Changed the format of parameter tccaAux_inx to array of flags rather than list...

%            2 - 2 step size [s]

%            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

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

% regressors. 0 for the indices of unused aux channels, 1 for included

% aux channels.

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

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

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

% PARAMETERS:

% flagtCCA: 1

% tCCAparams: [3 0.08 0.3]

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

% tCCAaux_inx: [1 1 1 1 0 0 0 0]

% rhoSD_ssThresh: 15.0

% ss_ch_inx: [1 2 3 4 5]

% runIdxResting: 1

%%

%% flags and tCCA settings

tCCAaux_inx = find(tCCAaux_inx); % Convert flags to list of indices

flags.pcaf =  [0 0]; % no pca of X or AUX

% flags.shrink = true; % perform shrinkage in the CCA

flags.shrink = false;  % JD: set to false because rtcca generate error, "Undefined function or variable 'cshrink'".

        end

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

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

        if length(lstSS) == 0

           errordlg('No short separation channels fall within rhoSD_ssThresh!');

        end

        if ss_ch_inx ~= 0

            lstSS = lstSS(ss_ch_inx);