gdcmraw (1) Linux Manual Page

gdcmraw – .TH "gdcmraw" 1 "Fri Oct 29 2010" "Version 2.0.16" "GDCM"

Name

gdcmraw – .SH "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) ?? 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

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

*

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.

See Also

gdcmdump(1), gdcmraw(1)

Copyright

Copyright (c) 2006-2010 Mathieu Malaterre