using avid for 3d functional region of interest (roi) creation jeff hoerle [email protected] friday...
Post on 18-Dec-2015
213 views
TRANSCRIPT
![Page 1: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/1.jpg)
Using AVID for 3D Functional Region Of Interest (ROI) Creation
Jeff [email protected]
Friday ForumNovember 5th, 2004
![Page 2: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/2.jpg)
AVID - Outline
• Motivation
• Initial Concepts
• Solution and Demonstration
• Implementation
• User Study Overview
• Future Work
![Page 3: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/3.jpg)
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
![Page 4: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/4.jpg)
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
![Page 5: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/5.jpg)
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
![Page 6: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/6.jpg)
AVID - Motivation
• Example: Functional ROI Drawing Tool
![Page 7: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/7.jpg)
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)?
![Page 8: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/8.jpg)
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
![Page 9: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/9.jpg)
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)
![Page 10: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/10.jpg)
AVID – Initial Concepts
• Scheme Three – use a magic wand tool to select an entire cluster (connected component) of activation
![Page 11: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/11.jpg)
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?
![Page 12: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/12.jpg)
AVID
Demonstration
![Page 13: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/13.jpg)
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
![Page 14: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/14.jpg)
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
![Page 15: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/15.jpg)
AVID - Implementation
Human Heart Simulation
Reservoir Model - GeoMap
- Univ of OsloAbdomen Segmentation – SINTEF CactusX
![Page 16: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/16.jpg)
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
![Page 17: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/17.jpg)
AVID - Implementation
Collaboration Diagram
Inheritance Diagram
![Page 18: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/18.jpg)
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
![Page 19: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/19.jpg)
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?
![Page 20: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/20.jpg)
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
![Page 21: Using AVID for 3D Functional Region Of Interest (ROI) Creation Jeff Hoerle jeffh@cs.duke.edu Friday Forum November 5 th, 2004](https://reader030.vdocument.in/reader030/viewer/2022032703/56649d245503460f949fb086/html5/thumbnails/21.jpg)
AVID - Acknowledgements
• Rachael Brady – VTG
• Allen Song – BIAC
• Melanie Wright – Human Simulation Lab
• Josh Bizzell – BIAC