Merge pull request #48 from mayucel/development

% SYNTAX:

% [cc, ml, cc_thresh] = hmrR_CrossCorrelation(data, cc_thresh, plot_on)

%

% UI NAME:

% hmrR_CrossCorrelation

%

% DESCRIPTION:

% This script calculates cross correlation across all channel pairs.

%

%

% INPUTS:

% data - this is the concentration data with dimensions #time points x [HbO/HbR/HbT] x #channels

% cc_thresh - cross correlation theshold, sets any correlation below cc_thresh to 0 in plots (display purpose only)

% plot_on - (1) displays cross correlation for HbO and HbR for each run; (0) no display

%

% OUTPUTS:

% cc -  cross correlation matrix

% ml -  measurement list

% cc_thresh - cross correlation theshold, sets any correlation below cc_thresh to 0 in plots (display purpose only)

%

% USAGE OPTIONS:

% hmrR_CrossCorrelation_conc: [cc, ml, cc_thresh] = hmrR_CrossCorrelation(dc, cc_thresh, plot_on)

%

% PARAMETERS:

% cc_thresh: 0.4

% plot_on: 0

%

% PREREQUISITES:

% GLM_HRF_Drift_SS_Concentration: [dcAvg, dcAvgStd, nTrials, dcNew, dcResid, dcSum2, beta, R, hmrstats] = hmrR_GLM(dc, stim, probe, mlActAuto, Aaux, tIncAuto, rcMap, trange, glmSolveMethod, idxBasis, paramsBasis, rhoSD_ssThresh, flagNuisanceRMethod, driftOrder, c_vector)

function [cc, ml, cc_thresh] = hmrR_CrossCorrelation(data, cc_thresh, plot_on)

for iBlk=1:length(data)

    y      = data(iBlk).GetDataTimeSeries('reshape');

    ml     = data(iBlk).GetMeasListSrcDetPairs();

end

% HbO

dc = squeeze(y(:,1,:));

dc = (dc-ones(length(dc),1)*mean(dc,1))./(ones(length(dc),1)*std(dc,[],1));

cc(:,:,1) = dc'*dc / length(dc);

% HbR

dc = squeeze(y(:,2,:));

dc = (dc-ones(length(dc),1)*mean(dc,1))./(ones(length(dc),1)*std(dc,[],1));

cc(:,:,2) = dc'*dc / length(dc);

%% plot

if plot_on == 1

    nch = length(ml);

    tlabel = '';

    for ii = 1:length(ml)

        tlabel = sprintf( '%s,''%c%d''',tlabel,char(64+ml(ii,1)), ml(ii,2) );

    end

    tlabel(1) = [];

    % HbO

    figure;

    cc0 = cc(:,:,1);

    cc0(find(abs(cc(:,:,1))<cc_thresh))=0;

    imagesc(cc0,[-1 1])

    colorbar

    set(gca,'xtick',[1:nch])

    set(gca,'xticklabel',eval(sprintf('{%s}', tlabel)) )

    set(gca,'ytick',[1:nch])

    set(gca,'yticklabel',eval(sprintf('{%s}', tlabel)) )

    title( 'HbO Cross-Correlation')

    % HbR

    figure;

    cc0 = cc(:,:,2);

    cc0(find(abs(cc(:,:,2))<cc_thresh))=0;

    imagesc(cc0,[-1 1])

    colorbar

    set(gca,'xtick',[1:nch])

    set(gca,'xticklabel',eval(sprintf('{%s}', tlabel)) )

    set(gca,'ytick',[1:nch])

    set(gca,'yticklabel',eval(sprintf('{%s}', tlabel)) )

    title( 'HbR Cross-Correlation')

end

 No newline at end of file

March 24, 2021, 13:27:41

Running Homer3 v1.31.2, R2019b

============

SYSTEM INFO:

============

Platform Arch  : PCWIN64

RAM Total      : 17.1 GB

RAM Free       : 6.3 GB

HD Space Total : 482.8 GB

HD Space Free  : 180.8 GB

Opened application config file C:/Users/mayucel/Documents/PROJECTS/CODES/Homer3_Meryem_fork/Homer3/AppSettings.cfg

MainGUI: March 24, 2021, 13:27:43 -  Will load group folder #1 - C:/Users/mayucel/Documents/PROJECTS/FNIRS TEST DATA/mci/Subj1/

Current GroupClass version 1.2

DataTreeClass.FindAndLoadGroups: Found 2 data files in 1 folders

Current GroupClass version 1.2

Added group Subj1 to dataTree.

   Added subject run1_seq1 to group Subj1.

     Added run run1_seq1.snirf to subject run1_seq1.

   Added subject run2_seq2 to group Subj1.

     Added run run2_seq2.snirf to subject run2_seq2.

Loaded acquisition data in 2.2 seconds

Saved group data, version 1.2 exists

Loaded data set in 3.6 seconds

Loaded saved registry C:/Users/mayucel/Documents/PROJECTS/CODES/Homer3_Meryem_fork/Homer3/FuncRegistry/UserFunctions/Registry.mat

Displaying channels [] in data blocks [1]

Logger: Chapter 1

MainGUI: March 24, 2021, 13:27:59 - Startup time - 16.1 seconds

Displaying channels [] in data blocks [1]

Processing iGroup=1, iSubj=1, iRun=1

Processing iGroup=1, iSubj=1, iRun=0

Processing iGroup=1, iSubj=2, iRun=1

Processing iGroup=1, iSubj=2, iRun=0

Processing iGroup=1, iSubj=0, iRun=0

Saving group 1 in C:/Users/mayucel/Documents/PROJECTS/FNIRS TEST DATA/mci/Subj1/groupResults.mat

Saving processed data in C:/Users/mayucel/Documents/PROJECTS/FNIRS TEST DATA/mci/Subj1/groupResults.mat

Auto-saving processing results ...

Current GroupClass version 1.2

Completed saving groupResults.mat for all groups in 1.912 seconds.

Displaying channels [] in data blocks [1]

24-Mar-2021 13:27:42