1GDCMIMG(1) DICOM Manipulation. GDCMIMG(1)
2
6 gdcmimg - Manipulate DICOM image file.
7 gdcmimg is a low level tool to allow de-/encapsulation from/to DICOM
9 image. This tool does not understand Transfer Syntax conversion. It
10 will encapsulate the raw data as-is. This has some impact in some
11 cases, see special warnings below.
12 It is important to note that gdcmimg can only encapsulate proper input
14 file, for instance JPG and or JP2 are accepted since an associated
15 DICOM Transfer Syntax can be found. However input such as TIFF and/or
16 PNG are not, since DICOM does not support those. See instead a tool
17 such as gdcm2vtk.
18
20 gdcmimg [options] file-in file-out
21
23 The gdcmimg command line tool can be used in two fashions:
24 • 1. Converting a recognized file format into its encapsulated DICOM
26 counterpart,
27 • 2. Anonymizing a rectangular portion of a DICOM file.
29
32 file-in input filename (non-DICOM)
33 file-out DICOM output filename
35
37 -i --input Input filename
38 -o --output Output filename
39
41 --endian %s Endianness (LSB/MSB).
42 -d --depth %d Depth (Either 8/16/32 or BitsAllocated eg. 12 when known).
43 --sign %s Pixel sign (0/1).
44 --spp %d Sample Per Pixel (1/3).
45 --pc [01] Change planar configuration.
46 --pi [str] Change photometric interpretation.
47 --pf %d,%d,%d Change pixel format: (BA,BS,HB).
48 -s --size %d,%d Size.
49 --offset %ull Start Offset.
50 -C --sop-class-uid SOP Class UID (name or value).
51 -T --study-uid Study UID.
52 -S --series-uid Series UID.
53 --template Template DICOM file.
54 --keep-meta Keep meta info from template file (advanced users only).
55 --root-uid Root UID.
56
58 -R --region %d,%d Region.
59 -F --fill %d Fill with pixel value specified.
60
62 -h --help
63 print this help text and exit
64 -v --version
66 print version information and exit
67 -V --verbose
69 verbose mode (warning+error).
70 -W --warning
72 warning mode, print warning information
73 -E --error
75 error mode, print error information
76 -D --debug
78 debug mode, print debug information
79
81 GDCM_ROOT_UID Root UID
82
84 gdcmimg will base it's conversion process based on the file extension.
85 Follows the list of recognized file extension. When no extension is
86 found, DICOM file is assumed.
87 input format
89 * RAW (raw, rawl, gray, rgb)
91 * RLE (rle)
92 * PNM (pgm, pnm, ppm)
93 * JPEG-LS (jls)
94 * JPEG 2000 (jp2, j2k, j2c, jpx, jpc)
95 * JPEG (jpg, jpeg, ljpg, ljpeg)
96 * DICOM ()
97 output format:
99 * PGM (pgm, pnm, ppm)
101 * DICOM ()
102 For RAW file format, you should take special care of the –endian
104 option. For the (old) JPEG file format, both the lossy and lossless
105 format are supported, user should pay attention to the –sign option.
106 For file format such as RLE or RAW, user is expected to fill in
107 information required to find the dimension and type of input data as
108 there is no other way to find this information. For all other file
109 format, the properties are derived from the file format itself.
110 PNM file are supposed to be big endian (important for depth > 8)
112
114 Remove a rectangular part of the image
115 To fill the region [0,100]x[0,100] of a DICOM image simply do:
116 $ gdcmimg --fill 0 --region 0,100,0,100 -i input.dcm -o output_black.dcm
118 Warning: if the Pixel Data is compressed, the image is first
120 decompressed so that pixel can be set to 0, but it is not
121 re-compressed.
122 Convert RAW to DICOM
124 Recognized extension is .raw, .rawl, .gray or .rgb (case insensitive)
125 $ gdcmimg --size 512,512 --depth 16 -i input.raw -o output.dcm
127 the image will be a Secondary Capture.
129 When the input is 3 component, one need to specify explicitly the
131 Samples Per Pixel:
132 $ gdcmimg --size 512,512 --spp 3 input_rgb.raw output_rgb.dcm
134 When the filename contains .rgb as file extension output is
136 automatically recognized as RGB no need to specify –spp
137 $ gdcmimg --size 512,512 input.rgb output_rgb.dcm
139 You can use the dd cmd line to skip any header you would like to
141 discard, for instance, if you would like to skip the first 108 bytes,
142 simply do:
143 $ dd skip=108 bs=1 if=input.raw of=output.raw
145 .raw and .rawl extension are equivalent. You need to explicitly specify
147 the endianness manually:
148 $ gdcmimg --endian MSB --size 512,512 --depth 16 -i input.raw -o output.dcm
150 or
152 $ gdcmimg --endian LSB --size 512,512 --depth 16 -i input.raw -o output.dcm
154 Convert PGM/PNM/PPM to DICOM
156 Recognized extensions are .pgm, .pnm, .ppm (case insensitive)
157 $ gdcmimg -i input.pgm -o output.dcm
159 the image will be a Secondary Capture
161 Convert RLE to DICOM
163 Recognized extension is .rle (case insensitive)
164 $ gdcmimg --size 512,512 --depth 16 -i input.rle -o output.dcm
166 the image will be a Secondary Capture
168 Convert JPEG to DICOM
170 Recognized extensions are .jpg, .jpeg, .ljpg, .ljpeg (case insensitive)
171 $ gdcmimg -i input.ljpeg -o output.dcm
173 the image will be a Secondary Capture
175 Convert J2K to DICOM
177 Recognized extensions are .j2k, .jp2, .jpc, jpx, j2c (case insensitive)
178 $ gdcmimg -i input.j2k -o output.dcm
180 the image will be a Secondary Capture.
182 All Pixel information (Bits Stored/Allocated...) will be derived from
184 the image itself, and not from the command line options.
185 Specifying a SOP Class UID
187 Instead of the default Secondary Capture Image Storage, one may want to
188 specify, say VL Photographic Image Storage.
189 $ gdcmimg --sop-class-uid 1.2.840.10008.5.1.4.1.1.77.1.4 input.jpg output.dcm
191 Specifying a template DICOM file
193 Instead of the default Secondary Capture Image Storage, generated with
194 default values, one may want to specify a DICOM file that will serve as
195 template to fill in the DICOM attributes.
196 $ gdcmimg --sign 1 --template template.dcm input.jpg output.dcm
198 Pay attention that any values from template.dcm that are not consistent
200 with what is found inside the reference image will be overridden (eg.
201 image size). On particular case should be of concern: the Pixel
202 Representation for the JPEG family.
203
205 gdcmimg handle nicely a set of files (for instance jpeg):
206 $ gdcmimg -C 1.2.840.10008.5.1.4.1.1.12.1 1.jpg 2.jpg 3.jpg 4.jpg output.dcm
208 It is important to specify an SOP Class that supports multi-frames
210 images otherwise gdcmimg will fail.
211
213 In some case, one may want to create a 2D slice from an arbitrary
214 volume (e.g 3D). In which case –offset becomes handy:
215 $ gdcmimg --offset 4954104330 --size 1673,1673 Input3D_1673_1673_1775.raw slice_1770.dcm
217
219 There are a couple of issues with gdcmimg implementation:
220 For RAW file, one should pay attention that when using –endian MSB the
222 Pixel Data will be encapsulated as is (not touched by gdcmimg).
223 Therefore the only possible transfer syntax available is Implicit VR
224 Big Endian DLX (G.E Private). GDCM does handle this private Transfer
225 Syntax. So if you need to convert this Transfer Syntax to another one
226 (and allow Pixel Data manipulation), you can use:
227 $ gdcmconv --raw --force input_big_endian_dlx.raw -o output_implicit_vr_little_endian.dcm
229 For JFIF file and JP2 file (with header) the header is copied into the
231 Pixel Data element which is illegal for JP2. Use gdcmconv to properly
232 re-encode a JP2/JFIF file into J2K/JPG.
233 $ gdcmimg input.jp2 output_jp2.dcm
235 $ gdcmconv --j2k --force output_jp2.dcm output_j2k.dcm
236 For RLE file, no check is done for crossing the row boundary. It is
238 recommended to use gdcmconv –rle to re-encode into a proper RLE file in
239 case of doubt.
240 Of course if the compression is not ok with your setup, you can always
242 de-encapsulated the DICOM file (typically JPEG) to a non-encapsulated
243 form, using gdcmconv:
244 $ gdcmconv --raw input_jpeg.dcm output_raw.dcm
246
248 gdcmdump(1), gdcm2vtk(1), gdcmraw(1), convert(1), dd(1)
249
251 Mathieu Malaterre
252 Main developer
253
255 Copyright © 2006, 2011 Mathieu Malaterre
256GDCM 3.0.12 08/02/2022 GDCMIMG(1)