Elastic Registration Research Articles

A Nomogram to predict parotid gland overdose in head and neck IMRT.

PurposesTo generate a nomogram to predict parotid gland (PG) overdose and to quantify the dosimetric benefit of weekly replanning based on its findings, in the context of intensity-modulated radiotherapy (IMRT) for locally-advanced head and neck carcinoma (LAHNC).Material and methodsTwenty LAHNC patients treated with radical IMRT underwent weekly computed tomography (CT) scans during IMRT. The cumulated PG dose was estimated by elastic registration. Early predictors of PG overdose (cumulated minus planned doses) were identified, enabling a nomogram to be generated from a linear regression model. Its performance was evaluated using a leave-one-out method. The benefit of weekly replanning was then estimated for the nomogram-identified PG overdose patients.ResultsClinical target volume 70 (CTV70) and the mean PG dose calculated from the planning and first weekly CTs were early predictors of PG overdose, enabling a nomogram to be generated. A mean PG overdose of 2.5Gy was calculated for 16 patients, 14 identified by the nomogram. All patients with PG overdoses >1.5Gy were identified. Compared to the cumulated delivered dose, weekly replanning of these 14 targeted patients enabled a 3.3Gy decrease in the mean PG dose.ConclusionBased on the planning and first week CTs, our nomogram allowed the identification of all patients with PG overdoses >2.5Gy to be identified, who then benefitted from a final 4Gy decrease in mean PG overdose by means of weekly replanning.

Local analysis of strains and rotations for macromolecular electron microscopy maps.

Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the different areas of the protein. The analysis of these local deformations may reveal important insight into the way proteins perform their tasks. In this paper we introduce a method to perform this kind of local analysis using Electron Microscopy volumes in a fully objective and automatic manner. For doing so, we exploit the continuous nature of the result of an elastic image registration using B-splines as its basis functions. We show that the results obtained by the new automatic method are consistent with previous observations on these macromolecules.

Detailed Evaluation of Five 3D Speckle Tracking Algorithms Using Synthetic Echocardiographic Recordings.

A plethora of techniques for cardiac deformation imaging with 3D ultrasound, typically referred to as 3D speckle tracking techniques, are available from academia and industry. Although the benefits of single methods over alternative ones have been reported in separate publications, the intrinsic differences in the data and definitions used makes it hard to compare the relative performance of different solutions. To address this issue, we have recently proposed a framework to simulate realistic 3D echocardiographic recordings and used it to generate a common set of ground-truth data for 3D speckle tracking algorithms, which was made available online. The aim of this study was therefore to use the newly developed database to contrast non-commercial speckle tracking solutions from research groups with leading expertise in the field. The five techniques involved cover the most representative families of existing approaches, namely block-matching, radio-frequency tracking, optical flow and elastic image registration. The techniques were contrasted in terms of tracking and strain accuracy. The feasibility of the obtained strain measurements to diagnose pathology was also tested for ischemia and dyssynchrony.

4D interventional device reconstruction from biplane fluoroscopy.

Biplane angiography systems provide time resolved 2D fluoroscopic images from two different angles, which can be used for the positioning of interventional devices such as guidewires and catheters. The purpose of this work is to provide a novel algorithm framework, which allows the 3D reconstruction of these curvilinear devices from the 2D projection images for each time frame. This would allow creating virtual projection images from arbitrary view angles without changing the position of the gantries, as well as virtual endoscopic 3D renderings. The first frame of each time sequence is registered to and subtracted from the following frame using an elastic grid registration technique. The images are then preprocessed by a noise reduction algorithm using directional adaptive filter kernels and a ridgeness filter that emphasizes curvilinear structures. A threshold based segmentation of the device is then performed, followed by a flux driven topology preserving thinning algorithm to extract the segments of the device centerline. The exact device path is determined using Dijkstra's algorithm to minimize the curvature and distance between adjacent segments as well as the difference to the device path of the previous frame. The 3D device centerline is then reconstructed using epipolar geometry. The accuracy of the reconstruction was measured in a vascular head phantom as well as in a cadaver head and a canine study. The device reconstructions are compared to rotational 3D acquisitions. In the phantom experiments, an average device tip accuracy of 0.35 ± 0.09 mm, a Hausdorff distance of 0.65 ± 0.32 mm, and a mean device distance of 0.54 ± 0.33 mm were achieved. In the cadaver head and canine experiments, the device tip was reconstructed with an average accuracy of 0.26 ± 0.20 mm, a Hausdorff distance of 0.62 ± 0.08 mm, and a mean device distance of 0.41 ± 0.08 mm. Additionally, retrospective reconstruction results of real patient data are presented. The presented algorithm is a novel approach for the time resolved 3D reconstruction of interventional devices from biplane fluoroscopic images, thus allowing the creation of virtual projection images from arbitrary view angles as well as virtual endoscopic 3D renderings. Availability of this technique would enhance the ability to accurately position devices in minimally invasive endovascular procedures.

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks.

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states.

Efficient Morphometric Techniques in Alzheimer’s Disease Detection: Survey and Tools

The development of advance techniques in the multiple fields such as image processing, data mining and machine learning are required for the early detection of Alzheimer’s Disease (AD) and to prevent the progression of the disease to the later stages. The longitudinal and cross sectional images of elderly subjects were obtained from the standard datasets like ADNI, OASIS, MIRIAD and ICBM. The subject image obtained from the dataset, can be geometrically aligned to the template image through the process of registration. The registration techniques like Mutual Information Registration, Fluid registration, Rigid registration, Spatial Transformation algorithm for registration, Elastic Registration are selected based on type of transformation and similarity measures to suit the required application. The registered images are then subjected to the process of segmentation in order to segment relevant tissues or desired region of interest that are significant in AD detection. The different types of segmentation techniques such as Tissue Segmentation, Atlas based Segmentation, Hippocampus Segmentation and other segmentation techniques have been discussed. The segmented images are then subjected to morphometry techniques to identify the morphological changes developed in an abnormal image. The different types of morphometry techniques used are Voxel Based Morphometry (VBM), Deformation Based Morphometry (DBM), Shape Based Morphometry (SBM) and Feature Based Morphometry (FBM). But in recent years, the main focus of researchers is towards the FBM and SBM to overcome the disadvantage of group analysis that existed in VBM and DBM. Further the data is classified into healthy normal and AD by supervised, unsupervised or probabilistic methods.

Automated brain region recognition based on elastic registration and atlas mapping

Automated brain region recognition based on elastic registration and atlas mapping

Multigrid solution of the nonlinear PDEs arising in elastic image registration with application to a group of monomodal images

Multigrid solution of the nonlinear PDEs arising in elastic image registration with application to a group of monomodal images

Discontinuity Preserving Image Registration through Motion Segmentation: A Primal-Dual Approach.

Image registration is a powerful tool in medical image analysis and facilitates the clinical routine in several aspects. There are many well established elastic registration methods, but none of them can so far preserve discontinuities in the displacement field. These discontinuities appear in particular at organ boundaries during the breathing induced organ motion. In this paper, we exploit the fact that motion segmentation could play a guiding role during discontinuity preserving registration. The motion segmentation is embedded in a continuous cut framework guaranteeing convexity for motion segmentation. Furthermore we show that a primal-dual method can be used to estimate a solution to this challenging variational problem. Experimental results are presented for MR images with apparent breathing induced sliding motion of the liver along the abdominal wall.

Atlas based brain volumetry: How to distinguish regional volume changes due to biological or physiological effects from inherent noise of the methodology

Fully-automated regional brain volumetry based on structural magnetic resonance imaging (MRI) plays an important role in quantitative neuroimaging. In clinical trials as well as in clinical routine multiple MRIs of individual patients at different time points need to be assessed longitudinally. Measures of inter- and intrascanner variability are crucial to understand the intrinsic variability of the method and to distinguish volume changes due to biological or physiological effects from inherent noise of the methodology.To measure regional brain volumes an atlas based volumetry (ABV) approach was deployed using a highly elastic registration framework and an anatomical atlas in a well-defined template space. We assessed inter- and intrascanner variability of the method in 51 cognitively normal subjects and 27 Alzheimer dementia (AD) patients from the Alzheimer's Disease Neuroimaging Initiative by studying volumetric results of repeated scans for 17 compartments and brain regions.Median percentage volume differences of scan–rescans from the same scanner ranged from 0.24% (whole brain parenchyma in healthy subjects) to 1.73% (occipital lobe white matter in AD), with generally higher differences in AD patients as compared to normal subjects (e.g., 1.01% vs. 0.78% for the hippocampus). Minimum percentage volume differences detectable with an error probability of 5% were in the one-digit percentage range for almost all structures investigated, with most of them being below 5%. Intrascanner variability was independent of magnetic field strength. The median interscanner variability was up to ten times higher than the intrascanner variability.

3D surface-based registration of ultrasound and histology in prostate cancer imaging

Several transrectal ultrasound (TRUS)-based techniques aiming at accurate localization of prostate cancer are emerging to improve diagnostics or to assist with focal therapy. However, precise validation prior to introduction into clinical practice is required. Histopathology after radical prostatectomy provides an excellent ground truth, but needs accurate registration with imaging. In this work, a 3D, surface-based, elastic registration method was developed to fuse TRUS images with histopathologic results. To maximize the applicability in clinical practice, no auxiliary sensors or dedicated hardware were used for the registration. The mean registration errors, measured in vitro and in vivo, were 1.5±0.2 and 2.1±0.5mm, respectively.

Deformable image registration with geometric changes

Geometric changes present a number of difficulties in deformable image registration. In this paper, we propose a global deformation framework to model geometric changes whilst promoting a smooth transformation between source and target images. To achieve this, we have developed an innovative model which significantly reduces the side effects of geometric changes in image registration, and thus improves the registration accuracy. Our key contribution is the introduction of a sparsity-inducing norm, which is typically L1 norm regularization targeting regions where geometric changes occur. This preserves the smoothness of global transformation by eliminating local transformation under different conditions. Numerical solutions are discussed and analyzed to guarantee the stability and fast convergence of our algorithm. To demonstrate the effectiveness and utility of this method, we evaluate it on both synthetic data and real data from traumatic brain injury (TBI). We show that the transformation estimated from our model is able to reconstruct the target image with lower instances of error than a standard elastic registration model.

Automatic detection of selective arterial devices for advanced visualization during abdominal aortic aneurysm endovascular repair

Here we address the automatic segmentation of endovascular devices used in the endovascular repair (EVAR) of abdominal aortic aneurysms (AAA) that deform vascular tissues. Using this approach, the vascular structure is automatically reshaped solving the issue of misregistration observed on 2D/3D image fusion for EVAR guidance. The endovascular devices we considered are the graduated pigtail catheter (PC) used for contrast injection and the stent-graft delivery device (DD). The segmentation of the DD was enhanced using an asymmetric Frangi filter. The segmented geometries were then analysed using their specific features to remove artefacts. The radiopaque markers of the PC were enhanced using a fusion of Hessian and newly introduced gradient norm shift filters. Extensive experiments were performed using a database of images taken during 28 AAA-EVAR interventions. This dataset was divided into two parts: the first half was used to optimize parameters and the second to compile performances using optimal values obtained. The radiopaque markers of the PC were detected with a sensitivity of 88.3% and a positive predictive value (PPV) of 96%. The PC can therefore be positioned with a majority of its markers localized while the artefacts were all located inside the vessel lumen. The major parts of the DD, the dilatator tip and the pusher surfaces, were detected accurately with a sensitivity of 85.9% and a PPV of 88.7%. The less visible part of the DD, the stent enclosed within the sheath, was segmented with a sensitivity of 63.4% because the radiopacity of this region is low and uneven. The centreline of the DD in this stent region was alternatively traced within a 0.74 mm mean error. The automatic segmentation of endovascular devices during EVAR is feasible and accurate; it could be useful to perform elastic registration of the vascular lumen during endovascular repair.

Bénéfice de la radiothérapie adaptative par bibliothèque de plans de traitement pour les cancers du col utérin ?

PurposeIn case of intensity-modulated radiotherapy (IMRT) for locally advanced cervix carcinoma, the objectives were to quantify the difference between the planned and the delivered doses by a standard irradiation, and to estimate the dosimetric benefit of a pretreatment planning library-based adaptive radiotherapy. Material and methodsTen patients with locally advanced cervix carcinoma had three planning CTs corresponding to three bladder volumes: empty, intermediate (vi) and full. On each CT, two IMRT plans were generated to deliver 45Gy to the planning target volume (PTV), with two different margins: clinical target volume (CTV)+10mm and CTV+15mm. Using bi-weekly CBCTs, three scenarios of treatment have been simulated and compared: standard IMRT (one vi planning) with 10 and 15mm margins and adaptive radiotherapy with 10mm margin. The cumulated dose in the organs at risk was estimated by elastic registration. ResultIn case of standard IMRT, the cumulated dose was significantly different than the planning dose, with an under-dose of the CTV and the bladder, and an over-dose of the rectum and the peritoneal cavity. For 54% of the fractions, the adaptive radiotherapy planning was not based on vi. Considering the cumulated dose and compared to IMRT with 10-mm margin, adaptive radiotherapy increased the dose to the CTV (1.4Gy for D98%) and decreased slightly the dose to the rectum and the peritoneal cavity. Compared to a standard IMRT with 15mm margin, adaptive radiotherapy decreased significantly the dose to the rectum (20% for V40), the bladder (13% for V40) and the peritoneal cavity (2% for V35). ConclusionA pretreatment planning library-based adaptive radiotherapy in cervix carcinoma decreases the dose to the organs at risk and increases the dose to the CTV.

Classified Scale-Invariant Feature Transform Feature Based Elastic Image Registration for 2-DE Gels

Classified Scale-Invariant Feature Transform Feature Based Elastic Image Registration for 2-DE Gels

Continuous ultrasound speckle tracking with Gaussian mixtures.

Speckle tracking echocardiography (STE) is now widely used for measuring strain, deformations, and motion in cardiology. STE involves three successive steps: acquisition of individual frames, speckle detection, and image registration using speckles as landmarks. This work proposes to avoid explicit detection and registration by representing dynamic ultrasound images as sparse collections of moving Gaussian elements in the continuous joint space-time space. Individual speckles or local clusters of speckles are approximated by a single multivariate Gaussian kernel with associated linear trajectory over a short time span. A hierarchical tree-structured model is fitted to sampled input data such that predicted image estimates can be retrieved by regression after reconstruction, allowing a (bias-variance) trade-off between model complexity and image resolution. The inverse image reconstruction problem is solved with an online Bayesian statistical estimation algorithm. Experiments on clinical data could estimate subtle sub-pixel accurate motion that is difficult to capture with frame-to-frame elastic image registration techniques.

Characterizing the DNA Damage Response by Cell Tracking Algorithms and Cell Features Classification Using High-Content Time-Lapse Analysis.

Traditionally, the kinetics of DNA repair have been estimated using immunocytochemistry by labeling proteins involved in the DNA damage response (DDR) with fluorescent markers in a fixed cell assay. However, detailed knowledge of DDR dynamics across multiple cell generations cannot be obtained using a limited number of fixed cell time-points. Here we report on the dynamics of 53BP1 radiation induced foci (RIF) across multiple cell generations using live cell imaging of non-malignant human mammary epithelial cells (MCF10A) expressing histone H2B-GFP and the DNA repair protein 53BP1-mCherry. Using automatic extraction of RIF imaging features and linear programming techniques, we were able to characterize detailed RIF kinetics for 24 hours before and 24 hours after exposure to low and high doses of ionizing radiation. High-content-analysis at the single cell level over hundreds of cells allows us to quantify precisely the dose dependence of 53BP1 protein production, RIF nuclear localization and RIF movement after exposure to X-ray. Using elastic registration techniques based on the nuclear pattern of individual cells, we could describe the motion of individual RIF precisely within the nucleus. We show that DNA repair occurs in a limited number of large domains, within which multiple small RIFs form, merge and/or resolve with random motion following normal diffusion law. Large foci formation is shown to be mainly happening through the merging of smaller RIF rather than through growth of an individual focus. We estimate repair domain sizes of 7.5 to 11 µm2 with a maximum number of ~15 domains per MCF10A cell. This work also highlights DDR which are specific to doses larger than 1 Gy such as rapid 53BP1 protein increase in the nucleus and foci diffusion rates that are significantly faster than for spontaneous foci movement. We hypothesize that RIF merging reflects a "stressed" DNA repair process that has been taken outside physiological conditions when too many DSB occur at once. High doses of ionizing radiation lead to RIF merging into repair domains which in turn increases DSB proximity and misrepair. Such finding may therefore be critical to explain the supralinear dose dependence for chromosomal rearrangement and cell death measured after exposure to ionizing radiation.

Estimation of intraoperative brain shift by combination of stereovision and doppler ultrasound: phantom and animal model study.

Combination of various intraoperative imaging modalities potentially can reduce error of brain shift estimation during neurosurgical operations. In the present work, a new combination of surface imaging and Doppler US images is proposed to calculate the displacements of cortical surface and deformation of internal vessels in order to estimate the targeted brain shift using a Finite Element Model (FEM). Registration error in each step and the overall performance of the method are evaluated. The preoperative steps include constructing a FEM from MR images and extracting vascular tree from MR Angiography (MRA). As the first intraoperative step, after the craniotomy and with the dura opened, a designed checkerboard pattern is projected on the cortex surface and projected landmarks are scanned and captured by a stereo camera (Int J Imaging Syst Technol 23(4):294-303, 2013. doi: 10.1002/ima.22064 ). This 3D point cloud should be registered to boundary nodes of FEM in the region of interest. For this purpose, we developed a new non-rigid registration method, called finite element drift that is more compatible with the underlying nature of deformed object. The presented algorithm outperforms other methods such as coherent point drift when the deformation is local or non-coherent. After registration, the acquired displacement vectors are used as boundary conditions for FE model. As the second step, by tracking a 2D Doppler ultrasound probe swept on the parenchyma, a 3D image of deformed vascular tree is constructed. Elastic registration of this vascular point cloud to the corresponding preoperative data results the second series of displacement vector applicable to closest internal nodes of FEM. After running FE analysis, the displacement of all nodes is calculated. The brain shift is then estimated as displacement of nodes in boundary of a deep target, e.g., a tumor. We used intraoperative MR (iMR) images as the references for measuring the performance of the brain shift estimator. In the present study, two set of tests were performed using: (a) a deformable brain phantom with surface data and (b) an alive brain of an approximately big dog with surface data and US Doppler images. In our designed phantom, small tubes connected to an inflatable balloon were considered as displaceable targets and in the animal model, the target was modeled by a cyst which was created by an injection. In the phantom study, the registration error for the surface points before FE analysis and for the target points after running FE model were <0.76 and 1.4 mm, respectively. In a real condition of operating room for animal model, the registration error was about 1 mm for the surface, 1.9 mm for the vascular tree and 1.55 mm for the target points. The proposed projected surface imaging in conjunction with the Doppler US data combined in a powerful biomechanical model can result an acceptable performance in calculation of deformation during surgical navigation. However, the projected landmark method is sensitive to ambient light and surface conditions and the Doppler ultrasound suffers from noise and 3D image construction problems, the combination of these two methods applied on a FEM has an eligible performance.

Skuller: A volumetric shape registration algorithm for modeling skull deformities.

We present an algorithm for volumetric registration of 3D solid shapes. In comparison to previous work on image based registration, our technique achieves higher efficiency by leveraging a template tetrahedral mesh. In contrast to point- and surface-based registration techniques, our method better captures volumetric nature of the data, such as bone thickness. We apply our algorithm to study pathological skull deformities caused by a particular condition, i.e., craniosynostosis. The input to our system is a pair of volumetric 3D shapes: a tetrahedral mesh and a voxelized object represented by a set of voxel cells segmented from computed tomography (CT) scans. Our general framework first performs a global registration and then launches a novel elastic registration process that uses as much volumetric information as possible while deforming the generic template tetrahedral mesh of a healthy human skull towards the underlying geometry of the voxel cells. Both data are high-resolution and differ by large non-rigid deformations. Our fully-automatic solution is fast and accurate, as compared with the state of the arts from the reconstruction and medical image registration fields. We use the resulting registration to match the ground-truth surfaces extracted from the medical data as well as to quantify the severity of the anatomical deformity.

Multiattribute probabilistic prostate elastic registration (MAPPER): application to fusion of ultrasound and magnetic resonance imaging.

Transrectal ultrasound (TRUS)-guided needle biopsy is the current gold standard for prostate cancer diagnosis. However, up to 40% of prostate cancer lesions appears isoechoic on TRUS. Hence, TRUS-guided biopsy has a high false negative rate for prostate cancer diagnosis. Magnetic resonance imaging (MRI) is better able to distinguish prostate cancer from benign tissue. However, MRI-guided biopsy requires special equipment and training and a longer procedure time. MRI-TRUS fusion, where MRI is acquired preoperatively and then aligned to TRUS, allows for advantages of both modalities to be leveraged during biopsy. MRI-TRUS-guided biopsy increases the yield of cancer positive biopsies. In this work, the authors present multiattribute probabilistic postate elastic registration (MAPPER) to align prostate MRI and TRUS imagery. MAPPER involves (1) segmenting the prostate on MRI, (2) calculating a multiattribute probabilistic map of prostate location on TRUS, and (3) maximizing overlap between the prostate segmentation on MRI and the multiattribute probabilistic map on TRUS, thereby driving registration of MRI onto TRUS. MAPPER represents a significant advancement over the current state-of-the-art as it requires no user interaction during the biopsy procedure by leveraging texture and spatial information to determine the prostate location on TRUS. Although MAPPER requires manual interaction to segment the prostate on MRI, this step is performed prior to biopsy and will not substantially increase biopsy procedure time. MAPPER was evaluated on 13 patient studies from two independent datasets—Dataset 1 has 6 studies acquired with a side-firing TRUS probe and a 1.5 T pelvic phased-array coil MRI; Dataset 2 has 7 studies acquired with a volumetric end-firing TRUS probe and a 3.0 T endorectal coil MRI. MAPPER has a root-mean-square error (RMSE) for expert selected fiducials of 3.36 ± 1.10 mm for Dataset 1 and 3.14 ± 0.75 mm for Dataset 2. State-of-the-art MRI-TRUS fusion methods report RMSE of 3.06-2.07 mm. MAPPER aligns MRI and TRUS imagery without manual intervention ensuring efficient, reproducible registration. MAPPER has a similar RMSE to state-of-the-art methods that require manual intervention.