1GDCMRAW(1)                    DICOM Manipulation.                   GDCMRAW(1)
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NAME

6       gdcmraw - Extract Data Element Value Field.
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SYNOPSIS

9           gdcmraw [options] file-in file-out
10

DESCRIPTION

12       The gdcmraw tool is mostly used for development purpose. It is used to
13       extract a specific binary field from a DICOM DataSet.
14

PARAMETERS

16           file-in   DICOM input filename
17
18           file-out  output filename
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OPTIONS

21             -i --input     Input filename
22             -o --output    Output filename
23             -t --tag       Specify tag to extract value from.
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SPECIFIC OPTIONS

26             -S --split-frags  Split fragments into multiple files.
27             -p --pattern      Specify trailing file pattern (see split-frags).
28             -P --pixel-data   Pixel Data trailing 0.
29

GENERAL OPTIONS

31             -h   --help
32                    print this help text and exit
33
34             -v   --version
35                    print version information and exit
36
37             -V   --verbose
38                    verbose mode (warning+error).
39
40             -W   --warning
41                    warning mode, print warning information
42
43             -E   --error
44                    error mode, print error information
45
46             -D   --debug
47                    debug mode, print debug information
48

TYPICAL USAGE

50   Copy Attribute Value to file
51       This will extract the value at Tag (0025,101b):
52
53           $ gdcmraw -i GE_MR_0025xx1bProtocolDataBlock.dcm -t 25,101b -o pdb.raw
54
55   Extract Pixel Data
56       If you do not specify any tag, the Pixel Data element is the default
57       one. So for instance to grab the Pixel Data from an image:
58
59           $ gdcmraw -i test.acr -o test.raw
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61       You can then for example compute the md5sum of this pixel data (very
62       useful):
63
64           $ md5sum test.raw
65           f845c8f283d39a0204c325654493ba53  test.raw
66
67   Encapsulated Syntax
68       When the Pixel Data is encapsulated, multiple fragments can be used to
69       store a single slice image:
70
71           $ gdcmdump D_CLUNIE_CT1_J2KR.dcm
72
73           ...
74           (7fe0,0010) OB                                                    # u/l,1 Pixel Data
75             (fffe,e000) ?? []                           # 0,1 Item
76             (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
77             (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
78             (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
79           (fffe,e0dd) 0
80
81       In order to create a J2K image out of it, we need to extract each
82       fragments and concatenate them:
83
84           $ gdcmraw -i D_CLUNIE_CT1_J2KR.dcm -o D_CLUNIE_CT1_J2KR.j2k
85
86       This is a valid J2K file, using the Kakadu software package:
87
88           $ kdu_expand -i D_CLUNIE_CT1_J2KR.j2k -o D_CLUNIE_CT1_J2KR.tiff -record D_CLUNIE_CT1_J2KR.txt
89
90           $ cat D_CLUNIE_CT1_J2KR.txt
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92           Sprofile=PROFILE2
93           Scap=no
94           Sextensions=0
95           Ssize={512,512}
96           Sorigin={0,0}
97           Stiles={512,512}
98           Stile_origin={0,0}
99           Scomponents=1
100           Ssigned=yes
101           Sprecision=16
102           Ssampling={1,1}
103           Sdims={512,512}
104           Cycc=no
105           Cmct=0
106           Clayers=1
107           Cuse_sop=no
108           Cuse_eph=no
109           Corder=LRCP
110           Calign_blk_last={no,no}
111           Clevels=5
112           Cads=0
113           Cdfs=0
114           Cdecomp=B(-:-:-)
115           Creversible=yes
116           Ckernels=W5X3
117           Catk=0
118           Cuse_precincts=no
119           Cblk={64,64}
120           Cmodes=0
121           Qguard=1
122           Qabs_ranges=18,19,19,20,19,19,20,19,19,20,19,19,20,19,19,20
123
124           >> New attributes for tile 0:
125
126   Extract fragments as single file
127       Sometimes each fragments is in fact a single slice, so we would not
128       need to concatenate them:
129
130           $ gdcmdump 00191113.dcm
131
132           ...
133           (7fe0,0010) OB                                                    # u/l,1 Pixel Data
134             (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
135             (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
136             (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
137             (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
138             (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
139           (fffe,e0dd) 0
140
141       Let's try to extract those 4 individual Lossless jpeg individually:
142
143           $ gdcmraw --split-frags -i 00191113.dcm -o jpeg --pattern %02d.ljpeg
144
145       This will output 4 files:
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147           -rw-r--r--  1 mathieu mathieu   81512 2008-08-08 22:10 jpeg03.ljpeg
148           -rw-r--r--  1 mathieu mathieu   81694 2008-08-08 22:10 jpeg02.ljpeg
149           -rw-r--r--  1 mathieu mathieu   81564 2008-08-08 22:10 jpeg01.ljpeg
150           -rw-r--r--  1 mathieu mathieu   79970 2008-08-08 22:10 jpeg00.ljpeg
151

FOOTNOTE ABOUT JPEG FILES

153       It is a common misunderstanding to interchange 'JPEG 8bits lossy' with
154       simply JPEG file. The JPEG specification is much broader than simply
155       the common lossy 8bits file (as found on internet).
156
157       You can have:
158
159       •   JPEG Lossy 8bits
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161       •   JPEG Lossy 12bits
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163       •   JPEG Lossless 2-16bits
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165       Those are what is defined in ITU-T T.81, ISO/IEC IS 10918-1.
166

SEE ALSO

168       gdcmdump(1), gdcmraw(1)
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AUTHOR

171       Mathieu Malaterre
172           Main developer
173
175       Copyright © 2006, 2011 Mathieu Malaterre
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179GDCM 3.0.9                        08/14/2021                        GDCMRAW(1)
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