read_GE_BIDS.m

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



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

% find the individual EXAM numbers

for i=1:size(files,1);
    if strcmp(files(i).name(1),'e')
        BIDS.input.data_dir(end+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
    max = size(BIDS.input.data_dir(i).subdir,2);
    n_day(i) = 0;
    
    for j=3:max
        i
        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 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
    
    % sanity check required!!!!
end