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GPU-based ray-casting of non-rigid deformations: a comparison between direct and indirect approaches
Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
Linköping University, Center for Medical Image Science and Visualization (CMIV). Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology. Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Health Sciences.ORCID iD: 0000-0002-7750-1917
2014 (English)In: Proceedings of SIGRAD 2014, Visual Computing, June 12-13, 2014, Göteborg, Sweden / [ed] Mohammad Obaid; Daniel Sjölie; Erik Sintorn; Morten Fjeld, Linköping University Electronic Press, 2014, 67-74 p.Conference paper (Refereed)
Abstract [en]

For ray-casting of non-rigid deformations, the direct approach (as opposed to the traditional indirect approach) does not require the computation of an intermediate volume to be used for the rendering step. The aim of this study was to compare the two approaches in terms of performance (speed) and accuracy (image quality).

The direct and the indirect approach were carefully implemented to benefit of the massive GPU parallel power, using CUDA. They were then tested with Computed Tomography (CT) datasets of varying sizes and with a synthetic image, the Marschner-Lobb function.

The results show that the direct approach is dependent on the ray sampling steps, number of landmarks and image resolution. The indirect approach is mainly affected by the number of landmarks, if the volume is large enough.

These results exclude extreme cases, i.e. if the sampling steps are much smaller than the voxel size and if the image resolution is much higher than the ones used here. For a volume of size 512×512×512, using 100 landmarks and image resolution of 1280×960, the direct method performs better if the ray sampling steps are approximately above 1 voxel. Regarding accuracy, the direct method provides better results for multiple frequencies using the Marschner-Lobb function.

The conclusion is that the indirect method is superior in terms of performance, if the sampling along the rays is high, in comparison to the voxel grid, while the direct is superior otherwise. The accuracy analysis seems to point out that the direct method is superior, in particular when the implicit function is used.

Place, publisher, year, edition, pages
Linköping University Electronic Press, 2014. 67-74 p.
Linköping Electronic Conference Proceedings, ISSN 1650-3686 (print), 1650-3740 (online) ; 106
National Category
Computer Vision and Robotics (Autonomous Systems)
URN: urn:nbn:se:liu:diva-107553ISBN: 9789175192123OAI: diva2:725259
Swedish Computer Graphics Association (SIGRAD), Göteborg, Sweden, June 12-13, 2014
Available from: 2014-06-16 Created: 2014-06-16 Last updated: 2016-09-15Bibliographically approved
In thesis
1. Guidance and Visualization for Brain Tumor Surgery
Open this publication in new window or tab >>Guidance and Visualization for Brain Tumor Surgery
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Image guidance and visualization play an important role in modern surgery to help surgeons perform their surgical procedures. Here, the focus is on neurosurgery applications, in particular brain tumor surgery where a craniotomy (opening of the skull) is performed to access directly the brain region to be treated. In this type of surgery, once the skull is opened the brain can change its shape, and this deformation is known as brain shift. Moreover, the boundaries of many types of tumors are difficult to identify by the naked eye from healthy tissue. The main goal of this work was to study and develop image guidance and visualization methods for tumor surgery in order to overcome the problems faced in this type of surgery.

Due to brain shift the magnetic resonance dataset acquired before the operation (preoperatively) no longer corresponds to the anatomy of the patient during the operation (intraoperatively). For this reason, in this work methods were studied and developed to compensate for this deformation. To guide the deformation methods, information of the superficial vessel centerlines of the brain was used. A method for accurate (approximately 1 mm) reconstruction of the vessel centerlines using a multiview camera system was developed. It uses geometrical constraints, relaxation labeling, thin plate spline filtering and finally mean shift to find the correct correspondences between the camera images.

A complete non-rigid deformation pipeline was initially proposed and evaluated with an animal model. From these experiments it was observed that although the traditional non-rigid registration methods (in our case coherent point drift) were able to produce satisfactory vessel correspondences between preoperative and intraoperative vessels, in some specific areas the results were suboptimal. For this reason a new method was proposed that combined the coherent point drift and thin plate spline semilandmarks. This combination resulted in an accurate (below 1 mm) non-rigid registration method, evaluated with simulated data where artificial deformations were performed.

Besides the non-rigid registration methods, a new rigid registration method to obtain the rigid transformation between the magnetic resonance dataset and the neuronavigation coordinate systems was also developed.

Once the rigid transformation and the vessel correspondences are known, the thin plate spline can be used to perform the brain shift deformation. To do so, we have used two approaches: a direct and an indirect. With the direct approach, an image is created that represents the deformed data, and with the indirect approach, a new volume is first constructed and only after that can the deformed image be created. A comparison of these two approaches, implemented for the graphics processing units, in terms of performance and image quality, was performed. The indirect method was superior in terms of performance if the sampling along the ray is high, in comparison to the voxel grid, while the direct was superior otherwise. The image quality analysis seemed to indicate that the direct method is superior.

Furthermore, visualization studies were performed to understand how different rendering methods and parameters influence the perception of the spatial position of enclosed objects (typical situation of a tumor enclosed in the brain). To test these methods a new single-monitor-mirror stereoscopic display was constructed. Using this display, stereo images simulating a tumor inside the brain were presented to the users with two rendering methods (illustrative rendering and simple alpha blending) and different levels of opacity. For the simple alpha blending method an optimal opacity level was found, while for the illustrative rendering method all the opacity levels used seemed to perform similarly.

In conclusion, this work developed and evaluated 3D reconstruction, registration (rigid and non-rigid) and deformation methods with the purpose of minimizing the brain shift problem. Stereoscopic perception of the spatial position of enclosed objects was also studied using different rendering methods and parameter values.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2016. 70 p.
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1762
National Category
Medical Image Processing Radiology, Nuclear Medicine and Medical Imaging Surgery Computer Engineering
urn:nbn:se:liu:diva-130791 (URN)10.3384/diss.diva-130791 (DOI)9789176857724 (Print) (ISBN)
Public defence
2016-09-30, Hugo Theorellsallen (norra entrén), Campus US, Linköping, 09:00 (English)
Swedish Foundation for Strategic Research Knowledge FoundationVINNOVAVårdal Foundation, 2009/0079Swedish Childhood Cancer Foundation, MT2013-0036
Available from: 2016-08-24 Created: 2016-08-24 Last updated: 2016-09-09Bibliographically approved

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