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.

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Writing Accountability Groups (WAGs)

Recently, 7 other students and myself joined the first writing accountability group (WAG) for students in our biostatistics department. Johns Hopkins has a set of WAGs all around campus, but we are the first student-only group.

What's a WAG?

I posted before about strategies of How to Write a Lot based on Paul Silvia's Book of the same name. One of his recommendations (especially for junior faculty) was to start what he calls an “agraphia group”, where you discuss goals, go on your way, and then come back and discuss if you met those goals or not. He (and I believe in this) seemed rigorous in this regard: if you came 2 times saying “I didn't do anything”- you were out.

The WAG is the implementation of such a group. The group consists of 3 parts:

  1. 15 minutes of discussing previous goals and goals for the 30 minute writing session.
  2. 30 minutes of “writing” – where writing means accomplishing the goals set in 1.
  3. 15 minutes of discussing if the goals were met from the 30 minute session and setting goals for the next week.

The WAG Makeup

The group consists of 4-8 participants. Don't have more than that – you won't have enough time in an hour and it will become unruly. Also, it's good when you can spot in a second who is missing. It runs for 10 weeks (it can run more), but gives a good concrete timeframe. This inhibits participants from saying “I'll come next time”. There are only 10 sessions, show up – a maximum of 2 misses are allowed.

Why did we start the group?

Now, why did we start this group – why not “just write”?

  1. Peer pressure can be used for good. No one wants to say “I've done nothing”. Even if you get 1 paragraph done as a last-ditch effort before the meetings, it's > 0 paragraphs.
  2. Goals are hard to set; it's easier with others flushing out your ideas.
  3. You are writing for 30 minutes even if you get nothing else done that week.

Overall Goals

Types of overall goals are group are trying to accomplish:
1. Write a paper.
2. Edit a paper for review/submission.
3. Write background/significance section on a grant.
4. Write more in a blog

30-minute Session Goals

These are large and somewhat abstract. In a goal-setting session for the 30 minute writing, we have more concrete goals such as:
1. Write 2 paragraphs of the results section for a paper.
2. Make patient demographics table
3. Incorporate all comments from collaborator 1.
4. Get 1 polished paragraph for background section
5. Write 3 sections of blog post, post by end of day

15-minute End Goal Creation

Examples of these goals are:
1. Write 2 pages of paper 1.
2. Make patient demographics table and 3 figures.
3. Incorporate all comments from all collaborators and format for journal.
4. “Lock down” background section as done.
5. Post blog post, write second for editing next Monday.

How do I start one?

If you are at Hopkins, please visit the WAG facebook group above. If not, just get a few people together and follow the above setup. Make people commit to a timeline (maybe even sign a pseudo contract so they know what they're getting into) that is short, concrete, and has a seeable end. I recommend buying a few of the Write a Lot books (as well as others) to share and discuss.

Additional WAG-related Time

The students in our group have also discussed that the 30 minutes in our WAG is helpful, and an additional 30 minutes would be helpful. We are testing an additional writing “meeting” and we will try to determine its effect. We will adapt based on our WAG (like 10 min goals, 45 mins writing, 5 end goals).