Error with dicomwrite: Attribute has wrong data type.

Hello! I am trying to anonymize dicom files by loading the original file with dicominfo and dicomread, changing some fields, and then writing the new file. However, I encountered the error below:

Error using dicom_add_attr>validate_data (line 118)

Attribute (7FE0,0010) has wrong data type.

Error in dicom_add_attr (line 103)

attr_str(pos).Data = validate_data(data, attr_str(pos), specificCharacterSet);

Error in dicom_convert_meta_to_attr (line 39)

attr = dicom_add_attr([], tag(1), tag(2), dictionary, specificCharacterSet, data, VR);

Error in dicom_convert_meta_to_attr>encode_item (line 151)

new_attr = dicom_convert_meta_to_attr(attr_names{p}, item_struct, dictionary, txfr, specificCharacterSet);

Error in dicom_convert_meta_to_attr>encode_SQ (line 125)

data = encode_item(SQ_struct.(items{p}), dictionary, txfr, specificCharacterSet);

Error in dicom_convert_meta_to_attr (line 26)

data = encode_SQ(metadata.(attr_name), dictionary, txfr, specificCharacterSet);

Error in dicom_copy_IOD (line 49)

new_attr = dicom_convert_meta_to_attr(attr_name, metadata, dictionary, options.txfr, specificCharacterSet);

Error in dicomwrite>write_message (line 277)

[attrs, status] = dicom_copy_IOD(X, map, ...

Error in dicomwrite (line 208)

[status, options] = write_message(X, filename, map, metadata, options);

I have also tried simply reading in the original file and writing out the new file (without changing any fields) -

>> y = dicomread('original.dcm');

>> x = dicominfo('original.dcm');

>> dicomwrite(y,'new.dcm',x,'WritePrivate',true,'CreateMode','Copy');

- but these actions produced the same error, as did using dicomanon. Any guidance would be much appreciated!

[Rik]

What data type does your PixelData have?

[Theodore Turesky]

Thanks for the prompt response, Rik! dicomdisp seems to show two types:

0071508 2 (7FE0,0010) OW 4096 bytes - PixelData *Binary*

0075616 0 (7FE0,0010) OW 131072 bytes - PixelData []

The problem may be unique to this particular dataset, as I have been able to write new, anonymized dicoms from other datasets. Still, I would think that even a dicom that was originally written with oddities in certain fields should be able to be rewritten (e.g., using dicomwrite), preserving those same oddities...

Thank you!

[Ralph Buchert]

Dear Theodore,

I'm currently trying to use dicomanon to anonymize MRI data from more than 100 different MR scanners. I encounter exactly the same problem you described in about 10% of the cases. Did you find a solution? I would very much appreciate your help.

With very best wishes, Ralph.

[Theodore Turesky]

Yes! I spoke with some other folks locally about this and they suggested removing the attribute, which can be found in IconImageSequence. It has to do with color info being erroneously added. Because of this, you won't be able to use dicomanon, but you can effectively make your own anonymization script using the dicomread, dicominfo, and dicomwrite, as below:

>> y = dicomread('original.dcm');

>> x = dicominfo('original.dcm');

>> x.PatientName = 'anon'; %you'll need to do something like this for every header field that you want to anonymize

>> x.IconImageSequence = []; % this is the key line for avoiding the attribute error

>> dicomwrite(y,'new.dcm',x,'WritePrivate',true,'CreateMode','Copy');

I'm also attaching my code, which you're welcome to use.

I compared the pixel data for original and de-identified images using numpy code and they were the same. I also converted the images to nifti and the resulting image arrays for original and de-identified files were identical.

[Ralph Buchert]

Dear Theodore,

thank you so much. Removing IconImageSequence from the header solved my problem in all cases expect one. I'm very happy, thank you so much :-). Below please find my code, perhapy you find it useful.

With very best wishes

Ralph

function numScans = htpAnonymize(searchDir,anonDir,firstImageOnly)
% anonymize MRI dicom scans
% - works on all dicom data in searchDir and all its subdirectories
% - assumes that each directory containes (at most) one series
% - the anonymized serieses are copied to anonDir, one directory per series
% - generates the txt-file "Codes_<date>" in anonDir that lists IDs, the number of
%   images in each series, the number of failures per series etc.
% - generates the log-file "AnonLog_<date>" in anonDir
% - ATTENTION: I did not manage to make sure that the last block of the SOPInstanceUID
%   of the images belonging to the same sequence are consecutive numbers
%   (neither 'keep' nor 'update' seems to work for SOPInstanceUID). As a consequence, some dicom
%   viewers might not recognize that the anonymized images belong to the same series,
%   although StudyInstanceUID and SeriesInstanceUID are equal for all images
%   of the series ('update' works for StudyInstanceUID and SeriesInstanceUID)%
% - seems to work properly in about 90% of the cases.
%   In the remaining 10% of the cases, there is either an error or a warning.
%   most frequent error: "Attribute (7FE0,0010) has wrong data type" (= PixelData)
%   In these cases (use dicomdisp):
%       0097588    2   (7FE0,0010) OW       4096 bytes - PixelData *Binary* 
%       0101696    0   (7FE0,0010) OW     131072 bytes - PixelData []
%   In 'normal' cases:
%       0009912    0   (7FE0,0010) OW     247808 bytes - PixelData []
%   Solution (Theodore Turesky):
%       The problem might be related to errorneous color info (suggesting    %       color but providing gray), try to
%       remove IconImageSequence from the header.
%       If this does not work, use another tool (e.g.,
%       MicroDicom) to read and export the scan. Then try again.
% - if firstImageOnly == true, only the first dicom image in each subdirectory
%   is anonymized. This might be usefull to check for errors and warnings
%   before processing a large number of series
%
% Ralph Buchert, January 28, 2021, [e-mail]
%
 
values.PatientAddress = 'unknown';
 
if nargin < 1
    searchDir = uigetdir('Select directory to be searched for DICOM data (including all subdirectories)');
end
if nargin < 2
    anonDir = uigetdir('Select directory to write anonymized DICOM data');
end
if nargin < 3
    firstImageOnly = false;
end
 
% get subdirs of searchDir
subdirs = genpath(searchDir);
semicolon = regexp(subdirs,';');
numSemicolon = max(size(semicolon));
dirs = {subdirs(1:semicolon(1)-1)};
for i = 1:numSemicolon-1
    dirs = [dirs; subdirs(semicolon(i)+1:semicolon(i+1)-1)];
end
dirs = [dirs; subdirs(semicolon(numSemicolon)+1:length(subdirs))];
numDirs = size(dirs,1);
 
% prepare file for scan name codes
fnameCodes = strcat(anonDir,filesep,'Codes',strrep(strrep(datestr(now),' ','-'),':','-'),'.txt');
fid = fopen(fnameCodes,'w');
if fid == -1
    error('ERROR(hptAnonymize): cannot open file to list codes\n\n');
end
fprintf(fid,'%s\t%s\t%s\t%s\t%s\t','original','code','numSlices','numFailures','numFailuresUnresolved');
fprintf(fid,'%s\t%s\t%s\t%s\t','manufacturer','model','fieldStrength','acquisitionDate');
fprintf(fid,'%s\t%s\n','sex','age');
 
 
fnameLog = strcat(anonDir,filesep,'AnonLog',strrep(strrep(datestr(now),' ','-'),':','-'),'.txt');
eval(['diary ' fnameLog]);
 
% do the work
numScans = 0;
for i = 1:numDirs   
    D = dir(dirs{i});
    num_files = size(D,1);
    numSlices = 0;
    numFailures = 0;
    numFailuresUnresolved = 0;
    for j = 1:num_files
        if (D(j).isdir ~= 1)
            slice = strcat(dirs{i},filesep,D(j).name);
            if firstImageOnly
                condition = isdicom(slice) & (numSlices < 1);
            else
                condition = isdicom(slice);
            end
            if condition
                numSlices = numSlices + 1;
                if numSlices == 1
                    numScans = numScans + 1;
                    scan = dirs{i}(length(searchDir)+2:length(dirs{i}));        
                    ind = findstr(dirs{i},filesep);
                    %newScan = sprintf('Scan%04d',str2num(dirs{i}(ind(length(ind)-1)+1:ind(length(ind))-1))); 
                    newScan = sprintf('Scan%04d',numScans);
                    mkdir(anonDir,newScan);
                    newDir = strcat(anonDir,filesep,newScan);
                    values.StudyInstanceUID = dicomuid;
                    values.SeriesInstanceUID = dicomuid;
                    values.StudyID = sprintf('4711%04d',numScans);
                    values.PatientName.FamilyName = newScan;
                    values.PatientName.GivenName = newScan;
                    fprintf('\n\nCurrently working on %s\n\n',scan);
                    hdr = dicominfo(slice);
                end
                %anonSlice = strcat(newDir,filesep,D(j).name); 
                anonSlice = strcat(newDir,filesep,newScan,sprintf('Image%04d',numSlices-1),'.dcm');
                try
                    dicomanon(slice,anonSlice,'keep', {'PatientAge', 'PatientSex', 'StudyDescription'},'update',values,'WritePrivate',false);
                catch
                    numFailures = numFailures + 1;
                    values.IconImageSequence = [];
                    try                       
                        dicomanon(slice,anonSlice,'keep', {'PatientAge', 'PatientSex', 'StudyDescription'},'update',values,'WritePrivate',false);
                    catch
                        numFailuresUnresolved = numFailuresUnresolved+1;
                    end
                    rmfield(values,'IconImageSequence');
                end
            end
        end
    end
    if numSlices > 0
        fprintf(fid,'%s\t%s\t%d\t%d\t%d\t',scan,newScan,numSlices,numFailures,numFailuresUnresolved);
        try
            fprintf(fid,'%s\t',hdr.Manufacturer);
        catch
            fprintf(fid,'%s\t','na');
        end
        try
            fprintf(fid,'%s\t',hdr.ManufacturerModelName);
        catch
            fprintf(fid,'%s\t','na');
        end
        try
            fprintf(fid,'%3.1f\t',hdr.MagneticFieldStrength);
        catch
            fprintf(fid,'%s\t','na');
        end
        try
            fprintf(fid,'%s\t',hdr.AcquisitionDate);
        catch
            fprintf(fid,'%s\t','na');
        end
        try
            fprintf(fid,'%s\t',hdr.PatientSex);
        catch
            fprintf(fid,'%s\t','na');
        end
        try
            fprintf(fid,'%s\n',hdr.PatientAge);
        catch
            fprintf(fid,'%s\n','na');
        end
    end
end
 
fclose(fid);
diary;
 
fprintf('\n\nDone\n\n');
 
end

[Theodore Turesky]

Looks great, Ralph! Thank you. Also, I want to credit Ross Mair for identifying the color problem and suggesting I remove the problematic tag.

Answer 1

[Theodore Turesky]

>> y = dicomread('original.dcm');

>> x = dicominfo('original.dcm');

>> x.PatientName = 'anon'; %you'll need to do something like this for every header field that you want to anonymize

>> x.IconImageSequence = []; % this is the key line for avoiding the attribute error

>> dicomwrite(y,'new.dcm',x,'WritePrivate',true,'CreateMode','Copy');