Remove flagMotionCorrect param from the GLM function (#24) (2c7986d6) · Commits · github_fork / Homer3

Docs/DesignNotes.ppt

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FuncRegistry/UserFunctions/hmrR_GLM.m

+20 −22

Original line number	Diff line number	Diff line
		% SYNTAX:
		% [yavg, yavgstd, tHRF, nTrials, ynew, yresid, ysum2, beta, R] = hmrR_GLM(data, stim, probe, mlActAuto, Aaux, tIncAuto, trange, rcMap, glmSolveMethod, idxBasis, paramsBasis, rhoSD_ssThresh, flagNuisanceRMethod, driftOrder, flagMotionCorrect )
		% [yavg, yavgstd, tHRF, nTrials, ynew, yresid, ysum2, beta, R] = hmrR_GLM(data, stim, probe, mlActAuto, Aaux, tIncAuto, trange, rcMap, glmSolveMethod, idxBasis, paramsBasis, rhoSD_ssThresh, flagNuisanceRMethod, driftOrder)
		%
		% UI NAME:
		% GLM_HRF_Drift_SS
		@@ -68,7 +68,6 @@
		% 3. uses tCCA regressors for nuisance regression, in Aaux,
		% mapped by rcMap, provided by hmr_tCCA()
		% driftOrder - Polynomial drift correction of this order
		% flagMotionCorrect - set to 1 to baseline correct between motion epochs indicated in tIncAuto, otherwise set to 0
		%
		%
		% OUTPUTS:
		@@ -87,7 +86,7 @@
		%
		%
		% USAGE OPTIONS:
		% GLM_HRF_Drift_SS_Concentration: [dcAvg, dcAvgStd, nTrials, dcNew, dcResid, dcSum2, beta, R] = hmrR_GLM(dc, stim, probe, mlActAuto, Aaux, tIncAuto, rcMap, trange, glmSolveMethod, idxBasis, paramsBasis, rhoSD_ssThresh, flagNuisanceRMethod, driftOrder, flagMotionCorrect)
		% GLM_HRF_Drift_SS_Concentration: [dcAvg, dcAvgStd, nTrials, dcNew, dcResid, dcSum2, beta, R] = hmrR_GLM(dc, stim, probe, mlActAuto, Aaux, tIncAuto, rcMap, trange, glmSolveMethod, idxBasis, paramsBasis, rhoSD_ssThresh, flagNuisanceRMethod, driftOrder)
		%
		%
		% PARAMETERS:
		@@ -98,11 +97,10 @@
		% rhoSD_ssThresh: 15.0
		% flagNuisanceRMethod: 1
		% driftOrder: 3
		% flagMotionCorrect: 0
		%
		%
		function [data_yavg, data_yavgstd, nTrials, data_ynew, data_yresid, data_ysum2, beta_blks, yR_blks] = ...
		hmrR_GLM(data_y, stim, probe, mlActAuto, Aaux, tIncAuto, rcMap, trange, glmSolveMethod, idxBasis, paramsBasis, rhoSD_ssThresh, flagNuisanceRMethod, driftOrder, flagMotionCorrect)
		hmrR_GLM(data_y, stim, probe, mlActAuto, Aaux, tIncAuto, rcMap, trange, glmSolveMethod, idxBasis, paramsBasis, rhoSD_ssThresh, flagNuisanceRMethod, driftOrder)

		% Init output
		data_yavg = DataClass().empty();
		@@ -381,25 +379,25 @@ for iBlk=1:length(data_y)
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		% Expand design matrix for Motion Correction
		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
		if flagMotionCorrect==1
		idxMA = find(diff(tInc)==1); % number of motion artifacts
		if isempty(idxMA)
		% if flagMotionCorrect==1
		% idxMA = find(diff(tInc)==1); % number of motion artifacts
		% if isempty(idxMA)
		nMC = 0;
		Amotion = [];
		else
		nMA = length(idxMA);
		nMC = nMA+1;
		Amotion = zeros(nT,nMC);
		Amotion(1:idxMA(1),1) = 1;
		for ii=2:nMA
		Amotion((idxMA(ii-1)+1):idxMA(ii),ii) = 1;
		end
		Amotion((idxMA(nMA)+1):end,end) = 1;
		end
		else
		nMC = 0;
		Amotion = [];
		end
		% else
		% nMA = length(idxMA);
		% nMC = nMA+1;
		% Amotion = zeros(nT,nMC);
		% Amotion(1:idxMA(1),1) = 1;
		% for ii=2:nMA
		% Amotion((idxMA(ii-1)+1):idxMA(ii),ii) = 1;
		% end
		% Amotion((idxMA(nMA)+1):end,end) = 1;
		% end
		% else
		% nMC = 0;
		% Amotion = [];
		% end
		lstInc = find(tInc==1);

		%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

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