gdcmraw - Extract Data Element Value Field.

MathieuMalaterre
           Main developer

       Copyright © 2006, 2011 Mathieu Malaterre

GDCM 3.0.24                                        03/08/2025                                         GDCMRAW(1)

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

       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:

       •   JPEG Lossy 8bits

       •   JPEG Lossy 12bits

       •   JPEG Lossless 2-16bits

       Those are what is defined in ITU-T T.81, ISO/IEC IS 10918-1.

             -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

       gdcmraw - Extract Data Element Value Field.

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

           file-in   DICOM input filename

           file-out  output filename

gdcmdump(1), gdcmraw(1)

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

           gdcmraw [options] file-in file-out

CopyAttributeValuetofile
       This will extract the value at Tag (0025,101b):

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

   ExtractPixelData
       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

   EncapsulatedSyntax
       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:

   Extractfragmentsassinglefile
       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