1gdcmimg(1) GDCM gdcmimg(1)
2
6 gdcmimg - Manipulate DICOM image file.
7
9 gdcmimg [options] file-in file-out
10
12 The gdcmimg command line tool can be used in two fashions:
13 · 1. Converting a recognized file format into its encapsulated DICOM
15 counterpart,
16 · 2. Anonymizing a rectangular portion of a DICOM file.
18 file-in input filename
19 file-out output filename
22 PARAMETERS
23 -i --input Input filename
24 -o --output Output filename
25 OPTIONS
26 --endian %s Endianness (LSB/MSB).
27 -d --depth %d Depth (8/16/32).
28 --sign %s Pixel sign (0/1).
29 -s --size %d,%d Size.
30 -C --sop-class-uid SOP Class UID (name or value).
31 -T --study-uid Study UID.
32 -S --series-uid Series UID.
33 --root-uid Root UID.
34 fill options
35 -R --region %d,%d Region.
36 -F --fill %d Fill with pixel value specified.
37 general options
38 -h --help
39 print this help text and exit
40 -v --version
42 print version information and exit
43 -V --verbose
45 verbose mode (warning+error).
46 -W --warning
48 warning mode, print warning information
49 -E --error
51 error mode, print error information
52 -D --debug
54 debug mode, print debug information
55 environment variable
56 GDCM_ROOT_UID Root UID
58 gdcmimg will base it's conversion process based on the file extension.
59 Follows the list of recognized file extension. When no extension is
60 found, DICOM file is assumed.
61 input format
62 * RAW (raw)
63 * RLE (rle)
64 * PNM (pgm, pnm, ppm)
65 * JPEG-LS (jls)
66 * JPEG 2000 (jp2, j2k, j2c, jpc)
67 * JPEG (jpg, jpeg, ljpg, ljpeg)
68 * DICOM ()
69 output format:
71 * PGM (pgm, pnm, ppm)
72 * DICOM ()
73 For RAW file format, you should take special care of the --endian
75 option. For the (old) JPEG file format, both the lossy and lossless
76 format are supported, user should pay attention to the --sign option.
77 For file format such as RLE or RAW, user is expected to fill in
78 information required to find the dimension and type of input data as
79 there is no other way to find this information. For all other file
80 format, the properties are derived from the file format itself. PNM
81 file are supposed to be big endian.
83 Remove a rectangular part of the image
84 To fill the region [0,100]x[0,100] of a DICOM image simply do:
85 $ gdcmimg --fill 0 --region 0,100,0,100 -i input.dcm -o output_black.dcm
86 Warning: if the Pixel Data is compressed, the image is first
87 decompressed so that pixel can be set to 0, but it is not recompressed.
88 Convert RAW to DICOM
89 Recognized extension is .raw (case insensitive)
90 $ gdcmimg --size 512,512 --depth 16 -i input.raw -o output.dcm
91 the image will be a Secondary Capture
92 You can use the dd cmd line to skip any header you would like to
93 discard, for instance, if you would like to skip the first 108 bytes,
94 simply do:
95 $ dd skip=108 bs=1 if=input.raw of=output.raw
96 Convert PGM/PNM/PPM to DICOM
97 Recognized extensions are .pgm, .pnm, .ppm (case insensitive)
98 $ gdcmimg -i input.pgm -o output.dcm
99 the image will be a Secondary Capture
100 Convert RLE to DICOM
101 Recognized extension is .rle (case insensitive)
102 $ gdcmimg --size 512,512 --depth 16 -i input.rle -o output.dcm
103 the image will be a Secondary Capture
104 Convert JPEG to DICOM
105 Recognized extensions are .jpg, .jpeg, .ljpg, .ljpeg (case insensitive)
106 $ gdcmimg -i input.ljpeg -o output.dcm
107 the image will be a Secondary Capture
108 Convert J2K to DICOM
109 Recognized extensions are .j2k, .jp2, .jpc (case insensitive)
110 $ gdcmimg -i input.j2k -o output.dcm
111 the image will be a Secondary Capture
112 Specifying a SOP Class UID
113 Instead of the default Secondary Capture Image Storage, one may want to
114 specify, say VL Photographic Image Storage.
115 $ gdcmimg --sop-class-uid 1.2.840.10008.5.1.4.1.1.77.1.4 input.jpg output.dcm
117 gdcmimg handle nicely a set of files (for instance jpeg):
118 $ gdcmimg 1.jpg 2.jpg 3.jpg 4.jpg output.dcm
120 There are a couple of issues with gdcmimg implementation: For JFIF file
121 and JP2 file (with header) the header is copied into the Pixel Data
122 element which is illegal for JP2. Use gdcmconv to properly re-encode a
123 JP2/JFIF file into J2K/JPG.
124 $ gdcmimg input.jp2 output_jp2.dcm
125 $ gdcmconv --j2k --force output_jp2.dcm output_j2k.dcm
126 For RLE file, no check is done for crossing the row boundary. It is
127 recommended to use gdcmconv --rle to re-encode into a proper RLE file
128 in case of doubt.
129 Of course if the compression is not ok with your setup, you can always
130 de-encapsulated the DICOM file (typically JPEG) to a non-encapsulated
131 form, using gdcmconv:
132 $ gdcmconv --raw input_jpeg.dcm output_raw.dcm
134 gdcmdump(1), gdcmdump(1), gdcmraw(1), convert(1), dd(1)
136 Copyright (c) 2006-2010 Mathieu Malaterre
137Version 2.0.16 Tue Jul 26 2011 gdcmimg(1)