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MappingEffects_GLM.m
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MappingEffects_GLM.m
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function [ ] = MappingEffects_GLM(Animals,Channels)
%MappingEffects_GLM.m
% Analyze data from mapping effects experiment, see MappingEffects.m
% Three experimental conditions:
% 1) retinotopic mapping, followed by fake SRP (grey screen)
% 2) retinotopic mapping, followed by SRP
% 3) fake mapping (grey screen), followed by SRP
%
% Created: 2017/04/14
% Byron Price
% Updated: 2017/04/14
% By: Byron Price
cd('~/CloudStation/ByronExp/MappingEffects');
for ii=1:length(Animals)
dataFiles = dir(sprintf('MappingEffectsData*%d.plx',Animals(ii)));
stimFiles = dir(sprintf('MappingEffectsStim*%d.mat',Animals(ii)));
numFiles = length(dataFiles);
fprintf('Running animal %d\n\n',Animals(ii));
linkFun = -2;
pix_to_degree = cell(numFiles,1);
currentChannel = Channels{ii};
numChans = length(currentChannel);
B = cell(numFiles,numChans);
DEV = cell(numFiles,numChans,2);
SE = cell(numFiles,numChans);
DEV_RESIDUALS = cell(numFiles,numChans);
F_TEST = cell(numFiles,numChans);
VEP_MAGNITUDES = cell(numFiles,numChans);
STIMULUS_LOCATIONS = cell(numFiles,numChans);
ALL_VEPS = cell(numFiles,1);
% could add back check for "goodChannels"
if numChans ~= 0
for jj=1:numFiles
ePhysFileName = dataFiles(jj).name;
[ChanData,timeStamps,tsevs,svStrobed,~,sampleFreq] = ExtractSignal(ePhysFileName);
load(stimFiles(jj).name);
stimLen = round(0.5*sampleFreq); % 500 milliseconds
strobeStart = 33;
strobeTimes = tsevs{strobeStart};
if ConditionNumber == 1
centerVals = stimParams.centerVals;
Radius = stimParams.Radius;
reps = stimParams.reps;
w_pixels = stimParams.w_pixels;
h_pixels = stimParams.h_pixels;
numStimuli = stimParams.numStimuli;
mmPerPixel = stimParams.mmPerPixel;
DistToScreen = stimParams.DistToScreen*10;
pix_to_degree{jj} = mmPerPixel/DistToScreen;
% COLLECT DATA IN THE PRESENCE OF VISUAL STIMULI
Response = zeros(numChans,numStimuli,reps,stimLen);
meanResponse = zeros(numChans,numStimuli,stimLen);
meanVEPMagnitude = zeros(numChans,numStimuli);
for kk=1:numChans
for ll=1:numStimuli
stimStrobes = strobeTimes(svStrobed == ll);
for mm=1:reps
stimOnset = stimStrobes(mm);
[~,index] = min(abs(timeStamps-stimOnset));
temp = ChanData(index:index+stimLen-1,currentChannel(kk));
Response(kk,ll,mm,:) = temp;
end
meanResponse(kk,ll,:) = mean(squeeze(Response(kk,ll,:,:)),1);
[~,minLatency] = min(squeeze(meanResponse(kk,ll,:)));
minLatency = max(min(minLatency,200),40);
minWin = minLatency-30:minLatency+30;
maxWin = minLatency+30:minLatency+200;
meanVEPMagnitude(kk,ll) = abs(max(squeeze(meanResponse(kk,ll,maxWin)))-min(squeeze(meanResponse(kk,ll,minWin))));
end
ALL_VEPS{jj} = squeeze(Response);
X = [centerVals(:,1),centerVals(:,2),centerVals(:,1).^2,centerVals(:,2).^2];
[b,dev,stats] = glmfit(X,meanVEPMagnitude(kk,:)','normal','link',linkFun);
B{jj,kk} = b;
DEV{jj,kk,1} = dev;
SE{jj,kk} = stats.se;
DEV_RESIDUALS{jj,kk} = stats.residd;
[~,nullDev,~] = glmfit(ones(numStimuli,1),meanVEPMagnitude(kk,:)','normal','link',linkFun,'constant','off');
dev = real(dev);nullDev = real(nullDev);b = real(b);
fStat = ((nullDev-dev)/(length(b)-1))/(dev/(numStimuli-length(b)));
F_TEST{jj,kk} = fcdf(fStat,length(b)-1,numStimuli-length(b),'upper');
VEP_MAGNITUDES{jj,kk} = meanVEPMagnitude(kk,:)';
STIMULUS_LOCATIONS{jj,kk} = centerVals;
DEV{jj,kk,2} = nullDev;
Radius = round(Radius);
xPos = unique(centerVals(:,1));
yPos = unique(centerVals(:,2));
xDiff = mean(diff(xPos));
yDiff = mean(diff(yPos));
xconv = stimLen/xDiff;
yconv = 800/yDiff; % for height of the stimulus
figure();
for ww=1:numStimuli
tempx = centerVals(ww,1);
tempy = centerVals(ww,2);
plot(((1:1:stimLen)./xconv+centerVals(ww,1)-0.5*xDiff),...
(squeeze(meanResponse(kk,ww,:))'./yconv+centerVals(ww,2)),'k','LineWidth',2);
hold on;
plot((tempx-Radius)*ones(Radius*2+1,1),(tempy-Radius):(tempy+Radius),'k','LineWidth',2);
plot((tempx+Radius)*ones(Radius*2+1,1),(tempy-Radius):(tempy+Radius),'k','LineWidth',2);
plot((tempx-Radius):(tempx+Radius),(tempy-Radius)*ones(Radius*2+1,1),'k','LineWidth',2);
plot((tempx-Radius):(tempx+Radius),(tempy+Radius)*ones(Radius*2+1,1),'k','LineWidth',2);
hold on;
end
xPos = 1:w_pixels;yPos = 1:h_pixels;
[XPOS,YPOS] = meshgrid(xPos,yPos);
tempX = [XPOS(:),YPOS(:),XPOS(:).^2,YPOS(:).^2];
nx = length(xPos);ny = length(yPos);
yhat = glmval(b,tempX,linkFun);
imagesc(xPos,yPos,reshape(yhat,[ny,nx]),'AlphaData',0.5);set(gca,'YDir','normal');w=colorbar;
ylabel(w,'Mean VEP Magnitude (\muV)');colormap('jet');
title(sprintf('F test p-value: %3.2e',F_TEST{jj,kk}));
axis([0 w_pixels 0 h_pixels]);
hold off;
end
elseif ConditionNumber == 2
centerVals = stimParams.centerVals;
Radius = stimParams.Radius;
reps = stimParams.reps;
w_pixels = stimParams.w_pixels;
h_pixels = stimParams.h_pixels;
numStimuli = stimParams.numStimuli;
mmPerPixel = stimParams.mmPerPixel;
DistToScreen = stimParams.DistToScreen*10;
pix_to_degree{jj} = mmPerPixel/DistToScreen;
% COLLECT DATA IN THE PRESENCE OF VISUAL STIMULI
Response = zeros(numChans,numStimuli,reps,stimLen);
meanResponse = zeros(numChans,numStimuli,stimLen);
meanVEPMagnitude = zeros(numChans,numStimuli);
for kk=1:numChans
for ll=1:numStimuli
stimStrobes = strobeTimes(svStrobed == ll);
for mm=1:reps
stimOnset = stimStrobes(mm);
[~,index] = min(abs(timeStamps-stimOnset));
temp = ChanData(index:index+stimLen-1,currentChannel(kk));
Response(kk,ll,mm,:) = temp;
end
meanResponse(kk,ll,:) = mean(squeeze(Response(kk,ll,:,:)),1);
[~,minLatency] = min(squeeze(meanResponse(kk,ll,:)));
minLatency = max(min(minLatency,200),40);
minWin = minLatency-30:minLatency+30;
maxWin = minLatency+30:minLatency+200;
meanVEPMagnitude(kk,ll) = abs(max(squeeze(meanResponse(kk,ll,maxWin)))-min(squeeze(meanResponse(kk,ll,minWin))));
end
ALL_VEPS{jj} = squeeze(Response);
X = [centerVals(:,1),centerVals(:,2),centerVals(:,1).^2,centerVals(:,2).^2];
[b,dev,stats] = glmfit(X,meanVEPMagnitude(kk,:)','normal','link',linkFun);
B{jj,kk} = b;
DEV{jj,kk,1} = dev;
SE{jj,kk} = stats.se;
DEV_RESIDUALS{jj,kk} = stats.residd;
[~,nullDev,~] = glmfit(ones(numStimuli,1),meanVEPMagnitude(kk,:)','normal','link',linkFun,'constant','off');
dev = real(dev);nullDev = real(nullDev);b = real(b);
fStat = ((nullDev-dev)/(length(b)-1))/(dev/(numStimuli-length(b)));
F_TEST{jj,kk} = fcdf(fStat,length(b)-1,numStimuli-length(b),'upper');
DEV{jj,kk,2} = nullDev;
VEP_MAGNITUDES{jj,kk} = meanVEPMagnitude(kk,:)';
STIMULUS_LOCATIONS{jj,kk} = centerVals;
Radius = round(Radius);
xPos = unique(centerVals(:,1));
yPos = unique(centerVals(:,2));
xDiff = mean(diff(xPos));
yDiff = mean(diff(yPos));
xconv = stimLen/xDiff;
yconv = 800/yDiff; % for height of the stimulus
figure();
for ww=1:numStimuli
tempx = centerVals(ww,1);
tempy = centerVals(ww,2);
plot(((1:1:stimLen)./xconv+centerVals(ww,1)-0.5*xDiff),...
(squeeze(meanResponse(kk,ww,:))'./yconv+centerVals(ww,2)),'k','LineWidth',2);
hold on;
plot((tempx-Radius)*ones(Radius*2+1,1),(tempy-Radius):(tempy+Radius),'k','LineWidth',2);
plot((tempx+Radius)*ones(Radius*2+1,1),(tempy-Radius):(tempy+Radius),'k','LineWidth',2);
plot((tempx-Radius):(tempx+Radius),(tempy-Radius)*ones(Radius*2+1,1),'k','LineWidth',2);
plot((tempx-Radius):(tempx+Radius),(tempy+Radius)*ones(Radius*2+1,1),'k','LineWidth',2);
hold on;
end
xPos = 1:w_pixels;yPos = 1:h_pixels;
[XPOS,YPOS] = meshgrid(xPos,yPos);
tempX = [XPOS(:),YPOS(:),XPOS(:).^2,YPOS(:).^2];
nx = length(xPos);ny = length(yPos);
yhat = glmval(b,tempX,linkFun);
imagesc(xPos,yPos,reshape(yhat,[ny,nx]),'AlphaData',0.5);set(gca,'YDir','normal');w=colorbar;
ylabel(w,'Mean VEP Magnitude (\muV)');colormap('jet');
title(sprintf('F test p-value: %3.2e',F_TEST{jj,kk}));
axis([0 w_pixels 0 h_pixels]);
hold off;
end
end
end
% savefig(h,sprintf('MappingEffectsResults_%d.fig',Animals(ii)));
end
filename = sprintf('MappingEffectsGLMResults_%d.mat',Animals(ii));
if ConditionNumber == 1 || ConditionNumber == 2
save(filename,'ConditionNumber','pix_to_degree','w_pixels','h_pixels','currentChannel','numChans',...
'B','DEV','SE','DEV_RESIDUALS','F_TEST','VEP_MAGNITUDES','STIMULUS_LOCATIONS','ALL_VEPS');
end
fprintf('Done with animal %d\n\n',Animals(ii));pause(1);
end
end
function [ChanData,timeStamps,tsevs,svStrobed,numChans,sampleFreq] = ExtractSignal(EphysFileName)
% Extract LFP signals from allad, filter, get timestamps
% read in the .plx file
if exist(strcat(EphysFileName(1:end-4),'.mat'),'file') ~= 2
readall(EphysFileName);pause(0.1);
end
EphysFileName = strcat(EphysFileName(1:end-4),'.mat');
load(EphysFileName)
sampleFreq = adfreq;
Chans = find(~cellfun(@isempty,allad));
numChans = length(Chans);
% lowpass filter the data
dataLength = length(allad{1,Chans(1)});
ChanData = zeros(dataLength,numChans);
preAmpGain = 1;
for ii=1:numChans
voltage = 1000.*((allad{1,Chans(ii)}).*SlowPeakV)./(0.5*(2^SlowADResBits)*adgains(Chans(ii))*preAmpGain);
n = 100;
lowpass = 100/(sampleFreq/2); % fraction of Nyquist frequency
blo = fir1(n,lowpass,'low',hamming(n+1));
temp = filter(blo,1,voltage);
notch = 60/(sampleFreq/2);
bw = notch/n;
[b,a] = iirnotch(notch,bw);
ChanData(:,ii) = filter(b,a,temp);
end
timeStamps = 0:1/sampleFreq:dataLength/sampleFreq-1/sampleFreq;
if length(timeStamps) ~= dataLength
display('Error: Review allad cell array and timing')
return;
end
end