Commit eba57454 authored by Meryem Ayse Yucel's avatar Meryem Ayse Yucel
Browse files

Update hmrS_RunAvgStd2.m 

- Removed unnecessary input dcAvgRuns
- Adding a check for ml extraction. Resting runs do not save ml in yAvgStdRuns as opposed to rest of the runs, now the code is looping until it finds ml.
-added checks to avoid crashing if there is no trial for a condition in a specific run
parent e1d20c19

FuncRegistry/UserFunctions/hmrS_RunAvgStd2.m

+46 −25
Original line number Diff line number Diff line 
% SYNTAX:

% yAvgStd = hmrS_RunAvgStd2(yAvgRuns, yAvgStdRuns, nTrialsRuns)

% yAvgStd = hmrS_RunAvgStd2(yAvgStdRuns, nTrialsRuns)

%

% UI NAME:

% Run_Average_Standard_Deviation
@@ -8,7 +8,6 @@ 
% Calculates a weighted avearge of HRF standard deviation across runs within a subject.

%

% INPUTS:

% yAvgRuns:

% yAvgStdRuns:

% nTrialsRuns:

%
@@ -16,50 +15,72 @@ 
% yAvgStdOut: the standard deviation across runs

%

% USAGE OPTIONS:

% Run_Average_Standard_Deviation_on_Concentration_Data:  dcAvgStd  = hmrS_RunAvgStd2(dcAvgRuns, dcAvgStdRuns, nTrialsRuns)

% Run_Average_Standard_Deviation_on_Concentration_Data:  dcAvgStd  = hmrS_RunAvgStd2(dcAvgStdRuns, nTrialsRuns)

%



function yAvgStdOut = hmrS_RunAvgStd2(yAvgRuns, yAvgStdRuns, nTrialsRuns)

function yAvgStdOut = hmrS_RunAvgStd2(yAvgStdRuns, nTrialsRuns)



yAvgStdOut = DataClass();

N = 0;

var = 0;

nDataBlks = length(yAvgStdRuns{1});



% find max nCond

for i = 1:size(nTrialsRuns, 2); niC(i) = size(nTrialsRuns{i}{1},2); end

niC = max(niC);



for iBlk = 1:nDataBlks

    % get tHRF and ml from yAvgRuns

    tHRF    = yAvgRuns{1}(iBlk).GetTime();

    ml    = yAvgRuns{1}(iBlk).GetMeasListSrcDetPairs();

    for iRun = 1:length(yAvgStdRuns)

    tHRF    = yAvgStdRuns{iRun}(iBlk).GetTime();

    ml    = yAvgStdRuns{iRun}(iBlk).GetMeasListSrcDetPairs();

    if ~isempty(ml)

        break

    end

    end

    yAvgStdOut(iBlk).SetTime(tHRF);

    yAvg    = yAvgRuns{1}(iBlk).GetDataTimeSeries('reshape');

    

    

    for iC = 1:size(nTrialsRuns{1}{1},2) % across conditions

    for iC = 1:niC % across conditions

        

        % get total number of trials per given condition

        for iRun = 1:length(yAvgStdRuns)

            if ~isempty(nTrialsRuns{iRun}{iBlk})

                N = N + nTrialsRuns{iRun}{iBlk}(iC);

            end

        end

        

        %         if N ~= 0

        % get average of variance across runs weighted by number of trials within a run

        for iRun = 1:length(yAvgStdRuns)

            if  ~isempty(nTrialsRuns{iRun}{iBlk})

                if nTrialsRuns{iRun}{iBlk}(iC) ~= 0

                    yAvgStd    = yAvgStdRuns{iRun}(iBlk).GetDataTimeSeries('reshape');

                    if isempty(yAvgStd) ~= 1

                        var = var + (nTrialsRuns{iRun}{iBlk}(iC)-1)/(N-1) * yAvgStd(:,:,:,iC).^2;

                    end

                end

            end

        end

        

            % get std and append

            yAvgStd_wa = sqrt(var);

            if yAvgStd_wa == 0

               yAvgStd_wa = zeros(size(tHRF,1), 3, size(ml,1));

            end

            yAvgStdOut(iBlk).AppendDataTimeSeries(yAvgStd_wa);

            var = 0;

            N = 0;

            

            % add measlist field

        for iCh = 1:size(yAvg,3)

%             if ~isempty(ml)

                for iCh = 1:size(ml,1)

                    yAvgStdOut(iBlk).AddChannelHbO(ml(iCh,1), ml(iCh,2), iC);

                    yAvgStdOut(iBlk).AddChannelHbR(ml(iCh,1), ml(iCh,2), iC);

                    yAvgStdOut(iBlk).AddChannelHbT(ml(iCh,1), ml(iCh,2), iC);

                end

%             end

%         end

        

    end

end

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