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Orcun Goksel |
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Currently at: http://www.vision.ee.ethz.ch/~ogoksel/ |
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Post-doctoral Fellow in Robotics and Control Lab., ECE, UBC (2010 Jan-Dec) |
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= Variational Image Meshing (VIM) =This is the implementation of the meshing technique presented in [Goksel & Salcudean, ``Image-Based Variational Meshing'' IEEE TMI, 2011]. It uses an optimization scheme to generate meshes (specifically for FEM simulation) by discretizing given 3D voxel data such as medical images.The application executable, Matlab files for sample mesh generation, and a help file can be downloaded at the link below:
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| Journal Articles: |
| Jeffrey M. Abeysekera, Reza Zahiri-Azar, Orcun Goksel, Robert Rohling, and Septimiu E. Salcudean, "Analysis of 2-D Motion Tracking in Ultrasound with Dual Transducers", Ultrasonics, 2011, online pre-print |
| Abstract: We study displacement and strain measurement error of dual transducers (two linear arrays, aligned orthogonally and coplanar). Displacements along the beam of each transducer are used to obtain measurements in two-dimensions. Simulations (5 MHz) and experiments (10 MHz) are compared to measurements with a single linear array, with and without angular compounding. Translation simulations demonstrate factors of 1.07 larger and 8 smaller biases in the axial and lateral directions respectively, for dual transducers compared to angular compounding. As the angle between dual transducers decreases from 90 to 40 degrees, for 1% compression simulations, the lateral RMS error ranges from 2.1-3.9 microns compared to 9 microns with angular compounding. Simulation of dual transducer misalignment of 1 mm and 2 degrees result in errors of less than 9 microns. Experiments demonstrate factors of 3.0 and 5.2 lower biases for dual transducers in the axial and lateral directions respectively compared to angular compounding. |
BibTeX:
@article{Abeysekera_analysis_11,
author = {Jeffrey M. Abeysekera and Reza Zahiri-Azar and Orcun Goksel and Robert Rohling and Septimiu E. Salcudean},
title = {Analysis of 2-D Motion Tracking in Ultrasound with Dual Transducers},
journal = {Ultrasonics},
year = {2011},
volume = {in press},
pages = {online},
doi = {http://dx.doi.org/10.1016/j.ultras.2011.07.011}
}
|
| Orcun Goksel, Kirill Sapchuk, and Septimiu E. Salcudean, "Haptic Simulator for Prostate Brachytherapy with Simulated Needle and Probe Interaction", IEEE Transactions on Haptics 4(3):188-198, 2011. |
| Abstract: This paper presents a haptic simulator for prostate brachytherapy. Both needle insertion and the manipulation of the transrectal ultrasound (TRUS) probe are controlled via haptic devices. Tissue interaction forces that are computed by a deformable tissue model based on the finite element method (FEM) are rendered to the user by these devices. The needle insertion simulation employs 3D models of needle flexibility and asymmetric tip bevel. The needle-tissue simulation allows a trainee to practice needle insertion and targeting. The TRUS-tissue interaction simulation allows a trainee to practice the 3D intraoperative TRUS placement for registration with the preoperative volume study and to practice TRUS axial translation and rotation for imaging needles during insertions. Approaches to computational acceleration for real-time haptic performance are presented. Trade-offs between accuracy and speed are discussed. A graphics-card implementation of the numerically intensive mesh-adaptation operation is also presented. The simulator can be used for training, rehearsal, and treatment planning. |
BibTeX:
@article{Goksel_haptic_11,
author = {Orcun Goksel and Kirill Sapchuk and Septimiu E. Salcudean},
title = {Haptic Simulator for Prostate Brachytherapy with Simulated Needle and Probe Interaction},
journal = {IEEE Transactions on Haptics},
year = {2011},
volume = {4},
number = {3},
pages = {188-198},
doi = {http://dx.doi.org/10.1109/TOH.2011.34}
}
|
| Abstract: This paper presents a haptic simulator for prostate brachytherapy. Both needle insertion and the manipulation of the transrectal ultrasound (TRUS) probe are controlled via haptic devices. Tissue interaction forces that are computed by a deformable tissue model based on the finite element method (FEM) are rendered to the user by these devices. The needle insertion simulation employs 3D models of needle flexibility and asymmetric tip bevel. The needle-tissue simulation allows a trainee to practice needle insertion and targeting. The TRUS-tissue interaction simulation allows a trainee to practice the 3D intraoperative TRUS placement for registration with the preoperative volume study and to practice TRUS axial translation and rotation for imaging needles during insertions. Approaches to computational acceleration for real-time haptic performance are presented. Trade-offs between accuracy and speed are discussed. A graphics-card implementation of the numerically intensive mesh-adaptation operation is also presented. The simulator can be used for training, rehearsal, and treatment planning. |
BibTeX:
@article{Goksel_haptic_11,
author = {Orcun Goksel and Kirill Sapchuk and Septimiu E. Salcudean},
title = {Haptic Simulator for Prostate Brachytherapy with Simulated Needle and Probe Interaction},
journal = {IEEE Transactions on Haptics},
year = {2011},
volume = {in press},
pages = {online},
doi = {http://dx.doi.org/10.1109/TOH.2011.34}
}
|
| Hani Eskandari, Orcun Goksel, Septimiu E. Salcudean, and Robert Rohling, "Bandpass Sampling of High Frequency Tissue Motion", IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 58(7):1332-1343, Jul 2011. |
| Abstract: The characterization of tissue viscoelastic properties requires the measurement of tissue motion over a region of interest at frequencies that significantly exceed the frame rates of conventional ultrasound systems. In this paper, we propose that the bandpass sampling technique be applied to tissue motion sampling. With this approach, high-frequency signals limited to a frequency band can be sampled and reconstructed without aliasing at a sampling frequency that is lower than the Nyquist rate. We first review this approach and discuss the selection of the tissue excitation frequency band and of the feasible sampling frequencies that allow signal reconstruction without aliasing. We then demonstrate the approach using simulations based on the finite element method and ultrasound simulations. Finally, we perform experiments on tissue-mimicking materials and demonstrate accurate motion estimation using a lower sampling rate than that required by the conventional sampling theorem. The estimated displacements were used to measure the elasticity and viscosity in a phantom in which an inclusion has been correctly delineated. Thus, with bandpass sampling, it is feasible to use conventional beamforming on diagnostic ultrasound systems to perform high-frequency dynamic elastography. The method is simple to implement because it does not require beam interleaving, additional hardware, or synchronization. |
BibTeX:
@article{Eskandari_bandpass_11,
author = {Hani Eskandari and Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
title = {Bandpass Sampling of High Frequency Tissue Motion},
journal = {IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control},
year = {2011},
volume = {58},
number = {7},
pages = {1332-1343},
doi = {http://dx.doi.org/10.1109/TUFFC.2011.1953}
}
|
| Orcun Goksel and Septimiu E. Salcudean, "Image-Based Variational Meshing", IEEE Transactions on Medical Imaging 30(1):11-21, Jan 2011. |
| Abstract: In medical simulations involving tissue deformation, the finite element method (FEM) is a widely used technique, where the size, shape, and placement of the elements in a model are important factors that affect the interpolation and numerical errors of a solution. Conventional model generation schemes for FEM consist of a segmentation step delineating the anatomy followed by a meshing step generating elements conforming to this segmentation. In this paper, a single-step model generation technique is proposed based on optimization. Starting from an initial mesh covering the domain of interest, the mesh nodes are adjusted to minimize an objective function which penalizes intra-element intensity variations and poor element geometry for the entire mesh. Trade-offs between mesh geometry quality and intra-element variance are achieved by adjusting the relative weights of the geometric and intensity variation components of the cost function. This meshing approach enables a more accurate rendering of shapes with fewer elements and provides more accurate models for deformation simulation, especially when the image intensities represent a mechanical feature of the tissue such as the elastic modulus. The use of the proposed mesh optimization is demonstrated in 2D and 3D on synthetic phantoms, MR images of the brain, and CT images of the kidney. A comparison with previous meshing techniques that do not account for image intensity is also provided demonstrating the benefits of our approach. |
BibTeX:
@article{goksel_image-based_10,
author = {Orcun Goksel and Septimiu E. Salcudean},
title = {Image-Based Variational Meshing},
journal = {IEEE Transactions on Medical Imaging},
year = {2011},
volume = {30},
number = {1},
pages = {11-21},
doi = {http://dx.doi.org/10.1109/TMI.2010.2055884}
}
|
| Reza Zahiri-Azar, Orcun Goksel, and Septimiu E. Salcudean, "Sub-sample Displacement Estimation from Digitized Ultrasound RF Signals Using Multi-Dimensional Polynomial Fitting of the Cross-correlation Function", IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control 57(11):2403-2420, 2010. |
| Abstract: A widely used time-domain technique for motion or delay estimation between digitized ultrasound RF signals involves the maximization of a discrete pattern-matching function, usually the cross-correlation. To achieve sub-sample accuracy, the discrete pattern-matching function is interpolated using the values at the discrete maximizer and adjacent samples. In prior work, only 1-D fit, applied separately along the axial, lateral, and elevational axes, has been used to estimate the sub-sample motion in 1-D, 2-D, and 3-D. In this paper, we explore the use of 2-D and 3-D polynomial fitting for this purpose. We quantify the estimation error in noise-free simulations using Field II and experiments with a commercial ultrasound machine. In simulated 2-D translational motions, function fitting with quartic spline polynomials leads to maximum bias of 0.2% of the sample spacing in the axial direction and 0.4% of the sample spacing in the lateral direction, corresponding to 38 nm and 1.31 mu m, respectively. The maximum standard deviations were approximately 1% of the sample spacing in both the axial and the lateral directions, corresponding to 193 nm axially and 4.43 mu m laterally. In simulated 1% axial strain, the same function fitting leads to mean absolute displacement estimation errors of 255 nm in the axial direction and 4.77 mu m in the lateral direction. In experiments with a linear array transducer, 2-D quartic spline fitting leads to maximum bias of 458 nm and 6.27 mu m in the axial and the lateral directions, respectively. These results are more than one order of magnitude smaller than those obtained with separate 1-D fit when applied to the same data set. Simulations and experiments in 3-D yield similar results when comparing 3-D polynomial fitting with 1-D fitting along the axial, lateral, and elevational directions. |
BibTeX:
@article{zahiri-azar_sub-sample_10,
author = {Reza Zahiri-Azar and Orcun Goksel and Septimiu E. Salcudean},
title = {Sub-sample Displacement Estimation from Digitized Ultrasound RF Signals Using Multi-Dimensional Polynomial Fitting of the Cross-correlation Function},
journal = {IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control},
year = {2010},
volume = {57},
number = {11},
pages = {2403-2420},
doi = {http://dx.doi.org/10.1109/TUFFC.2010.1708}
}
|
| Orcun Goksel and Septimiu E. Salcudean, "B-Mode Ultrasound Image Simulation in Deformable 3-D Medium", IEEE Transactions on Medical Imaging 28(11):1657-1669, Nov 2009. |
| Abstract: 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. |
BibTeX:
@article{goksel_b-mode_09,
author = {Orcun Goksel and Septimiu E. Salcudean},
title = {B-Mode Ultrasound Image Simulation in Deformable 3-D Medium},
journal = {IEEE Transactions on Medical Imaging},
year = {2009},
volume = {28},
number = {11},
pages = {1657-1669},
doi = {http://dx.doi.org/10.1109/TMI.2009.2016561}
}
|
| Orcun Goksel, Ehsan Dehghan, and Septimiu E. Salcudean, "Modeling and Simulation of Flexible Needles", Medical Engineering and Physics 31(9):1069-1078, Nov 2009. |
| Abstract: Needle insertion is performed in many clinical and therapeutic procedures. Tissue displacement and needle bending which result from needle–tissue interaction make accurate targeting difficult. For performing physicians to gain essential needle targeting skills, needle insertion simulators can be used for training. An accurate needle bending model is essential for such simulators. These bending models are also needed for needle path planning. In this paper, three different models are presented to simulate the deformations of a needle. The first two models use the finite element method and take the geometric nonlinearity into account. The third model is a series of rigid bars connected by angular springs. The models were compared to recorded deformations during experiments of applying lateral tip forces on a brachytherapy needle. The model parameters were identified and the simulation results were compared to the experimental data. The results show that the angular spring model, which is computationally the most efficient model, is also the most accurate in modeling the bending of the brachytherapy needle. |
BibTeX:
@article{goksel_modeling_09,
author = {Orcun Goksel and Ehsan Dehghan and Septimiu E. Salcudean},
title = {Modeling and Simulation of Flexible Needles},
journal = {Medical Engineering and Physics},
year = {2009},
volume = {31},
number = {9},
pages = {1069-1078},
doi = {http://dx.doi.org/10.1016/j.medengphy.2009.07.007}
}
|
| Orcun Goksel, Septimiu E. Salcudean, and Simon P. DiMaio, "3D Simulation of Needle-Tissue Interaction with Application to Prostate Brachytherapy", Computer Aided Surgery 11(6):279-288, Nov 2006. |
| Abstract: This paper presents a needle-tissue interaction model that is a 3D extension of prior work based on needle and tissue models discretized using the Finite Element Method. The use of flexible needles necessitates remeshing the tissue during insertion, since simple mesh-node snapping to the tip can be detrimental to the simulation. In this paper, node repositioning and node addition are the two methods of mesh modification examined for coarse meshes. Our focus is on numerical approaches for fast implementation of these techniques. Although the two approaches compared, namely the Woodbury formula (matrix inversion lemma) and the boundary condition switches, have the same computational complexity, the Woodbury formula is shown to perform faster due to its cache-efficient order of operations. Furthermore, node addition is applied in constant time for both approaches, whereas node repositioning requires longer and variable computational times. A method for rendering the needle forces during simulated insertions into a 3D prostate model has been implemented. Combined with a detailed anatomical segmentation, this will be useful in teaching the practice of prostate brachytherapy. Issues related to discretization of such coupled (e.g., needle-tissue) models are also discussed. |
BibTeX:
@article{goksel_3d_06,
author = {Orcun Goksel and Septimiu E. Salcudean and Simon P. DiMaio},
title = {3D Simulation of Needle-Tissue Interaction with Application to Prostate Brachytherapy},
journal = {Computer Aided Surgery},
year = {2006},
volume = {11},
number = {6},
pages = {279-288},
doi = {http://dx.doi.org/10.1080/10929080601089997}
}
|
| Danny G. French, James Morris Morris, Mira Keyes, Orcun Goksel, and Septimiu E. Salcudean, "Computing Intraoperative Dosimetry for Prostate Brachytherapy Using TRUS and Fluoroscopy", Academic Radiology 12(10):1262-1272, 2005. |
| Abstract: Rationale and Objectives: There is a need to provide real-time dosimetric feedback during prostate brachytherapy based on the location of the implanted seeds. The objective of our approach is to develop a system to accurately locate seeds with minimal impact on the current protocol for prostate brachytherapy and without additional imaging equipment. Materials and Methods: A new approach for intraoperatively computing dosimetry for prostate brachytherapy is presented. The approach uses transrectal ultrasound (TRUS) and fluoroscopic images. A fluoroscopic image of the TRUS probe is required to register the fluoroscopic and ultrasound images. The C-arm is not moved during the procedure and all images are acquired from the same C-arm angles. A needle path is interpolated for each needle based on the location of the needle tip in TRUS images and the known entry point of the needle. Throughout the procedure, fluoroscopic images are acquired to determine the coronal plane coordinates of the seeds and the remaining coordinate of each seed is computed from the needle path. For accurate results, intraoperative seed motion tracking is advised and a method to achieve such tracking is also presented. Results: Experimentally, the TRUS and fluoroscopic images are registered with a mean and maximum error of 1.3 mm and 5.8 mm, respectively. In a phantom, 12 seeds are located using our approach and compared with the known locations, with a mean error in the x, y, and z direction of 0.96 mm, 0.33, and 0.68 mm, respectively, and a corresponding maximum error of 1.85 mm, 0.56 mm, and 1.63 mm. Experimental results show motion tracking in the y-direction with submillimeter accuracy. The feasibility of our approach is tested on five cases of clinical data using a semiautomated version of our system and the resulting dosimetry is compared with that found using postoperative computed tomography images. The D90 and V100 metrics computed using our approach and the computed tomography images differ by a maximum of 16.6% and 1.7%, respectively. Conclusions: TRUS can be combined with single pose fluoroscopic images to compute delivered dose intraoperatively for prostate brachytherapy. Phantom results demonstrate the accuracy of the method and preliminary clinical results show its potential. |
BibTeX:
@article{french_computing_05,
author = {Danny G. French and James Morris Morris and Mira Keyes and Orcun Goksel and Septimiu E. Salcudean},
title = {Computing Intraoperative Dosimetry for Prostate Brachytherapy Using TRUS and Fluoroscopy},
journal = {Academic Radiology},
year = {2005},
volume = {12},
number = {10},
pages = {1262-1272},
doi = {http://dx.doi.org/10.1016/j.acra.2005.05.026}
}
|
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Refereed Conferences: |
| Hani Eskandari, Orcun Goksel, Septimiu E. Salcudean, and Robert Rohling, "Bandpass Sampling of High Frequency Tissue Motion", In International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC), pp. 71, Utah, USA, Oct 2010. |
BibTeX:
@inproceedings{eskandari_bandpass_10,
author = {Hani Eskandari and Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
title = {Bandpass Sampling of High Frequency Tissue Motion},
booktitle = {International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC)},
year = {2010},
pages = {71}
}
|
| Orcun Goksel and Septimiu E. Salcudean, "FEM Simulation of Harmonic Tissue Excitation for Prostate Elastography", In International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC), pp. 93, Utah, USA, Oct 2010. |
BibTeX:
@inproceedings{goksel_fem_10,
author = {Orcun Goksel and Septimiu E. Salcudean},
title = {FEM Simulation of Harmonic Tissue Excitation for Prostate Elastography},
booktitle = {International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC)},
year = {2010},
pages = {93}
}
|
| Orcun Goksel, Hani Eskandari, and Septimiu E. Salcudean, "Mesh Adaptation for Improving Inverse-Problem Reconstruction", In International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC), pp. 96, Utah, USA, Oct 2010. |
BibTeX:
@inproceedings{goksel_mesh_10,
author = {Orcun Goksel and Hani Eskandari and Septimiu E. Salcudean},
title = {Mesh Adaptation for Improving Inverse-Problem Reconstruction},
booktitle = {International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC)},
year = {2010},
pages = {96}
}
|
| Orcun Goksel and Septimiu E. Salcudean, "Haptic Simulator for Prostate Brachytherapy with Simulated Ultrasound", In International Symposium on Biomedical Simulation (ISBMS), pp. 150-159, Jan 2010. |
| Abstract: This paper presents a medical simulator for prostate brachytherapy procedure. Needles are inserted in deformable tissue models using a haptic device while the force feedback computed using a needletissue interaction model is rendered on the user’s hand. Transrectal ultrasound images of the region of interest are also displayed in real-time using an interpolation scheme accounting for the mesh-based tissue deformation. Employing a 3D ultrasound volume data reconstructed a priori, this simulation method achieves realistic ultrasound feedback coupled with immediate tissue deformation. Models for simulating tissue deformation using the finite element method are obtained by segmented the relevant anatomy on MR slices. These models are rigidly registered to the ultrasound voxel volume using the prostate surface. The presented simulation system is suitable for brachytherapy training using haptic control/feedback. It can also be used for treatment planning. |
BibTeX:
@inproceedings{goksel_haptic_10,
author = {Orcun Goksel and Septimiu E. Salcudean},
title = {Haptic Simulator for Prostate Brachytherapy with Simulated Ultrasound},
booktitle = {International Symposium on Biomedical Simulation (ISBMS)},
year = {2010},
pages = {150-159},
doi = {http://dx.doi.org/10.1007/978-3-642-11615-5_16}
}
|
| Amir Haddadi, Orcun Goksel, Septimiu E. Salcudean, and Keyvan Hashtrudi-Zaad, "On the Controllability of Dynamic Model-Based Needle Insertion in Soft Tissue", In IEEE Engineering in Medicine and Biology Conference (EMBC), pp. 2287-2291, Buenos Aires, Argentina, Sep 2010. |
BibTeX:
@inproceedings{haddadi_controllability_10,
author = {Amir Haddadi and Orcun Goksel and Septimiu E. Salcudean and Keyvan Hashtrudi-Zaad},
title = {On the Controllability of Dynamic Model-Based Needle Insertion in Soft Tissue},
booktitle = {IEEE Engineering in Medicine and Biology Conference (EMBC)},
year = {2010},
pages = {2287-2291},
doi = {http://dx.doi.org/10.1109/IEMBS.2010.5627676}
}
|
| Orcun Goksel and Septimiu E. Salcudean, "Automatic Prostate Segmentation from Transrectal Ultrasound Elastography Images Using Geometric Active Contours", In International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC), pp. 34, Vlissingen, Netherlands, Sep 2009. |
BibTeX:
@inproceedings{goksel_automatic_09,
author = {Orcun Goksel and Septimiu E. Salcudean},
title = {Automatic Prostate Segmentation from Transrectal Ultrasound Elastography Images Using Geometric Active Contours},
booktitle = {International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC)},
year = {2009},
pages = {34}
}
|
| Orcun Goksel and Septimiu E. Salcudean, "High-Quality Model Generation for Finite Element Simulation of Tissue Deformation", In Medical Image Computation and Computer Assisted Intervention (MICCAI), pp. 248-256, London, UK, Sep 2009. |
| Abstract: In finite element simulation, size, shape, and placement of the elements in a model are significant factors that affect the interpolation and numerical errors of a solution. In medical simulations, such models are desired to have higher accuracy near features such as anatomical boundaries (surfaces) and they are often required to have element faces lying along these surfaces. Conventional modelling schemes consist of a segmentation step delineating the anatomy followed by a meshing step generating elements conforming to this segmentation. In this paper, a one-step energy-based model generation technique is proposed. An objective function is minimized when each element of a mesh covers similar image intensities while, at the same time, having desirable FEM characteristics. Such a mesh becomes essential for accurate models for deformation simulation, especially when the image intensities represent a mechanical feature of the tissue such as the elastic modulus. The use of the proposed mesh optimization is demonstrated on synthetic phantoms, 2D/3D brain MR images, and prostate ultrasound-elastography data. |
BibTeX:
@inproceedings{goksel_high-quality_09,
author = {Orcun Goksel and Septimiu E. Salcudean},
title = {High-Quality Model Generation for Finite Element Simulation of Tissue Deformation},
booktitle = {Medical Image Computation and Computer Assisted Intervention (MICCAI)},
year = {2009},
pages = {248-256},
doi = {http://dx.doi.org/10.1007/978-3-642-04271-3_31}
}
|
| Sara Mahdavi, Orcun Goksel, and Septimiu E. Salcudean, "3D Prostate Segmentation in Ultrasound Images Based on Tapered and Deformed Ellipsoids", In Medical Image Computation and Computer Assisted Intervention (MICCAI), pp. 960-967, London, UK, Sep 2009. |
| Abstract: Prostate segmentation from trans-rectal transverse B-mode ultrasound images is required for radiation treatment of prostate cancer. Manual segmentation is a time-consuming task, the results of which are dependent on image quality and physicians’ experience. This paper introduces a semi-automatic 3D method based on super-ellipsoidal shapes. It produces a 3D segmentation in less than 15 seconds using a warped, tapered ellipsoid fit to the prostate. A study of patient images shows good performance and repeatability. This method is currently in clinical use at the Vancouver Cancer Center where it has become the standard segmentation procedure for low dose-rate brachytherapy treatment. |
BibTeX:
@inproceedings{mahdavi_3d_09,
author = {Sara Mahdavi and Orcun Goksel and Septimiu E. Salcudean},
title = {3D Prostate Segmentation in Ultrasound Images Based on Tapered and Deformed Ellipsoids},
booktitle = {Medical Image Computation and Computer Assisted Intervention (MICCAI)},
year = {2009},
pages = {960-967},
doi = {http://dx.doi.org/10.1007/978-3-642-04271-3_116}
}
|
| Reza Zahiri-Azar, Orcun Goksel, and Septimiu E. Salcudean, "Application of 2D Polynomial Fitting to Beam Steering for Motion Estimation with Sub-Sample Accuracy", In International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC), pp. 124, Vlissingen, Netherlands, Sep 2009. |
BibTeX:
@inproceedings{zahiri-azar_application_09,
author = {Reza Zahiri-Azar and Orcun Goksel and Septimiu E. Salcudean},
title = {Application of 2D Polynomial Fitting to Beam Steering for Motion Estimation with Sub-Sample Accuracy},
booktitle = {International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC)},
year = {2009},
pages = {124}
}
|
| Reza Zahiri-Azar, Orcun Goksel, and Septimiu E. Salcudean, "Methods for the Estimation of the Sub-Sample Motion Using Digitized Ultrasound Echo Signals in Three Dimensions", In International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC), pp. 88, Vlissingen, Netherlands, Sep 2009. |
BibTeX:
@inproceedings{zahiri-azar_methods_09,
author = {Reza Zahiri-Azar and Orcun Goksel and Septimiu E. Salcudean},
title = {Methods for the Estimation of the Sub-Sample Motion Using Digitized Ultrasound Echo Signals in Three Dimensions},
booktitle = {International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC)},
year = {2009},
pages = {88}
}
|
| Reza Zahiri-Azar, Orcun Goksel, T.S. Yao, Ehsan Dehghan, Joseph Yan, and Septimiu E. Salcudean, "Multi-Dimensional Sub-Sample Motion Estimation: Initial Results", In IEEE Ultrasonics Symposium, pp. , Rome, Italy, Sep 2009. |
BibTeX:
@inproceedings{zahiri-azar_multi-dimensional_09,
author = {Reza Zahiri-Azar and Orcun Goksel and T.S. Yao and Ehsan Dehghan and Joseph Yan and Septimiu E. Salcudean},
title = {Multi-Dimensional Sub-Sample Motion Estimation: Initial Results},
booktitle = {IEEE Ultrasonics Symposium},
year = {2009},
doi = {C:\Program Files\Utilities\JabRef\plugins\listrefs.layout}
}
|
| Reza Zahiri-Azar, Orcun Goksel, T.S. Yao, Ehsan Dehghan, Joseph Yan, and Septimiu E. Salcudean, "Methods for the Estimation of Sub-sample Motion of Digitized Ultrasound Echo Signals in 2D", In IEEE Engineering in Medicine and Biology Conference (EMBC), pp. 5581-5584, Vancouver, BC, Canada, Aug 2008. |
| Abstract: Motion estimation in sequences of ultrasound echo signals is essential for a wide range of modern ultrasound-based signal processing applications. Pattern matching algorithms are generally used for finding the motion within sampling accuracy. Subsequently, 1D interpolation techniques are employed to find any motion smaller than sampling accuracy. In this paper, we propose several interpolation schemes that are suited for 2D motion estimation. Simulations using Field II ultrasound simulation software and experiments using an Ultrasonix Sonix RP imaging system with a L9-4/38 linear array transducer are used to study these techniques and compare their performance to other methods reported in the literature. The results show that the proposed interpolation methods outperform other common techniques in terms of bias and jitter. The axial and the lateral bias of the proposed methods are measured to be less than 1$m and 5 $m, respectively, in both the simulated and the experimental data. |
BibTeX:
@inproceedings{zahiri-azar_methods_08,
author = {Reza Zahiri-Azar and Orcun Goksel and T.S. Yao and Ehsan Dehghan and Joseph Yan and Septimiu E. Salcudean},
title = {Methods for the Estimation of Sub-sample Motion of Digitized Ultrasound Echo Signals in 2D},
booktitle = {IEEE Engineering in Medicine and Biology Conference (EMBC)},
year = {2008},
pages = {5581-5584},
doi = {http://dx.doi.org/10.1109/IEMBS.2008.4650479}
}
|
| Orcun Goksel and Septimiu E. Salcudean, "Fast B-Mode Ultrasound Image Simulation of Deformed Tissue", In IEEE Engineering in Medicine and Biology Conference (EMBC), pp. 87-90, Lyon, France, Aug 2007. |
| Abstract: This paper presents a fast image synthesis procedure inside elastic volumes under deformation simulated by the finite element method (FEM). Given the node displacements of a mesh and the 3D image voxel data of a volume prior to deformation, the method maps the image pixels, to be synthesized, from the deformed configuration back to the nominal pre-deformed configuration, where the pixel intensities are obtained easily through interpolation in the regular-grid structure of the voxel volume. This mapping requires the identification of the mesh element enclosing each image pixel, in order to use its corresponding shape function for smooth interpolation. To accelerate this point location operation, a fast method of marking the projection of the deformed mesh on the image pixels at every frame is introduced. In order to evaluate our method, a deformable tissue phantom was constructed and its 3D ultrasound volume was acquired in its nominal state. B-mode images of the phantom were then synthesized under the simulated deformation of an ultrasound probe. Results show that realistic B-mode images can be simulated in real-time with the proposed technique, even under large deformations. The technique is also implemented on a real-time system for ultrasound exploration with deformation. |
BibTeX:
@inproceedings{goksel_fast_07,
author = {Orcun Goksel and Septimiu E. Salcudean},
title = {Fast B-Mode Ultrasound Image Simulation of Deformed Tissue},
booktitle = {IEEE Engineering in Medicine and Biology Conference (EMBC)},
year = {2007},
pages = {87-90},
doi = {http://dx.doi.org/10.1109/IEMBS.2007.4352229}
}
|
| Orcun Goksel and Septimiu E. Salcudean, "Real-time Synthesis of Image Slices in Deformed Tissue from Nominal Volume Images", In Medical Image Computation and Computer Assisted Intervention (MICCAI), pp. 401-408, Brisbane, QLD, Australia, Oct 2007. |
| Abstract: This paper presents a fast image synthesis procedure for elastic volumes under deformation. Given the node displacements of a mesh and the 3D image voxel data of an undeformed volume, the method maps the image plane pixels to be synthesized from the deformed configuration back to the nominal pre-deformed configuration, where the pixel intensities are obtained easily through interpolation in the regular-grid structure of the voxel volume. For smooth interpolation, this mapping requires the identification of the mesh element enclosing each image pixel. To accelerate this point location procedure, a fast method of marking the image pixels is employed by finding the intersection of the mesh and the image, and marking this intersection on the image pixels using Bresenham’s line drawing algorithm. A deformable tissue phantom was constructed, it was modeled using the finite element method, and its 3D ultrasound volume was acquired in its undeformed state. Actual B-mode images of the phantom under deformation by the ultrasound probe were then compared with the corresponding synthesized images simulated for the same deformations. Results show that realistic images can be synthesized in real-time using the proposed technique. |
BibTeX:
@inproceedings{goksel_real-time_07,
author = {Orcun Goksel and Septimiu E. Salcudean},
title = {Real-time Synthesis of Image Slices in Deformed Tissue from Nominal Volume Images},
booktitle = {Medical Image Computation and Computer Assisted Intervention (MICCAI)},
year = {2007},
pages = {401-408},
doi = {http://dx.doi.org/10.1007/978-3-540-75757-3_49}
}
|
| Orcun Goksel, Reza Zahiri-Azar, and Septimiu E. Salcudean, "Simulation of Ultrasound Radio-Frequency Signals in Deformed Tissue for Validation of 2D Motion Estimation with Sub-Sample Accuracy", In IEEE Engineering in Medicine and Biology Conference (EMBC), pp. 2159-2162, Lyon, France, Aug 2007. |
BibTeX:
@inproceedings{goksel_simulation_07,
author = {Orcun Goksel and Reza Zahiri-Azar and Septimiu E. Salcudean},
title = {Simulation of Ultrasound Radio-Frequency Signals in Deformed Tissue for Validation of 2D Motion Estimation with Sub-Sample Accuracy},
booktitle = {IEEE Engineering in Medicine and Biology Conference (EMBC)},
year = {2007},
pages = {2159-2162},
url = {http://www.ece.ubc.ca/~orcung/pubs/Goksel07_embc_SubSamp_.pdf},
doi = {http://dx.doi.org/10.1109/IEMBS.2007.4352750}
}
|
| Reza Zahiri-Azar, Orcun Goksel, and Septimiu E. Salcudean, "Real-Time Tissue Deformation Visualization", In International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC), pp. 117, Santa Fe, New Mexico, USA, Nov 2007. |
BibTeX:
@inproceedings{zahiri-azar_real-time_07,
author = {Reza Zahiri-Azar and Orcun Goksel and Septimiu E. Salcudean},
title = {Real-Time Tissue Deformation Visualization},
booktitle = {International Conference on Ultrasonic Measurement and Imaging of Tissue Elasticity (ITEC)},
year = {2007},
pages = {117},
url = {http://www.uth.tmc.edu/schools/med/rad/elasto/conference/prior_conf/2007/2007Proceedings.pdf}
}
|
| Ehsan Dehghan, Orcun Goksel, and Septimiu E. Salcudean, "A Comparison of Needle Bending Models", In Medical Image Computation and Computer Assisted Intervention (MICCAI), pp. 305-312, Copenhagen, Denmark, Oct 2006. |
| Abstract: Modeling the deflection of flexible needles is an essential part of needle insertion simulation and path planning. In this paper, three models are compared in terms of accuracy in simulating the bending of a prostate brachytherapy needle. The first two utilize the finite element method, one using geometric non-linearity and triangular plane elements, the other using non-linear beam elements. The third model uses angular springs to model cantilever deflection. The simulations are compared with the experimental bent needle configurations. The models are assessed in terms of geometric conformity using independently identified and pre-identified model parameters. The results show that the angular spring model, which is also the simplest, simulates the needle more accurately than the others. |
BibTeX:
@inproceedings{dehghan_comparison_06,
author = {Ehsan Dehghan and Orcun Goksel and Septimiu E. Salcudean},
title = {A Comparison of Needle Bending Models},
booktitle = {Medical Image Computation and Computer Assisted Intervention (MICCAI)},
year = {2006},
pages = {305-312},
doi = {http://dx.doi.org/10.1007/11866565_38}
}
|
| Orcun Goksel, Septimiu E. Salcudean, and Robert Rohling, "Image Synthesis of Deformed Tissue with Application to Ultrasound for Prostate Brachytherapy", In Canadian Medical and Biological Engineering Conference (CMBEC), pp. , Vancouver, BC, Canada, Jun 2006. |
BibTeX:
@inproceedings{goksel_image_06,
author = {Orcun Goksel and Septimiu E. Salcudean and Robert Rohling},
title = {Image Synthesis of Deformed Tissue with Application to Ultrasound for Prostate Brachytherapy},
booktitle = {Canadian Medical and Biological Engineering Conference (CMBEC)},
year = {2006}
}
|
| Orcun Goksel, Simon P. DiMaio, Septimiu E. Salcudean, Robert Rohling, and James Morris, "3D Needle-Tissue Interaction Simulation for Prostate Brachytherapy", In Medical Image Computation and Computer Assisted Intervention (MICCAI), pp. 827-834, Palm Springs, CA, USA, Oct 2005. |
| Abstract: This paper presents a needle-tissue interaction model that is a 3D extension of a prior work based on the finite element method. The model is also adapted to accommodate arbitrary meshes so that the anatomy can effectively be meshed using third-party algorithms. Using this model a prostate brachytherapy simulator is designed to help medical residents acquire needle steering skills. This simulation uses a prostate mesh generated from clinical data segmented as contours on parallel slices. Node repositioning and addition, which are methods for achieving needle-tissue coupling, are discussed. In order to achieve real-time haptic rates, computational approaches to these methods are compared. Specifically, the benefit of using the Woodbury formula (matrix inversion lemma) is studied. Our simulation of needle insertion into a prostate is shown to run faster than 1 kHz. |
BibTeX:
@inproceedings{goksel_3d_05,
author = {Orcun Goksel and Simon P. DiMaio and Septimiu E. Salcudean and Robert Rohling and James Morris},
title = {3D Needle-Tissue Interaction Simulation for Prostate Brachytherapy},
booktitle = {Medical Image Computation and Computer Assisted Intervention (MICCAI)},
year = {2005},
pages = {827-834},
doi = {http://dx.doi.org/10.1007/11566465_102}
}
|
PhD Thesis:
- O. Goksel: "Meshing and Rendering of Patient-Specific Deformation Models With Application to Needle Insertion Simulation", PhD Thesis, University of British Columbia, 2009.
Master’s Thesis:
- O. Goksel: "Ultrasound Image and 3D Finite Element based Tissue Deformation Simulator for Prostate Brachytherapy", M.A.Sc. Thesis, University of British Columbia, 2005.
Other Contributions:
- O. Goksel, S.E. Salcudean, and R. Rohling: "3D Needle-Tissue Interaction Simulation for Prostate Brachytherapy", Poster presentation at IS 2005: 15th Annual Canadian Conference on Intelligent Systems, 2005. [national; received the Best Poster Award]
- O. Goksel, S.E. Salcudean, and R. Rohling: "Towards a Prostate Brachytherapy Haptic Simulator", Poster at the BC ASI (Advanced Systems Institute) Exchange, 2004.
[provincial, received the ASI Innovation Award and the ASI Communication Award]
Orcun Goksel