Compressed DICOMs

Sometimes you might come across DICOM data which is in a compressed format.

In ImageJ an error will pop up saying "java.io.IOException ImageJ cannot open compressed DICOM images Transfer Syntax UID = 1.2.840.10008.1.2.4.70"

In eFilm, the DICOM file will open as a blank white image like this:

... which isn't very useful.

It appears some kind of JPEG or JPEG2000 compression is used.

Unfortunately, there is not lots of information on the internet as to how to deal with this.

But after having the help of a colleague (thanks Timo!) we worked out how to deal with it:

1) Install the GDCM ("Grassroots DICOM") software from here (make sure you follow their instructions as otherwise the next steps won't work)

2) Go to the command line and to the directory with your data

3) The generic command:

gdcmconv --raw test.dcm output_raw.dcm

...works to just create the uncompressed DICOM.

test.dcm = your compressed DICOM file

output_raw.dcm = the output file name

The image should be able to be opened then in any standard DICOM.

Likely, you will have lots of compressed MR images to uncompress. In this case, you'll need to write a DOS-script or similar, which can be very entertaining. If you want some tips on how to do this, go to this site: https://sites.google.com/site/commandlineocr/ and have a look under the section "Automating the conversion of lots of .JPGs to .PGM and then.."