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Example 4 Simulation Study B

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Junpeng Lao edited this page Aug 18, 2016 · 2 revisions

In this hypothetical experiment, two groups of subjects participated in a free viewing experiment of face recognition. We introduced a main effect between groups that control subject display a triangle pattern whereas the patient group only look at the month. However, there is an effect of the eye region for the patient group only: if they fixated on the eye they gave more accurate response (Interaction between group and accuracy).

We used Gaussian mixture model in Matlab for 2D data generation:

%% Generate dataset - GMM
clear all;clc;
p=userpath;
addpath(genpath([ p(1:end-1) '/Apps/iMAP']));

nsamp=10000;
% save current random generation state
defaultStream = RandStream.getGlobalStream();
savedState = defaultStream.State;
% use the Multiplicative Lagged Fibonacci algotrithm for independent substreams
mystream = RandStream.create('mlfg6331_64','NumStreams',nsamp,'StreamIndices',1);
RandStream.setGlobalStream(mystream);
reset(defaultStream); % allows restarting allays the same

xSize=100;
ySize=100;

muG=[40,55;60,55;50,30;50,48];
sigma(:,:,1) = [35 0; 0 30];
sigma(:,:,2) = [35 0; 0 30];
sigma(:,:,3) = [50 0; 0 60];
sigma(:,:,4) = [35 0; 0 60];
p = [30,30,50,10];% the mixing parameter for GMM

obj = gmdistribution(muG,sigma,p);
subplot(1,3,1)
ezsurf(@(x,y)pdf(obj,[x y]),[0 xSize],[0 ySize])
zlim([0,10])

subplot(1,3,2)
Nfix=10; % total number of fixation
Y = random(obj,Nfix);

plot(Y(:,1),Y(:,2),'o')
axis([0 xSize 0 ySize],'square')
%
% smooth map
smoothingpic=5;
[x, y] = meshgrid(-floor(ySize/2)+.5:floor(ySize/2)-.5, -floor(xSize/2)+.5:floor(xSize/2)-.5);
gaussienne = exp(- (x .^2 / smoothingpic ^2) - (y .^2 / smoothingpic ^2));
gaussienne = (gaussienne - min(gaussienne(:))) / (max(gaussienne(:)) - min(gaussienne(:)));
f_fil = fft2(gaussienne);
% fixation matrix
coordX = round(Y(:,2));
coordY = round(Y(:,1));
intv=normrnd(0.4,.085,length(Y),1);
indx1=coordX>0 & coordY>0 & coordX<xSize & coordY<ySize;
rawmap=full(sparse(coordX(indx1),coordY(indx1),intv(indx1),ySize,xSize));

f_mat = fft2(rawmap); % 2D fourrier transform on the points matrix
filtered_mat = f_mat .* f_fil;
smoothpic = real(fftshift(ifft2(filtered_mat)));
subplot(1,3,3)
imagesc(smoothpic);colorbar
set(gca,'YDir','normal');
axis('square','off')

The above code showed an example of one subject one trial.
example4-1

Genearte a dataset:

%% Dataset generation
Ns=10;
Group={'CN','PA'};% control group and patient group
Ntrial=25;
MeanNfix=14;
stdNfix=3;
Meandur=.4;
Stddur=.085;
MC=0;
itt=0;
descriptemp=zeros(Ns*length(Group)*Ntrial,10);
FixMap=zeros(Ns*length(Group)*Ntrial,ySize,xSize);
RawMap=FixMap;

for ig=1:length(Group)
    %%
    figure;
    vidObj = VideoWriter(char(['Group' num2str(ig) '.avi']));
    open(vidObj)
    for is=1:Ns
        % set seed
        MC=MC+1;
        mystream = RandStream.create('mlfg6331_64','NumStreams',nsamp,'StreamIndices',MC);
        RandStream.setGlobalStream(mystream);
        if ig==1
            % for Control group, only one type of generative model
            p = [30,30,50,10];% the mixing parameter for GMM
            shif=5-randi(10,1,4);
            shifmn=5-randi(10,size(muG));
            shifsd=randi(10,size(sigma));shifsd(2,1,:)=shifsd(1,2,:);
            pnew=p+shif;
            obj = gmdistribution(muG+shifmn,sigma+shifsd,pnew);
        else
            % for patient group, two generative model
            p1 = [30,30,50,10];% the mixing parameter for GMM
            shif=5-randi(10,1,4);
            shifmn=5-randi(10,size(muG));
            shifsd=randi(10,size(sigma));shifsd(2,1,:)=shifsd(1,2,:);
            pnew1=p1+shif;
            obj1 = gmdistribution(muG+shifmn,sigma+shifsd,pnew1);
            p2 = [6,6,50,10];% the mixing parameter for GMM
            shif=5-randi(10,1,4);
            shifmn=5-randi(10,size(muG));
            shifsd=randi(10,size(sigma));shifsd(2,1,:)=shifsd(1,2,:);
            pnew2=p2+shif;
            obj2 = gmdistribution(muG+shifmn,sigma+shifsd,pnew2);
        end
        if ig==1
            ACC=(rand(1,Ntrial)>.6)+1;% 1 correct, 2 incorrect
        else
            ACC=(rand(1,Ntrial)>.4)+1;% 1 correct, 2 incorrect
        end
        % ACC=(rand(1,Ntrial)>.5)+1;% 1 correct, 2 incorrect
        ACCtmp=rand(size(ACC));
        [a,b]=sort(ACC);
        ACC2=zeros(size(ACC));
        ACC2(b)=1-sort(ACCtmp);
        for it=1:Ntrial
            itt=itt+1;
            Nfix=ceil(normrnd(MeanNfix,stdNfix)); % total number of fixation
            if ig==2
                if ACC(it)==1;
                    obj=obj1;
                else
                    obj=obj2;
                    Nfix=ceil(normrnd(MeanNfix*.78,stdNfix)); % total number of fixation
                end
            end
            
            Ytmp = random(obj,Nfix);
            Ytmp2= [randi(xSize,2,1) randi(ySize,2,1)];
            Y=[Ytmp;Ytmp2];
            hold on
            plot(Y(:,1),Y(:,2),'.','color',[0 0 0])
            drawnow
            axis([0 xSize 0 ySize],'square','off')
            currFrame = getframe;
            writeVideo(vidObj,currFrame);
            
            rawmap = zeros(ySize, xSize);
            coordX = xSize-round(Y(:,2));
            coordY = round(Y(:,1));
            pathlength=diag(squareform(pdist([coordY,coordX])),1);
            intv=normrnd(Meandur,Stddur,length(Y),1)*1000;
            indx1=coordX>0 & coordY>0 & coordX<xSize & coordY<ySize;
            rawmap=full(sparse(coordX(indx1),coordY(indx1),intv(indx1),ySize,xSize));
            
            f_mat = fft2(rawmap); % 2D fourrier transform on the points matrix
            filtered_mat = f_mat .* f_fil;
            smoothpic = real(fftshift(ifft2(filtered_mat)));
            mm=mean(smoothpic(:));
            stdm=std(smoothpic(:));
            FixMap(itt,:,:)=(smoothpic-mm)./stdm;
            RawMap(itt,:,:)=rawmap;
            descriptemp(itt,:)=[Nfix,sum(intv),sum(intv)/Nfix,sum(pathlength),mean(pathlength),ig,ACC(it),is+Ns*(ig-1),it,ACC2(it)];
        end
    end
    close(vidObj);
end

The code above also create two video files, you might already see a group differences around the eye.

We can format the matrix and save them:

table_header2 = [{'FixNum'},{'sumFixDur'},{'meanFixDur'},{'totalPathLength'},...
    {'meanPathLength'},{'Grp'},{'ACC'},{'Sbj'},{'Trial'},{'ACC2'}];
DescriptvM1 = [table_header2;num2cell(descriptemp)];
DescriptvM1 = cell2dataset(DescriptvM1);

DescriptvM1.Trial=nominal(DescriptvM1.Trial);
DescriptvM1.Sbj=nominal(DescriptvM1.Sbj);
DescriptvM1.Grp=nominal(DescriptvM1.Grp,Group);
DescriptvM1.ACC=nominal(DescriptvM1.ACC,{'hit','miss'});

PredictorM=DescriptvM1(:,6:end);
DescriptvM=DescriptvM1(:,1:end-2);

Mask=squeeze(mean(FixMap,1))>.1;

%% save matrix
save(strcat('./FixMap_single_trial_scaled'),'FixMap','-v7.3');
save(strcat('./PredictorM_single_trial'),'PredictorM','-v7.3');
save(strcat('./DescriptvM_single_trial'),'DescriptvM','-v7.3');
save(strcat('./RawMap_single_trial_scaled'),'RawMap','-v7.3');
save(strcat('./Mask_single_trial_scaled'),'Mask','-v7.3');

Descriptive result can be display quite easily:

descriptive_part(DescriptvM,FixMap)

Running the core functions for model fitting and hypothesis testing:

%% LMM
tic
opt.singlepredi=1;
[LMMmap,lmexample]=imapLMM(FixMap,PredictorM,Mask,opt,'PixelIntensity ~ Grp * ACC + (1|Sbj)','DummyVarCoding','effect');
save('LMMmap_ACC.mat','LMMmap','-v7.3');
toc

%% plot model fitting
opt1.type='model';
% perform contrast
[StatMap]=imapLMMcontrast(LMMmap,opt1);
% output figure;
imapLMMdisplay(StatMap,0)

%% plot fixed effec(anova result using the cell mean DS and its related contrast)
% close all
opt=struct;% clear structure
opt.type='predictor beta';
opt.c=limo_OrthogContrasts([2,2]);
opt.name={'Grp','ACC','Interaction'};
opt.alpha=.05;
% perform contrast
[StatMap]=imapLMMcontrast(LMMmap,opt);
imapLMMdisplay(StatMap,0);

mccopt=struct;
mccopt.methods='bootstrap';
mccopt.bootopt=1;
mccopt.bootgroup={'Grp'};
mccopt.nboot=1000;

% 
[StatMap_c]=imapLMMmcc(StatMap,LMMmap,mccopt,FixMap);
imapLMMdisplay(StatMap_c,0);

%% post-hoc
[Posthoc]=imapLMMposthoc(StatMap_c,RawMap,LMMmap,'mean')

And we can replace one of the catigorical predictor to a continous predictor while maintaining the same linear relationship (ACC2 in this case, see above). The model fitting result is highly similar:

%% LMM 2
tic
opt.singlepredi=1;
[LMMmap2,lmexample]=imapLMM(FixMap,PredictorM,Mask,opt,'PixelIntensity ~ Grp * ACC2 + (1|Sbj)','DummyVarCoding','effect');
save('LMMmap_ACC2.mat','LMMmap2','-v7.3');
toc

%% plot model fitting
opt1.type='model';
% perform contrast
[StatMap]=imapLMMcontrast(LMMmap2,opt1);
% output figure;
imapLMMdisplay(StatMap,0)

%% plot fixed effec(anova result using the cell mean DS and its related contrast)
close all
opt=struct;% clear structure
opt.type='fixed';
% perform contrast
[StatMap]=imapLMMcontrast(LMMmap2,opt);
imapLMMdisplay(StatMap,0);

mccopt=struct;
mccopt.methods='bootstrap';
mccopt.bootopt=1;
mccopt.bootgroup={'Grp'};
mccopt.nboot=1000;

% 
[StatMap_c]=imapLMMmcc(StatMap,LMMmap2,mccopt,FixMap);
imapLMMdisplay(StatMap_c,0);

%%
opt=struct;% clear structure
opt.type='model beta';
% perform contrast
[StatMap]=imapLMMcontrast(LMMmap2,opt);
imapLMMdisplay(StatMap,0);

mccopt=struct;
mccopt.methods='bootstrap';
mccopt.bootopt=1;
mccopt.bootgroup={'Grp'};
mccopt.nboot=1000;

% 
[StatMap_c]=imapLMMmcc(StatMap,LMMmap2,mccopt,FixMap);
imapLMMdisplay(StatMap_c,0);

You can find the simulation code here

This wiki is adapted from the original iMap4 guidebook.

If you have any questions about the iMap4 usage, please email [email protected]

Getting started

Theory

Data structures and function usage

Example 1 (GUI)

Example 2 (Code)

Example 3 (Code)

Example 4 (Code)

Future development

Additional information

Clone this wiki locally