# Blog Archives

## The Statistical Whitening Transform

In a number of modeling scenarios, it is beneficial to transform the to-be-modeled data such that it has an identity covariance matrix, a procedure known as Statistical Whitening. When data have an identity covariance, all dimensions are statistically independent, and the variance of the data along each of the dimensions is equal to one. (To get a better idea of what an identity covariance entails, see the following post.)

Enforcing statistical independence is useful for a number of reasons. For example, in probabilistic models of data that exist in multiple dimensions, the joint distribution–which may be very complex and difficult to characterize–can factorize into a product of many simpler distributions when the dimensions are statistically independent. Forcing all dimensions to have unit variance is also useful. For instance, scaling all variables to have the same variance treats each dimension with equal importance.

In the remainder of this post we derive how to transform data such that it has an identity covariance matrix, give some examples of applying such a transformation to real data, and address some interpretations of statistical whitening in the scope of theoretical neuroscience.

## Decorrelation: Transforming Data to Have a Diagonal Covariance Matrix

Let’s say we have some data matrix $X$ composed of $K$ dimensions and $n$ observations ($X$ has  size $[K \times n]$).  Let’s also assume that the rows of $X$ have been centered (the mean has been subracted across all observations) . The covariance $\Sigma$ of each of the dimensions with respect to the other is

$\Sigma = Cov(X) = \mathbb E[X X^T]$                                                                                        (1)

Where the covariance $\mathbb E[X X^T]$ can be estimated from the data matrix as follows:

$\mathbb E[X X^T] \approx \frac{X X^T}{n}$                                                                                            (2)

The covariance matrix $\Sigma$, by definition (Equation 2) is symmetric and positive semi-definite (if you don’t know what that means, don’t worry it’s not terribly important for this discussion). Thus we can write the matrix as the product of two simpler matrices $E$ and $D$, using a procedure known as Eigenvalue Decomposition:

$\Sigma = EDE^{-1}$                                                                                                 (3)

The matrix $E$ is an $[K \times K]$-sized matrix, where each column is an eigenvector of $\Sigma$, and $D$ is a diagonal matrix whose diagonal elements $D_{ii}$ are eigenvalues that correspond to the eigenvectors of the $i$-th column of $E$.  For more details on eigenvectors and eigenvalues see the following. From Equation (3), and using a little algebra, we can transform $\Sigma$ into the diagonal matrix $D$

$E^{-1} \Sigma E = D$                                                                                                 (4)

Now, imagine the goal is to transform the data matrix $X$ into a new data matrix $Y$

$Y = W_DX$                                                                                                   (5)

whose dimensions are uncorrelated (i.e. $Y$ has a diagonal covariance $D$). Thus we want to determine the transformation $W_D$ that makes:

$D = Cov(Y) = \mathbb E[YY^T]$                                                                                   (6)

Here we derive the expression for $W_D$ using Equations (2), (4), (5), and (6):

$D = \frac{W_DX(W_DX)^T}{n}$                                                       (a la Equations (5) and (6))

$D = W_D W_D^T \Sigma$                                                                       (via Equation (2))

$E^{-1}\Sigma E = W_D W_D^T \Sigma$                                                                   (via Equation (4))

$\Sigma^{-1}E^{-1} \Sigma E = \Sigma^{-1}W_D W_D^T \Sigma$

now, because $E^{-1} = E^T$                                             (see following link for details)

$E^TE = W_DW_D^T$ and thus

$W_D = E^T$                                                                                                   (7)

This means that we can transform $X$ into an uncorrelated (i.e. orthogonal) set of variables by premultiplying data matrix $X$ with the transpose of the the eigenvectors of data covariance matrix $\Sigma$.

## Whitening: Transforming data to have an Identity Covariance matrix

Ok, so now we have a way of transforming our data so that the dimensions are uncorrelated. However, this only gives us a diagonal covariance matrix, not an Identity covariance matrix. In order to obtain an Identity covariance, we also need to scale each dimension so that its variance is equal to one. How can we determine this transformation? We know how to transform our data so that the covariance is equal to $D$. If we can determine the transformation that leaves $D = I$, then we can apply this transformation to our decorrelated covariance to give us the desired whitening transform. We can determine this from the somewhat trivial notion that

$D^{-1}D = I$                                                                                                        (8)

and further that

$D^{-1} = D^{-1/2}ID^{-1/2}$                                                                                             (9)

Now, using Equation (4) along with Equation (8), we can see that

$D^{-1/2}E^{-1}\Sigma E D^{-1/2} = I$                                                                                      (10)

Now say that we define a variable $Y = W_W X$, where $W_W$ is the desired whitening transform, that leaves the covariance of $Y$ equal to the identity matrix. Using essentially the same set of derivation steps as above to solve for $W_D$, but starting from Equation (9) we find that

$W_W = D^{-1/2}E^T$                                                                                                  (11)

$= D^{-1/2}W_D$                                                                                                 (12)

Thus, the whitening transform is simply the decorrelation transform, but scaled by the inverse of the square root of the $D$ (here the inverse and square root can be performed element-wise because $D$ is a diagonal matrix).

## Interpretation of the Whitening Transform

So what does the whitening transformation actually do to the data (below, blue points)? We investigate this transformation below: The first operation decorrelates the data by premultiplying the data with the eigenvector matrix $E^T$, calculated from the data covariance. This decorrelation can be thought of as a rotation that reorients the data so that the principal axes of the data are aligned with the axes along which the data has the largest (orthogonal) variance. This rotation is essentially the same procedure as the oft-used Principal Components Analysis (PCA), and is shown in the middle row.

The second operation, scaling by $D^{-1/2}$ can be thought of squeezing the data–if the variance along a dimension is larger than one–or stretching the data–if the variance along a dimension is less than one. The stretching and squeezing forms the data into a sphere about the origin (which is why whitening is also referred to as “sphering”). This scaling operation is depicted in the bottom row in the plot above.

The MATLAB to make make the plot above is here:

% INITIALIZE SOME CONSTANTS
mu = [0 0];
S = [1 .9; .9 3];

% SAMPLE SOME DATAPOINTS
nSamples = 1000;
samples = mvnrnd(mu,S,nSamples)';

% WHITEN THE DATA POINTS...
[E,D] = eig(S);

% ROTATE THE DATA
samplesRotated = E*samples;

% TAKE D^(-1/2)
D = diag(diag(D).^-.5);

% SCALE DATA BY D
samplesRotatedScaled = D*samplesRotated;

% DISPLAY
figure;

subplot(311);
plot(samples(1,:),samples(2,:),'b.')
axis square, grid
xlim([-5 5]);ylim([-5 5]);
title('Original Data');

subplot(312);
plot(samplesRotated(1,:),samplesRotated(2,:),'r.'),
axis square, grid
xlim([-5 5]);ylim([-5 5]);
title('Decorrelate: Rotate by V');

subplot(313);
plot(samplesRotatedScaled(1,:),samplesRotatedScaled(2,:),'ko')
axis square, grid
xlim([-5 5]);ylim([-5 5]);
title('Whiten: scale by D^{-1/2}');


The transformation in Equation (11) and implemented above  whitens the data but leaves the data aligned with principle axes of the original data. In order to observe the data in the original space, it is often customary “un-rotate” the data back into it’s original space. This is done by just multiplying the whitening transform by the inverse of the rotation operation defined by the eigenvector matrix. This gives the whitening transform:

$W =E^{-1}D^{-1/2}E^T$                                                                                                   (13)

Let’s take a look an example of using statistical whitening for a more complex problem: whitening patches of images sampled from natural scenes.

## Example: Whitening Natural Scene Image Patches

Modeling the local spatial structure of pixels in natural scene images is important in many fields including computer vision and computational neuroscience. An interesting model of natural scenes is one that can account for interesting, high-order statistical dependencies between pixels. However, because natural scenes are generally composed of continuous objects or surfaces, a vast majority of the spatial correlations in natural image data can be explained by local pairwise dependencies. For example, observe the image below.

% LOAD AND DISPLAY A NATURAL IMAGE
im = double(imread('cameraman.tif'));
figure
imagesc(im); colormap gray; axis image; axis off;
title('Base Image')


Given one of the gray pixels in the upper portion of the image, it is very likely that all pixels within the local neighborhood will also be gray. Thus there is a large amount of correlation between pixels in local regions of natural scenes. Statistical models of local structure applied to natural scenes will be dominated by these pairwise correlations, unless they are removed by preprocessing. Whitening provides such a preprocessing procedure.

Below we create and display a dataset of local image patches of size $16 \times 16$ extracted at random from the image above. Each patch is rastered out into a column vector of size $(16)16 \times 1$. Each of these patches can be thought of as samples of the local structure of this natural scene. Below we use the whitening transformation to remove pairwise correlations between pixels in each patch and scale the variance of each pixel to be one.

On the left is the dataset of extracted image patches, along with the corresponding covariance matrix for the image patches on the right. The large local correlation within the neighborhood of each pixel is indicated by the large bright diagonal regions throughout the covariance matrix.

The MATLAB code to extract and display the patches shown above is here:

% CREATE PATCHES DATASET FROM NATURAL IMAGE
rng(12345)
imSize = 256;
nPatches = 400;  % (MAKE SURE SQUARE)
patchSize = 16;
patches = zeros(patchSize*patchSize,nPatches);
patchIm = zeros(sqrt(nPatches)*patchSize);

% PAD IMAGE FOR EDGE EFFECTS
im = padarray(im,[patchSize,patchSize],'symmetric');

% EXTRACT PATCHES...
for iP = 1:nPatches
pix = ceil(rand(2,1)*imSize);
rows = pix(1):pix(1)+patchSize-1;
cols = pix(2):pix(2)+patchSize-1;
tmp = im(rows,cols);
patches(:,iP) = reshape(tmp,patchSize*patchSize,1);
rowIdx = (ceil(iP/sqrt(nPatches)) - 1)*patchSize + ...
1:ceil(iP/sqrt(nPatches))*patchSize;
colIdx = (mod(iP-1,sqrt(nPatches)))*patchSize+1:patchSize* ...
((mod(iP-1,sqrt(nPatches)))+1);
patchIm(rowIdx,colIdx) = tmp;
end

% CENTER IMAGE PATCHES
patchesCentered = bsxfun(@minus,patches,mean(patches,2));

% CALCULATE COVARIANCE MATRIX
S = patchesCentered*patchesCentered'/nPatches;

% DISPLAY PATCHES
figure;
subplot(121);
imagesc(patchIm);
axis image; axis off; colormap gray;
title('Extracted Patches')

% DISPLAY COVARIANCE
subplot(122);
imagesc(S);
axis image; axis off; colormap gray;
title('Extracted Patches Covariance')


Below we implement the whitening transformation described above to the extracted image patches and display the whitened patches that result.

On the left, we see that the whitening procedure zeros out all areas in the extracted patches that have the same value (zero is indicated by gray). The whitening procedure also boosts the areas of high-contrast (i.e. edges). The right plots the covariance matrix for the whitened patches. The covarance matrix is diagonal, indicating that pixels are now independent. In addition, all diagonal entries have the same value, indicating the that all pixels now have the same variance (i.e. 1). The MATLAB code used to whiten the image patches and create the display above is here:

%% MAIN WHITENING

% DETERMINE EIGENECTORS & EIGENVALUES
% OF COVARIANCE MATRIX
[E,D] = eig(S);

% CALCULATE D^(-1/2)
d = diag(D);
d = real(d.^-.5);
D = diag(d);

% CALCULATE WHITENING TRANSFORM
W = E*D*E';

% WHITEN THE PATCHES
patchesWhitened = W*patchesCentered;

% DISPLAY THE WHITENED PATCHES
wPatchIm = zeros(size(patchIm));
for iP = 1:nPatches
rowIdx = (ceil(iP/sqrt(nPatches)) - 1)*patchSize + 1:ceil(iP/sqrt(nPatches))*patchSize;
colIdx = (mod(iP-1,sqrt(nPatches)))*patchSize+1:patchSize* ...
((mod(iP-1,sqrt(nPatches)))+1);
wPatchIm(rowIdx,colIdx) = reshape(patchesWhitened(:,iP),...
[patchSize,patchSize]);
end

figure
subplot(121);
imagesc(wPatchIm);
axis image; axis off; colormap gray; caxis([-5 5]);
title('Whitened Patches')

subplot(122);
imagesc(cov(patchesWhitened'));
axis image; axis off; colormap gray; %colorbar
title('Whitened Patches Covariance');


## Investigating the Whitening Matrix: implications for theoretical neuroscience

So what does the whitening matrix look like, and what does it do? Below is the whitening matrix $W$ calculated for the image patches dataset:

% DISPLAY THE WHITENING MATRIX
figure; imagesc(W);
axis image; colormap gray; colorbar
title('The Whitening Matrix W')


Each column of $W$ is the operation that scales the variance of the corresponding pixel to be equal to one and forces that pixel independent of the others in the $16 \times 16$ patch. So what exactly does such an operation look like? We can get an idea by reshaping a column of W back into the shape of the image patches. Below we show what the 86th column of W looks like when reshaped in such a way (the index 86 has no particular significance, it was chosen at random):

% DISPLAY A COLUMN OF THE WHITENING MATRIX
figure; imagesc(reshape(W(:,86),16,16)),
colormap gray,
axis image, colorbar
title('Column 86 of W')


We see that the operation is essentially an impulse centered on the 86th pixel in the image (counting pixels starting in the upper left corner, proceeding down columns). This impulse is surrounded by inhibitory weights. If we were to look at the remaining columns of $W$, we would find that that the same center-surround operation is being replicated at every pixel location in each image patch. Essentially, the whitening transformation is performing a convolution of each image patch with a center-surround filter whose properties are estimated from the patches dataset. Similar techniques are common in computer vision edge-detection algorithms.

## Implications for theoretical neuroscience

A theoretical function of the primate retina is data compression: a large number of photoreceptors  pass data from the retina into a physiological bottleneck, the optic nerve, which has far fewer fibers than retinal photoreceptors. Thus removing redundant information is an important task that the retina must perform. When observing the whitened image patches above, we see that redundant information is nullified; pixels that have similar local values to one another are zeroed out. Thus, statistical whitening is a viable form of data compression

It turns out that there is a large class of ganglion cells in the retina whose spatial receptive fields exhibit…that’s right center-surround activation-inhibition like the operation of the whitening matrix shown above! Thus it appears that the primate visual system may be performing data compression at the retina by means of a similar operation to statistical whitening. Above, we derived the center-surround whitening operation based on data sampled from a natural scene. Thus it is seems reasonable that the primate visual system may have evolved a similar data-compression mechanism through experience with natural scenes, either through evolution, or development.

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## fMRI in Neuroscience: Estimating Voxel Selectivity & the General Linear Model (GLM)

In a typical fMRI experiment  a series of stimuli are presented to an observer and evoked brain activity–in the form of blood-oxygen-level-dependent (BOLD) signals–are measured from tiny chunks of the brain called voxels. The task of the researcher is then to infer the tuning of the voxels to features in the presented stimuli based on the evoked BOLD signals. In order to make this inference quantitatively, it is necessary to have a  model of how BOLD signals are evoked in the presence of stimuli. In this post we’ll develop a model of evoked BOLD signals, and from this model recover the tuning of individual voxels measured during an fMRI experiment.

## Modeling the Evoked BOLD Signals — The Stimulus and Design Matrices

Suppose we are running an event-related fMRI experiment where we present $C$ different stimulus conditions to an observer while recording the BOLD signals evoked in their brain over a series of $T$ consecutive fMRI measurements (TRs). We can represent the stimulus presentation quantitatively with a $T \times C$ binary Stimulus Matrix, $D$, whose entries indicate the onset of each stimulus condition (columns) at each point in time (rows). Now let’s assume that we have an accurate model of how a voxel is activated by a single, very short stimulus. This activation model is called hemodynamic response function (HRF), $h$, for the voxel, and, as we’ll discuss in a later post, can be estimated from the measured BOLD signals. Let’s assume for now that the voxel is also activated to an equal degree to all stimuli. In this scenario we can represent the BOLD signal evoked over the entire experiment with another $T \times C$ matrix $X$ called the Design Matrix that is the convolution of the stimulus matrix $D$ with the voxel’s HRF $h$.

$X = D * h$

Note that this model of the BOLD signal is an example of the Finite Impulse Response (FIR) model that was introduced in the previous post on fMRI Basics.

To make the concepts of $D$ and $X$ more concrete, let’s say our experiment consists of $C = 3$ different stimulus conditions: a light, a tone, and heat applied to the palm. Each stimulus condition is presented twice in a staggered manner during 80 TRs of fMRI measurements. The stimulus matrix and the design matrix are simulated here in Matlab:

TR = 1; % REPETITION TIME
t = 1:TR:20; % MEASUREMENTS
h = gampdf(t,6) + -.5*gampdf(t,10); % HRF MODEL
h = h/max(h); % SCALE HRF TO HAVE MAX AMPLITUDE OF 1

trPerStim = 30; % # TR PER STIMULUS
nRepeat = 2; % # OF STIMULUS REPEATES
nTRs = trPerStim*nRepeat + length(h);
impulseTrain0 = zeros(1,nTRs);

% VISUAL STIMULUS
impulseTrainLight = impulseTrain0;
impulseTrainLight(1:trPerStim:trPerStim*nRepeat) = 1;

% AUDITORY STIMULUS
impulseTrainTone = impulseTrain0;
impulseTrainTone(5:trPerStim:trPerStim*nRepeat) = 1;

% SOMATOSENSORY STIMULUS
impulseTrainHeat = impulseTrain0;
impulseTrainHeat(9:trPerStim:trPerStim*nRepeat) = 1;

% COMBINATION OF ALL STIMULI
impulseTrainAll = impulseTrainLight + impulseTrainTone + impulseTrainHeat;

% SIMULATE VOXELS WITH VARIOUS SELECTIVITIES
visualTuning = [4 0 0]; % VISUAL VOXEL TUNING
auditoryTuning = [0 2 0]; % AUDITORY VOXEL TUNING
somatoTuning = [0 0 3]; % SOMATOSENSORY VOXEL TUNING
noTuning = [1 1 1]; % NON-SELECTIVE

beta = [visualTuning', ...
auditoryTuning', ...
somatoTuning', ...
noTuning'];

% EXPERIMENT DESIGN / STIMULUS SEQUENCE
D = [impulseTrainLight',impulseTrainTone',impulseTrainHeat'];

% CREATE DESIGN MATRIX FOR THE THREE STIMULI
X = conv2(D,h'); % X = D * h
X(nTRs+1:end,:) = []; % REMOVE EXCESS FROM CONVOLUTION

% DISPLAY STIMULUS AND DESIGN MATRICES
subplot(121); imagesc(D); colormap gray;
xlabel('Stimulus Condition')
ylabel('Time (TRs)');
title('Stimulus Train, D');
set(gca,'XTick',1:3); set(gca,'XTickLabel',{'Light','Tone','Heat'});

subplot(122);
imagesc(X);
xlabel('Stimulus Condition')
ylabel('Time (TRs)');
title('Design Matrix, X = D * h')
set(gca,'XTick',1:3); set(gca,'XTickLabel',{'Light','Tone','Heat'});



Stimulus presentation matrix, D (left) and the Design Matrix X for an experiment with three stimulus conditions: a light, a tone, and heat applied to the palm

Each column of the design matrix above (the right subpanel in the above figure) is essentially a model of the BOLD signal evoked independently by each stimulus condition, and the total signal is simply a sum of these independent signals.

## Modeling Voxel Tuning — The Selectivity Matrix

In order to develop the concept of the design matrix we assumed that our theoretical voxel is equally tuned to all stimuli. However, few voxels in the brain exhibit such non-selective tuning. For instance, a voxel located in visual cortex will be more selective for the light than for the tone or the heat stimulus. A voxel in auditory cortex will be more selective for the tone than for the other two stimuli. A voxel in the somoatorsensory cortex will likely be more selective for the heat than the visual or auditory stimuli. How can we represent the tuning of these different voxels?

A simple way to model tuning to the stimulus conditions in an experiment is to multiplying each column of the design matrix by a weight that modulates the BOLD signal according to the presence of the corresponding stimulus condition. For example, we could model a visual cortex voxel by weighting the first column of $X$ with a positive value, and the remaining two columns with much smaller values (or even negative values to model suppression). It turns out that we can model the selectivity of $V$ individual voxels simultaneously through a $C \times V$ Selectivity Matrix$\beta$. Each entry in $\beta$ is the amount that the $v$-th voxel (columns) is tuned to the $c$-th stimulus condition (rows). Given the design matrix and the selectivity matrix, we can then predict the BOLD signals $y$ of selectively-tuned voxels with a simple matrix multiplication:

$y = X\beta$

Keeping with our example experiment, let’s assume that we are modeling the selectivity of four different voxels: a strongly-tuned visual voxel, a moderately-tuned somatosensory voxel, a weakly tuned auditory voxel, and an unselective voxel that is very weakly tuned to all three stimulus conditions. We can represent the tuning of these four voxels with a $3 \times 4$ selectivity matrix. Below we define a selectivity matrix that represents the tuning of these 4 theoretical voxels and simulate the evoked BOLD signals to our 3-stimulus experiment.

% SIMULATE NOISELESS VOXELS' BOLD SIGNAL
% (ASSUMING VARIABLES FROM ABOVE STILL IN WORKSPACE)
y0 = X*beta;

figure;
subplot(211);
imagesc(beta); colormap hot;
axis tight
ylabel('Condition')
set(gca,'YTickLabel',{'Visual','Auditory','Somato.'})
xlabel('Voxel');
set(gca,'XTick',1:4)
title('Voxel Selectivity, \beta')

subplot(212);
plot(y0,'Linewidth',2);
legend({'Visual Voxel','Auditory Voxel','Somato. Voxel','Unselective'});
xlabel('Time (TRs)'); ylabel('BOLD Signal');
title('Activity for Voxels with Different Stimulus Tuning')
set(gcf,'Position',[100 100 750 540])
subplot(211); colorbar


Selectivity matrix (top) for four theoretical voxels and GLM BOLD signals (bottom) for a simple experiment

The top subpanel in the simulation output visualizes the selectivity matrix defined for the four theoretical voxels. The bottom subpanel plots the columns of the $T \times V$ matrix of voxel responses $y$. We see that the maximum response of the strongly-tuned visual voxel (plotted in blue) is larger than that of the other voxels, corresponding to the larger weight upper left of the selectivity matrix. Also note that the response for the unselective voxel (plotted in cyan) demonstrates the linearity property of the FIR model. The attenuated but complex BOLD signal from the unselective voxel results from the sum of small independent signals evoked by each stimulus.

## Modeling Voxel Noise

The example above demonstrates how we can model BOLD signals evoked in noisless theoretical voxels. Though this noisless scenario is helpful for developing a modeling framework, real-world voxels exhibit variable amounts of noise (noise is any signal that cannot be accounted by the FIR model). Therefore we need to incorporate a noise term into our BOLD signal model.

The noise in a voxel is often modeled as a random variable $\epsilon$. A common choice for the noise model is a zero-mean Normal/Gaussian distribution with some variance $\sigma^2$:

$\epsilon \sim \mathcal N(0,\sigma^2)$

Though the variance of the noise model may not be known apriori, there are methods for estimating it from data. We’ll get to estimating noise variance in a later post when we discuss various sources of noise and how to account for them using more advance techniques. For simplicity, let’s just assume that the noise variance is 1 as we proceed.

## Putting It All Together — The General Linear Model (GLM)

So far we have introduced on the concepts of the stimulus matrix, the HRF, the design matrix, selectivity matrix, and the noise model. We can combine all of these to compose a comprehensive quantitative model of BOLD signals measured from a set of voxels during an experiment:

$y = X\beta + \epsilon \\ = (D * h)\beta + \epsilon$

This is referred to as the General Linear Model (GLM).

In a typical fMRI experiment the researcher controls the stimulus presentation $D$, and measures the evoked BOLD responses $y$ from a set of voxels. The problem then is to estimate the selectivities of the voxels based on these measurments. Specifically, we want to determine the parameters $\hat \beta$ that best explain the measured BOLD signals during our experiment. The most common way to do this is a method known as Ordinary Least Squares (OLS) Regression. Using OLS the idea is to adjust the values of $\hat \beta$ such that the predicted model BOLD signals are as similar to the measured signals as possible. In other words, the goal is to infer the selectivity each voxel would have to exhibit in order to produce the measured BOLD signals. I showed in an earlier post that the optimal OLS solution for the selectivities $\hat \beta$ is given by:

$\hat \beta = (X^T X)^{-1} X^T y$

Therefore, given a design matrix $X$ and a set of voxel responses $y$ associated with the design matrix, we can calculate the selectivities of voxels to the stimulus conditions represented by the columns of the design matrix. This works even when the BOLD signals are noisy. To get a better idea of this process at work let’s look at a quick example based on our toy fMRI experiment.

## Example: Recovering Voxel Selectivity Using OLS

Here the goal is to recover the selectivities of the four voxels in our toy experiment they have been corrupted with noise. First, we add noise to the voxel responses. In this example the variance of the added noise is based on a concept known as signal-to-noise-ration or SNR.  As the name suggests, SNR is the ratio of the underlying signal to the noise “on top of” the signal. SNR is a very important concept when interpreting fMRI analyses. If a voxel exhibits a low SNR, it will be far more difficult to estimate its tuning. Though there are many ways to define SNR, in this example it is defined as the ratio of the maximum signal amplitude to the variance of the noise model. The underlying noise model variance is adjusted to be one-fifth of the maximum amplitude of the BOLD signal, i.e. an SNR of 5.  Feel free to try different values of SNR by changing the value of the variable $\text{SNR}$ in the Matlab simulation. Noisy versions of the 4 model BOLD signals are plotted in the top subpanel of the figure below. We see that the noisy signals are very different from the actual underlying BOLD signals.

Noisy BOLD signals from 4 voxels (top) and GLM predictions (bottom) of the underlying BOLD signals

Here we estimate the selectivities $\hat \beta$ from the GLM using OLS, and then predict the BOLD signals in our experiment with this estimate. We see in the bottom subpanel of the above figure that the resulting GLM predictions of are quite accurate. We also compare the estimated selectivity matrix $\hat \beta$ to the actual selectivity matrix $\beta$ below. We see that OLS is able to recover the selectivity of all the voxels.

Actual (top) and estimated (bottom) selectivity matrices.

% SIMULATE NOISY VOXELS & ESTIMATE TUNING
% (ASSUMING VARIABLES FROM ABOVE STILL IN WORKSPACE)

SNR = 5; % (APPROX.) SIGNAL-TO-NOISE RATIO
noiseSTD = max(y0(:))./SNR; % NOISE LEVEL FOR EACH VOXEL
noise = bsxfun(@times,randn(size(y0)),noiseSTD);
y = y0 + noise;

betaHat = inv(X'*X)*X'*y % OLS
yHat = X*betaHat; % GLM PREDICTION

figure
subplot(211);
plot(y,'Linewidth',3);
xlabel('Time (s)'); ylabel('BOLD Signal');
legend({'Visual Voxel','Auditory Voxel','Somato. Voxel','Unselective'});
title('Noisy Voxel Responses');

subplot(212)
h1 = plot(y0,'Linewidth',3); hold on
h2 = plot(yHat,'-o');
legend([h1(end),h2(end)],{'Actual Responses','Predicted Responses'})
xlabel('Time (s)'); ylabel('BOLD Signal');
title('Model Predictions')
set(gcf,'Position',[100 100 750 540])

figure
subplot(211);
imagesc(beta); colormap hot(5);
axis tight
ylabel('Condition')
set(gca,'YTickLabel',{'Visual','Auditory','Somato.'})
xlabel('Voxel');
set(gca,'XTick',1:4)
title('Actual Selectivity, \beta')

subplot(212)
imagesc(betaHat); colormap hot(5);
axis tight
ylabel('Condition')
set(gca,'YTickLabel',{'Visual','Auditory','Somato.'})
xlabel('Voxel');
set(gca,'XTick',1:4)
title('Noisy Estimated Selectivity')
drawnow


## Wrapping Up

Here we introduced the GLM commonly used for fMRI data analyses and used the GLM framework to recover the selectivities of simulated voxels. We saw that the GLM is quite powerful of recovering the selectivity in the presence of noise. However, there are a few details left out of the story.

First, we assumed that we had an accurate (albeit exact) model for each voxel’s HRF. This is generally not the case. In real-world scenarios the HRF is either assumed to have some canonical shape, or the shape of the HRF is estimated the experiment data. Though assuming a canonical HRF shape has been validated for block design studies of peripheral sensory areas, this assumption becomes dangerous when using event-related designs, or when studying other areas of the brain.

Additionally, we did not include any  physiological noise signals in our theoretical voxels. In real voxels, the BOLD signal changes due to physiological processes such as breathing and heartbeat can be far larger than the signal change due to underlying neural activation. It then becomes necessary to either account for the nuisance signals in the GLM framework, or remove them before using the model described above. In two upcoming posts we’ll discuss these two issues: estimating the HRF shape from data, and dealing with nuisance signals.