Commit 8d7c811d authored by jayd1860's avatar jayd1860
Browse files

v1.17 

-- Removed group avg pass (grpAvgPass) variable which excludes subject channel data based on standard deviation threshold from the group level averaging.
-- Update .nirs support in Homer3 in some hmr*_Nirs.m user functions and in NirsClass.
-- Update unit test processOpt_*.cfg files for new hmrG_SubjAvg function definition which removes 3 arguments relating to group avg pass variable.
-- Add conversion to full path to convertToStandardPath.m
parent fc6f8b01

DataTree/AcquiredData/DataFiles/mydir.m

+1 −1
Original line number Diff line number Diff line
@@ -17,7 +17,7 @@ for ii=1:length(dirs) 
    foo = FileClass(dirs(ii));

    if ~foo.IsEmpty()

        files(kk) = foo;

        files(kk).pathfull = fileparts(fullpath(str));

        files(kk).pathfull = convertToStandardPath(fileparts(fullpath(str)));

        kk=kk+1;

    end

end

DataTree/AcquiredData/Nirs/NirsClass.m

+4 −0
Original line number Diff line number Diff line
@@ -267,6 +267,10 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass 
        

        % ---------------------------------------------------------

        function val = GetTime(obj, iBlk)

            val = [];

            if iBlk>1

                return

            end

            val = obj.t;

        end

DataTree/RunClass.m

+1 −5
Original line number Diff line number Diff line
@@ -63,11 +63,7 @@ classdef RunClass < TreeNodeClass 
                return;

            end

            if nargin==1 || isempty(dirname)

                dirname = '.';

            end

            dirname(dirname=='\') = '/';

            if dirname(end) ~= '/'

                dirname(end+1) = '/';

                dirname = convertToStandardPath('.');

            end

            

            if obj.IsNirs()

FuncRegistry/UserFunctions/Archive/hmrG_SubjAvg_Nirs.m

+30 −80
Original line number Diff line number Diff line 
function [yAvg, yAvgStd, tHRF, nTrials, grpAvgPass] = hmrG_SubjAvg_Nirs(yAvgSubjs, yAvgStdSubjs, tHRFSubjs, SDSubjs, nTrialsSubjs, tRange, thresh0)

function [yAvg, tHRF, nTrials] = hmrG_SubjAvg_Nirs(yAvgSubjs, tHRFSubjs, nTrialsSubjs)

% SYNTAX:

% [yAvg, yAvgStd, tHRF, nTrials, grpAvgPass] = hmrG_SubjAvg_Nirs(yAvgSubjs, yAvgStdSubjs, tHRFSubjs, SDSubjs, nTrialsSubjs, tRange, thresh)

% [yAvg, tHRF, nTrials] = hmrG_SubjAvg_Nirs(yAvgSubjs, tHRFSubjs, nTrialsSubjs)

%

% UI NAME:

% Subj_Average
@@ -10,72 +10,51 @@ function [yAvg, yAvgStd, tHRF, nTrials, grpAvgPass] = hmrG_SubjAvg_Nirs(yAvgSubj 
%

% INPUTS:

% yAvgSubjs:

% yAvgStdSubjs:

% tHRFSubjs: 

% SDSubjs:

% nTrialsSubjs:

% trange: Defines the range for the block average

% thresh: Threshold for excluding channels if it's data deviates too much

%         from mean 

%

% OUTPUTS:

% yavg: the averaged results

% yAvgStd: the standard deviation across trials

% tHRF: the time vector

% nTrials: the number of trials averaged for each condition across all

%          subjects

% grpAvgPass:

%

% USAGE OPTIONS:

% Subj_Average_on_Concentration_Data: [dcAvg, dcAvgStd, tHRF, nTrials, grpAvgPass] = hmrG_SubjAvg_Nirs(dcAvgSubjs, dcAvgStdSubjs, tHRFSubjs, SDSubjs, nTrialsSubjs, tRange, thresh)

% Subj_Average_on_Delta_OD_Data:      [dodAvg, dodAvgStd, tHRF, nTrials, grpAvgPass] = hmrG_SubjAvg_Nirs(dodAvgSubjs, dodAvgStdSubjs, tHRFSubjs, SDSubjs, nTrialsSubjs, tRange, thresh)

% Subj_Average_on_Concentration_Data: [dcAvg, tHRF, nTrials] = hmrG_SubjAvg_Nirs(dcAvgSubjs, tHRFSubjs, nTrialsSubjs)

% Subj_Average_on_Delta_OD_Data:      [dodAvg, tHRF, nTrials] = hmrG_SubjAvg_Nirs(dodAvgSubjs, tHRFSubjs, nTrialsSubjs)

%

% PARAMETERS:

% tRange: [5.0, 10.0]

% thresh: [5.0]

%



yAvg       = [];

yAvgStd    = [];

tHRF       = [];

nTrials    = [];

grpAvgPass = [];

    

subjCh = [];

nStim = 0;

grp1=[];

nSubj = length(yAvgSubjs);



% chkFlag is a parameter that if true requires, for each channel, ALL corresponding 

% subjects channels to pass before averaging that channel. TBD: Currently we set it to 

% false unconditionally. In the future chkFlag should be a user-settable input parameter.

chkFlag = false;



for iSubj = 1:nSubj

    

    if isempty(yAvgSubjs{iSubj}) || isempty(yAvgStdSubjs{iSubj}) || isempty(tHRFSubjs{iSubj}) || isempty(nTrialsSubjs{iSubj}) || isempty(SDSubjs{iSubj})

    if isempty(yAvgSubjs{iSubj}) || isempty(tHRFSubjs{iSubj}) || isempty(nTrialsSubjs{iSubj})

        continue;

    end

    

    yAvg      = yAvgSubjs{iSubj};

    yAvgStd   = yAvgStdSubjs{iSubj};

    tHRF      = tHRFSubjs{iSubj};

    nTrials   = nTrialsSubjs{iSubj};

    SD        = SDSubjs{iSubj};

        

    nCond = size(nTrials,2);

    

    if ndims(yAvg) == (4-(nCond<2))

        thresh = thresh0 * 1e-6;

        

        if iSubj==1

            lstT = find(tHRF>=tRange(1) & tHRF<=tRange(2));

            grp1 = zeros(size(yAvg,1), size(yAvg,2), size(yAvg,3), nCond);

        end

        

        nCh  = size(yAvg,3);

        if isempty(subjCh)

            subjCh = zeros(size(yAvg,3), nCond);

            grpAvgPass = zeros(size(yAvg,3), nCond, nSubj);

            subjCh = zeros(nCh, nCond);

        end

        

        for iC = 1:nCond
@@ -83,33 +62,21 @@ for iSubj = 1:nSubj 
                continue;

            end

            

            % Calculate which channels to include and exclude from the group HRF avg,

            % based on the subjects' standard error and store result in lstPass

            % also need to consider if channel was manually or

            % automatically included

            lstPass = find( (squeeze(mean(yAvgStd(lstT,1,:,iC),1))./sqrt(nTrials(:,iC)+eps)) <= thresh &...

                            (squeeze(mean(yAvgStd(lstT,2,:,iC),1))./sqrt(nTrials(:,iC)+eps)) <= thresh &...

                            nTrials(:,iC)>0 );

            

            if chkFlag==false | length(lstPass)==size(yAvg,3)

            if iSubj==1 | iC>nStim

                    for iPass=1:length(lstPass)

                for iCh = 1:size(yAvg,3)

                    for iHb=1:3

                            grp1(:,iHb,lstPass(iPass),iC) = interp1(tHRF,yAvg(:,iHb,lstPass(iPass),iC),tHRF(:));

                        grp1(:,iHb,iCh,iC) = interp1(tHRF,yAvg(:,iHb,iCh,iC),tHRF(:));

                    end

                end

                    subjCh(size(yAvg,3),iC)=0;

                nStim = iC;

            else

                    for iPass=1:length(lstPass)

                for iCh = 1:size(yAvg,3)

                    for iHb=1:3

                            grp1(:,iHb,lstPass(iPass),iC) = grp1(:,iHb,lstPass(iPass),iC) + interp1(tHRF,yAvg(:,iHb,lstPass(iPass),iC),tHRF(:));

                        grp1(:,iHb,iCh,iC) = grp1(:,iHb,iCh,iC) + interp1(tHRF,yAvg(:,iHb,iCh,iC),tHRF(:));

                    end

                end

            end

                subjCh(lstPass,iC) = subjCh(lstPass,iC) + 1;

            end

            grpAvgPass(lstPass,iC,iSubj) = 1;

            subjCh(:,iC) = subjCh(:,iC) + 1; %#ok<*AGROW>

        end

        

        yAvg = [];
@@ -124,47 +91,35 @@ for iSubj = 1:nSubj 
        end

        

    elseif ndims(yAvg) == (3-(nCond<2))

        thresh = thresh0;

        

        if iSubj==1

            lstT  = find(tHRF>=tRange(1) & tHRF<=tRange(2));

            grp1 = zeros(size(yAvg,1),size(yAvg,2),nCond);

        end

        

        nCh  = size(yAvg,2);

        if isempty(subjCh)

            subjCh = zeros(size(yAvg,2),nCond);

            grpAvgPass = zeros(size(yAvg,2),nCond,nSubj);

            subjCh = zeros(nCh, nCond);

        end

        

        for iC = 1:nCond

            if nTrials(:,iC)==0

                continue;

            end

            

            for iWl = 1:2

                % Calculate which channels to include and exclude from the group HRF avg,

                % based on the subjects' standard error and store result in lstPass

                lstWl = find(SD.MeasList(:,4)==iWl);

                lstPass = find( ((squeeze(mean(yAvgStd(lstT,lstWl,iC),1))./sqrt(nTrials(lstWl,iC)'+eps)) <= thresh) &...

                                 nTrials(lstWl,iC)'>0 );

                lstPass = lstWl(lstPass);

                

                if chkFlag==false | length(lstPass)==size(yAvg,2)

                if iSubj==1 | iC>nStim

                        for iPass=1:length(lstPass)

                            grp1(:,lstPass(iPass),iC) = interp1(tHRF,yAvg(:,lstPass(iPass),iC),tHRF(:));

                    for iCh = 1:size(yAvg,2)

                        grp1(:,iCh,iC) = interp1(tHRF,yAvg(:,iCh,iC),tHRF(:));

                    end

                        subjCh(size(yAvg,2),iC)=0;

                    nStim = iC;

                else

                        for iPass=1:length(lstPass)

                            grp1(:,lstPass(iPass),iC) = grp1(:,lstPass(iPass),iC) + interp1(tHRF,yAvg(:,lstPass(iPass),iC),tHRF(:));

                    for iCh = 1:size(yAvg,3)

                        grp1(:,iCh,iC) = grp1(:,iCh,iC) + interp1(tHRF,yAvg(:,iCh,iC),tHRF(:));

                    end

                end

                    subjCh(lstPass,iC) = subjCh(lstPass,iC) + 1;

                subjCh(:,iC) = subjCh(:,iC) + 1;

            end

        end

            grpAvgPass(lstPass,iC,iSubj) = 1;

        end

        

        yAvg = [];

        if ~isempty(grp1)
@@ -175,12 +130,7 @@ for iSubj = 1:nSubj 
                    yAvg(:,iCh,iC) = grp1(:,iCh,iC) / subjCh(iCh,iC);

                end

            end            

            grpAvgPass = grpAvgPass(1:size(yAvg,2)/2 ,:,:);            

        end

        

    end

end
 


% TBD: Calculate Standard deviation

yAvgStd = [];

FuncRegistry/UserFunctions/Archive/hmrR_MotionArtifact_Nirs.m

+3 −2
Original line number Diff line number Diff line
@@ -87,9 +87,10 @@ end 


if isempty(tIncMan)

    tIncMan = ones(size(d,1),1);

else

    tIncMan = tIncMan{1};

end



tInc = ones(size(d,1),1);

tInc = tIncMan;



% Calculate the diff of d to to set the threshold if ncssesary

diff_d=diff(d);

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