Pipeline_infants_NocovReg.m

    function rMatrix = Pipeline_Huiqing_NocovReg(SubjectID,SessionID)
    fmri_root='/export/bedny/Projects/dHCP_3rel/rel3_dhcp_fmri_pipeline';
    ROI_root='/export/bedny/Projects/dHCP_3rel/ROIs';
    
    fmri_dir=[fmri_root,filesep,SubjectID,filesep,SessionID,filesep,'func'];
    ROI_dir=[ROI_root,filesep,'ROI_individual_nooverlap'];

    file_motion_regressor=[fmri_dir,filesep,'confound.txt'];
    file_fMRI=[fmri_dir,filesep,SubjectID,'_',SessionID,'_task-rest_desc-preproc_bold.nii.gz'];
    MaskData = [fmri_dir,filesep,SubjectID,'_',SessionID,'_task-rest_desc-brain_mask.nii.gz'];

    ROIs={'A1','math_frontal','lang_frontal','gngc_frontal','SMC','math_occ','gngc_occ','lang_occ','V1'};
    hemi={'lh','rh'};
    ROIDef=cell(1,size(ROIs,2)*2);
%     for iROI=1:size(ROIs,2)
%         for iHemi=1:2
%             %--copy ROI to fMRI folder
%             file_ROI_orig=[ROI_dir,filesep,ROIs{1,iROI},'_',SubjectID,'_',SessionID,'.',hemi{iHemi},'.nii.gz'];
%             file_ROI_dest=[fmri_dir,filesep,ROIs{1,iROI},'_',SubjectID,'_',SessionID,'.',hemi{iHemi},'.nii.gz'];
%             copyfile(file_ROI_orig,file_ROI_dest);
%             %--reslicing
%             file_ROI_reslice = [fmri_dir,filesep,'r_',ROIs{1,iROI},'_',SubjectID,'_',SessionID,'.',hemi{iHemi},'.nii'];
%             y_Reslice(file_ROI_dest,file_ROI_reslice,'',0, MaskData);
%             ROIDef{1,(iROI-1)*2+iHemi}=file_ROI_reslice;
%         end
%     end
    
    %===============use ROI files in the ROI folder
     for iROI=1:size(ROIs,2)
        for iHemi=1:2
            file_ROI_orig=[ROI_dir,filesep,ROIs{1,iROI},'_',SubjectID,'_',SessionID,'.',hemi{iHemi},'.nii.gz'];
            ROIDef{1,(iROI-1)*2+iHemi}=file_ROI_orig;
        end
     end
    %-----------------

    OutputName=[fmri_dir,filesep,'ROI_signal'];

    %===========Regress covariates=================
    %--Regress covariates
%     mask_dir = '/export/bedny/Projects/dHCP_3rel/MASK_func';
%     %mask_file_WM = [SubjectID,'_',SessionID,'-WM.nii.gz'];
%     mask_file_CSF = [SubjectID,'_',SessionID,'-CSF_func.nii.gz'];
%         
%     DataDir = [fmri_dir,filesep,'tmp_DPABI'];
%     if ~isdir(DataDir)
%         mkdir(DataDir)
%     end
%     copyfile(file_fMRI,DataDir);
%     CovMask_list = {mask_file_CSF};
%    % CovMask_list = {mask_file_CSF,mask_file_WM};
%     Postfix='_Covremoved';
%     MaskFilename = MaskData;
%     ImgCovModel = 1;
%     for iCovMask = 1:size(CovMask_list,2)
%         file_CovMask_orig=[mask_dir,filesep,CovMask_list{1,iCovMask}];
%         file_CovMask_dest=[fmri_dir,filesep,CovMask_list{1,iCovMask}];
%         copyfile(file_CovMask_orig,file_CovMask_dest);
%          %--reslicing
%         file_CovMask_reslice = [fmri_dir,filesep,'r_',CovMask_list{1,iCovMask}];
%         y_Reslice(file_CovMask_dest,file_CovMask_reslice,'',0, MaskData);
%         CovariablesDef.CovMask{1,iCovMask}=file_CovMask_reslice(1:end-3);
%     end
%     y_RegressOutImgCovariates(DataDir,CovariablesDef,Postfix,MaskFilename,ImgCovModel);
%     file_fMRI_Covremoved = [fmri_dir,filesep,'tmp_DPABI_Covremoved',filesep,'CovRegressed_4DVolume.nii'];


    %===========QC with motion outlier==============
    %--read motion regressor
    %file_motion_regressor='confound.txt'; %confound.txt should be generated by fsl
    motion_regressor=dlmread(file_motion_regressor);
    %--generate temporal mask '1' to keep and '0' to remove
    outlier_mask = sum(motion_regressor,2);
    temporal_mask = ~outlier_mask;
    %--total number of outliers in sliding windows (continuous set) of 1600 volumne
    total_length = 2300;
    window_length = 1600;
    number_window = total_length - window_length + 1;
    vector_outlier_number = zeros(1,number_window);
    for i_window = 1:number_window
        vector_outlier_number(1,i_window) = sum(outlier_mask(i_window:i_window + window_length - 1,1));
    end
    %--sliding window with minimum number of motion-outliers
    [minimum_outlier,window_minimum_outlier] = min(vector_outlier_number);
    continuous_set_mask = zeros(2300,1);
    continuous_set_mask(window_minimum_outlier:window_minimum_outlier + window_length - 1) =  1;
    %--QC
    if minimum_outlier > 160 % not pass QC
        %%%%%%% Do Something %%%%%
        rMatrix = [];
        disp([SubjectID, ':Not pass QC!']);
        return % end the procedure    
    end

    
    %============= Processing the fMRI==============
    DataDir = [fmri_dir,filesep,'tmp_DPABI'];
    if ~isdir(DataDir)
        mkdir(DataDir)
    end
    file_fMRI=[fmri_dir,filesep,SubjectID,'_',SessionID,'_task-rest_desc-preproc_bold.nii.gz'];    
    file_fMRIcopy = [DataDir,filesep,SubjectID,'_',SessionID,'_task-rest_desc-preproc_bold.nii.gz'];
    copyfile(file_fMRI,file_fMRIcopy);
    gunzip(file_fMRIcopy,DataDir);
    file_fMRIcopy = [DataDir,filesep,SubjectID,'_',SessionID,'_task-rest_desc-preproc_bold.nii'];
    %file_fMRI = '/export/bedny/Projects/dHCP/sub_passed_QC_allROI/Scrubbing/sub-CC00109XX10_ses-36901_task-rest_desc-preproc_bold.nii';
    [Data, VoxelSize, FileList, Header] = y_ReadAll(file_fMRIcopy);
    
    %[Data, VoxelSize, FileList, Header] = y_ReadAll(file_fMRI_Covremoved);
    %file_fMRI = '/export/bedny/Projects/dHCP/sub_passed_QC_allROI/Scrubbing/sub-CC00109XX10_ses-36901_task-rest_desc-preproc_bold.nii';
    %[Data, VoxelSize, FileList, Header] = y_ReadAll(file_fMRI);
    %[Data, VoxelSize, FileList, Header] = y_ReadAll(file_fMRI_Covremoved);
    
    Data_continuous_set = Data(:,:,:,logical(continuous_set_mask));
    AllVolume = Data_continuous_set;
    % OutputName = 'test.nii';
    % MaskData = '/export/bedny/Projects/dHCP/sub_passed_QC_allROI/Scrubbing/sub-CC00109XX10_ses-36901_task-rest_desc-preproc_space-bold_brainmask.nii';
    % TemporalMask = logical(temporal_mask(logical(continuous_set_mask)));
    % ScrubbingMethod='cut';
    % ScrubbingTiming = 'AfterFiltering';
    % IsNeedDetrend = 0;
    % Band = [0,0.08];
    % TR = 0.392;
    % 
    % [AllVolumeBrain, Header_Out] = y_Scrubbing(AllVolume, OutputName, MaskData, TemporalMask, ScrubbingMethod, ScrubbingTiming, IsNeedDetrend, Band, TR, Header);

    %y_Reslice('A1_sub-CC00109XX10_ses-36901.lh.nii','r_A1_sub-CC00109XX10_ses-36901.lh.nii','',0, '/export/bedny/Projects/dHCP/sub_passed_QC_allROI/Scrubbing/sub-CC00109XX10_ses-36901_task-rest_desc-preproc_space-bold_brainmask.nii');
    %y_Reslice('gngcFrontal_sub-CC00109XX10_ses-36901.lh.nii','r_gngcFrontal_sub-CC00109XX10_ses-36901.lh.nii','',0, '/export/bedny/Projects/dHCP/sub_passed_QC_allROI/Scrubbing/sub-CC00109XX10_ses-36901_task-rest_desc-preproc_space-bold_brainmask.nii');
    %ROIDef={'r_A1_sub-CC00109XX10_ses-36901.lh.nii','r_gngcFrontal_sub-CC00109XX10_ses-36901.lh.nii'};
    %OutputName='test_ROI_signal';
    %MaskData = '/export/bedny/Projects/dHCP/sub_passed_QC_allROI/Scrubbing/sub-CC00109XX10_ses-36901_task-rest_desc-preproc_space-bold_brainmask.nii';
    IsMultipleLabel=0;
    IsNeedDetrend=1;
    Band = [0,0.08];
    TR = 0.392;
    TemporalMask = logical(temporal_mask(logical(continuous_set_mask)));
    ScrubbingMethod='cut';
    ScrubbingTiming = 'AfterFiltering';
    CUTNUMBER=10;
    [ROISignals] = y_ExtractROISignal(AllVolume, ROIDef, OutputName, MaskData, IsMultipleLabel, IsNeedDetrend, Band, TR, TemporalMask, ScrubbingMethod, ScrubbingTiming, Header,CUTNUMBER); 
    rMatrix=corr(ROISignals);
end