function data = execute_sort_and_convert_Callback(data)
%whether the conversion is carried out or not depends on the parameter
%data.current_conversion = 'dicom';
%data.current_conversion = 'convert'
%data.current_conversion = 'list';
readfile_dir = data.readfile_dir;
writefile_dir_selected = data.writefile_dir_selected;
default_startpath = data.default_startpath;
data.not_one_series_option = 'Not Set';
%if no output directory is selected (it is still == default), set the
%output directory to be the readfile_dir
if strcmp(writefile_dir_selected, default_startpath) ==1
writefile_dir_selected = readfile_dir;
end
% get the directory contents
flist = dir(fullfile(readfile_dir,data.readfile_filter));
nfiles = length(flist);
data.total_number_of_files = nfiles;
if(nfiles == 0)
warndlg(sprintf('No %s files in %s\n', data.readfile_filter, readfile_dir), 'dlgname');
return;
end
% get the subject ID and accession number from any scan in the series to
% make a new directory name
[res, dcminfo] = isdicomfile(fullfile(readfile_dir,flist(1).name));
if strcmp(dcminfo.PatientID, 'Anonymous') ~= 1
anon_subdir = [strip_banned_characters_func(dcminfo.PatientID) '_' strip_banned_characters_func(dcminfo.AccessionNumber)];
else
anon_subdir = strip_banned_characters_func(dcminfo.PatientID);
end
data.anon_subdir = anon_subdir;
%set a subdirectory, or not
switch data.define_writefile_subdir
case 'yes'
writefile_dir_stem = fullfile(writefile_dir_selected, anon_subdir);
otherwise
writefile_dir_stem = writefile_dir_selected;
end
%set the dicom directory always to be called dicom
switch data.current_conversion
case 'dicom'
writefile_dir = fullfile(writefile_dir_stem, 'dicom') ;
case 'convert'
switch data.convert_format
case {'analyze','nifti'}
writefile_dir = fullfile(writefile_dir_stem, 'nifti') ;
otherwise
error('Convert format could not be determined');
end
case 'list'
writefile_dir = fullfile(writefile_dir_stem, 'list') ;
otherwise
error('Current conversion could not be determined');
end
data.writefile_dir = writefile_dir;
try
s = warning ('query', 'MATLAB:MKDIR:DirectoryExists') ; % get current state
warning ('off', 'MATLAB:MKDIR:DirectoryExists') ;
mkdir(writefile_dir);
warning (s) ; % restore state
catch
errordlg(['You do not have permission to write to ' data.writefile_dir ' , use the "Select Destination Directory" to choose a folder where you may write']);
end
%Need to establish the form of the filename - how many full stops before
%the scan number?
% See if the anonymise parameter is set
try
switch dcminfo.DerivationDescription
case 'Force Anonymity'
nfullstopsoffset = 0;
otherwise
nfullstopsoffset = 1;
end
catch
nfullstopsoffset = 1;
end
data.nfullstopsoffset = nfullstopsoffset;
disp(['Processing files in ' data.readfile_dir]);
disp('Checking all files belong to the same subject and series...');
subject_name = get_dicom_fieldname_func(flist(1).name, 0);
series_name = get_dicom_fieldname_func(flist(1).name, nfullstopsoffset+10);
for n = 1:nfiles
%check its the same subject
current_subject_name = get_dicom_fieldname_func(flist(n).name, 0);
data.current_subject_name = current_subject_name;
if strcmp(subject_name, current_subject_name) ~= 1
errordlg(sprintf('Not all images to be sorted belong to the same subject \nSeparate before sorting'), 'dlgname');
return;
end
%check its the same series
current_series_name = get_dicom_fieldname_func(flist(n).name, nfullstopsoffset+10);
data.current_series_name = current_series_name;
if strcmp(series_name, current_series_name) ~= 1
if (strcmp(data.not_one_series_option, 'Stop and separate the data into separate directories') ~= 1 && strcmp(data.not_one_series_option, 'Continue') ~= 1)
data.not_one_series_option = questdlg(sprintf('All images to be sorted belong to the same subject, \nbut are not in the same export series \nThis could arise from exporting\ntwo parts of a session separately\nbut could also indicate multiple versions of the same data, \nwhich will lead to the data becoming mixed. \n\nDo you want to'), ...
'Mixed Series Alert', ...
'Stop and separate the data into separate directories', ...
'Continue', ...
'Stop and separate the data into separate directories');
switch data.not_one_series_option
case 'Stop and separate the data into separate directories'
return;
case 'Continue'
end
end
end
end
disp('Done');
%sort by scan number, which is field number 3 (anon), 4 (norm)
disp('Sorting by scan number ...');
flist = sortlist_func2(flist, nfullstopsoffset+2);
disp('Done');
%create a list of the scan names
scan_names=cell(nfiles,1);
for n = 1:nfiles
%for VB17, need to remove leading '0's (cheat by going to int and back to cell)
scan_names(n) = cellstr(num2str(str2num(get_dicom_fieldname_func(flist(n).name, nfullstopsoffset+2))));
end
%sort by image number, which is field number 4 (anon), 5 (norm)
disp('Sorting scans by image number ...');
int_scan_names = str2num(char(scan_names));
first_scan = min(int_scan_names(:));
last_scan = max(int_scan_names(:));
for n = first_scan: last_scan
files_in_scan_series = find(int_scan_names(:)==n);
if length(files_in_scan_series) > 1
flist(files_in_scan_series) = sortlist_func2(flist(files_in_scan_series), nfullstopsoffset+3);
end
end
data.flist = flist ;
disp('Done');
for n = 1:nfiles
%if this is the first file with this scan number, make a new directory
%and calls the conversion for this list
if (n == 1)
new_scan = 'yes';
else
if strcmp(char(scan_names(n)),char(scan_names(n-1))) ~= 1
new_scan = 'yes';
else
new_scan = 'no';
image_counter = image_counter+1;
end
end
current_scan = char(scan_names(n));
data.current_scan = current_scan;
flist_IX = find(int_scan_names(:)==str2num(current_scan));
data.fsublist = data.flist(flist_IX);
n_files_in_series = length(data.fsublist);
switch data.scanlistonly
case 'no'
case 'yes'
if strcmp(data.workbar_off,'no')
workbar(n/nfiles, ['Processing ' int2str(n_files_in_series) ' files in scan series ' data.current_scan], 'Overall Progress');
end
end
% open log file and set a parameter to decide which things to write to file log
if strcmp(data.first_scan,'yes') == 1
scanlistfile = fullfile(writefile_dir_stem,'scan_list.txt');
data.fp_scanlog = fopen(scanlistfile, 'w');
if data.fp_scanlog == -1
errordlg('Can''t write to scan log in this directory: Select output directory with the "Select Destination Directory" button');
end
data.write_to_log = 'yes';
data.current_dir = fullfile(writefile_dir, current_scan);
write_introductory_comments(data);
data.first_scan = 'no';
end
if strcmp(new_scan,'yes')
disp(['Scan ' data.current_scan ': processing ' int2str(n_files_in_series) ' files in series ']);
current_dir = fullfile(writefile_dir, current_scan);
data.current_dir = current_dir;
if strcmp(data.current_conversion, 'list') ~=1
s = warning ('query', 'MATLAB:MKDIR:DirectoryExists') ; % get current state
warning ('off', 'MATLAB:MKDIR:DirectoryExists') ;
mkdir(current_dir);
warning (s) ; % restore state
end
image_counter = 1;
if strcmp(data.current_conversion, 'convert') || strcmp(data.current_conversion, 'list')
% need to update the dcminfo in case this isn't really a scan at
% all
[res, dcminfo] = isdicomfile(fullfile(readfile_dir,flist(n).name));
if isvar('dcminfo.DerivationDescription')
if strcmp(dcminfo.DerivationDescription, 'MEDCOM RESAMPLED')
fprintf(data.fp_scanlog, 'Scan %s: MEDCOM RESAMPLED; not processing\n', current_scan);
continue;
end
end
% can pick other types of sequences not to convert
if isvar('dcminfo.ProtocolName')
switch dcminfo.ProtocolName
case 'one hour delay fid'
fprintf(data.fp_scanlog, 'Scan %s: 1 hour pause; not processing\n', current_scan);
case 'svs_se_270'
fprintf(data.fp_scanlog, 'Scan %s: spectroscopy sequence; not processing\n', current_scan);
this_warning_text = sprintf('Scan %s was a spectroscopy sequence and was not processed\n', current_scan);
data.warning_present = 'yes';
data.warning_text = sprintf('%s %s', data.warning_text, this_warning_text);
continue;
end
end
if isvar('dcminfo.SeriesDescription')
switch dcminfo.SeriesDescription
case 'StartFMRI'
fprintf(data.fp_scanlog, 'Scan %s: Dummy scan StartFMRI; not processing\n', current_scan);
continue;
case 'intermediate t-Map'
fprintf(data.fp_scanlog, 'Scan %s: ; intermediate t-Map; not processing\n', current_scan);
continue;
case 'Design'
fprintf(data.fp_scanlog, 'Scan %s: ; fMRI Design matrix; not processing\n', current_scan);
continue;
end
end
data.current_readfile_stem = get_readfile_stem_func(flist(n).name, current_scan);
data = convert_to_analyze_func(data);
try
fclose(data.writefile_th_fp);
catch
end
end
end
% Now for DICOM sorting: read, anonymise, rename and write the file
if strcmp(data.current_conversion, 'dicom')
if strcmp(data.workbar_off,'no')
workbar(n/nfiles, ['Sorting DICOM data, ' int2str(n_files_in_series) ' files in scan series ' data.current_scan], 'Overall Progress');
end
writefile_name = ('Image0000.dcm');
try
writefile_name(10-ceil(log10(image_counter+1)):9)=int2str(image_counter);
catch
errordlg('Cannot attribute filename: Are there more than 9999 files in this scan?', 'dlgname');
end
readfile_dcm = fullfile(readfile_dir, flist(n).name);
writefile_name_full = fullfile(current_dir, writefile_name);
% try to read the image and get the header info
try
dcm_header = dicominfo(readfile_dcm);
dcm_image = dicomread(readfile_dcm);
catch
error(['Could not read ' readfile_dcm]);
end
if (strcmp(new_scan,'yes') && (data.number_of_operations == 1))
disp('');
end
switch data.anonymise
case 'yes'
version_number = version;
if ((size(findstr(version_number, '(R2006b)'),1) ~= 0) || size(findstr(version_number, '(R2007a)'),1) ~= 0 || (size(findstr(version_number, '(R2007b)'),1) ~= 0) || (size(findstr(version_number, '(R2008a)'),1) ~= 0) || (size(findstr(version_number, '(R2008b)'),1) ~= 0) || (size(findstr(version_number, '(R2009a)'),1) ~= 0) )
% % NEW STYLE ANONIMISATION
% % get dicom info for first image in scan - leave InstanceNumber because it's not the same for every scan in the series
if (strcmp(dcm_header.Private_0029_10xx_Creator,'SIEMENS CSA NON-IMAGE') ~= 1)
if strcmp(new_scan,'yes')
if strcmp(data.first_scan,'yes')
disp('Doing new style DICOM anon');
data.first_scan = 'no';
end
[res, dcminfo] = isdicomfile(fullfile(readfile_dir,flist(n).name));
if isvar('dcm_header.PatientName') ; values.PatientName = 'Anonymised by dicom_sort_convert'; end
if isvar('dcm_header.PatientID') ; values.PatientID = dcm_header.PatientID; end
if isvar('dcm_header.AccessionNumber'); values.AccessionNumber = dcm_header.AccessionNumber; end
if isvar('dcm_header.InstitutionAddress'); values.InstitutionAddress = dcm_header.InstitutionAddress; end
if isvar('dcm_header.InstitutionName'); values.InstitutionName = dcm_header.InstitutionName; end
if isvar('dcm_header.StationName') ; values.StationName = dcm_header.StationName; end
if isvar('dcm_header.StudyDescription'); values.StudyDescription = dcm_header.StudyDescription; end
if isvar('dcm_header.SeriesDescription'); values.SeriesDescription = dcm_header.SeriesDescription; end
if isvar('dcm_header.PerformingPhysicianName'); values.PerformingPhysicianName = dcm_header.PerformingPhysicianName; end
if isvar('dcm_header.OperatorName'); values.OperatorName = dcm_header.OperatorName; end
if isvar('dcm_header.PatientBirthDate'); values.PatientBirthDate = dcm_header.PatientBirthDate; end
if isvar('dcm_header.PatientSex'); values.PatientSex = dcm_header.PatientSex; end
if isvar('dcm_header.PatientAge'); values.PatientAge = dcm_header.PatientAge; end
if isvar('dcm_header.PatientWeight'); values.PatientWeight = dcm_header.PatientWeight; end
if isvar('dcm_header.PatientComments'); values.PatientComments = dcm_header.PatientComments; end
if isvar('dcm_header.DeviceSerialNumber'); values.DeviceSerialNumber = dcm_header.DeviceSerialNumber; end
if isvar('dcm_header.ProtocolName'); values.ProtocolName = dcm_header.ProtocolName; end
if isvar('dcm_header.StudyInstanceUID'); values.StudyInstanceUID = dcm_header.StudyInstanceUID; end
if isvar('dcm_header.SeriesInstanceUID'); values.SeriesInstanceUID = dcm_header.SeriesInstanceUID; end
if isvar('dcm_header.StudyID'); values.StudyID = dcm_header.StudyID; end
if isvar('dcm_header.AcquisitionNumber'); values.AcquisitionNumber = dcm_header.AcquisitionNumber; end
% if isvar('dcm_header.InstanceNumber'); values.InstanceNumber = dcm_header.InstanceNumber; end
if isvar('dcm_header.FrameOfReferenceUID'); values.FrameOfReferenceUID = dcm_header.FrameOfReferenceUID ; end
% values.Private_0029_10xx_Creator = dcm_header.Private_0029_10xx_Creator;
% values.Private_0029_11xx_Creator = dcm_header.Private_0029_11xx_Creator;
% values.Private_0029_12xx_Creator = dcm_header.Private_0029_12xx_Creator;
% values.Private_0029_1008 = dcm_header.Private_0029_1008;
% values.Private_0029_1009 = dcm_header.Private_0029_1009;
% values.Private_0029_1018 = dcm_header.Private_0029_1018;
% values.Private_0029_1019 = dcm_header.Private_0029_1019;
% values.Private_0029_1131 = dcm_header.Private_0029_1131;
% values.Private_0029_1132 = dcm_header.Private_0029_1132;
% values.Private_0029_1133 = dcm_header.Private_0029_1133;
% values.Private_0029_1134 = dcm_header.Private_0029_1134;
% values.Private_0029_1260 = dcm_header.Private_0029_1260;
end
dicomanon(readfile_dcm, writefile_name_full, 'update', values);
end
elseif (size(findstr(version_number, '(R2006a)'),1) ~= 0) %(size(findstr(version_number, '(R2007a)'),1) ~= 0 || (size(findstr(version_number, '(R2006b)'),1) ~= 0))%
% OLD STYLE ANONIMISATION
disp('Doing old style DICOM anon');
if (strcmp(dcm_header.Private_0029_10xx_Creator,'SIEMENS CSA NON-IMAGE') ~= 1)
dcm_header.PatientName = 'Anonymised by dicom_sort_convert';
end_of_string_marker = strfind(dcm_header.Filename, '.MR.');
dcm_header.Filename = ['ANONYMISED' dcm_header.Filename(end_of_string_marker:end)];
if length(end_of_string_marker) == 0;
dcm_header.Filename = ['ANONYMISED:couldnt_sep_filestring'];
end
try
dicomwrite(dcm_image, writefile_name_full, dcm_header);
catch
disp('');
end
if n==1
this_warning_text = sprintf('If you plan to use DICOM images with Brain Voyager\nyou will need to run\nthis program with MATLAB 2006b or later\nYou are using %s.', version_number);
data.warning_text = sprintf('%s %s', data.warning_text,this_warning_text);
data.warning_present = 'yes';
end
end
else
error(['Do not know what to do for anonimisation in version ' version]);
end
case 'no'
if (strcmp(data.first_scan,'yes'))
button = questdlg('This data will not be anonymised: do you want to continue', ...
'Anonymisation Alert!',...
'continue',...
'stop',...
'stop');
if strcmp(button,'continue')
error('Not anonymising data not allowed');
%dicomwrite(dcm_image, writefile_name_full, dcm_header);
this_warning_text = '!!!Warning!!! Data has not been anonymised';
data.warning_present = 'yes';
data.warning_text = sprintf('%s \n%s', data.warning_text, data.current_scan, this_warning_text);
end
end
end
end
end
disp('');
