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General Linear Model in fMRI Analysis

The document provides an overview of the general linear model (GLM) approach used for analyzing functional magnetic resonance imaging (fMRI) data. It discusses how the GLM treats fMRI data as a linear combination of model functions and noise. A standard GLM expresses the blood oxygen level dependent (BOLD) signal as a design matrix multiplied by regression coefficients plus error. It also notes that the GLM allows for incorporating knowledge about the signal and noise properties of fMRI data to construct appropriate models and estimates.

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2 views13 pages

General Linear Model in fMRI Analysis

The document provides an overview of the general linear model (GLM) approach used for analyzing functional magnetic resonance imaging (fMRI) data. It discusses how the GLM treats fMRI data as a linear combination of model functions and noise. A standard GLM expresses the blood oxygen level dependent (BOLD) signal as a design matrix multiplied by regression coefficients plus error. It also notes that the GLM allows for incorporating knowledge about the signal and noise properties of fMRI data to construct appropriate models and estimates.

Uploaded by

augustus1189
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Module 10: The General Linear Model

Data Processing Pipeline


! !Experimental Design !

Data Acquisition !

Preprocessing ! !

Reconstruction!

Slice-time ! ! ! Correction! ! ! !Motion Correction,! ! Co-registration &! ! !Normalization! ! ! ! Spatial! ! Smoothing! !

Data Analysis! ! ! Localizing !


! Brain Activity! ! ! ! ! Connectivity! ! ! ! ! ! Prediction! ! !

Statistical Analysis
" There are multiple goals in the statistical analysis of fMRI data. " They include:
" localizing brain areas activated by the task; " determining networks corresponding to brain function; and " making predictions about psychological or disease states.

Human Brain Mapping


" The most common use of fMRI to date has been to localize areas of the brain that activate in response to a certain task. " These types of human brain mapping studies are necessary for the development of biomarkers and increasing our understanding of brain function.

Massive Univariate Approach


" Typically analysis is performed by constructing a separate model at each voxel
" The massive univariate approach. " Assumes an improbable independence between voxel pairs......

" Typically dependencies between voxels are dealt with later using random field theory, which makes assumptions about the spatial dependencies between voxels.

General Linear Model


" The general linear model (GLM) approach treats the data as a linear combination of model functions (predictors) plus noise (error). " The model functions are assumed to have known shapes, but their amplitudes are unknown and need to be estimated. " The GLM framework encompasses many of the commonly used techniques in fMRI data analysis (and data analysis more generally).

Illustration
" Consider an experiment of alternating blocks of finger-tapping and rest. " Construct a model to study data from a single voxel for a single subject. " We seek to determine whether activation is higher during finger-tapping compared with rest.

fMRI Data

Design matrix

Model parameters

Residuals

&' 0 # $' ! % 1"

BOLD signal

Intercept

Predicted task response

H 0 : !1 = 0

GLM
A standard GLM can be written:

Y = X" + !
where

! ~ N (0, V )

&Y1 # &1 X 11 " X 1 p # & ) 0 # & (1 # ! $) ! $ ! $Y ! $1 X " X (2 ! 21 2p! $ 1 ! $ 2! = $ $ ' + ! ! ! $ ! ! $!! $ ! ! $! ! $ ! $ ! $ ! $1 X " X Y np np " % ) p " % n" % %( n "

V is the covariance matrix whose format depends on the noise model.

fMRI Data

Design matrix

Noise

Regression coefficients

The quality of the model depends on our choice of X and V.

Estimation
" If ! is i.i.d., then Ordinary Least Square (OLS) estimate is optimal
model estimate

Y = X" + !

!1 ! = ( X' X) X' Y

" If Var(!) =V"2 # I"2, then Generalized Least Squares (GLS) estimate is optimal
model estimate

Y = X" + !

= ( X' V !1X) !1 X' V !1Y !

Model Refinement
" This model has a number of shortcomings. " We want to use our understanding of the signal and noise properties of BOLD fMRI to aid us in constructing appropriate models. " This includes deciding on an appropriate design matrix, as well as an appropriate noise model.

Issues
1." BOLD responses have a delayed and dispersed form. 2." The fMRI signal includes substantial amounts of lowfrequency noise.! 3." The data are serially correlated which needs to be considered in the model.!

End of Module

@fMRIstats

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