1dcm2json(1) OFFIS DCMTK dcm2json(1)
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6 dcm2json - Convert DICOM file and data set to JSON
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10 dcm2json [options] dcmfile-in [jsonfile-out]
11
13 The dcm2json utility converts the contents of a DICOM file (file format
14 or raw data set) to JSON (JavaScript Object Notation). The output
15 refers to the 'DICOM JSON Model', which is found in DICOM Part 18
16 Section F.
17 If dcm2json reads a raw data set (DICOM data without a file format
19 meta-header), it will attempt to guess the transfer syntax by examining
20 the first few bytes of the file. It is not always possible to correctly
21 guess the transfer syntax and it is better to convert a data set to a
22 file format whenever possible (using the dcmconv utility). It is also
23 possible to use the -f and -t[ieb] options to force dcm2json to read a
24 data set with a particular transfer syntax.
25
27 dcmfile-in DICOM input filename to be converted
28 jsonfile-out JSON output filename (default: stdout)
30
32 general options
33 -h --help
34 print this help text and exit
35 --version
37 print version information and exit
38 --arguments
40 print expanded command line arguments
41 -q --quiet
43 quiet mode, print no warnings and errors
44 -v --verbose
46 verbose mode, print processing details
47 -d --debug
49 debug mode, print debug information
50 -ll --log-level [l]evel: string constant
52 (fatal, error, warn, info, debug, trace)
53 use level l for the logger
54 -lc --log-config [f]ilename: string
56 use config file f for the logger
57 input options
59 input file format:
60 +f --read-file
62 read file format or data set (default)
63 +fo --read-file-only
65 read file format only
66 -f --read-dataset
68 read data set without file meta information
69 input transfer syntax:
71 -t= --read-xfer-auto
73 use TS recognition (default)
74 -td --read-xfer-detect
76 ignore TS specified in the file meta header
77 -te --read-xfer-little
79 read with explicit VR little endian TS
80 -tb --read-xfer-big
82 read with explicit VR big endian TS
83 -ti --read-xfer-implicit
85 read with implicit VR little endian TS
86 processing options
88 encoding of infinity and not-a-number:
89 -es --encode-strict
90 report error for 'inf' and 'nan' (default)
91 -ee --encode-extended
93 permit 'inf' and 'nan' in JSON numbers
94 output options
96 output format:
97 +fc --formatted-code
99 enable whitespace formatting (default)
100 # prints additional spaces and newlines for increased
102 # readability
103 -fc --compact-code
105 print only required characters
106 +m --write-meta
108 write data set with meta information
109 (warning: not conforming to the DICOM standard)
110
112 The basic structure of the JSON output created from a DICOM file looks
113 like the following (see DICOM Part 18 Section F for details):
114 {
116 "00080005": {
117 "vr": "CS",
118 "Value": [
119 "ISO_IR 192"
120 ]
121 },
122 "00080020": {
123 "vr": "DT",
124 "Value": [
125 "20130409"
126 ]
127 },
128 "00080030": {
129 "vr": "TM",
130 "Value": [
131 "131600.0000"
132 ]
133 },
134 "00080050": {
135 "vr": "SH",
136 "Value": [
137 "11235813"
138 ]
139 },
140 "00080056": {
141 "vr": "CS",
142 "Value": [
143 "ONLINE"
144 ]
145 },
146 "00080061": {
147 "vr": "CS",
148 "Value": [
149 "CT",
150 "PET"
151 ]
152 },
153 "00080090": {
154 "vr": "PN",
155 "Value": [
156 {
157 "Alphabetic": "^Bob^^Dr."
158 }
159 ]
160 },
161 "00081190": {
162 "vr": "UR",
163 "Value": [
164 "http://wado.nema.org/studies/
165 1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873"
166 ]
167 },
168 "00090010": {
169 "vr": "LO",
170 "Value": [
171 "Vendor A"
172 ]
173 },
174 "00091002": {
175 "vr": "UN",
176 "InlineBinary": "z0x9c8v7"
177 },
178 "00100010": {
179 "vr": "PN",
180 "Value": [
181 {
182 "Alphabetic": "Wang^XiaoDong"
183 }
184 ]
185 },
186 "00100020": {
187 "vr": "LO",
188 "Value": [
189 "12345"
190 ]
191 },
192 "00100021": {
193 "vr": "LO",
194 "Value": [
195 "Hospital A"
196 ]
197 },
198 "00100030": {
199 "vr": "DA",
200 "Value": [
201 "19670701"
202 ]
203 },
204 "00100040": {
205 "vr": "CS",
206 "Value": [
207 "M"
208 ]
209 },
210 "00101002": {
211 "vr": "SQ",
212 "Value": [
213 {
214 "00100020": {
215 "vr": "LO",
216 "Value": [
217 "54321"
218 ]
219 },
220 "00100021": {
221 "vr": "LO",
222 "Value": [
223 "Hospital B"
224 ]
225 }
226 },
227 {
228 "00100020": {
229 "vr": "LO",
230 "Value": [
231 "24680"
232 ]
233 },
234 "00100021": {
235 "vr": "LO",
236 "Value": [
237 "Hospital C"
238 ]
239 }
240 }
241 ]
242 },
243 "0020000D": {
244 "vr": "UI",
245 "Value": [
246 "1.2.392.200036.9116.2.2.2.1762893313.1029997326.945873"
247 ]
248 },
249 "00200010": {
250 "vr": "SH",
251 "Value": [
252 "11235813"
253 ]
254 },
255 "00201206": {
256 "vr": "IS",
257 "Value": [
258 4
259 ]
260 },
261 "00201208": {
262 "vr": "IS",
263 "Value": [
264 942
265 ]
266 }
267 }
268 Bulk Data
270 Binary data, i.e. DICOM element values with Value Representations (VR)
271 of OB or OW, as well as OD, OF, OL, OV and UN values are always written
272 as 'InlineBinary' (base64 encoding) to the JSON output. A future
273 version of this tool might optionally use a 'BulkDataURI' instead, i.e.
274 the WADO-RS URL of a bulk data item that contains the element value.
275 This would be particularly useful for large amounts of data, such as
276 pixel data.
277
279 Numbers as Strings
280 The DICOM standard allows certain numeric DICOM value representations,
281 DS, IS, SV and UV, to be converted either to a JSON number or a JSON
282 string. dcm2json converts DS and IS values to JSON numbers if they are
283 valid decimal strings or integer strings, and to strings if they
284 contain any illegal character. dcm2json converts SV and UV values to
285 numbers if they are not larger than 9007199254740991ll or smaller than
286 -9007199254740991ll, and to strings otherwise. While the JSON
287 specification permits larger numbers, these are the largest integers
288 that JavaScript can handle. Therefore, many JSON parsers cannot process
289 larger numbers.
290 Character Encoding
292 As required by the DICOM JSON encoding, dcm2json always creates output
293 in Unicode UTF-8 encoding and converts DICOM datasets accordingly. If
294 this is not possible, for example because DCMTK has been compiled
295 without either iconv or ICU library, an error is returned.
296
298 The level of logging output of the various command line tools and
299 underlying libraries can be specified by the user. By default, only
300 errors and warnings are written to the standard error stream. Using
301 option --verbose also informational messages like processing details
302 are reported. Option --debug can be used to get more details on the
303 internal activity, e.g. for debugging purposes. Other logging levels
304 can be selected using option --log-level. In --quiet mode only fatal
305 errors are reported. In such very severe error events, the application
306 will usually terminate. For more details on the different logging
307 levels, see documentation of module 'oflog'.
308 In case the logging output should be written to file (optionally with
310 logfile rotation), to syslog (Unix) or the event log (Windows) option
311 --log-config can be used. This configuration file also allows for
312 directing only certain messages to a particular output stream and for
313 filtering certain messages based on the module or application where
314 they are generated. An example configuration file is provided in
315 <etcdir>/logger.cfg.
316
318 All command line tools use the following notation for parameters:
319 square brackets enclose optional values (0-1), three trailing dots
320 indicate that multiple values are allowed (1-n), a combination of both
321 means 0 to n values.
322 Command line options are distinguished from parameters by a leading '+'
324 or '-' sign, respectively. Usually, order and position of command line
325 options are arbitrary (i.e. they can appear anywhere). However, if
326 options are mutually exclusive the rightmost appearance is used. This
327 behavior conforms to the standard evaluation rules of common Unix
328 shells.
329 In addition, one or more command files can be specified using an '@'
331 sign as a prefix to the filename (e.g. @command.txt). Such a command
332 argument is replaced by the content of the corresponding text file
333 (multiple whitespaces are treated as a single separator unless they
334 appear between two quotation marks) prior to any further evaluation.
335 Please note that a command file cannot contain another command file.
336 This simple but effective approach allows one to summarize common
337 combinations of options/parameters and avoids longish and confusing
338 command lines (an example is provided in file <datadir>/dumppat.txt).
339
341 The dcm2json utility uses the following exit codes when terminating.
342 This enables the user to check for the reason why the application
343 terminated.
344 general
346 EXITCODE_NO_ERROR 0
347 EXITCODE_COMMANDLINE_SYNTAX_ERROR 1
348 input file errors
350 EXITCODE_CANNOT_READ_INPUT_FILE 20
351 EXITCODE_NO_INPUT_FILES 21
352 output file errors
354 EXITCODE_CANNOT_WRITE_OUTPUT_FILE 40
355 processing errors
357 EXITCODE_CANNOT_CONVERT_TO_UNICODE 80
358 EXITCODE_CANNOT_WRITE_VALID_JSON 81
359
361 The dcm2json utility will attempt to load DICOM data dictionaries
362 specified in the DCMDICTPATH environment variable. By default, i.e. if
363 the DCMDICTPATH environment variable is not set, the file
364 <datadir>/dicom.dic will be loaded unless the dictionary is built into
365 the application (default for Windows).
366 The default behavior should be preferred and the DCMDICTPATH
368 environment variable only used when alternative data dictionaries are
369 required. The DCMDICTPATH environment variable has the same format as
370 the Unix shell PATH variable in that a colon (':') separates entries.
371 On Windows systems, a semicolon (';') is used as a separator. The data
372 dictionary code will attempt to load each file specified in the
373 DCMDICTPATH environment variable. It is an error if no data dictionary
374 can be loaded.
375
377 Copyright (C) 2016-2022 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
378 Germany.
379Version 3.6.7 Fri Apr 22 2022 dcm2json(1)