OPTIMA_read_GE_BIDS.m

function BIDS = OPTIMA_read_GE_BIDS(BIDS)
%
% reads GE raw data structure
%
%
% file history:
% created M. Czisch & F. Binder 8.11.2017
% last 22.5.2019 M.Czisch



files = dir;
BIDS.input.data_dir = '';

fprintf('read GE data structure\n');

% find the individual EXAM numbers

for i = 1:size(files,1)
    if logical(strcmp(files(i).name(1),'e'))
        %BIDS.input.data_dir(end+1).name = files(i).name;
        BIDS.input.data_dir(1).name = files(i).name;
    end
end


% find the individual SERIES numbers

for i=1:size(BIDS.input.data_dir,2)
    cd(BIDS.input.dir);
    cd(BIDS.input.data_dir(i).name)
    files = dir;
    for j=1:size(files,1)
        BIDS.input.data_dir(i).subdir{j} = files(j).name;
    end
end

% loop over the days and read dicom file information

for i=1:2
    
    if i==2 && size(BIDS.input.data_dir,2) == 1
        break;
    else
        fprintf('reading day %d\n', i);
        
        max = size(BIDS.input.data_dir(i).subdir,2);
        n_day(i) = 0;
        
        for j=3:max
            if ~logical(strcmp(BIDS.input.data_dir(i).subdir(j),'.'))
                
                filename = [BIDS.input.dir,'/',BIDS.input.data_dir(i).name,'/',BIDS.input.data_dir(i).subdir{j},'/*.1'];
                image = dir(filename);
                BIDS.input.data_dir(i).image{j} = image.name;
                
                filename = [BIDS.input.dir,'/',BIDS.input.data_dir(i).name,'/',BIDS.input.data_dir(i).subdir{j},'/',BIDS.input.data_dir(i).image{j}];
                
                myfile = dicominfo(filename);
                BIDS.input.data_dir(i).Filename{j} = myfile.Filename;
                BIDS.input.data_dir(i).PatientID{j} = myfile.PatientID;
                BIDS.input.data_dir(i).StudyDate{j} = myfile.StudyDate;
                BIDS.input.data_dir(i).StudyTime{j} = myfile.StudyTime;
                BIDS.input.data_dir(i).ContentTime{j} = myfile.ContentTime;
                BIDS.input.data_dir(i).ProtocolName{j} = myfile.ProtocolName;
                BIDS.input.data_dir(i).SeriesDescription{j} = myfile.SeriesDescription;
                %BIDS.input.data_dir(i).ImagesInAcquisition{j} = myfile.ImagesInAcquisition;
                
                if strfind(myfile.ImageType,'DERIVED\') %if GE produces mean images of previous fMRI time series
                    data_dir(i).ImagesInAcquisition{j} = 0;
                else
                    data_dir(i).ImagesInAcquisition{j} = myfile.ImagesInAcquisition;
                end
                
                if isfield(myfile, 'NumberOfTemporalPositions')
                    BIDS.input.data_dir(i).NumberOfTemporalPositions{j} = myfile.NumberOfTemporalPositions;
                else
                    BIDS.input.data_dir(i).NumberOfTemporalPositions{j} = 1;
                end
                BIDS.input.data_dir(i).SequenceName{j} = myfile.Private_0019_109c;
            end
        end
    end
    
    % sanity check required!!!!
end