National Alliance for Medical Image Computing Slicer fMRI introduction.

National Alliance for Medical Image Computing http://na-mic.org

Slicer fMRI introduction


• Todo: stress that the current effort is basic infrastructure…


Goal…

augment slicer to be a platform for fMRI analysis


strong coupling to anatomical analysis

• situate fMRI results in anatomy of individual

• make ROIs for use in fMRI analysis


workflow / human factors

• easy to use

• Wendy Plesniak


open source

• Matlab $$$

• buy in from research community– distributed development


Slicer workshop: prototype tools for fMRI and multi-volume applications

•Functional Magnetic Resonance Imaging & fMRI data

•Protocols and modeling

•Analysis and inference

•Visualization

•Tools: Ibrowser, fMRIEngine

(hands-on demos)

Wendy Plesniak, Haiying Liu



• What is BOLD-fMRI?

BOLD-fMRI is a technique for determining which parts of the brain are activated by different types of sensation (sight, sound), activity (tapping a finger), or by performing cognitive tasks.

This functional "brain mapping" is achieved by detecting the increased blood flow to the activated areas of the brain during a sequence of MRI scans.



•How is it being used?

Mapping of the brain

Informing neurosurgery

Understanding of disease/disease processes

…

Neuromarketing...



Functional Magnetic Resonance Imaging

MRI: single volumetric dataset to study brain structure

fMRI: volumetric time-series, e.g. acquire one volume every 2 sec for 5 min, to study brain function over time.

(Same slices from three volumes.) Low res: ~3mm3 voxels

(One slice in a single volume.)

High res: 1mm3 voxels


fMRI Setup



fMRI: data

•Takes temporal volumetric sampling of blood oxygen level in blood flow (BOLD signal) in brain of subject performing a motor or cognitive task, or attending to a sensory stimulus.

•Experimental protocol: blocked or event-related design

•Data collected: a time-series of brain volumes (e.g. 150 x 64 x 64 x 32 voxels)

Blood Oxygenation Level Dependent (BOLD) signal indirect measure of neural activity

neural activity blood oxygen fMRI signal



time

extract voxel or ROI timecourse…

t

fMRISignal

(% change)

voxel or ROI time course

protocol

...~ 11+ min

… and compare to protocol

t

fMRI: simple signal detection overview

Rest (c1)

Auditory (c2)

…

…

…

…

c1

c2



Form statistical inferences:

• test hypothesis that protocol-related signal is present in the data e.g. using t-test

• Convert into a p-value

• Threshold to form a parametric map of activation



1. Statistical parametric map of activation (superimposed on high resolution anatomical MRI

image)

fMRI: what to visualize?

2. Interactive plot of voxel time-course, compared to protocol

(visual check)



Other new techniques (future work fMRIEngine):

Techniques based on the mutual information between the protocol and the voxel timecourse:

Junmo Kim, John W. Fisher III, Andy Tsai, Cindy Wible, Alan S. Willsky, William M. Wells III. “Incorporating Spatial Priors into an Information Theoretic Approach for fMRI Data Analysis.” MICCAI 2000: 62-71.

Andy Tsai, John W. Fisher III, Cindy Wible, William M. Wells III, Junmo Kim, Alan S. Willsky. “Analysis of Functional MRI Data Using Mutual Information.” MICCAI 1999; 473-480.

Techniques that incorporate spatial priors:

Eric Cosman, John Fisher, Wanmei Ou, and William Wells“Exact MAP Activity Detection in fMRI Using A GLM with an Ising Spatial Prior”. MICCAI 2004.

Wanmei Ou : MS thesis

National Alliance for Medical Image Computing Slicer fMRI introduction.

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