Merge branch 'master' of https://github.com/BUNPC/Homer3

% SYNTAX:

% [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, runIdxResting, tResting)

% [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

%

% UI NAME:

% hmrR_tCCA

%          if you do not want to regress the short separation measurements.

%          Follows the static estimate procedure described in Gagnon et al (2011).

%          NeuroImage, 56(3), 1362?1371.

% ss_ch_inx - short separation channel index, starts from one ends with the

% total number of short separation channels

% runIdxResting - resting state run index

% tResting - start/stop time [s] to use from resting data for tCCA training

%

%           Only relevant when flagICRegressors = 1.

%

% USAGE OPTIONS:

% hmrR_tCCA_Concentration_Data: [Aaux, rcMap] = hmrR_tCCA(dc, aux, probe, iRun, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, runIdxResting, tResting)

% hmrR_tCCA_OD_Data: [Aaux, rcMap] = hmrR_tCCA(dod, aux, probe, iRun, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, runIdxResting, tResting)

% hmrR_tCCA_Concentration_Data: [Aaux, rcMap] = hmrR_tCCA(dc, aux, probe, iRun, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

% hmrR_tCCA_OD_Data: [Aaux, rcMap] = hmrR_tCCA(dod, aux, probe, iRun, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

%

%

% PARAMETERS:

% tCCAparams: [3 2 0.3]

% tCCAaux_inx: [1 2 3 4 5 6 7 8]

% rhoSD_ssThresh: 15.0

% ss_ch_inx: 0

% runIdxResting: 1

% tResting: [30 210]

%

function [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, runIdxResting, tResting)

function [Aaux, rcMap] = hmrR_tCCA(data, aux, probe, runIdx, flagtCCA, tCCAparams, tCCAaux_inx, rhoSD_ssThresh, ss_ch_inx, runIdxResting, tResting)

%% COMMENTS/THOUGHTS/QUESTIONS ALEX

% 2) Output canonical correlation coefficients as quality metric?

        lstSS = lst(find(rhoSD<=rhoSD_ssThresh)); %#ok<*FNDSB>

        lstLS = lst(find(rhoSD>rhoSD_ssThresh));

        if ss_ch_inx ~= 0

            lstSS = lstSS(ss_ch_inx);

        end

        %% get long and short separation data

        if strncmp(datatype{1}, 'Hb', 2)

            dHbO = squeeze(d(:,1,:));