Merge branch 'master' of https://github.com/BUNPC/Homer3 (d735fe16) · Commits · github_fork / Homer3

FuncRegistry/UserFunctions/hmrS_CalcPvalue.m

+60 −53

Original line number	Diff line number	Diff line
		% SYNTAX:
		% pValues = hmrS_CalcPvalue(yRuns, stimRuns, baselineRange, hrfTimeWindow)
		% [pValuesS, pValuesS_cond] = hmrS_CalcPvalue(yRuns, stimRuns, mlActRuns, baselineRange, hrfTimeWindow)
		%
		% UI NAME:
		% Pvalues_on_Session
		@@ -10,21 +10,21 @@
		% INPUTS:
		% yRuns:
		% stimRuns:
		% mlActRuns:
		% baselineRange:
		% hrfTimeWindow:
		%
		% OUTPUTS:
		% pValues:
		%
		% pValuesS:
		% pValuesS_cond
		% USAGE OPTIONS:
		% Pvalues_on_Session_Concentration_Data: pValues = hmrS_CalcPvalue(dcRuns, stimRuns, baselineRange, hrfTimeWindow)
		% Pvalues_on_Session_Delta_OD_Data: pValues = hmrS_CalcPvalue(dodRuns, stimRuns, baselineRange, hrfTimeWindow)
		% Pvalues_on_Session_Concentration_Data: [pValuesS, pValuesS_cond] = hmrS_CalcPvalue(dcRuns, stimRuns, mlActRuns, baselineRange, hrfTimeWindow)
		%
		% PARAMETERS:
		% baselineRange: [-2.0, 0.0]
		% hrfTimeWindow: [-2.0, 20.0]
		%
		function pValues = hmrS_CalcPvalue(yRuns, stimRuns,baselineRange, hrfTimeWindow)

		function [pValuesS, pValuesS_cond] = hmrS_CalcPvalue(yRuns, stimRuns, mlActRuns, baselineRange, hrfTimeWindow)

		pValues = cell(length(yRuns{1}),1);

		@@ -36,8 +36,10 @@ t = snirf.GetTimeCombined();
		s = snirf.GetStims(t);
		ncond = size(s,2);
		fq = abs(1/(t(1)-t(2)));
		nDataBlks = length(yRuns{1});

		%% BASELINE vs CONDITION, PAIRED T-TEST
		for iBlk = 1:nDataBlks
		for cond = 1:ncond % for each condition
		for iRun = 1:length(yRuns)

		@@ -50,13 +52,18 @@ for cond = 1:ncond % for each condition

		% extract HRF at baselineRange and at hrfTimeWindow
		lst_stim = find(s(:,cond)==1);
		for iBlk = 1:length(yRuns)

		% get active measuremnt list for each run
		% 1) IS THIS HOW WE EXTRACT MEASLISTACT
		if ~exist('mlActAuto')
		mlActAuto{iBlk} = ones(size(ml,1),1);
		if isempty(mlActRuns{iRun})
		mlActRuns{iRun} = cell(length(nDataBlks),1);
		end
		mlAct = mlActAuto{iBlk};
		ml = yRuns{iRun}(iBlk).GetMeasListSrcDetPairs();

		if isempty(mlActRuns{iRun}{iBlk})
		mlActRuns{iRun}{iBlk} = ones(size(ml,1),1);
		end
		mlAct = mlActRuns{iRun}{iBlk}(1:size(ml,1));

		% GetDataMatrix() extract data in old homer2 dimensions (time X Hb X channel)
		y = yRuns{iRun}(iBlk).GetDataMatrix();% yRuns{iRun}(iBlk).GetDataMatrix(); % data matrix for run iRun, data block iBlk
		for hb = 1:3 % across HbO/HbR/HbT
		@@ -85,8 +92,6 @@ for cond = 1:ncond % for each condition
		% get stats
		if isempty(pValues{iBlk})
		for ch = 1:size(MEAN_Hb_peak,2) % channels
		if mlAct(ch) ~=0
		format long
		for hb = 1:3% HbO/HbR/HbT
		[h,p,c,stats] = ttest(MEAN_Hb_baseline(:,ch,hb),(MEAN_Hb_peak(:,ch,hb)));
		pValuesS(hb,ch,cond) = p;
		@@ -94,13 +99,13 @@ for cond = 1:ncond % for each condition
		% 2) Pvalue SHOULD BE CONVERTED TO DATA CLASS IN THE RIGHT DIM AT THE END

		end
		else
		pValuesS(hb,ch,cond) = 'NaN';
		end
		end
		end
		end

		pValuesS(:,find(mlAct==0),:) = NaN;




		%% CONDITION vs CONDITION, UNPAIRED T-TEST
		@@ -111,18 +116,23 @@ for i = 1:ncond
		lst_stim_all{i} = find(s(:,i)==1);
		end

		for iBlk = 1:length(nDataBlks)
		for comb_inx = 1:size(cond_2_comb,1) % for each condition
		% get current combin.
		foo = cond_2_comb(comb_inx,:);

		for iRun = 1:length(yRuns)
		for iBlk = 1:length(yRuns)
		% get active measuremnt list for each run
		% 1) IS THIS HOW WE EXTRACT MEASLISTACT
		if ~exist('mlActAuto')
		mlActAuto{iBlk} = ones(size(ml,1),1);
		if isempty(mlActRuns{iRun})
		mlActRuns{iRun} = cell(length(nDataBlks),1);
		end
		mlAct = mlActAuto{iBlk};
		ml = yRuns{iRun}(iBlk).GetMeasListSrcDetPairs();

		if isempty(mlActRuns{iRun}{iBlk})
		mlActRuns{iRun}{iBlk} = ones(size(ml,1),1);
		end
		mlAct = mlActRuns{iRun}{iBlk}(1:size(ml,1));

		% GetDataMatrix() extract data in old homer2 dimensions (time X Hb X channel)
		y = yRuns{iRun}(iBlk).GetDataMatrix(); % data matrix for run iRun, data block iBlk
		for hb = 1:3 % across HbO/HbR/HbT
		@@ -154,8 +164,6 @@ for comb_inx = 1:size(cond_2_comb,1) % for each condition
		% get stats
		if ~exist('pValuesS_cond')
		for ch = 1:size(MEAN_Hb_peak,2) % channels
		if mlAct(ch) ~=0
		format long
		for hb = 1:3% HbO/HbR/HbT
		[h,p,c,stats] = ttest2(MEAN_Hb_peak1(:,ch,hb),(MEAN_Hb_peak2(:,ch,hb)));
		pValuesS_cond(hb,ch,comb_inx) = p;
		@@ -164,9 +172,8 @@ for comb_inx = 1:size(cond_2_comb,1) % for each condition
		% 2) Pvalue SHOULD BE CONVERTED TO DATA CLASS IN THE RIGHT DIM AT THE END

		end
		else
		pValuesS_cond(hb,ch,comb_inx) = 'NaN';
		end
		end
		end
		end
		pValuesS_cond(:,find(mlAct==0),:) = NaN;
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

FuncRegistry/UserFunctions/tcca_glm/hmrR_tCCA.m

+2 −10

Original line number	Diff line number	Diff line
		@@ -48,20 +48,16 @@
		% rhoSD_ssThresh: 15.0

		%% COMMENTS/THOUGHTS/QUESTIONS ALEX
		% 1) I think we can remove the original perf_temp_emb_cca.m function (done)
		% 2) Output canonical correlation coefficients as quality metric?
		% 3) Output fNIRS signal(s)/Aux regressors for visualization/quality control?
		% 4) Add single channel (regressor) feature - flag - how do we provide the individual outputs?
		% 5) Implement the variable low/bandpass filter coefficients from previous processing stream
		% Q1) why the flagtCCA?
		%%

		function [Aaux] = hmrR_tCCA(data, aux, probe, yRuns, flagtCCA, tCCAparams, tCCAaux_inx, tCCArest_inx, rhoSD_ssThresh)
		%% flags
		flags.pcaf = [0 0]; % no pca of X or AUX
		flags.shrink = true;
		% perform regularized (rtcca) (alternatively old approach)
		rtccaflag = true;
		flag_conc = true; % if 1 CCA inputs are in conc, if 0 CCA inputs are in intensity

		%% extract user input
		@@ -87,10 +83,6 @@ if flagtCCA
		t = data_y(iBlk).GetTime();
		fq = 1/(t(2)-t(1));
		ml = data_y(iBlk).GetMeasListSrcDetPairs();
		if isempty(mlActAuto{iBlk})
		mlActAuto{iBlk} = ones(size(ml,1),1);
		end
		mlAct = mlActAuto{iBlk};
		end

		%% find the list of short and long distance channels
		@@ -101,8 +93,8 @@ if flagtCCA
		rhoSD(iML) = sum((SrcPos(ml(lst(iML),1),:) - DetPos(ml(lst(iML),2),:)).^2).^0.5;
		posM(iML,:) = (SrcPos(ml(lst(iML),1),:) + DetPos(ml(lst(iML),2),:)) / 2;
		end
		lstSS = lst(find(rhoSD<=rhoSD_ssThresh & mlAct(lst) == 1));
		lstLS = lst(find(rhoSD>rhoSD_ssThresh & mlAct(lst) == 1));
		lstSS = lst(find(rhoSD<=rhoSD_ssThresh));
		lstLS = lst(find(rhoSD>rhoSD_ssThresh));


		%% get long and short channels

getpaths.m

+1 −0

Original line number	Diff line number	Diff line
		@@ -15,6 +15,7 @@ paths = {...
		'/FuncRegistry'; ...
		'/FuncRegistry/UserFunctions'; ...
		'/FuncRegistry/UserFunctions/Archive'; ...
		'/FuncRegistry/UserFunctions/tcca_glm'; ...
		'/MainGUI'; ...
		'/Install'; ...
		'/PlotProbeGUI'; ...

hmrR_tCCA.m

0 → 100644

+0 −0

Empty file added.

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