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TWIXDeIdentify.m
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function TWIXDeIdentify(fnames)
%% TWIXDeIdentify(fnames)
% Reads Siemens TWIX files (*.dat) and removes participant information. New
% de-identified TWIX files are then output, with filenames appended with
% '_noID'. The original files are not overwritten.
%
% If TWIXDeIdentify has already been run, and de-identified files are
% found within the directory, the user will be asked whether these files
% should be overwritten.
%
% NOTE: The user must make sure that filenames themselves do not contain
% information that can personally identify participants. This function
% will only de-identify the content of the TWIX file.
%
% NOTE: This code has been tested with TWIX files from
% VB17A
% VB20P
% VD13D
% VE11A
% VE11C
%
% However, for your particular configuration/software version, it can not be
% guaranteed that the code is running without error, or catching all
% files that are to be de-identified. Please check back if you are unsure
% whether de-identification has worked for you.
%
% Usage:
% TWIXDeIdentify, by itself, de-identifies all TWIX files found
% within the current directory.
%
% TWIXDeIdentify(fnames) de-identifies TWIX files listed in the
% cell array fnames.
%
% Example:
% c = {'MRS_01.dat', 'MRS_02.dat'};
% TWIXDeIdentify(c);
%
% Author:
% Dr. Georg Oeltzschner (Johns Hopkins University, 2016-08-25)
%
% Credits:
% This code is a modification of previous work:
% PhilipsDeIdentify.m
% (Dr. Mark Mikkelsen, Johns Hopkins University)
%
% This code is heavily relying on TWIX parsing code bits from:
% mapVBVD.m
% read_twix_hdr.m
% loop_mdh_read.m
% (Dr. Philipp Ehses, University of Tuebingen)
%
% History:
% 2016-08-25: First version of the code.
% 2016-08-26: Added various fields to be de-identified.
% 2017-02-02: Fixed errors for certain header formats.
% Added various fields to be de-identified.
% 2017-02-07: Added further fields to be de-identified.
% 2018-09-14: Added further fields to be de-identified.
% 2018-09-25: Minor bug fix.
if nargin < 1 % De-identify all DAT files in current directory
flist = dir('*.dat');
flist = flist(cellfun(@isempty, strfind({flist.name}, '._'))); %#ok<*STRCLFH>
for ii = 1:length(flist)
fnames(ii) = cellstr(flist(ii).name);
end
nArgs = nargin;
[exitFunc, fnames] = CheckForOutput(nArgs, fnames);
if exitFunc
return
end
else % De-identify DAT files user has listed in fnames
% Check if filenames include a .dat extension
for ii = 1:length(fnames)
ext = fnames{ii}(end-3:end);
assert(strcmpi(ext, '.dat'), ...
['The filename ' fnames{ii} ' (' num2str(ii) ')' ' in ' inputname(1) ...
' does not include a .dat extension.']);
end
% Check if files can be found
for ii = 1:length(fnames)
assert(any(exist(fnames{ii}, 'file')), ...
['The file ' fnames{ii} ' (' num2str(ii) ')' ' cannot be found.' ...
' Check spelling of filenames in ' inputname(1) ...
' (TWIX files must include a .dat extension in their filename).' ...
' Also check that you are in the right directory.']);
end
nArgs = nargin;
[exitFunc, fnames] = CheckForOutput(nArgs, fnames);
if exitFunc
return
end
end
% Loop over all input DAT files, make copies, and edit these copies.
for ii = 1:length(fnames)
% Make a copy of the DAT file that is to be worked on.
fnames_noid = cell(size(fnames));
fnames_noid{ii} = [fnames{ii}(1:end-4) '_noID' fnames{ii}(end-3:end)];
copyfile(fnames{ii}, fnames_noid{ii});
% Open this new file.
fid = fopen(fnames_noid{ii}, 'r+','l','US-ASCII');
% *** TAKEN FROM MAPVBVD.M ***
% start of actual measurement data (sans header)
fseek(fid,0,'bof');
firstInt = fread(fid,1,'uint32');
secondInt = fread(fid,1,'uint32');
% lazy software version check (VB or VD?)
if and(firstInt < 10000, secondInt <= 64)
version = 'vd';
disp('Software version: VD (!?)');
% number of different scans in file stored in 2nd in
NScans = secondInt;
measID = fread(fid,1,'uint32');
fileID = fread(fid,1,'uint32');
% measOffset: points to beginning of header, usually at 10240 bytes
measOffset = fread(fid,1,'uint64');
measLength = fread(fid,1,'uint64');
fseek(fid,measOffset,'bof');
hdrLength = fread(fid,1,'uint32');
else
% in VB versions, the first 4 bytes indicate the beginning of the
% raw data part of the file
version = 'vb';
disp('Software version: VB (!?)');
measOffset = 0;
hdrLength = firstInt;
NScans = 1; % VB does not support multiple scans in one file
end
datStart = measOffset + hdrLength;
%SRY read data correction factors
% do this for all VB datasets, so that the factors are available later
% in the image_obj if the user chooses to set the correction flag
if (strcmp(version, 'vb')) % not implemented/tested for vd, yet
frewind(fid);
while ( (ftell(fid) < datStart) && ~exist('rawfactors', 'var'))
line = fgetl(fid);
%find the section of the protocol
%note: the factors are also available in <ParamArray."CoilSelects">
%along with element name and FFT scale, but the parsing is
%significantly more difficult
if (~isempty(strfind(line, '<ParamArray."axRawDataCorrectionFactor">')))
while (ftell(fid) < datStart)
line = fgetl(fid);
%find the line with correction factors
%the factors are on the first line that begins with this
%pattern
if (~isempty(strfind(line, '{ { { ')))
line = strrep(line, '} { } ', '0.0');
line = strrep(line, '{', '');
line = strrep(line, '}', '');
rawfactors = textscan(line, '%f');
rawfactors = rawfactors{1}; %textscan returns a 1x1 cell array
% this does not work in this location because the MDHs
% have not been parsed yet
% if (length(rawfactors) ~= 2*max(image_obj.NCha))
% error('Number of raw factors (%f) does not equal channel count (%d)', length(rawfactors)/2, image_obj.NCha);
% end;
if (mod(length(rawfactors),2) ~= 0)
error('Error reading rawfactors');
end
%note the transpose, this makes the vector
%multiplication during the read easier
arg.rawDataCorrectionFactors = rawfactors(1:2:end).' + 1i*rawfactors(2:2:end).';
break;
end
end
end
end
disp('Read raw data correction factors');
end
cPos = measOffset;
% Loop over all scans within the TWIX file (only VD and higher!)
for s=1:NScans
fseek(fid,cPos,'bof');
hdr_len = fread(fid, 1,'uint32');
% Call routine to read in the header data and de-identify them.
change_twix_hdr(fid);
% Jump to first mdh
cPos = cPos + hdr_len;
fseek( fid, cPos, 'bof' );
% Find out where this scan ends.
[~, filePos, ~] = loop_mdh_read( fid, version );
% Jump to end
cPos = filePos( end );
filePos( end ) = [];
end
fclose(fid);
% Perform sanity check on file size (should be unchanged):
bytes_old = cell(size(fnames));
bytes_noid = cell(size(fnames));
bytes_old{ii} = getfield(dir(fnames{ii}), 'bytes');
bytes_noid{ii} = getfield(dir(fnames_noid{ii}), 'bytes');
if bytes_old{ii} ~= bytes_noid{ii}
msg = sprintf('*** WARNING! *** Filesizes of %s (%i) and %s (%i) do not agree! Check for errors!',fnames{ii},fnames_noid{ii},bytes_old{ii},bytes_noid{ii});
else
msg = sprintf('*** SUCCESSFULLY DEIDENTIFIED! *** Filesizes of %s (%i) and %s (%i) agree!',fnames{ii},bytes_old{ii},fnames_noid{ii},bytes_noid{ii});
end
disp(msg);
end
end
function [mdh_blob, filePos, isEOF] = loop_mdh_read( fid, version )
%% This is a modified version of loop_mdh_read by Philipp Ehses (University of Tübingen)
% This slightly shortened code just rushes through the mdh bits
% of the TWIX file to determine the bit where they end, i.e. where the next scan
% begins with a new header of its own to be de-identified.
%
% Author:
% Dr. Georg Oeltzschner (Johns Hopkins University, 2016-08-25)
%
% Credits:
% This code is heavily relying on TWIX parsing code bits from:
% loop_mdh_read.m
% (Dr. Philipp Ehses, University of Tuebingen)
switch version
case 'vb'
isVD = false;
byteMDH = 128;
case 'vd'
isVD = true;
byteMDH = 184;
szScanHeader = 192; % [bytes]
szChannelHeader = 32; % [bytes]
otherwise
% arbitrary assumptions:
isVD = false;
byteMDH = 128;
warning( [mfilename() ':UnknownVer'], 'Software version "%s" is not supported.', version );
end
cPos = ftell(fid);
n_acq = 0;
allocSize = 4096;
ulDMALength = byteMDH;
isEOF = false;
mdh_blob = zeros( byteMDH, 0, 'uint8' );
szBlob = size( mdh_blob, 2 );
filePos = zeros(0, 1, class(cPos)); % avoid bug in Matlab 2013b: https://scivision.co/matlab-fseek-bug-with-uint64-offset/
% get file size
fseek(fid,0,'eof');
fseek(fid,cPos,'bof');
% ======================================
% constants and conditional variables
% ======================================
bit_0 = uint8(2^0);
bit_5 = uint8(2^5);
mdhStart = 1-byteMDH;
u8_000 = zeros( 3, 1, 'uint8'); % for comparison with data_u8(1:3)
% 20 fill bytes in VD (21:40)
evIdx = uint8( 21 + 20*isVD); % 1st byte of evalInfoMask
dmaIdx = uint8((29:32) + 20*isVD); % to correct DMA length using NCol and NCha
if isVD
dmaOff = szScanHeader;
dmaSkip = szChannelHeader;
else
dmaOff = 0;
dmaSkip = byteMDH;
end
% ======================================
while true
% Read mdh as binary (uint8) and evaluate as little as possible to know...
% ... where the next mdh is (ulDMALength / ushSamplesInScan & ushUsedChannels)
% ... whether it is only for sync (MDH_SYNCDATA)
% ... whether it is the last one (MDH_ACQEND)
% evalMDH() contains the correct and readable code for all mdh entries.
try
% read everything and cut out the mdh
data_u8 = fread( fid, ulDMALength, 'uint8=>uint8' );
data_u8 = data_u8( mdhStart+end : end );
catch exc
warning( [mfilename() ':UnxpctdEOF'], ...
[ '\nAn unexpected read error occurred at this byte offset: %d (%g GiB)\n'...
'Will stop reading now.\n' ...
'=== MATLABs error message ================\n' ...
exc.message ...
'\n=== end of error =========================\n' ...
], cPos, cPos/1024^3 )
isEOF = true;
break
end
bitMask = data_u8(evIdx); % the initial 8 bit from evalInfoMask are enough
if isequal( data_u8(1:3), u8_000 ) ... % probably ulDMALength == 0
|| bitand(bitMask, bit_0) % MDH_ACQEND
% ok, look closer if really all *4* bytes are 0:
data_u8(4)= bitget( data_u8(4),1); % ubit24: keep only 1 bit from the 4th byte
ulDMALength = double( typecast( data_u8(1:4), 'uint32' ) );
if ulDMALength == 0 || bitand(bitMask, bit_0)
cPos = cPos + ulDMALength;
% jump to next full 512 bytes
if mod(cPos,512)
cPos = cPos + 512 - mod(cPos,512);
end
break;
end
end
if bitand(bitMask, bit_5) % MDH_SYNCDATA
data_u8(4)= bitget( data_u8(4),1); % ubit24: keep only 1 bit from the 4th byte
ulDMALength = double( typecast( data_u8(1:4), 'uint32' ) );
cPos = cPos + ulDMALength;
continue
end
% pehses: the pack bit indicates that multiple ADC are packed into one
% DMA, often in EPI scans (controlled by fRTSetReadoutPackaging in IDEA)
% since this code assumes one adc (x NCha) per DMA, we have to correct
% the "DMA length"
% if mdh.ulPackBit
% it seems that the packbit is not always set correctly
NCol_NCha = double( typecast( data_u8(dmaIdx), 'uint16' ) ); % [ushSamplesInScan ushUsedChannels]
ulDMALength = dmaOff + (8*NCol_NCha(1) + dmaSkip) * NCol_NCha(2);
n_acq = n_acq + 1;
% grow arrays in batches
if n_acq > szBlob
filePos( end + allocSize ) = 0;
end
filePos( n_acq ) = cPos;
cPos = cPos + ulDMALength;
end % while true
if isEOF
n_acq = n_acq-1; % ignore the last attempt
end
filePos( n_acq+1 ) = cPos; % save pointer to the next scan
filePos = reshape( filePos(1:n_acq+1), 1, [] ); % row vector
end % of loop_mdh_read()
function change_twix_hdr(fid)
%% Reads in the distinct TWIX header parts, calls the search and replace
% function parse_deid.m, and overwrites the data directly in the file.
%
% Author:
% Dr. Georg Oeltzschner (Johns Hopkins University, 2016-08-25)
%
% This code is heavily relying on TWIX parsing code bits from:
% read_twix_hdr.m
% (Dr. Philipp Ehses, University of Tuebingen)
nbuffers = fread(fid, 1,'uint32');
for b=1:nbuffers
namesz = 0;
byte = 1;
while byte~=0 % look for NULL-character
byte = fread(fid, 1, 'uint8');
namesz = namesz+1;
end
fseek(fid,-namesz,'cof');
bufname = fread(fid,namesz,'char=>char').';
bufname(end) = []; % delete NULL character
buflen = fread(fid, 1,'uint32');
if buflen > 1e9 % MM (190213)
continue
end
buffer = fread(fid, buflen, 'char=>char').';
buff.(bufname) = buffer;
% Search for patient info and replace with XXX happens now:
newbuff.(bufname) = parse_deid(buff.(bufname));
% Rewind by length of buffer and overwrite with new buffer
fseek(fid,-buflen,'cof');
fwrite(fid,newbuff.(bufname),'char');
end
end % of change_twix_hdr()
function newbuffer = parse_deid(buffer)
%% This contains the regular expressions needed to filter out the
% information that requires de-identification.
%
% The code replaces the values assigned to the long/string parameter fields
% PatientID
% PatientBirthDay
% PatientBirthDate
% tPatientName
% PatientsName
% PatientName
% lPatientSex
% PatientSex
% FrameOfReference (2017-02-02)
% tFrameOfReference (2017-02-02)
% FOR (2017-02-02)
% ExamMemoryUID (2017-02-02)
% tReferenceImage0 (2017-02-02)
% tReferenceImage1 (2017-02-02)
% tReferenceImage2 (2017-02-02)
% DeviceSerialNumber (2017-02-06)
% PatientLOID/PatientLoid (2018-09-14)
% StudyLOID/StudyLoid (2018-09-14)
% SeriesLOID (2018-09-14)
% Study (2018-09-14)
% Patient (2018-09-14)
% InstitutionAddress (2018-09-14)
% InstitutionName (2018-09-14)
% StudyLOIDS4Split (2018-09-14)
% MppsLOIDS4Split (2018-09-14)
% SeriesLOIDS4Split (2018-09-14)
% StudyLOIDS4SplitAndPause (2018-09-14)
% MppsLOIDS4SplitAndPause (2018-09-14)
% SeriesLOIDS4SplitAndPause (2018-09-14)
% ParentLoid (2018-09-14)
% ParentUid (2018-09-14)
% DefaultSeriesLoid (2018-09-14)
%
% the double parameter fields with "precision" tag
% flUsedPatientWeight
% flPatientAge
% PatientWeight
% PatientAge
%
% the double parameter fields with "unit" tag
% flPatientHeight
%
% the string parameter fields with "visible" tag
% PatientName
% PatientBirthDay
% PatientSex
% PatientID
% PatientBirthDate
% FrameOfReference (2017-02-02)
% tFrameOfReference (2017-02-02)
% FOR (2017-02-02)
% ExamMemoryUID (2017-02-02)
%
% the double parameter fields with "visible" tag
% PatientAge
% PatientWeight
%
% the array parameter fields with "default" tag
% ReferencedImageSequence (2017-02-02)
% Studyloids4Split (2018-09-14)
% MppsLoids4Split (2018-09-14)
% DefaultSeriesLoids4Split (2018-09-14)
%
% the simple text field in the MeasYaps header part
% tReferenceImage0 (2017-02-07)
% tReferenceImage1 (2017-02-07)
% tReferenceImage2 (2017-02-07)
%
% If your specific implementation requires more fields to be de-identified,
% please note the author.
%
% Author: Dr. Georg Oeltzschner
% Johns Hopkins University, 08/23/2016
%
% History: 2016-08-23: First version.
% 2017-02-02: Added fields containing date stamps.
% 2017-02-07: Added fields containing device IDs.
% 2018-09-14: Added fields containing scan dates and unique IDs.
newbuffer1 = regexprep(buffer, '<Param(?:Bool|Long|String)\."(?:PatientID|PatientBirthDay|tPatientName|PatientName|PatientsName|PatientSex|lPatientSex|PatientBirthDate|FrameOfReference|tFrameOfReference|FOR|ExamMemoryUID|tReferenceImage0|tReferenceImage1|tReferenceImage2|DeviceSerialNumber|PatientLOID|PatientLoid|StudyLOID|StudyLoid|SeriesLOID|Study|Patient|InstitutionAddress|InstitutionName|ParentLoid|ParentUid|DefaultSeriesLoid)">\s*\n*\s*{\s*([^}]*)','${write_xxx($0,$1)}');
newbuffer2 = regexprep(newbuffer1, '<ParamDouble\."(?:flPatientAge|flUsedPatientWeight|PatientAge|PatientWeight)">\s*{\s*(<Precision>\s*[0-9]*)?\s*([^}]*)','${write_xxx($0,$2)}');
newbuffer3 = regexprep(newbuffer2, '<ParamDouble\."(?:flPatientHeight)">\s*{\s*<Unit>.*"\[mm\]"\s*(<Precision>\s*[0-9]*)?\s*([^}]*)','${write_xxx($0,$2)}');
newbuffer4 = regexprep(newbuffer3, '<Param(?:Bool|Long|String)\."(?:PatientName|PatientBirthDay|PatientSex|PatientID|PatientBirthDate|FrameOfReference|tFrameOfReference|FOR|ExamMemoryUID)">\s*{\s*(<Visible>\s*"\w*")?\s*([^}]*)','${write_xxx($0,$2)}');
newbuffer5 = regexprep(newbuffer4, '<ParamArray\."ReferencedImageSequence">\s*{\s*(<Default>\s*<ParamString."">)?\s*{\s*}\s*{\s*([^}]*)','${write_xxx($0,$2)}');
newbuffer6 = regexprep(newbuffer5, '<ParamArray\."ReferencedImageSequence">\s*{\s*(<Default>\s*<ParamString."">)?\s*{\s*}\s*{\s*([^}]*)}\s*{\s*([^}]*)}\s*{\s*([^}]*)','${write_xxx($0,$3)}');
newbuffer7 = regexprep(newbuffer6, '<ParamArray\."ReferencedImageSequence">\s*{\s*(<Default>\s*<ParamString."">)?\s*{\s*}\s*{\s*([^}]*)}\s*{\s*([^}]*)}\s*{\s*([^}]*)','${write_xxx($0,$4)}');
newbuffer8 = regexprep(newbuffer7,'"\d*\.\d*\.\d*\.\d*\.\d*\.\d*\.\d*\.\d*\.\d*\.\d*"','${write_xxx($0,$0)}');
newbuffer9 = regexprep(newbuffer8, '<Param(?:Bool|Long|String)\."(?:PatientID|PatientBirthDay|tPatientName|PatientName|PatientsName|PatientSex|lPatientSex|PatientBirthDate|FrameOfReference|tFrameOfReference|FOR|ExamMemoryUID|tReferenceImage0|tReferenceImage1|tReferenceImage2|DeviceSerialNumber|PatientLOID|StudyLOID|SeriesLOID|Study|Patient|InstitutionAddress|InstitutionName|StudyLOIDS4Split|MppsLOIDS4Split|SeriesLOIDS4Split|StudyLOIDS4SplitAndPause|MppsLOIDS4SplitAndPause|SeriesLOIDS4SplitAndPause)">\s*{\s*<MinSize>\s*[0-9]*\s*<MaxSize>\s*[0-9]*\s*([^}]*)','${write_xxx($0,$1)}');
newbuffer10 = regexprep(newbuffer9, '<ParamArray\."(?:Studyloids4Split|MppsLoids4Split|DefaultSeriesLoids4Split)">\s*{\s*<Default>\s*<ParamString."">\s*{\s*}\s*{\s*([^}]*)','${write_xxx($0,$1)}');
newbuffer11 = regexprep(newbuffer10, '<ParamArray\."(?:Studyloids4Split|MppsLoids4Split|DefaultSeriesLoids4Split)">\s*{\s*<MinSize>\s*[0-9]*\s*<MaxSize>\s*[0-9]*\s*<Default>\s*<ParamString."">\s*{\s*}\s*{\s*([^}]*)','${write_xxx($0,$1)}');
newbuffer = regexprep(newbuffer11, '<ParamDouble\."(?:PatientAge|PatientWeight)">\s*{\s*(<Visible>\s*"\w*")\s*(<Precision>\s*[0-9]*)?\s*([^}]*)','${write_xxx($0,$3)}');
end % of parse_deid()
function [exitFunc, fnames] = CheckForOutput(nArgs, fnames)
%% Check if any de-identified files have already been output and ask user if
% they want to overwrite them
% Author:
% Dr. Mark Mikkelsen, Johns Hopkins University
exitFunc = 0;
if nArgs < 1
if any(~cellfun('isempty', strfind(fnames, '_noID')))
resp = input('\nDe-identified files found in the directory! Proceed and overwrite? [y/n]: ','s');
if strcmpi(resp, 'y')
disp('Overwriting...');
elseif strcmpi(resp, 'n')
disp('Exiting...');
exitFunc = 1;
return
end
ind1 = strfind(fnames, '_noID');
ind2 = find(~cellfun('isempty', ind1));
fnames(ind2) = []; %#ok<FNDSB>
end
else
for ii = 1:length(fnames)
fnames_noID{ii} = [fnames{ii}(1:end-5) '_noID' fnames{ii}(end-4:end)];
end
if any(cellfun(@exist, fnames_noID))
resp = input('\nDe-identified files found in the directory! Proceed and overwrite? [y/n]: ','s');
if strcmpi(resp, 'y')
disp('Overwriting...');
elseif strcmpi(resp, 'n')
disp('Exiting...');
exitFunc = 1;
return
end
end
end
end % of CheckForOutput()