Using AVID for 3D Functional Region Of Interest (ROI) Creation
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Transcript of Using AVID for 3D Functional Region Of Interest (ROI) Creation
Using AVID for 3D Functional Region Of Interest (ROI) Creation
Jeff [email protected]
Friday ForumNovember 5th, 2004
AVID - Outline
• Motivation• Initial Concepts• Solution and Demonstration• Implementation• User Study Overview• Future Work
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 xx
x = Functional Image Acquisition
AVID - Motivation
Functional Volumes
Event List (What and when)
SPMtstatprofile
Activation Map
• 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
AVID - Motivation
• What is a region of interest (ROI)?- any sub-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
AVID - Motivation
• Example: Functional ROI Drawing Tool
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)?
AVID – Initial Concepts
• Scheme One(1) Specify a bounding polygon or circle(2) Adjust the endplanes of the projected volume(3) Accept or reject volume
Step One Step Two
AVID – Initial Concepts• Scheme Two
(1) Click any point in the 3D volume(2) Select a point along the ray cast through the volume to
serve as the midpoint for the to-be-created sphere(3) Use mouse to modify the diameter and placement of the
sphere (and possibly shape too – make the sphere an ellipsoid)
AVID – Initial Concepts• Scheme Three
– use a magic wand tool to select an entire cluster (connected component) of activation
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?
AVID
Demonstration
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
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
AVID - Implementation
Human Heart Simulation
Reservoir Model - GeoMap
- Univ of OsloAbdomen Segmentation – SINTEF CactusX
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
AVID - Implementation
Collaboration Diagram
Inheritance Diagram
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
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?
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
AVID - Acknowledgements
• Rachael Brady – VTG• Allen Song – BIAC• Melanie Wright – Human Simulation Lab• Josh Bizzell – BIAC