gdcmconv - Online in the Cloud

PROGRAM:

NAME

gdcmconv - Tool to convert DICOM to DICOM.

SYNOPSIS

gdcmconv [options] file-in file-out

DESCRIPTION

The gdcmconv command line program takes as input a DICOM file (file-in) and process it to
generate an output DICOM file (file-out). The command line option dictate the type of
operation(s) gdcmconv will use to generate the output file.

PARAMETERS

file-in DICOM input filename

file-out DICOM output filename

OPTIONS

-i --input DICOM filename
-o --output DICOM filename

SPECIFIC OPTIONS

-X --explicit Change Transfer Syntax to explicit.
-M --implicit Change Transfer Syntax to implicit.
-U --use-dict Use dict for VR (only public by default).
--with-private-dict Use private dict for VR (advanced user only).
-C --check-meta Check File Meta Information (advanced user only).
--root-uid Root UID.
--remove-gl Remove group length (deprecated in DICOM 2008).
--remove-private-tags Remove private tags.
--remove-retired Remove retired tags.

IMAGE OPTIONS

-l --apply-lut Apply LUT (non-standard, advanced user only).
-P --photometric-interpretation %s Change Photometric Interpretation (when possible).
-w --raw Decompress image.
-d --deflated Compress using deflated (gzip).
-J --jpeg Compress image in jpeg.
-K --j2k Compress image in j2k.
-L --jpegls Compress image in jpeg-ls.
-R --rle Compress image in rle (lossless only).
-F --force Force decompression/merging before recompression/splitting.
--generate-icon Generate icon.
--icon-minmax %d,%d Min/Max value for icon.
--icon-auto-minmax Automatically commpute best Min/Max values for icon.
--compress-icon Decide whether icon follows main TransferSyntax or remains uncompressed.
--planar-configuration [01] Change planar configuration.
-Y --lossy Use the lossy (if possible) compressor.
-S --split %d Write 2D image with multiple fragments (using max size)

JPEG OPTIONS

-q --quality %*f set quality.

JPEG-LS OPTIONS

-e --lossy-error %*i set error.

J2K OPTIONS

-r --rate %*f set rate.
-q --quality %*f set quality.
-t --tile %d,%d set tile size.
-n --number-resolution %d set number of resolution.
--irreversible set irreversible.

GENERAL OPTIONS

-h --help
print this help text and exit

-v --version
print version information and exit

-V --verbose
verbose mode (warning+error).

-W --warning
warning mode, print warning information

-E --error
error mode, print error information

-D --debug
debug mode, print debug information

SPECIAL OPTIONS

-I --ignore-errors convert even if file is corrupted (advanced users only, see disclaimers).

ENVIRONMENT VARIABLE

GDCM_ROOT_UID Root UID

SIMPLE USAGE

gdcmconv is a great tool to convert broken DICOM implementation into properly parsable
DICOM file. Usage is simply:

$ gdcmconv input.dcm output.dcm

or if you prefer being explicit:

$ gdcmconv -i input.dcm -o output.dcm

Even though gdcmconv can overwrite directly on the same file (input.dcm = output.dcm), it
is recommended that user should first convert into a different file to make sure the bug
is properly handled by GDCM.

Typical cases where you would want to use gdcmconv in its simple form:

· convert non-cp246 conforming file into conforming cp246,

· convert implicit little endian transfer syntax file meta header into proper explicit
little endian transfer syntax,

· convert the GE-13 bytes bug,

· convert dual syntax file: implicit/explicit,

· convert Philips dual Little Endian/Big Endian file,

· convert GDCM 1.2.0 broken UN-2-bytes fields,

· &...

· All other broken files listed in the supported refsection.

When no option other is used, only the dataset is inspected. So encapsulated Pixel Data,
for instance, is not inspected for well known bugs.

When doing this kind of work, this is usually a good idea to perform some kind of quality
control, see gdcmconv Quality Control refsection (down below).

TYPICAL USAGE

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:

· When Pixel Data is missing data / is padded with junk

· When you would like to make sure GDCM can handle decompression & recompression cycle

Decompressing a Compressed DICOM
$ gdcmconv --raw compressed.dcm uncompressed.dcm

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
attibute. 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

LOSSLESS CONVERSION

When talking about lossless conversion, there is an ambiguity that need to be understood.
To achieve higher compression ratio, the RGB color space is usually not used, in favor of
a YBR one. Changing from one color space to the other is (bit level) not lossless.

For more detail, see what are the true lossless transformations as described:

http://gdcm.sourceforge.net/wiki/index.php/Color_Space_Transformations

QUALITY CONTROL

One important part when using gdcmconv it to have a way to quality control the output.

You can use 3rd party tool to check the output of gdcmconv is correct.

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 DCMTK use: dcmdump

· For dicom3tools use: dcdump

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

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