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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