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Using AVID for 3D Functional Region Of Interest (ROI) Creation

Using AVID for 3D Functional Region Of Interest (ROI) Creation. Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th , 2004. AVID - Outline. Motivation Initial Concepts Solution and Demonstration Implementation User Study Overview Future Work. AVID - Motivation.

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Using AVID for 3D Functional Region Of Interest (ROI) Creation

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  1. Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5th, 2004

  2. AVID - Outline • Motivation • Initial Concepts • Solution and Demonstration • Implementation • User Study Overview • Future Work

  3. AVID - Motivation • Where does the data used by AVID come from? Cognitive Neuroscience • Simple Example x x x x x x x x x x x x x x x x = Functional Image Acquisition

  4. AVID - Motivation • Activation Map – contains a statistical score (e.g. t-statistic) for each voxel in the functional volume that indicates the likelihood of activation due to a specific stimuli Generating an Activation Map SPM tstatprofile Functional Volumes Event List (What and when) Activation Map

  5. AVID - Motivation • What is a region of interest (ROI)? - anysub-region in space that possesses some “interesting” feature which requires further investigation • How is an ROI specified? - for a 3D volume, it typically involves a slice-by-slice investigation and selection of voxels - problem: time-consuming

  6. AVID - Motivation • Example: Functional ROI Drawing Tool

  7. AVID - Motivation • Can we use a 3D interface and interaction scheme to improve ROI creation? • What is the best way to navigate and interact in 3D using 2D interaction devices (e.g. mouse, desktop monitors)?

  8. Step One Step Two AVID – Initial Concepts • Scheme One • Specify a bounding polygon or circle • Adjust the endplanes of the projected volume • Accept or reject volume

  9. AVID – Initial Concepts • Scheme Two • Click any point in the 3D volume • Select a point along the ray cast through the volume to serve as the midpoint for the to-be-created sphere • Use mouse to modify the diameter and placement of the sphere (and possibly shape too – make the sphere an ellipsoid)

  10. AVID – Initial Concepts • Scheme Three – use a magic wand tool to select an entire cluster (connected component) of activation

  11. AVID - Solution • AVID uses a 3D magic wand • Pros: - Takes advantage of inherent clustering in activation maps - Very simple, avoid multi-step process • Cons: - What if the desired ROI consists of many small clusters of activation? - Region growth can extend beyond the desired anatomical region. What can be done to prevent this?

  12. AVID Demonstration

  13. AVID - Implementation • Windows… but why? - User population (BIAC) almost exclusively consists of Windows users • Visualization Toolkit (VTK) - Vastly sped the development of the 3D interface • Written in C++ using MFC library - VTK written in C++, making C++ an obvious choice for AVID

  14. AVID - Implementation • VTK - developed by Kitware (http://public.kitware.com/VTK) - open-source, object-oriented graphics library - written in C++ using OpenGL or Mesa as graphics API - can interface graphics API using Cocoa, Carbon, Win32 or X - has bindings written for Java, Tcl, Python

  15. AVID - Implementation Human Heart Simulation Abdomen Segmentation – SINTEF CactusX - Univ of Oslo Reservoir Model - GeoMap

  16. AVID – Implementation • VTK Pros: - design intelligently, factory classes allow the same code can be compiled for Linux, Mac, Windows (ideally) - speeds development, has pre-built visualization algorithms • VTK Cons: - VTK is HUGE and complex… over 900 classes with deep class hierarchies - doing things the “non-VTK way” can be (very) painful - not enough documentation

  17. AVID - Implementation Collaboration Diagram Inheritance Diagram

  18. AVID – User Study • Intended to be used as a feedback tool to improve functionality and extend feature set • NOT intended to provide a quality measurement of AVID based on some set of metrics • Recruit five to seven end-users to participate in a 20 – 30 minute session

  19. AVID – User Study • How does user expectation align with AVID functionality? • Do system defaults make sense? • What is the most intuitive mechanism to add/remove voxels from an ROI? - Can we think of ROI creation in terms of file selection?

  20. AVID – Future Work • Incorporate feedback from user study into new releases of AVID • Revisit the idea of 3D selection - will one of our existing schemes work? - are others out there? • Develop a “true” volumetric rendering option • Find the source of 3D rendering anomalies on VTK

  21. AVID - Acknowledgements • Rachael Brady – VTG • Allen Song – BIAC • Melanie Wright – Human Simulation Lab • Josh Bizzell – BIAC

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