Converting JPEG2000 DICOMs to Uncompressed DICOM

TL;DR – Neuroimaging-specific post. Some files can't be converted by programs if they are encoded one way – present Matlab program to fix that.

JPEG2000 DICOM data

Recently, I had some DICOM data that is stored in the JPEG2000 format from OsiriX. I wanted to convert these to a NIfTI format using dcm2nii but it was not a fan of the compression, specifically the transfer syntax (which tells you how the data is encoded).

It spit out the error:

Unsupported Transfer Syntax 1.2.840.10008.1.2.4.91 Solution: use MRIcro

Using Matlab's Image Processing Toolbox

For most of my endeavors, I try to use R for everything, but that's not always possible. For example the oro.dicom package is great for working with DICOM data, but the JPEG2000 compression format is not supported. Therefore, I went into Matlab, which has the image processing toolbox. You will need an updated version, as described here, Matlab 2009b version will not work.

The Code for Conversion

Overall, the code takes a directory, lists all the files, removing directories. . The for loop goes through each DICOM file, reads in the header information with dicominfo, reads in the data matrix with dicomread. The transfer syntax is changed using newsyntax, creates a new filename (within a specified output directory outdir) and writes the DICOM file using dicomwrite. The createmode can either be Create or Copy. Using Create is the default option and has error and missing checking. The Copy mode bypasses many of these checks, but this may be required for certain DICOM files to be written.

rundir = pwd;
updir = fileparts(rundir);
outdir = fullfile(updir, 'Converted');
addon = '';
newsyntax = '1.2.840.10008.1.2';
createmode = 'Copy'; % could be 'Create';
x = dir(rundir);
nodir = ~[x.isdir]';
x = x(nodir);
x = {x.name}';
ifile = 1;
for ifile = 1:length(x)
    name = x{ifile};
    stub = regexprep(name, '(.*)[.].*', '$1');
    stub = [stub addon '.dcm']; %#ok<AGROW>
    name = fullfile(rundir, name);
    stub = fullfile(outdir, stub);
    dinfo = dicominfo(name);
    dinfo.TransferSyntaxUID = newsyntax;
    X = dicomread(name);
    dicomwrite(X, stub, dinfo, 'CreateMode', createmode);
end

After this conversion, dcm2nii worked as usual for converting.

Other Options

Other options exist such as the DICOM JPEG 2000 Module, but this must be licensed and Matlab has implemented this in imread. Just figured if you ran into this problem, this may help.