performAutoKinMod.m

function outputArg1 = performAutoKinMod(pathInputFolder, app, keepTempfiles,FolderNameSetOfNormals, numberOfFramesToModel)


addpath('setup');


try
    app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' processing started']}, app.ProtocolTextArea.Value(:)'];
end


%% Step -1: Select steps to be performed

performDICOMImport = true;
performMovCor = true;
performACOrig = true;
performSpatialNorm = true;
performKinMod = true;
performZTrans = true;
performReportOutput = true;

%Try to read status of checkboxes in GUI
try
    performDICOMImport = app.chkDicom.Value;
    performMovCor = app.chkMovCor.Value;
    performACOrig = app.chkACOrig.Value;
    performSpatialNorm = app.chkSpatialNorm.Value;
    performKinMod = app.chkKinMod.Value;
    performZTrans = app.chkZTrans.Value;
    performReportOutput = app.chkReportOutput.Value;
    
    disp(performDICOMImport);
end


%% Step 0: Create Workdir


try
    app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' create workdir']}, app.ProtocolTextArea.Value(:)'];
end

%Append filesep to path, if missing
if ~strcmp(pathInputFolder(end), filesep)
    pathInputFolder = [pathInputFolder filesep];
end

mkdir([pathInputFolder 'workdir']);

%% Step 1: DICOM Import

if performDICOMImport
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' import DICOM']}, app.ProtocolTextArea.Value(:)'];
    end
    
    addpath('BatchDICOM_Import');
    
    foldersForInput = dir([pathInputFolder]);
    
    % remove linux folder-dots .. . and workidr
    foldersForInput(strcmp({foldersForInput.name}, '..')) = [];
    foldersForInput(strcmp({foldersForInput.name}, '.')) = [];
    foldersForInput(strcmp({foldersForInput.name}, 'workdir')) = [];
    % only folders
    foldersForInput = foldersForInput([foldersForInput(:).isdir]);
    
    for i=1:length(foldersForInput)
        fcnDICOMImportBatch([pathInputFolder foldersForInput(i).name], [pathInputFolder foldersForInput(i).name], '','noGUI');
    end
    
    %remove intermediate file from DICOM import
    try
        delete('DICOMImportBatch_jobINTERMEDIATE.m')
    end
    
    rmpath('BatchDICOM_Import');
    
    % Move created nifti files to workdir
    
    for i=1:length(foldersForInput)
        filesInFolder = dir([pathInputFolder foldersForInput(i).name filesep '*.nii']);
        for j=1:length(filesInFolder)
            movefile([filesInFolder(j).folder filesep filesInFolder(j).name], [pathInputFolder 'workdir']);
        end
    end
    
end

%% Step 2: Movement Correction

if performMovCor
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' Movement Correction started']}, app.ProtocolTextArea.Value(:)'];
    end
    
    addpath('MovementCorrection');
    fcnMovementCorrection([pathInputFolder 'workdir' filesep], 'noGUI');
    
    rmpath('MovementCorrection');
    
    %remove intermediate file from Movement Correction
    try
        delete('MovCor_job_INTERMEDIATE.m')
    end
    
end

%% Step 3: convert to 4D Nifti

if performMovCor
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' 4D Nifti conversion']}, app.ProtocolTextArea.Value(:)'];
    end
    
    addpath('ConvertTo4D');
    if ~exist('numberOfFramesToModel','var')
        numberOfFramesToModel = 23;
    end
    conversion4DSuccessful = fcnConvert4D([pathInputFolder 'workdir' filesep], 'movCor_*.nii', numberOfFramesToModel, 'noGUI');
    
    if conversion4DSuccessful
        % delete non4D files
        delete([pathInputFolder 'workdir' filesep '4D*.mat']);
        delete([pathInputFolder 'workdir' filesep 'movCor_*.nii']);
    end
    
    rmpath('ConvertTo4D');
    
    %remove intermediate file from 4D Conversion
    try
        delete('Convert4D_job_INTERMEDIATE.m')
    end
    
end

%% Step 4: SetAC origin

if performACOrig
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' Set AC Origin ']}, app.ProtocolTextArea.Value(:)'];
    end
    
    addpath('SetACOrigin');
    
    fcnSetACOrigin([pathInputFolder 'workdir' filesep], [pathInputFolder 'workdir' filesep], '4D*.nii', numberOfFramesToModel);
    
    rmpath('SetACOrigin');
    
end

%% Step 5: Normalize against perfusion template

if performSpatialNorm
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' Spatial normalization started']}, app.ProtocolTextArea.Value(:)'];
    end
    
    addpath('NormalizePerfusionPETbased');
    
    fcnNormalizePerfusionPETbased([pathInputFolder 'workdir' filesep], 'noGUI');
    
    rmpath('NormalizePerfusionPETbased');
    
    %remove intermediate file from spatial normalization
    try
        delete('normalizePerfusionBased_batch_INTERMEDIATE.m')
    end
    
end


%% Step 6: Run qmodeling with the Normalized Dataset to

if performKinMod
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' kinetic modeling started']}, app.ProtocolTextArea.Value(:)'];
    end
    
    addpath('autoQModeling');
    
    % clear qModeling input folder of nifti files
    delete(['autoQModeling' filesep 'workdir' filesep 'studies' filesep 'automatedCGN' filesep '*.nii']);
    delete(['autoQModeling' filesep 'workdir' filesep 'studies' filesep 'automatedCGN' filesep '*.hdr']);
    delete(['autoQModeling' filesep 'workdir' filesep 'studies' filesep 'automatedCGN' filesep '*.img']);
    
    %delete qModeling results fodler
    try
        rmdir(['autoQModeling' filesep 'workdir' filesep 'results'], 's');
    end
    try
        mkdir(['autoQModeling' filesep 'workdir' filesep 'results']);
    end
    
    %move normalized 4D file to qModeling input folder
    normalized4DNifti = dir([pathInputFolder 'workdir' filesep 'wAC*.nii']);
    copyfile([normalized4DNifti(1).folder filesep normalized4DNifti(1).name], ['autoQModeling' filesep 'workdir' filesep 'studies' filesep 'automatedCGN']);
    
    oldfolder = cd('autoQModeling');
    
    run('localPathDefinition.m');
    addpath(path_qmodeling);
    autoQModelingCGN();
    cd(oldfolder);
    
    % move results files back to orginal directory and rename folder
    movefile(['autoQModeling' filesep 'workdir' filesep 'results'], pathInputFolder);
    movefile([pathInputFolder filesep 'results'], [pathInputFolder filesep 'results_kinetic_modeling' filesep]);
    
    rmpath(path_qmodeling);
    
end

%% Step 7: Create z transformed deviation map

if performZTrans
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' Create z transformed deviation map']}, app.ProtocolTextArea.Value(:)'];
    end
    
    addpath('zTransformation');
    
    FolderNameSetOfNormals = 'PI2620_HC_Piramal';
    fcnZtransform([pathInputFolder 'results_kinetic_modeling' filesep],'*SRTM2_BPnd*', FolderNameSetOfNormals);
    
    rmpath('zTransformation');
    
end

%% Step 8: Skull stripping

if performZTrans
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' Remove skull']}, app.ProtocolTextArea.Value(:)'];
    end
    
    addpath('skullStripping');
    
    fcnSkullStrip([pathInputFolder 'results_kinetic_modeling' filesep]);
    
    rmpath('skullStripping');
    
end

%% Step 9: Human readable Output as Png-image and dicom

if performReportOutput
    
    try
        app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' Overview-Output Sheet']}, app.ProtocolTextArea.Value(:)'];
    end
    
    overlaySlices([pathInputFolder 'results_kinetic_modeling' filesep 'BET_zDev_automatedCGN_SRTM2_BPnd_image.nii'], [pathInputFolder 'results_kinetic_modeling' filesep 'BET_zDev_automatedCGN_SRTM2_BPnd_image.nii'], pathInputFolder, [pathInputFolder 'results_kinetic_modeling' filesep]);
    
end

%% Finished 

rmpath('setup');

try
    app.ProtocolTextArea.Value = [{[datestr(datetime('now')) ' done']}, app.ProtocolTextArea.Value(:)'];
end

end