File Meta Header¶

Running

$ gdcmconv input.dcm output.dcm

Is not enough to recompute file meta header, when input file is buggy. You may want to use: –check-meta

$ gdcmconv --check-meta input.dcm output.dcm

See typical cases such as: GE_DLX-8-MONO2-PrivateSyntax.dcm or PICKER-16-MONO2-No_DicomV3_Preamble.dcm from gdcmData.

Conversion to Explicit Transfer Syntax¶

To convert a file that was written using Implicit Transfer Syntax into Explicit Transfer Syntax simply use:

$ gdcmconv --explicit uncompressed.dcm compressed.dcm

Compressing to lossless JPEG¶

To compress an uncompressed DICOM file to a JPEG Lossless encapsulated format:

$ gdcmconv --jpeg uncompressed.dcm compressed.dcm

Compressing to lossy JPEG¶

To compress an uncompressed DICOM file to a JPEG Lossy encapsulated format:

$ gdcmconv --lossy --jpeg -q 90 uncompressed.dcm compressed.dcm

Note:

  -q is just one of the many way to specify lossy quality, you need to inspect the other cmd line flag to specify lossyness properties.

Compressing to lossless JPEG-LS¶

To compress an uncompressed DICOM file to a JPEG-LS Lossless encapsulated format:

$ gdcmconv --jpegls uncompressed.dcm compressed.dcm

Compressing to lossy JPEG-LS¶

To compress an uncompressed DICOM file to a JPEG-LS Lossy encapsulated format:

$ gdcmconv --lossy --jpegls -e 2 uncompressed.dcm lossy_compressed.dcm

Note:

-e (or –lossy-error) means that the maximum tolerate error is 2 for each pixel value

Compressing to lossless J2K¶

To compress an uncompressed DICOM file to a JPEG-2000 Lossless encapsulated format:

$ gdcmconv --j2k uncompressed.dcm compressed.dcm

Compressing to lossy J2K¶

To compress an uncompressed DICOM file to a JPEG-2000 Lossy encapsulated format:

$ gdcmconv --lossy -q 55,50,45 --j2k uncompressed.dcm lossy_compressed.dcm

Note:

  -q is just one of the many way to specify lossy quality, you need to inspect the other cmd line flag to specify lossyness properties.

Compressing to lossless RLE¶

To compress an uncompressed DICOM file to a RLE Lossless encapsulated format:

$ gdcmconv --rle uncompressed.dcm compressed.dcm

There is no such thing as lossy RLE compression.

Split encapsulated DICOM:¶

To split an encapsulated stream into smaller chunk (1024 bytes each):

$ gdcmconv --split 1024 rle.dcm rle_1024.dcm

If an odd number of bytes is passed it will be rounded down to the next even number (eg. 1025 -> 1024) since DICOM only allow even number for Value Length.

Forcing (re)compression¶

Sometime it is necessary to use the –force option. By default when user specify –j2k and input file is already in JPEG 2000 encapsulated DICOM format then no operation takes places. By using –force you make sure that (re)compression operation takes places.

Real life example of why you would use –force:

Decompressing a Compressed DICOM¶

$ gdcmconv --raw compressed.dcm uncompressed.dcm

In the case of uncompress file (Explicit and Implicit) the behavior is to keep the original Transfer Syntax (so Implicit remains Implit)

Decompressing a Compressed DICOM as implicit¶

$ gdcmconv --raw --implicit compressed.dcm uncompressed_implicit.dcm

By symmetry it is also possible to use gdcmconv --raw --explicit to make sure that target file is always Explicit TS.

Compressing an uncompressed Icon¶

By default when compressing a DICOM Image file, gdcmconv will not compress the icon. A user option needs to be turned on to explicitly force the compression of the Icon Image Sequence Pixel Data

For example, by default we will not compress the Icon Image Sequence Pixel Data attribute:

$ gdcmconv --jpeg gdcmData/simpleImageWithIcon.dcm uncompressed_icon.dcm

In the following example we will explicitly compress the Icon Image Sequence Pixel Data attribute. In that case the same Transfer Syntax is being used for both the main Pixel Data and the Pixel Data from the Icon Image Sequence:

$ gdcmconv --jpeg --compress-icon gdcmData/simpleImageWithIcon.dcm compressed_icon.dcm

Generating an Icon¶

For some application it might be necessary to produce a small preview of the main image to be able to quickly load that short preview instead of the main image. In that case:

$ gdcmconv --raw --generate-icon gdcmData/test.acr test_icon.dcm

In some cases the main Pixel Data element is expressed as pixel defined on 16bits. Since Icon can only store at most pixel of size 8bits, a rescale operation needs to take place. In order to properly select a better interval for doing the rescale operation user can specify the min max used for the rescale operation:

$ gdcmconv --raw --generate-icon --icon-minmax 0,192 gdcmData/012345.002.050.dcm icon_minmax.dcm

Changing the planar Configuration¶

Often RLE files are compressed using a different Planar Configuration (RRR ... GGG... BBB...) instead of the usual triplet (RGB ... RGB ... RGB ). So upon decompression the Planar Configuration is 1. This is perfectly legal in DICOM, however this is unconventional, and thus it may be a good idea to also change the planar configuration and set it to the default :

$ gdcmconv --raw --planar-configuration 0 compressed.dcm uncompressed1.dcm

To reinvert the planar configuration of file 'uncompressed1.dcm', simply do:

$ gdcmconv --raw --planar-configuration 1 uncompressed1.dcm uncompressed2.dcm

DCMTK / dicom3tools¶

Using another DICOM implementation such as the one from DCMTK or dicom3tools can be a good process to check the output of gdcmconv.

For reference, gdcmconv --raw will act as dcmdjpeg +cn +px, since it never tries to convert color space.

VIM: vimdiff¶

You can setup your favorite editor to compare the output, for instance in vim:

autocmd BufReadPre *.dcm set ro
autocmd BufReadPost *.dcm silent %!dcmdump -M +uc "%"

then simply do:

$ vimdiff input.dcm output.dcm

vbindiff¶

On UNIX you can visually compare binary file using the vbindiff command:

$ vbindiff input.dcm output.dcm