RegistrationShop - An Interactive 3D Medical Volume Registration System
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RegistrationShop - An Interactive 3D Medical Volume Registration System
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Slides for the RegistrationShop talk I gave at the EG Visual Computing in Biology and Medicine (VCBM) 2014 conference in Vienna. Demo video: https://vimeo.com/112264446 Abstract: In medical imaging, registration is used to combine images containing information from different modalities or to track treatment effects over time in individual patients. Most registration software packages do not provide an easy-to-use interface that facilitates the use of registration. 2D visualization techniques are often used for visualizing 3D datasets. RegistrationShop was developed to improve and ease the process of volume registration using 3D visualizations and intuitive interactive tools. It supports several basic visualizations of 3D volumetric data. Interactive rigid and non-rigid transformation tools can be used to manipulate the volumes and immediate visual feedback for all rigid transformation tools allows the user to examine the current result in real-time. In this context, we introduce 3D comparative visualization techniques, as well as a way of placing landmarks in 3D volumes. Finally, we evaluated our approach with domain experts, who underlined the potential and usefulness of RegistrationShop.
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RegistrationShop - An Interactive 3D Medical Volume Registration System
- 1. RegistrationShop: An Interactive 3D Medical Volume Registration System Noeska N. Smit1, Berend Klein Haneveld1, Marius Staring2, Elmar Eisemann1, Charl P. Botha3 and Anna Vilanova1 1 Computer Graphics and Visualization group, Intelligent Systems, TU Delft, The Netherlands 2 Division of Image Processing, Department of Radiology, LUMC, The Netherlands 3 vxlabs, South Africa RegistrationShop Noeska Smit
- 2. Pre- and post treatment RegistrationShop Noeska Smit
- 3. Multiple modalities RegistrationShop Noeska Smit http://www.osirix-viewer.com/Snapshots.html
- 4. Atlas-based Segmentation RegistrationShop Noeska Smit
- 6. Registration Functionality • AMIDE • AMILab • FusionSync • Ezys • Elastix • MITK • Mirada Medical • PMOD • Slicer • VolView • Voreen • … RegistrationShop Noeska Smit
- 7. Slicer RegistrationShop Noeska Smit
- 8. Elastix RegistrationShop Noeska Smit
- 9. Comparison • Typically only 2D visualizations of the registration result or missing required transformation tools • Not always suitable for non-image processing experts RegistrationShop Noeska Smit
- 10. What if… • simple interaction techniques • + real-time 3D visual feedback • = simplified registration process for novice users? RegistrationShop Noeska Smit
- 11. Landmark placement Corresponding landmark pairs: – Method 1: surface picker RegistrationShop Noeska Smit
- 12. Landmark placement Corresponding landmark pairs: – Method 1: surface picker – Method 2: two-step picker RegistrationShop Noeska Smit
- 13. Simple visualization techniques Direct volume rendering: Double thresholds MIP RegistrationShop Noeska Smit
- 14. Multi-volume rendering Real-time visual feedback on the current registration result: THR/THR MIP/THR MIP/MIP RegistrationShop Noeska Smit
- 16. Implementation • Source code freely available via GitHub: • github.com/berendkleinhaneveld/Registrationshop • Installable builds coming soon! RegistrationShop Noeska Smit
- 18. Evaluation • Four domain experts: – Medical radiation therapist – Radiologist – Medical imaging researcher: + registration frequency – Medical imaging researcher: - registration frequency • Two use-cases: – CT lung – Full body MRI RegistrationShop Noeska Smit
- 19. Evaluation Setup 1. Prior experience interview 2. Live demo: artificial dataset 3. Performing registration of clinical datasets 4. Survey RegistrationShop Noeska Smit
- 20. Evaluation Results • 3D visualizations • Transformation tools • Conclusion: – RegistrationShop: a promising volume registration tool with the potential to make registration more accessible to clinicians and researchers in the future. RegistrationShop Noeska Smit
- 21. Future Work • Visualizing registration quality • Visualizing non-rigid registration deformation field • Experimenting with compositing operations and transfer function definitions • Examining clinical potential in larger follow-up user study RegistrationShop Noeska Smit
- 22. Conclusion • RegistrationShop: medical volume registration system • Simple transformation techniques: – manual and landmark transformations • Instant visual feedback: – 2D/3D inspection of current registration result RegistrationShop Noeska Smit
- 23. Acknowledgements • This work is supported by the Technology Foundation STW via project 10903: “High-definition Atlas-based surgical planning for Pelvic Surgery” • CT lung datasets shown in this presentation are available from the Elastix test suite • We would like to thank our collaborators and domain experts for their participation in the user study RegistrationShop Noeska Smit
- 24. Thank you! @_Noeska_ , @berendkleinhane @medvisorg github.com/berendkleinhaneveld/Registrationshop RegistrationShop Noeska Smit
Editor's Notes
- Imagine you have a pre- and post-treatment scan of a patient and we want to examine the treatment effects. There is one small problem, the patient is not in the exact same position in both scans Wouldn’t it be great if we can just register these two scans to spot the differences?
- The same holds for combining two scans from different modalities to enrich them with additional information? T1: anatomy structural information DWI: water diffusion which can indicate tumor characteristics
- What about using an atlas to segment an unseen dataset?
- We need an easy way to register all these dataset pairs together
- Many tools that perform registrations exist, but they are often complex for novice users
- We could try to manually align the datasets using rigid transformations in a tool like Slicer But is using sliders and 2D overlays really the easiest way to do this? Or to place corresponding landmark pairs and align the scans based on these But we only see the result of the transformation once all landmark pairs are set
- We could use a command-line tool such as Elastix to perform deformable registrations But it has no direct visual feedback on intermediate registration results and the learning curve for novice users is steep
- When we compare these tools, often only 2D visualization or missing transformation tools What if I’m not an image processing expert but a clinician or researcher from a different field?
- What if we use simple interaction techniques and real-time visual feedback to simplify the registration process? With this in mind, we designed a system that allow a user to import two volumes and create simple 3D visualizations. The user can perform transformations by interacting with the moving volume to register it to the target volume, while our system provides feedback on the current registration result. After each registrationstep, the user can evaluate the results and either adjust the transformations or accept the result to iteratively converge to a satisfactory registration result
- Placing landmarks in the intended location can be challenging in 3D. Therefore we introduce two techniques to easily place corresponding landmarks in 3D. If a surface can be visualized for a structure of interest, the user can place landmarks directly on the surface using the surface picker. The arrow indicates the surface normal and is used as a cursor for landmark picking
- When the structures of interest can not be clearly visualized as a surface and occlusion is present, the two-step picker can be used. In the first step, the user defines a ray from the camera to the selected point, while in the second step, the intended depth along the ray can be picked. An intensity profile of the values encountered along the ray with a linked cursor aids the user in specifying the correct depth
- We introduce simple visualization techniques to quickly visualize structures of interest in 3D Double thresholds and opacity values can be set to make simple 3D visualizations. When the structures of interest are of high intensity a maximum intensity projection can be selected.
- We visualize the current registration result using multivolume-rendering techniques in 3D for each of the three potential visualization combinations. By always displaying the target volume in orange and the moving volume in blue, the volumes can be identified. Furthermore, in the MIP+MIP view, these colors sum to white when there is overlap.
- The full system is called RegistrationShop. It combines the aforementioned techniques and several more features in a single application. Target volume left in orange Moving volume right in blue Registration result in the center
- RegistrationShop is implemented in Python using VTK extended with custom multi-volume rendering features. We rely on Elastix for advanced registration techniques.
- Let’s take a look at some of these features in a short demo video.
- We evaluated RegistrationShop with four domain experts. RegistrationShop was considered a promising volume registration tool with the potential to make registration more accessible to clinicians and researchers in the future.
- We evaluated RegistrationShop with four domain experts. RegistrationShop was considered a promising volume registration tool with the potential to make registration more accessible to clinicians and researchers in the future.
- 3D: Appreciated, but need to become familiar with them first 2D is required for detailed inspection of the results Transformation tools: Good manual initialization possible for subsequent steps Two-step landmark picking was considered useful Real-time visualization of intermediate registration result very helpful
- There is still room for improvements such as visualizing registration quality, visualizing non-rigid deformation field, experimenting with compositing operations or transfer function definitions, examining clinical potential in follow-up user study.
- We presented the RegistrationShop system: a prototype registration software tool that provides users with simple transformation tools combined with visual feedback of the registration result