gdcmconv(1)							       GDCM							       gdcmconv(1)

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
   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

       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:

       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
   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 explicitely
       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 explicitely 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 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
       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
SEE ALSO

       gdcmdump(1), gdcmraw(1), gdcminfo(1)
COPYRIGHT

       Copyright (c) 2006-2011 Mathieu Malaterre

Version 2.2.0							  Tue Feb 5 2013						       gdcmconv(1)