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

Jeff Hoerlejeffh@cs.duke.edu

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