minor documentation updates

%

% DESCRIPTION:

% This script generates regressors using the regularized temporally embedded

% Canonical Correlation Anlaysis described in detail in von Lhmann, NI,

% 2020. Generated Aaux and rcMap are to be passed as an input to GLM function.

% Reference code:  https://github.com/avolu/tCCA-GLM

%

% If you apply this method or want to learn more about it, please use the following

% CITATION:

% Canonical Correlation Anlaysis described in detail in von Lhmann, NeuroImage,

% 2020. If you use this method, please use the following CITATION:

% von Lhmann, Alexander, et al. "Improved physiological noise regression

% in fNIRS: A multimodal extension of the General Linear Model using temporally

% embedded Canonical Correlation Analysis." NeuroImage 208 (2020): 116472.

% runIdx - the index of the run in a multi-run session

% flagtCCA - turns the function on / off

% flagICRegressors - selects regressor generation strategy:

%            0/false - common set of regressors for all fNIRS channels (default)

%            1/true - one individual regressor per fNIRS channel (true)

%            (0/false): common set of regressors for all fNIRS channels

%            (default), (1/true): one individual regressor per fNIRS channel

% tCCAparams - These are the parameters for tCCA function

%            1 - timelag

%            2 - sts: step size

%            3 - ctr: if <1  correlation threshold, if =>1 number of regressors.

%            1 - 1 timelag [s]

%            2 - 2 step size [samples]

%            3 - 3 ctr if <1  correlation threshold, if =>1 number of regressors.

%                   Redundant if flagICRegressors = 1;

% tCCAaux_inx -  Indices of the aux channels to be used to generate regressors

% rhoSD_ssThresh - max distance for a short separation measurement. Set =0

% Homer3 (v1.20.1)

% group

@ hmrG_SubjAvg [dcAvg,nTrials] (dcAvgSubjs,nTrialsSubjs

@ hmrG_SubjAvgStd dcAvgStd (dcAvgSubjs

% subj

@ hmrS_RunAvg [dcAvg,nTrials] (dcAvgRuns,mlActRuns,nTrialsRuns 

@ hmrS_RunAvgStd2 dcAvgStd (dcAvgRuns,dcSum2Runs,mlActRuns,nTrialsRuns 

% run

@ hmrR_Intensity2OD dod (data

@ hmrR_BandpassFilt dod (dod hpf %0.3f 0.01 lpf %0.3f 0.5

@ hmrR_BandpassFilt aux (aux hpf %0.3f 0.01 lpf %0.3f 0.5

@ hmrR_OD2Conc_new dc (dod,probe ppf %0.1f_%0.1f 1_1

@ hmrR_tCCA [Aaux,rcMap] (dc,aux,probe,iRun flagtCCA %d 1 flagICRegressors %d 0 tCCAparams %d_%d_%0.1f 3_2_0.3 tCCAaux_inx %d_%d_%d_%d_%d_%d_%d_%d 1_2_3_4_5_6_7_8 rhoSD_ssThresh %0.1f 15 runIdxResting %d 1

@ hmrR_GLM [dcAvg,dcAvgStd,nTrials,dcNew,dcResid,dcSum2,beta,R] (dc,stim,probe,mlActAuto,Aaux,tIncAuto,rcMap trange %0.1f_%0.1f -2_20 glmSolveMethod %d 1 idxBasis %d 2 paramsBasis %0.1f_%0.1f_%0.1f_%0.1f_%0.1f_%0.1f 0.1_3_10_1.8_3_10 rhoSD_ssThresh %0.1f 15 flagNuisanceRMethod %d 3 driftOrder %d 3 flagMotionCorrect %d 0

@ hmrR_BlockAvg [dcAvg,dcAvgStd,nTrials,dcSum2] (dc,stim trange %0.1f_%0.1f -2_20