GDCMRAW(1)

📦
version 3.0.24 · 12 versions
, in opensuse-leap 16.0

🌸 NAME 🌸

gdcmraw — Extract Data Element Value Field.

okay bestie, welcome to the gdcmraw(1) manual page from the DICOM Manipulation set. This tool is giving dev-purpose energy, and it’s here to extract a specific binary field from a DICOM DataSet. That’s the whole assignment. 💅

✨ 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. Lowkey iconic for a tiny little extractor, ngl.

🎀 PARAMETERS 🎀

  • file-in — DICOM input filename
  • file-out — output filename

💅 OPTIONS 💅

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

🌈 SPECIFIC 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)

👑 AUTHOR 👑

Mathieu Malaterre

  • Main developer

Copyright © 2006, 2011 Mathieu Malaterre

💖 source/version GDCM 3.0.24, date 12/25/2025 — that’s the whole page, bestie; go extract something iconic 💅

📦 where this page comes from