WiscPlan_v2/WiscPlanPhotonkV125/matlab_frontend/nrrd2ROI.m

function Geometry=nrrd2ROI(Geometry, patient_dir)

    %% -----===== Get ROI mask =====-----
    while true
        newRoi = questdlg('Do you want to load another ROI?','New ROI','Yes','No','No');
        switch newRoi
            case 'Yes'
                
                [ROI_in, ROI_path, filterIdx] = uigetfile([{'*.nrrd'; '*.am'}], 'Select ROI image', Geometry.data_dir);
                switch filterIdx
                    case 0
                        warning('No file selected, aborting!')
                        return 
                    case 1
                        [ROI_img, meta]=nrrdread([ROI_path, ROI_in]);
                        disp('NRRD file loaded!')
                    case 2
                        ROI_img = am2mat([ROI_path, ROI_in]);
                        ROI_img = permute(ROI_img.data, [2,1,3]);
                        disp('AM file loaded!')
                    case 3
                        error('please do not select *all* in file selection')
                    otherwise
                        error('You should never see this.')
                end
                
                WiscPlan_preferences.patientDataPath = Geometry.patient_dir;
                save(which('WiscPlan_preferences.mat'), 'WiscPlan_preferences');
                
                Geometry.ROIS{end+1}.ind = find(ROI_img>0);
                str = inputdlg('Enter ROI name:')
                Geometry.ROIS{end}.name= str{1};
                save(fullfile(Geometry.patient_dir, 'matlab_files', 'Geometry.mat'), 'Geometry');

            case 'No'
                break
        end
    end
end