method outperformed the GBM. TREs of the novel method and the GBM were approximately the same. For the registration of 3DRX and CT images to X-ray images as few as 2-3 X-ray views were sufficient to obtain approximately 0.4 mm TREs, 7-9 mm capture range, and 80%-90% of successful registrations. To obtain similar results for MR to X-ray registrations, an image, reconstructed from at least 11 X-ray images was required. Reconstructions from more than 11 images had no effect on the registration results.     

2-D locally regularized tissue strain estimation from radio-frequency ultrasound images: theoretical developments and results on experimental data

In this paper, a 2-D locally regularized strain estimation method for imaging deformation of soft biological tissues from radio-frequency (RF) ultrasound (US) data is introduced. Contrary to most 2-D techniques that model the compression-induced local displacement as a 2-D shift, our algorithm also considers a local scaling factor in the axial direction. This direction-dependent model of tissue motion and deformation is induced by the highly anisotropic resolution of RF US images. Optimal parameters are computed through the constrained maximization of a similarity criterion defined as the normalized correlation coefficient. Its value at the solution is then used as an indicator of estimation reliability, the probability of correct estimation increasing with the correlation value. In case of correlation loss, the estimation integrates an additional constraint, imposing local continuity within displacement and strain fields. Using local scaling factors and regularization increase the method's robustness with regard to decorrelation noise, resulting in a wider range of precise measurements. Results on simulated US data from a mechanically homogeneous medium subjected to successive uniaxial loadings demonstrate that our method is theoretically able to accurately estimate strains up to 17%. Experimental strain images of phantom and cut specimens of bovine liver clearly show the harder inclusions.     

Semiautomatic 3-D image registration as applied to interventional MRI liver cancer treatment

We evaluated semiautomatic, voxel-based registration methods for a new application, the assessment and optimization of interventional magnetic resonance imaging (I-MRI) guided thermal ablation of liver cancer. The abdominal images acquired on a low-field-strength, open I-MRI system contain noise, motion artifacts, and tissue deformation. Dissimilar images can be obtained as a result of different MRI acquisition techniques and/or changes induced by treatments. These features challenge a registration algorithm. We evaluated one manual and four automated methods on clinical images acquired before treatment, immediately following treatment, and during several follow-up studies. Images were T2-weighted, T1-weighted Gd-DTPA enhanced, T1-weighted, and short-inversion-time inversion recovery (STIR). Registration accuracy was estimated from distances between anatomical landmarks. Mutual information gave better results than entropy, correlation, and variance of gray-scale ratio. Preprocessing steps such as masking and an initialization method that used two-dimensional (2-D) registration to obtain initial transformation estimates were crucial. With proper preprocessing, automatic registration was successful with all image pairs having reasonable image quality. A registration accuracy of approximately equal to 3 mm was achieved with both manual and mutual information methods. Despite motion and deformation in the liver, mutual information registration is sufficiently accurate and robust for useful applications in I-MRI thermal ablation therapy.     

Towards 3-D scene reconstruction from broadcast video

Three-dimensional (3-D) scene reconstruction from broadcast video is a challenging problem with many potential applications, such as 3-D TV, free-view TV, augmented reality or three-dimensionalization of two-dimensional (2-D) media archives. In this paper, a flexible and effective system capable of efficiently reconstructing 3-D scenes from broadcast video is proposed, with the assumption that there is relative motion between camera and scene/objects. The system requires no a priori information and input, other than the video sequence itself, and capable of estimating the internal and external camera parameters and performing a 3-D motion-based segmentation, as well as computing a dense depth field. The system also serves as a showcase to present some novel approaches for moving object segmentation, sparse and dense reconstruction problems. According to the simulations for both synthetic and real data, the system achieves a promising performance for typical TV content, indicating that it is a significant step towards the 3-D reconstruction of scenes from broadcast video.     

B-Mode Ultrasound Image Simulation in Deformable 3-D Medium

This paper presents an algorithm for fast image synthesis inside deformed volumes. Given the node displacements of a mesh and a reference 3-D image dataset of a predeformed volume, the method first maps the image pixels that need to be synthesized from the deformed configuration to the nominal predeformed configuration, where the pixel intensities are obtained easily through interpolation in the regular-grid structure of the reference voxel volume. This mapping requires the identification of the mesh element enclosing each pixel for every image frame. To accelerate this point location operation, a fast method of projecting the deformed mesh on image pixels is introduced in this paper. The method presented was implemented for ultrasound B-mode image simulation of a synthetic tissue phantom. The phantom deformation as a result of ultrasound probe motion was modeled using the finite element method. Experimental images of the phantom under deformation were then compared with the corresponding synthesized images using sum of squared differences and mutual information metrics. Both this quantitative comparison and a qualitative assessment show that realistic images can be synthesized using the proposed technique. An ultrasound examination system was also implemented to demonstrate that real-time image synthesis with the proposed technique can be successfully integrated into a haptic simulation.      

Model-based quantitation of 3-D magnetic resonance angiographic images

Quantification of the degree of stenosis or vessel dimensions are important for diagnosis of vascular diseases and planning vascular interventions. Although diagnosis from three-dimensional (3-D) magnetic resonance angiograms (MRA's) is mainly performed on two-dimensional (2-D) maximum intensity projections, automated quantification of vascular segments directly from the 3-D dataset is desirable to provide accurate and objective measurements of the 3-D anatomy. A model-based method for quantitative 3-D MRA is proposed. Linear vessel segments are modeled with a central vessel axis curve coupled to a vessel wall surface. A novel image feature to guide the deformation of the central vessel axis is introduced. Subsequently, concepts of deformable models are combined with knowledge of the physics of the acquisition technique to accurately segment the vessel wall and compute the vessel diameter and other geometrical properties. The method is illustrated and validated on a carotid bifurcation phantom, with ground truth and medical experts as comparisons. Also, results on 3-D time-of-flight (TOF) MRA images of the carotids are shown. The approach is a promising technique to assess several geometrical vascular parameters directly on the source 3-D images, providing an objective mechanism for stenosis grading.     

A 3-D reconstruction system for the human jaw using a sequence of optical images

This paper presents a model-based vision system for dentistry that will assist in diagnosis, treatment planning, and surgical simulation. Dentistry requires an accurate three-dimensional (3-D) representation of the teeth and jaws for diagnostic and treatment purposes. The proposed integrated computer vision system constructs a 3-D model of the patient's dental occlusion using an intraoral video camera. A modified shape from shading (SFS) technique, using perspective projection and camera calibration, extracts the 3-D information from a sequence of two-dimensional (2-D) images of the jaw. Data fusion of range data and 3-D registration techniques develop the complete jaw model. Triangulation is then performed, and a solid 3-D model is reconstructed. The system performance is investigated using ground truth data, and the results show acceptable reconstruction accuracy.     

Robust Gradient-Based 3-D/2-D Registration of CT and MR to X-Ray Images

One of the most important technical challenges in image-guided intervention is to obtain a precise transformation between the intrainterventional patient's anatomy and corresponding preinterventional 3-D image on which the intervention was planned. This goal can be achieved by acquiring intrainterventional 2-D images and matching them to the preinterventional 3-D image via 3-D/2-D image registration. A novel 3-D/2-D registration method is proposed in this paper. The method is based on robustly matching 3-D preinterventional image gradients and coarsely reconstructed 3-D gradients from the intrainterventional 2-D images. To improve the robustness of finding the correspondences between the two sets of gradients, hypothetical correspondences are searched for along normals to anatomical structures in 3-D images, while the final correspondences are established in an iterative process, combining the robust random sample consensus algorithm (RANSAC) and a special gradient matching criterion function. The proposed method was evaluated using the publicly available standardized evaluation methodology for 3-D/2-D registration, consisting of 3-D rotational X-ray, computed tomography, magnetic resonance (MR), and 2-D X-ray images of two spine segments, and standardized evaluation criteria. In this way, the proposed method could be objectively compared to the intensity, gradient, and reconstruction-based registration methods. The obtained results indicate that the proposed method performs favorably both in terms of registration accuracy and robustness. The method is especially superior when just a few X-ray images and when MR preinterventional images are used for registration, which are important advantages for many clinical applications.      

Patient-specific bronchoscopy visualization through BRDF estimation and disocclusion correction

This paper presents an image-based method for virtual bronchoscope with photo-realistic rendering. The technique is based on recovering bidirectional reflectance distribution function (BRDF) parameters in an environment where the choice of viewing positions, directions, and illumination conditions are restricted. Video images of bronchoscopy examinations are combined with patient-specific three-dimensional (3-D) computed tomography data through two-dimensional (2-D)/3-D registration and shading model parameters are then recovered by exploiting the restricted lighting configurations imposed by the bronchoscope. With the proposed technique, the recovered BRDF is used to predict the expected shading intensity, allowing a texture map independent of lighting conditions to be extracted from each video frame. To correct for disocclusion artefacts, statistical texture synthesis was used to recreate the missing areas. New views not present in the original bronchoscopy video are rendered by evaluating the BRDF with different viewing and illumination parameters. This allows free navigation of the acquired 3-D model with enhanced photo-realism. To assess the practical value of the proposed technique, a detailed visual scoring that involves both real and rendered bronchoscope images is conducted.     

Voxel-based 2-D/3-D registration of fluoroscopy images and CT scansfor image-guided surgery

Registration of intraoperative fluoroscopy images with preoperative 3D CT images can he used for several purposes in image-guided surgery. On the one hand, it can be used to display the position of surgical instruments, which are being tracked by a localizer, in the preoperative CT scan. On the other hand, the registration result can be used to project preoperative planning information or important anatomical structures visible in the CT image on to the fluoroscopy image. For this registration task, a novel voxel-based method in combination with a new similarity measure (pattern intensity) has been developed. The basic concept of the method is explained at the example of 2D/3D registration of a vertebra in an X-ray fluoroscopy image with a 3D CT image. The registration method is described, and the results for a spine phantom are presented and discussed. Registration has been carried out repeatedly with different starting estimates to study the capture range. Information about registration accuracy has been obtained by comparing the registration results with a highly accurate “ground-truth” registration, which has been derived from fiducial markers attached to the phantom prior to imaging. In addition, registration results for different vertebrae have been compared. The results show that the rotation parameters and the shifts parallel to the projection plane can accurately be determined from a single projection. Because of the projection geometry, the accuracy of the height above the projection plane is significantly lower     

A novel temporal calibration method for 3-D ultrasound

This paper examines a novel approach for temporal calibration of a three-dimensional (3-D) freehand ultrasound system. A localization system fixed on the probe gives the position and orientation of the probe. For quantitative use, calibration is needed to correctly localize a B-scan in four-dimensional (4-D) (3-D+t) space. Temporal latency estimation is defined in a general robust formulation using no specific probe motion constraints. Experiments were performed on synthetic and real data using a 3-D freehand ultrasound system. The achieved precision is lower than the image acquisition rate (40 ms). A validation study using a calibration phantom has been performed to evaluate the influence of incorrect latency estimation on the 3-D reconstruction procedure. We showed that for latency estimation errors less than 40 ms, the 3-D reconstruction errors are negligible for volume estimation.     

Noise characteristics of 3-D and 2-D PET images

The authors analyzed the noise characteristics of two-dimensional (2-D) and three-dimensional (3-D) images obtained from the GE Advance positron emission tomography (PET) scanner. Three phantoms were used: a uniform 20-cm phantom, a 3-D Hoffman brain phantom, and a chest phantom with heart and lung inserts. Using gated acquisition, the authors acquired 20 statistically equivalent scans of each phantom in 2-D and 3-D modes at several activity levels. From these data, they calculated pixel normalized standard deviations (NSD's), scaled to phantom mean, across the replicate scans, which allowed them to characterize the radial and axial distributions of pixel noise. The authors also performed sequential measurements of the phantoms in 2-D and 3-D modes to measure noise (from interpixel standard deviations) as a function of activity. To compensate for the difference in axial slice width between 2-D and 3-D images (due to the septa and reconstruction effects), they developed a smoothing kernel to apply to the 2-D data. After matching the resolution, the ratio of image-derived NSD values (NSD_2D/NSD_3D)² averaged throughout the uniform phantom was in good agreement with the noise equivalent count (NEC) ratio (NEC_3D/NEC_2D). By comparing different phantoms, the authors showed that the attenuation and emission distributions influence the spatial noise distribution. The estimates of pixel noise for 2-D and 3-D images produced here can be applied in the weighting of PET kinetic data and may be useful in the design of optimal dose and scanning requirements for PET studies. The accuracy of these phantom-based noise formulas should be validated for any given imaging situation, particularly in 3-D, if there is significant activity outside the scanner field of view     

Model evaluation and calibration for prospective respiratory motion correction in coronary MR angiography based on 3-D image registration

Image processing was used as a fundamental tool to derive motion information from magnetic resonance (MR) images, which was fed back into prospective respiratory motion correction during subsequent data acquisition to improve image quality in coronary MR angiography (CMRA) scans. This reduces motion artifacts in the images and, in addition, enables the usage of a broader gating window than commonly used today to increase the scan efficiency. The aim of the study reported in this paper was to find a suitable motion model to be used for respiratory motion correction in cardiac imaging and to develop a calibration procedure to adapt the motion model to the individual patient. At first, the performance of three motion models [one-dimensional translation in feet-head (FH) direction, three-dimensional (3-D) translation, and 3-D affine transformation] was tested in a small volunteer study. An elastic image registration algorithm was applied to 3-D MR images of the coronary vessels obtained at different respiratory levels. A strong intersubject variability was observed. The 3-D translation and affine transformation model were found to be superior over the conventional FH translation model used today. Furthermore, a new approach is presented, which utilizes a fast model-based image registration to extract motion information from time series of low-resolution 3-D MR images, which reflects the respiratory motion of the heart. The registration is based on a selectable global 3-D motion model (translation, rigid, or affine transformation). All 3-D MR images were registered with respect to end expiration. The resulting time series of model parameters were analyzed in combination with additionally acquired motion information from a diaphragmatic MR pencil-beam navigator to calibrate the respiratory motion model. To demonstrate the potential of a calibrated motion model for prospective motion correction in coronary imaging, the approach was tested in CMRA examinations in five volunteers.