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gdcmraw: Extract Data Element Value Field.


gdcmraw - Extract Data Element Value Field.


gdcmraw [options] file-in file-out


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


file-in DICOM input filename file-out output filename
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
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) ?? ff\4f\ff\51\00\29\00\00\00\00\02\00\00\00\02\00\00\00\00\00\00\00\00\00\00\00\02\00\00\00\02\00 # 65536,1 Item (fffe,e000) ?? 2c\b7\ee\68\de\e3\93\2d\b3\b8\ba\90\7b\42\3e\f8\42\16\64\88\46\30\37\d4\50\95\9b\b6\a5\c7\38\9b # 65536,1 Item (fffe,e000) ?? 48\3c\03\e8\c4\3f\44\e1\8a\5c\73\3b\02\0a\ad\a5\8f\e4\0c\81\76\a2\d7\1b\7f\b7\cd\bc\30\c6\6a\6a # 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) ?? 00\00\00\00\6b\38\01\00\10\77\02\00\37\b6\03\00\a7\f4\04\00 # 20,1 Item (fffe,e000) ?? ff\d8\ff\c3\00\0b\08\02\00\02\00\01\00\11\00\ff\c4\00\1b\00\01\01\01\01\01\01\01\01\00\00\00\00 # 79970,1 Item (fffe,e000) ?? ff\d8\ff\c3\00\0b\08\02\00\02\00\01\00\11\00\ff\c4\00\1b\00\01\01\01\01\01\01\01\01\00\00\00\00 # 81564,1 Item (fffe,e000) ?? ff\d8\ff\c3\00\0b\08\02\00\02\00\01\00\11\00\ff\c4\00\1b\00\01\01\01\01\01\01\01\01\00\00\00\00 # 81694,1 Item (fffe,e000) ?? ff\d8\ff\c3\00\0b\08\02\00\02\00\01\00\11\00\ff\c4\00\1b\00\01\01\01\01\01\01\01\01\00\00\00\00 # 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


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.


gdcmdump(1), gdcmraw(1)


Copyright (c) 2006-2010 Mathieu Malaterre GDCMRAW(1)

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