Group level paired t-test for "baseline vs cond" and "cond vs cond"

% SYNTAX:

% [hmrstatsG_base_cond] = hmrG_t_paired_baseline_HRF(yAvgSubjs, tHRFrange, cond)

%

% UI NAME:

% Paired_t-test_baseline_vs_HRF

%

% DESCRIPTION:

% Performs a paired t-test between baseline and the mean HRF for a single condition across all subjects

%

% INPUTS:

% yAvgSubjs:

% tHRFrange: tHRF range for HRF averaging

%

% OUTPUTS:

% hmrstatsG_base_cond: Statistical results from the MATLAB ttest (h,p,c,stats) and measurement list (ml) 

%

% USAGE OPTIONS:

% Stats_on_Concentration_Data: [hmrstatsG_base_cond] = hmrG_t_paired_baseline_HRF(dcAvgSubjs, tHRFrange, cond)

%

% PARAMETERS:

% tHRFrange: [0, 0]

%

function  [hmrstatsG_base_cond] = hmrG_t_paired_baseline_HRF(yAvgSubjs, tHRFrange)

% N subject included per channel da gerekiyor.

% fix name hrmstatsG

hmrstatsG_base_cond = [];

nDataBlks = length(yAvgSubjs{1});

nSubj = length(yAvgSubjs);

% get number of conditions

for iBlk = 1:nDataBlks

    for iSubj = 1:nSubj

        yAvg      = yAvgSubjs{iSubj}(iBlk).GetDataTimeSeries('reshape');

        ncond = size(yAvg,4);

        if iSubj == 1

            tHRF      = yAvgSubjs{iSubj}(iBlk).GetTime();

            fq = abs(1/(tHRF(1)-tHRF(2)));

            ml    = yAvgSubjs{iSubj}(iBlk).GetMeasListSrcDetPairs();

        end

        baseline_yAvg(iSubj,:,:,:) = mean(yAvg(round(fq*(tHRFrange(1) + abs(min(tHRF)))):round(fq*(tHRFrange(2) + abs(min(tHRF)))),:,:,:),1);

        mean_yAvg(iSubj,:,:,:) = mean(yAvg(1:round(fq*abs(min(tHRF))),:,:,:),1);

    end

    % get t-stats

    for iCond = 1:ncond

        for i = 1:size(yAvg, 2)  % HbO/R/T

            for j = 1:size(yAvg,3) % Channels

                [h,p,c,stats] = ttest(baseline_yAvg(:,i,j,iCond),mean_yAvg(:,i,j,iCond));

                pval(i,j,iCond) = p;

                hval(i,j,iCond) = h;

                cval(i,j,iCond,:) = c;

                tstats{i,j,iCond} = stats;

            end

        end

    end

end

% output

hmrstatsG_base_cond.pval = pval;

hmrstatsG_base_cond.hval = hval;

hmrstatsG_base_cond.cval = cval;

hmrstatsG_base_cond.tstats = tstats;

hmrstatsG_base_cond.ml = ml;

% SYNTAX:

% [hmrstatsG_contrast] = hmrG_t_paired_contrast(yAvgSubjs, tHRFrange, c_vector)

%

% UI NAME:

% Paired_t-test_contrast

%

% DESCRIPTION:

% Performs a paired t-test between the HRF of two conditions across all subjects.

%

% INPUTS:

% yAvgSubjs:

% tHRFrange: tHRF range for HRF averaging

% c_vector - Contrast vector, has values 1 or 0. E.g. to perform a paired t-test between cond

%           2 and cond 3 in an experimental paradigm with four conditions, c_vector is

%           [0 1 1 0]

%

% OUTPUTS:

% hrmstatsG_contrast: Statistical results from the MATLAB ttest (h,p,c,stats),

%           measurement list (ml) and contrast vector (c_vector)

%

% USAGE OPTIONS:

% Stats_on_Concentration_Data: [hmrstatsG_contrast] = hmrG_t_paired_contrast(dcAvgSubjs, tHRFrange, c_vector)

%

% PARAMETERS:

% tHRFrange: [0, 0]

% c_vector: [0, 0]

%

function  [hmrstatsG_contrast] = hmrG_t_paired_contrast(yAvgSubjs, tHRFrange, c_vector)

% N subject included per channel da gerekiyor.

% fix name hrmstatsG

hmrstatsG_contrast = [];

nDataBlks = length(yAvgSubjs{1});

nSubj = length(yAvgSubjs);

nCond = find(c_vector);

if ~isempty(nCond)

    for iBlk = 1:nDataBlks

        for iSubj = 1:nSubj

            yAvg      = yAvgSubjs{iSubj}(iBlk).GetDataTimeSeries('reshape');

            if iSubj == 1

                tHRF      = yAvgSubjs{iSubj}(iBlk).GetTime();

                fq = abs(1/(tHRF(1)-tHRF(2)));

                ml    = yAvgSubjs{iSubj}(iBlk).GetMeasListSrcDetPairs();

            end

            for iCond = nCond

                mean_yAvg(iSubj,iCond,:,:) = mean(yAvg(round(fq*(tHRFrange(1) + abs(min(tHRF)))):round(fq*(tHRFrange(2) + abs(min(tHRF)))),:,:,iCond),1);

            end

        end

        % get t-stats

        for i = 1:size(yAvg, 2)  % HbO/R/T

            for j = 1:size(yAvg,3) % Channels

                [h,p,c,stats] = ttest( mean_yAvg(:,nCond(1),i,j),mean_yAvg(:,nCond(2),i,j));

                pval(i,j) = p;

                hval(i,j) = h;

                cval(i,j,:) = c;

                tstats{i,j} = stats;

            end

        end

    end

end

% output

hmrstatsG_contrast.pval = pval;

hmrstatsG_contrast.hval = hval;

hmrstatsG_contrast.cval = cval;

hmrstatsG_contrast.tstats = tstats;

hmrstatsG_contrast.ml = ml;

hmrstatsG_contrast.c_vector = c_vector;