conn_batchexample_qcplot.m

% creates QC-FC plots separately within each site (for a multi-site study)

DOREMOVE = false;                                                                % set to false to create QC plots based on all subjects, set to true to create QC plots based on a chosen subset of "valid" subjects
DOCOMBI = false;                                                                 % computes QC-FC plots combining all sites
DOSITES = true;                                                                 % computes QC-FC plots separately for each site
if DOREMOVE
    foldername = 'validsubjects';                                               % output QA-report name (only needed if DOREMOVE=true)
    groupvariable = 'QC_ValidSubjects';                                        % 2nd-level covariate name containing "valid subjects" group (only needed if DOREMOVE=true)
else
    foldername = 'original';                                                    % output QA-report name (only needed if DOREMOVE=false)
    groupvariable = 'AllSubjects';                                              % 2nd-level covariate name containing "valid subjects" group (e.g. 'AllSubjects') (only needed if DOREMOVE=false)
end
sitevariable = '^SITE_'; %{'site_1','site_2','site_3'};                                    % 2nd-level covariate names containing SITES subject-groups (only needed if DOSITES=true)
QCvariables = {'QC_InvalidScans','QC_MeanMotion','QC_ProportionValidScans'};    % name of QC variables to use for QC-FC plots (only needed if DOSITES=true)
% conn load /myfolder/myproject.mat;                                            % uncomment this line to load a different conn project (by default it works on the currently-open project)  


% ------ END OF USER-DEFINED PARAMETERS --------
% ------ DO NOT MODIFY THE CODE BELOW   --------

[filepath,filename,fileext] = fileparts(conn_projectmanager('projectfile')); % project folder
filepath = conn_fullfile(filepath,filename);
[covs,covs_names]=conn_module('get','l2covariates');
idx=find(ismember(covs_names,groupvariable)); valid=covs(:,idx);
if ischar(sitevariable), sitevariable=covs_names(find(cellfun('length',regexp(covs_names,sitevariable))>0)); end
if DOSITES, sites=[]; for k=1:numel(sitevariable), idx=find(ismember(covs_names,sitevariable{k})); sites=[sites, covs(:,idx)]; end; end

if DOCOMBI
    conn_batch(...
        'QA.plots',         {'QA_DENOISE FC-QC'},...
        'QA.l2covariates',  QCvariables,...
        'subjects',         find(valid),...
        'QA.foldername',    fullfile(filepath,'results','qa',sprintf('QA_%s_all',foldername)) );
end

if DOSITES
    for k=1:numel(sitevariable),
        conn_batch(...
            'QA.plots',         {'QA_DENOISE FC-QC'},...
            'QA.l2covariates',  QCvariables,...
            'subjects',         find(sites(:,k)&valid),...
            'QA.foldername',    fullfile(filepath,'results','qa',sprintf('QA_%s_site%d',foldername,k)) );
    end
end