NAME
gdcmconv - .TH "gdcmconv" 1 "Sun Aug 8 2010" "Version 2.0.15" "GDCM"
NAME
gdcmconv - .SH "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
PARAMETERS
-i --input DICOM filename
-o --output DICOM filename
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.
--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
Eventhough 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:
o convert non-cp246 conforming file into conforming cp246,
o convert implicit little endian transfer syntax file meta header into
proper explicit little endian transfer syntax,
o convert the GE-13 bytes bug,
o convert dual syntax file: implicit/explicit,
o convert Philips dual Little Endian/Big Endian file,
o convert GDCM 1.2.0 broken UN-2-bytes fields,
o &...
o All other broken files listed in the supported section.
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 section
(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.
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:
o When Pixel Data is missing data / is padded with junk
o When you would like to make sure GDCM can handle decompression &
recompression cycle
Decompressing a Compressed DICOM
$ gdcmconv --raw compressed.dcm uncompressed.dcm
Changing the planar Configuration
Often RLE files are compressed using a different Planar Comnfiguration
(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://sourceforge.net/apps/mediawiki/gdcm/index.php?title=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.
o For DCMTK use: dcmdump
o For dicom3tools use: dcdump
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
SEE ALSO
gdcmdump(1), gdcmraw(1), gdcminfo(1)
COPYRIGHT
Copyright (c) 2006-2010 Mathieu Malaterre