Freehand 3D Research Articles

Soft tissue deformation for surgical simulation: a position-based dynamics approach

PurposeTo assist the rehearsal and planning of robot-assisted partial nephrectomy, a real-time simulation platform is presented that allows surgeons to visualise and interact with rapidly constructed patient-specific biomechanical models of the anatomical regions of interest. Coupled to a framework for volumetric deformation, the platform furthermore simulates intracorporeal 2D ultrasound image acquisition, using preoperative imaging as the data source. This not only facilitates the planning of optimal transducer trajectories and viewpoints, but can also act as a validation context for manually operated freehand 3D acquisitions and reconstructions.MethodsThe simulation platform was implemented within the GPU-accelerated NVIDIA FleX position-based dynamics framework. In order to validate the model and determine material properties and other simulation parameter values, a porcine kidney with embedded fiducial beads was CT-scanned and segmented. Acquisitions for the rest position and three different levels of probe-induced deformation were collected. Optimal values of the cluster stiffness coefficients were determined for a range of different particle radii, where the objective function comprised the mean distance error between real and simulated fiducial positions over the sequence of deformations.ResultsThe mean fiducial error at each deformation stage was found to be compatible with the level of ultrasound probe calibration error typically observed in clinical practice. Furthermore, the simulation exhibited unconditional stability on account of its use of clustered shape-matching constraints.ConclusionsA novel position-based dynamics implementation of soft tissue deformation has been shown to facilitate several desirable simulation characteristics: real-time performance, unconditional stability, rapid model construction enabling patient-specific behaviour and accuracy with respect to reference CT images.Electronic supplementary materialThe online version of this article (doi:10.1007/s11548-016-1373-8) contains supplementary material, which is available to authorized users.

Defining the medial-lateral axis of an anatomical femur coordinate system using freehand 3D ultrasound imaging

Hip rotation from gait analysis informs clinical decisions regarding correction of femoral torsional deformities. However, it is among the least repeatable due to discrepancies in determining the medial-lateral axis of the femur. Conventional or functional calibration methods may be used to define the axis but there is no benchmark to evaluate these methods. Freehand 3D ultrasound, the coupling of ultrasound with 3D motion capture, may provide such a benchmark.We measured the accuracy in vitro and repeatability in vivo of determining the femur condylar axis from freehand 3D ultrasound. The condylar axis provided the reference medial-lateral axis of the femur and was used to evaluate one conventional method and three functional calibration methods, applied to three calibration movements. Ten healthy subjects (20 limbs) underwent 3D gait analysis and freehand 3D ultrasound. The functional calibration methods were a transformation technique, a geometrical method and a method that minimises variance of knee varus-valgus kinematics (DynaKAD). The conventional method used markers over the femoral epicondyles.The condylar axis determined by 3D ultrasound showed good accuracy in vitro, 1.6° (SD: 0.3°) and good repeatability in vivo, 0.2° (RSMD: 2.3°). The DynaKAD method applied to the walking calibration movement determined the medial-lateral axis closest to the ultrasound reference. The average angular difference in the transverse plane was 3.1° (SD: 6.1°).Freehand 3D ultrasound offers an accurate, non-invasive and relatively fast method to locate the medial-lateral axis of the femur for gait analysis.

GPU-based real-time generation of large ultrasound volumes from freehand 3D sweeps

Abstract In the recent past, 3D ultrasound has been gaining relevance in many biomedical applications. One main limitation, however, is that typical ultrasound volumes are either very poorly resolved or only cover small areas. We have developed a GPU-accelerated method for live fusion of freehand 3D ultrasound sweeps to create one large volume. The method has been implemented in CUDA and is capable of generating an output volume with 0.5 mm resolution in real time while processing more than 45 volumes per second, with more than 300.000 voxels per volume. First experiments indicate that large structures like a whole forearm or high-resolution volumes of smaller structures like the hand can be combined efficiently. It is anticipated that this technology will be helpful in pediatric surgery where X-ray or CT imaging is not always possible.

Reliability and validity of 3D freehand ultrasound

Reliability and validity of 3D freehand ultrasound

A novel Bayesian-based nonlocal reconstruction method for freehand 3D ultrasound imaging

Freehand three-dimensional (3D) ultrasound imaging is an important medical imaging modality in computer-assisted clinical diagnosis and image-guided intervention. In this paper, we present a novel Bayesian-based nonlocal method for the accurate volume reconstruction of freehand 3D ultrasound imaging with irregularly spaced B-scans. In the algorithm, each pixel is represented as the Gamma distribution which corresponds to the speckle noise generated by the interaction of the acoustic wave with the tissues. The variational reconstruction functional is associated with a nonlocal denoising term and a nonlocal inpainting term. To suppress speckle noise in the ultrasound image, the observed data is filtered via nonlocal total variation method firstly. The nonlocal denoising model is adapted to the speckle noise by substituting the Pearson distance-based weight function for the Gaussian weight function. To interpolate the missing data, a new inpainting scheme derived from the nonlocal means filter and its implementation based on fast marching method are introduced to fill the empty regions. This makes interpolation of missing data more accurate and effective. The Pearson distance function derived from the Bayesian estimator is not only used for speckle reduction, but also serves as weight function for building nonlocal means-based inpainting algorithm. Experimental results on synthetic cube data, in-vitro ultrasound abdominal phantom and in-vivo liver of human subject and comparisons with some classical and recent algorithms are used to demonstrate its improvement in both speckle suppression and edge preservation in 3D ultrasound reconstruction.

Three-dimensional morphology and strain of the human Achilles free tendon immediately following eccentric heel drop exercise.

Our understanding of the immediate effects of exercise on Achilles free tendon transverse morphology is limited to single site measurements acquired at rest using 2D ultrasound. The purpose of this study was to provide a detailed 3D description of changes in Achilles free tendon morphology immediately following a single clinical bout of exercise. Freehand 3D ultrasound was used to measure Achilles free tendon length, and regional cross-sectional area (CSA), medio-lateral (ML) diameter and antero-posterior (AP) diameter in healthy young adults (N=14) at rest and during isometric muscle contraction, immediately before and after 3×15 eccentric heel drops. Post-exercise reductions in transverse strain were limited to CSA and AP diameter in the mid-proximal region of the Achilles free tendon during muscle contraction. The change in CSA strain during muscle contraction was significantly correlated to the change in longitudinal strain (r=-0.72) and the change in AP diameter strain (r=0.64). Overall findings suggest the Achilles free tendon experiences a complex change in 3D morphology following eccentric heel drop exercise that manifests under contractile but not rest conditions, is most pronounced in the mid-proximal tendon and is primarily driven by changes in AP diameter strain and not ML diameter strain.

Freehand sketching and 3D modeling commands correlation studies

Freehand sketching and 3D modeling commands correlation studies

Reconstruction of freehand 3D ultrasound based on kernel regression.

IntroductionFreehand three-dimensional (3D) ultrasound has the advantages of flexibility for allowing clinicians to manipulate the ultrasound probe over the examined body surface with less constraint in comparison with other scanning protocols. Thus it is widely used in clinical diagnose and image-guided surgery. However, as the data scanning of freehand–style is subjective, the collected B-scan images are usually irregular and highly sparse. One of the key procedures in freehand ultrasound imaging system is the volume reconstruction, which plays an important role in improving the reconstructed image quality.System and methodsA novel freehand 3D ultrasound volume reconstruction method based on kernel regression model is proposed in this paper. Our method consists of two steps: bin-filling and regression. Firstly, the bin-filling step is used to map each pixel in the sampled B-scan images to its corresponding voxel in the reconstructed volume data. Secondly, the regression step is used to make the nonparametric estimation for the whole volume data from the previous sampled sparse data. The kernel penalizes distance away from the current approximation center within a local neighborhood.Experiments and resultsTo evaluate the quality and performance of our proposed kernel regression algorithm for freehand 3D ultrasound reconstruction, a phantom and an in-vivo liver organ of human subject are scanned with our freehand 3D ultrasound imaging system. Root mean square error (RMSE) is used for the quantitative evaluation. Both of the qualitative and quantitative experimental results demonstrate that our method can reconstruct image with less artifacts and higher quality.ConclusionThe proposed kernel regression based reconstruction method is capable of constructing volume data with improved accuracy from irregularly sampled sparse data for freehand 3D ultrasound imaging system.

Technical Note: Millimeter precision in ultrasound based patient positioning: experimental quantification of inherent technical limitations.

To identify the relevant technical sources of error of a system based on three-dimensional ultrasound (3D US) for patient positioning in external beam radiotherapy. To quantify these sources of error in a controlled laboratory setting. To estimate the resulting end-to-end geometric precision of the intramodality protocol. Two identical free-hand 3D US systems at both the planning-CT and the treatment room were calibrated to the laboratory frame of reference. Every step of the calibration chain was repeated multiple times to estimate its contribution to overall systematic and random error. Optimal margins were computed given the identified and quantified systematic and random errors. In descending order of magnitude, the identified and quantified sources of error were: alignment of calibration phantom to laser marks 0.78 mm, alignment of lasers in treatment vs planning room 0.51 mm, calibration and tracking of 3D US probe 0.49 mm, alignment of stereoscopic infrared camera to calibration phantom 0.03 mm. Under ideal laboratory conditions, these errors are expected to limit ultrasound-based positioning to an accuracy of 1.05 mm radially. The investigated 3D ultrasound system achieves an intramodal accuracy of about 1 mm radially in a controlled laboratory setting. The identified systematic and random errors require an optimal clinical tumor volume to planning target volume margin of about 3 mm. These inherent technical limitations do not prevent clinical use, including hypofractionation or stereotactic body radiation therapy.

A Freehand 3D Ultrasound Imaging System using Open-Source Software Tools with Improved Edge-Preserving Interpolation

Ultrasound imaging is widely employed in various medical procedures. Most ultrasound procedures are performed with conventional 2D ultrasound systems, but visualizing the 3D anatomy using 2D ultrasound images is often challenging. This paper describes the use of open-source software tools to develop a freehand system for synthesizing high-quality 3D ultrasound volumes using electromagnetic tracking. In the proposed system, the spatial transformation between the 2D ultrasound images and the electromagnetic sensor attached to the ultrasound transducer was performed using an accurate spatial calibration method. A new interpolation method, called the edge-preserving distance-weighted (EPDW), is employed to reconstruct the 3D ultrasound volumes. The performance of the system is evaluated by performing a set of phantom experiments. The results showed that the reconstructed 3D ultrasound volumes have sub-millimeter accuracy. Moreover, the ultrasound volumes synthesized using the EPDW method demonstrated improved edge preservation compared with a previous interpolation method.

Behavioral-model-based freehand tracking in a Selection-Move-Release system

The development of three dimensional (3D) freehand tracking is motivated by the need for 3D freehand-based human computer interface in the Selection-Move-Release (SMR) system. The high dimensionality of articulated hand models is one of the major obstacles for tracking 3D hand in real time. A practical Task-Phase-Trajectory-Mentality (TPTM) model for the SMR system is built and a novel freehand tracking algorithm is introduced by using a camera that is calibrated by a charge-coupled device. The TPTM model is proposed and explained based on the cognitive theory in the proposed method. The manner by which the TPTM model guides the realtime design of freehand tracking is also shown. The proposed method reduces the high dimensionality down to eight degrees of freedom (DOF), optimizes the dynamic number of particles for each frame, and achieves realtime hand tracking and high accuracy of 3D full DOF hand gestures. The algorithm presented in this paper is successfully applied to a 3D virtual teaching system.

What does it take to walk normally with high femoral neck anteversion?—A case study

[1] SangeuxM, et al. Dophysical examination andCT-scanmeasures of femoral neck anteversion and tibial torsion relate to each other? ESMAC 2012. [2] Miller F, et al. Femoral version and neck shaft angle. J Pediatr Orthop 1993;13(3):382–8. [3] Peters A, et al. Validation of 3-D freehand ultrasound for the determination of the hip joint centre. Gait Posture 2010;31(4):530–2. [4] Gee A, et al. Stradwin, a tool for freehand 3D ultrasound calibration, acquisition, measurement and visualisation. Medical Imaging group at the Department of Engineering, University of Cambridge, UK. [5] Murphy SB, et al. Femoral anteversion. J Bone Joint Surg Am Vol 1987;69(8):1169–76. [6] Fedorov A, et al. 3D Slicer as an image computing platform for the Quantitative Imaging Network. Magn Reson Imaging 2012;30(9):1323–41.

Measuring femoral neck anteversion—Validation of a technique based on 3D freehand ultrasound

s / Gait & Posture 39S (2014) S1–S141 S53 Fig. 1. Change in GPS after 2y ML surgery vs baseline GPS. (age 6–24yrs), who could walk independently or with aids, had undergone SEMLS at our hospital, and had a pre-op as well as post-op gait analysis at around two years following surgery (conventional gait model). The Gait Profile Score (GPS) [2] was selected as a primary outcomemeasure. Predictor variables included (1) age at surgery, (2) pre-opGPS, (3) unilateral or bilateral surgery, and (4) soft tissueonlyorother surgery. Regressionanalysiswasperformed with significance set at p<0.05. Predictor variables were compared to both the post op GPS, as well as the change in GPS compared to pre-op. Results: Overall, 75% of patients demonstrated improvement that exceeded theMCID of 1.6◦, while only 2% deteriorated according to the same criteria. The average improvement in GPS was 3.2◦. Pre-op GPS was found to be the strongest predictor of change (b=0.57, p<0.001) (Fig. 1). It was also found to be a significantly associated with absolute GPS post-op (p<0.001). Age at surgery was found to be a significant predictor of change (p=0.02), but not absolute GPS following surgery (p=0.61). Bilateral compared to unilateral surgery was associated with a greater change (p=0.001) but post-op GPS was not significantly correlated (p=0.01). While the soft tissue surgery subjects, when compared to other surgeries,wasnot a significant predictor of change (p=0.60) or outcome (p=0.37). Discussion and conclusions: This study builds on previous work conducted elsewhere [3] which assessed outcomes one year following SEMLS, and confirms that pre-op GPS is the strongest predictor of improvement. The work presented here shows that this is maintained up to two years following surgery. In addition, pre-op GPS was demonstrated here to be a good predictor of absolute GPS post op. Significant correlation of change, but not final GPS, with bilateral/unilateral surgery would suggest this is related to severity of involvement. Interestingly, the same trend was not observed where soft tissue only surgery was performed, however this may be related to the relatively small sample size (around 10% of patients). Encouragingly, the vast majority of subjects improved following SEMLS by an average of 3.2◦, and this trend was maintained over a significant period of time. Based on the findings of this study the expected change in GPS following SEMLS can be approximated by the following equation: GPS Improvement = (0.6×pre-op GPS)− (0.1× age)−2.6. Reference [1] Thomason, et al. JBJS(A) 2014;93:451–60 [in press]. [2] Baker, et al. Gait Posture 2014;30:265–9 [in press]. [3] Rutz, et al. Gait Posture 2014;36:S6 [in press]. http://dx.doi.org/10.1016/j.gaitpost.2014.04.073

Freehand 3D Ultrasound to Measure Thrombus Volume in Patients with Acute Deep-Vein Thrombosis

Objective —Current imaging techniques are limited in their ability to quantify thrombus burden, progression, or resolution in patients with acute deep-vein thrombosis (DVT). These assessments are critical measures of therapeutic success when thrombolytic or thrombectomy treatment protocols are used for DVT. We have developed a novel freehand three-dimensional (3D) ultrasound method to measure thrombus volume. In this study, we evaluated the reliability of this new technology. Methods —We studied consecutive hospital inpatients with a first episode of acute DVT. Treatment decisions were not influenced by the study protocol. A combination of routine imaging in grayscale, color-flow, and power-Doppler modes along-with freehand 3D volumetric imaging with a linear transducer attached to an external tracking sensor was performed using a personal computer–based ultrasound scanner. Image-processing software loaded on the personal computer was used to process and reconstruct the serial cross-sectional images of the affected veins and outlined thrombus into a composite 3D image. Imaging and processing was performed twice by one sonographer, and repeated once by another sonographer. Results —The mean age of patients was 56.7 ± 15 years; 40% were women. A total of 70% of DVTs were in the lower extremity and 60% received anticoagulation. Thrombus volume was reliably determined by our protocol. The mean inter- and intraobserver differences in measurements were −0.09 ± 0.59 cm3 and 0.23 ± 0.43 cm3 (mean ± SD), which were well within 2 SD (Bland Altman statistics) of the mean volumes. Measurements of the second sonographer correlated well with those of the first (regression slope = 0.95 ± 0.07, p = 0.001) and those of the first observation correlated with the second observation performed by the same sonographer (regression slope = 0.91 ± 0.03, p = 0.001). Interrater agreement was good between the two sonographers (kappa = 0.71) and between two measurements by the same sonographer (kappa = 0.82). Conclusions —We have developed a novel freehand 3D-ultrasound imaging technique and protocol that reliably measures venous thrombus volume. There is good agreement in measurements between two observers and repeated measurements by one observer. The technique can be readily adapted for routine clinical practice. This protocol will be of increasing value as the appreciation for the deleterious effects of residual thrombus after DVT increases; and the use of aggressive thrombus removal treatments for acute DVT increases.

FhSPECT-US guided needle biopsy of sentinel lymph nodes in the axilla: is it feasible?

Until now, core needle biopsy of the axillary sentinel lymph nodes in early stage breast cancer patients is not possible, due to the lack of a proper combination of functional and anatomical information. In this work we present the first fully 3D freehand SPECT--ultrasound fusion, combining the advantages of both modalities. By using spatial positioning either with optical or with electromagnetic tracking for the ultrasound probe, and a mini gamma camera as radiation detector for freehand SPECT reconstructions, we investigate the capability of the introduced multi-model imaging system, where we compare both 3D freehand SPECT and 3D ultrasound to ground truth for a realistic breast mimicking phantom and further analyze the effect of tissue deformation by ultrasound. Finally, we also show its application in a real clinical setting.

Probe localization for freehand 3D ultrasound by tracking skin features.

Ultrasound probe localization with respect to the patient's body is essential for freehand three-dimensional ultrasound and image-guided intervention. However, current methods for probe localization generally involve bulky and expensive equipment. In this paper, a highly cost-effective and miniature-mobile system is described for 6-DoF probe localization that is robust to rigid patient motion. In this system, skin features in the scan region are recorded at each ultrasound scan acquisition by a lightweight camera rigidly mounted to the probe. A skin map is built based on the skin features and optimal probe poses are estimated in a Bayesian probabilistic framework that incorporates a prior motion model, camera frames, and ultrasound scans. Through freehand scanning on three different body parts, it is shown that on average, for every probe travel distance of 10 mm, the translational and rotational errors are 0.91 ± 0.49 mm and 0.55 degrees ± 0.17 degrees, respectively. The 3D reconstructions were also validated by comparison with real ultrasound scans.

3D free hand reconstruction in endosonography - is there some value for the gastroenterologist?

Purpose: 3D reconstruction in endosonography is a new tool for endoscopists. However because of the free hand reconstruction technique measurements cannot be done and therefore the scientific value is limited. This case control study should give an impression about the possibilities of the method and the future perspectives.

An accurate and effective FMM-based approach for freehand 3D ultrasound reconstruction

Freehand three-dimensional ultrasound imaging is a highly attractive research area because it is capable of volumetric visualization and analysis of tissues and organs. The reconstruction algorithm plays a key role to the construction of three-dimensional ultrasound volume data with higher image quality and faster reconstruction speed. However, a systematic approach to such problem is still missing. A new fast marching method (FMM) for three-dimensional ultrasound volume reconstruction using the tracked and hand-held probe is proposed in this paper. Our reconstruction approach consists of two stages: bin-filling stage and hole-filling stage. Each pixel in the B-scan images is traversed and its intensity value is assigned to its nearest voxel in the bin-filling stage. For the efficient and accurate reconstruction, we present a new hole-filling algorithm based on the fast marching method. Our algorithm advances the interpolation boundary along its normal direction and fills the area closest to known voxel points in first, which ensure that the structural details of image can be preserved. Experimental results on both ultrasonic abdominal phantom and in vivo urinary bladder of human subject and comparisons with some popular algorithms are used to demonstrate its improvement in both reconstruction accuracy and efficiency.

Surface Reconstruction from Sparse and Arbitrarily Oriented Contours in Freehand 3D Ultrasound

3D reconstruction for freehand 3D ultrasound is a challenging issue because the recorded B-scans are not only sparse, but also non-parallel (actually they may arbitrarily orient in 3D space and may intersect each other). Conventional volume reconstruction methods can’t reconstruct sparse data efficiently while not introducing geometrical artifacts and conventional surface reconstruction methods can’t reconstruct surfaces from contours that are arbitrarily oriented in 3D space. We developed a new surface reconstruction method for freehand 3D ultrasound based on variational implicit function which is presented by Greg Turk for shape transformation. In the new method, we first constructed on- and off-surface constraints from the segmented contours of all recorded B-scans and then used a variational interpolation technique to get a single implicit function in 3D. Finally, the implicit function was evaluated to extract the zero-valued surface as final reconstruction result. Two experiments was conducted to assess our variational surface reconstruction method and the experiment results have shown that the new method is capable of reconstructing surface smoothly from sparse contours which can be arbitrarily oriented in 3D space.

Surface Reconstruction from Sparse & Arbitrarily Oriented Contours in Freehand 3D Ultrasound

3D reconstruction for freehand 3D ultrasound is a challenging issue because the recorded B-scans are not only sparse, but also non-parallel (actually they may arbitrarily oriented in 3D space and may intersect each other). Conventional volume reconstruction methods can’t reconstruct sparse data efficiently while not introducing geometrical artifacts, and conventional surface reconstruction methods can’t reconstruct surfaces from contours that are arbitrarily oriented in 3D space. We developed a new surface reconstruction method for freehand 3D ultrasound based on variational implicit function which is presented by Greg Turk for shape transformation. In the new method, we first constructed on- & off-surface constraints from the segmented contours of all recorded B-scans, then used a variational interpolation technique to get a single implicit function in 3D. Finally, the implicit function was evaluated to extract the zero-valued surface as final reconstruction result. Two experiment was conducted to assess our variational surface reconstruction method, and the experiment results have shown that the new method is capable of reconstructing surface smoothly from sparse contours which can be arbitrarily oriented in 3D space.