debian man page for gdcmraw

gdcmraw(1)							       GDCM								gdcmraw(1)

NAME
       gdcmraw - Extract Data Element Value Field.

SYNOPSIS
       gdcmraw [options] file-in file-out

DESCRIPTION
       The gdcmraw tool is mostly used for development purpose. It is used to extract a specific binary field from a DICOM DataSet.

PARAMETERS
       file-in	 DICOM input filename

       file-out  output filename

options
   PARAMETERS
	 -i --input	Input filename
	 -o --output	Output filename
	 -t --tag	Specify tag to extract value from.

   options
	 -S --split-frags  Split fragments into multiple files.
	 -p --pattern	   Specify trailing file pattern (see split-frags).
	 -P --pixel-data   Pixel Data trailing 0.

   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

Typical usage
   Copy Attribute Value to file
       This will extract the value at Tag (0025,101b):

       $ gdcmraw -i GE_MR_0025xx1bProtocolDataBlock.dcm -t 25,101b -o pdb.raw

   Extract Pixel Data
       If you do not specify any tag, the Pixel Data element is the default one. So for instance to grab the Pixel Data from an image:

       $ gdcmraw -i test.acr -o test.raw

       You can then for example compute the md5sum of this pixel data (very useful):

       $ md5sum test.raw
       f845c8f283d39a0204c325654493ba53  test.raw

   Encapsulated Syntax
       When the Pixel Data is encapsulated, multiple fragments can be used to store a single slice image:

       $ gdcmdump D_CLUNIE_CT1_J2KR.dcm

       ...
       (7fe0,0010) OB							 # u/l,1 Pixel Data
	 (fffe,e000) ?? []			     # 0,1 Item
	 (fffe,e000) ?? ff4fff5102900002000200000000000200020 	# 65536,1 Item
	 (fffe,e000) ?? 2c7ee68dee3932d38a907b423ef842166488463037d450959b6a5c7389b 	# 65536,1 Item
	 (fffe,e000) ?? 483c3e8c43f44e18a5c733b2aada58fe4c8176a2d71b7f7cdc30c66a6a 	# 43308,1 Item
       (fffe,e0dd) 0

       In order to create a J2K image out of it, we need to extract each fragments and concatenate them:

       $ gdcmraw -i D_CLUNIE_CT1_J2KR.dcm -o D_CLUNIE_CT1_J2KR.j2k

       This is a valid J2K file, using the Kakadu software package:

       $ kdu_expand -i D_CLUNIE_CT1_J2KR.j2k -o D_CLUNIE_CT1_J2KR.tiff -record D_CLUNIE_CT1_J2KR.txt

       $ cat D_CLUNIE_CT1_J2KR.txt

       Sprofile=PROFILE2
       Scap=no
       Sextensions=0
       Ssize={512,512}
       Sorigin={0,0}
       Stiles={512,512}
       Stile_origin={0,0}
       Scomponents=1
       Ssigned=yes
       Sprecision=16
       Ssampling={1,1}
       Sdims={512,512}
       Cycc=no
       Cmct=0
       Clayers=1
       Cuse_sop=no
       Cuse_eph=no
       Corder=LRCP
       Calign_blk_last={no,no}
       Clevels=5
       Cads=0
       Cdfs=0
       Cdecomp=B(-:-:-)
       Creversible=yes
       Ckernels=W5X3
       Catk=0
       Cuse_precincts=no
       Cblk={64,64}
       Cmodes=0
       Qguard=1
       Qabs_ranges=18,19,19,20,19,19,20,19,19,20,19,19,20,19,19,20

       >> New attributes for tile 0:

   Extract fragments as single file
       Sometimes each fragments is in fact a single slice, so we would not need to concatenate them:

       $ gdcmdump 00191113.dcm

       ...
       (7fe0,0010) OB							 # u/l,1 Pixel Data
	 (fffe,e000) ?? 000006b381010772037630a7f440	    # 20,1 Item
	 (fffe,e000) ?? ffd8ffc30b8202010110ffc401b0111111110000 	# 79970,1 Item
	 (fffe,e000) ?? ffd8ffc30b8202010110ffc401b0111111110000 	# 81564,1 Item
	 (fffe,e000) ?? ffd8ffc30b8202010110ffc401b0111111110000 	# 81694,1 Item
	 (fffe,e000) ?? ffd8ffc30b8202010110ffc401b0111111110000 	# 81511 (81512),1 Item
       (fffe,e0dd) 0

       Let's try to extract those 4 individual Lossless jpeg individually:

       $ gdcmraw --split-frags -i 00191113.dcm -o jpeg --pattern %02d.ljpeg

       This will output 4 files:

       -rw-r--r--  1 mathieu mathieu   81512 2008-08-08 22:10 jpeg03.ljpeg
       -rw-r--r--  1 mathieu mathieu   81694 2008-08-08 22:10 jpeg02.ljpeg
       -rw-r--r--  1 mathieu mathieu   81564 2008-08-08 22:10 jpeg01.ljpeg
       -rw-r--r--  1 mathieu mathieu   79970 2008-08-08 22:10 jpeg00.ljpeg

Footnote about JPEG files
       It is a common misunderstanding to interchange 'JPEG 8bits lossy' with simply JPEG file. The JPEG specification is much broader than simply
       the common lossy 8bits file (as found on internet).

       You can have

       o JPEG Lossy 8bits
       o JPEG Lossy 12bits
       o JPEG Lossless 2-16bits
       Those are what is defined in ITU-T T.81, ISO/IEC IS 10918-1.
SEE ALSO
       gdcmdump(1), gdcmraw(1)
COPYRIGHT
       Copyright (c) 2006-2011 Mathieu Malaterre

Version 2.2.0							  Tue Feb 5 2013							gdcmraw(1)