gdcmraw (1)

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:

• 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.

gdcmdump(1), gdcmraw(1)

Copyright (c) 2006-2011 Mathieu Malaterre