1img2dcm(1) OFFIS DCMTK img2dcm(1)
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6 img2dcm - Convert standard image formats into DICOM format
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9 img2dcm [options] imgfile-in dcmfile-out
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12 The img2dcm tool serves as a conversion tool from a standard image
13 format like JPEG or BMP to DICOM. Different output SOP Classes can be
14 selected. The additional information (regarding patients, series, etc.)
15 stored in the DICOM output file can be extracted from other DICOM files
16 which serve as a 'template' for the resulting DICOM object. img2dcm can
17 also be configured to invent missing DICOM type 1 and type 2 attributes
18 to work even without any template dataset.
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21 imgfile-in image file to be imported
22 dcmfile-out DICOM output file
24
26 general options
27 -h --help
28 print this help text and exit
29 --version
31 print version information and exit
32 --arguments
34 print expanded command line arguments
35 -q --quiet
37 quiet mode, print no warnings and errors
38 -v --verbose
40 verbose mode, print processing details
41 -d --debug
43 debug mode, print debug information
44 -ll --log-level [l]evel: string constant
46 (fatal, error, warn, info, debug, trace)
47 use level l for the logger
48 -lc --log-config [f]ilename: string
50 use config file f for the logger
51 input options
53 general:
54 -i --input-format [i]nput file format: string
56 supported formats: JPEG (default), BMP
57 -df --dataset-from [f]ilename: string
59 use dataset from DICOM file f
60 -stf --study-from [f]ilename: string
62 read patient/study from DICOM file f
63 -sef --series-from [f]ilename: string
65 read patient/study/series from DICOM file f
66 -ii --instance-inc
68 increase instance number read from DICOM file
69 JPEG format:
71 -dp --disable-progr
73 disable support for progressive JPEG
74 -de --disable-ext
76 disable support for extended sequential JPEG
77 -jf --insist-on-jfif
79 insist on JFIF header existence
80 -ka --keep-appn
82 keep APPn sections (except JFIF)
83 processing options
85 attribute checking:
86 --do-checks
88 enable attribute validity checking (default)
89 --no-checks
91 disable attribute validity checking
92 +i2 --insert-type2
94 insert missing type 2 attributes (default)
95 (only with --do-checks)
96 -i2 --no-type2-insert
98 do not insert missing type 2 attributes
99 (only with --do-checks)
100 +i1 --invent-type1
102 invent missing type 1 attributes
103 (only with --do-checks)
104 -i1 --no-type1-invent
106 do not invent missing type 1 attributes
107 (only with --do-checks)
108 character set:
110 +l1 --latin1
112 set latin-1 as standard character set (default)
113 -l1 --no-latin1
115 keep 7-bit ASCII as standard character set
116 other processing options:
118 -k --key [k]ey: gggg,eeee="str", path or dictionary name="str"
120 add further attribute
121 output options
123 target SOP class:
124 -sc --sec-capture
126 write Secondary Capture SOP class
127 -nsc --new-sc
129 write new Secondary Capture SOP classes
130 -vlp --vl-photo
132 write Visible Light Photographic SOP class (default)
133 output file format:
135 +F --write-file
137 write file format (default)
138 -F --write-dataset
140 write data set without file meta information
141 group length encoding:
143 +g= --group-length-recalc
145 recalculate group lengths if present (default)
146 +g --group-length-create
148 always write with group length elements
149 -g --group-length-remove
151 always write without group length elements
152 length encoding in sequences and items:
154 +e --length-explicit
156 write with explicit lengths (default)
157 -e --length-undefined
159 write with undefined lengths
160 data set trailing padding (not with --write-dataset):
162 -p --padding-off
164 no padding (implicit if --write-dataset)
165 +p --padding-create [f]ile-pad [i]tem-pad: integer
167 align file on multiple of f bytes
168 and items on multiple of i bytes
169
171 Attribute Sources
172 For converting a general image format into DICOM format, the img2dcm
173 application may be fed with some additional input for filling mandatory
174 (and optional) attributes in the new DICOM file like patient, study and
175 series information. This information can be collected using different
176 approaches, which can be combined and are applied to the result file in
177 the following order:
178 · Using the --dataset-from option img2dcm is forced to import
180 attributes from an existing DICOM file. The given DICOM file is fully
181 imported and serves as the basis for all further export operations.
182 As an exception, the SOP Instance UID is not copied by this option.
183 Also image related data like Rows, Columns etc. is exchanged during
184 conversion. Note that img2dcm does not check any other attribute
185 values for validity, e. g. it does not look into sequences to adapt
186 any attributes to the new object (referenced images etc.). Therefore,
187 it is recommended to use the templates in the data directory for
188 (old) SC and VLP objects. See also section 'Input Templates'.
189 · The --study-from and --series-from options (mutually exclusive) can
190 be used to import patient, study and series information from an
191 existing DICOM file. If --series-from is specified, then the given
192 DICOM file is opened by img2dcm and all mandatory information down to
193 the series level is imported. Note that this includes patient, study
194 and series information. In case of --study-from, the series
195 information is excluded. The following attributes are taken over:
196 Patient Level:
197 Patient's Name
198 Patient ID
199 Patient's Sex
200 Patient's Birth Date
201 Specific Character Set
202 Study Level:
204 Study Instance UID
205 Study Date
206 Study Time
207 Referring Physician's Name
208 Study ID
209 Accession Number
210 Series Level (only in case of option --series-from):
212 Series Instance UID
213 Series Number
214 Manufacturer
215 · With the --insert-type2 and --invent-type1 options (both enabled per
217 default), missing attributes (type 2 attributes) and/or missing
218 attribute values (for type 1 attributes) are automatically added and
219 invented by img2dcm. Please note that these options are only
220 evaluated if option --do-checks is enabled (default). If the --no-
221 checks options is enabled, no automatic attribute insertion will take
222 place.
223 · The --key option can be used to add further attributes to the DICOM
224 output file. This option is applied at the very end, just before
225 saving the DICOM file. It is also possible to specify sequences,
226 items and nested attributes using the --key option. In these cases, a
227 special 'path' notation has to be used. Details on this path notation
228 can be found in the documentation of dcmodify.
229 UIDs
230 New Study and Series Instance UIDs are generated if necessary after
231 applying the --study-from and --series options. If Study Instance UID
232 or Series Instance UID are not present after these steps, they are
233 newly generated, independently from each other. A contrary behaviour is
234 choosen for the SOP Instance UID that one could expect to be taken over
235 when using the --dataset-from option. This is not the case, the SOP
236 Instance UID is not copied to the new object. This should be the
237 desirable behaviour for most use cases. However, if a certain SOP
238 Instance UID should be inserted into the new object, the --key option
239 should be used.
240 Input Templates
241 For supporting the conversion into DICOM, img2dcm comes with some pre-
242 defined templates which can be used for the --dataset-from option (see
243 sample files SC.dump and VLP.dump). These templates should be filled
244 with the desired values and then must be dumped (converted) to a DICOM
245 file before actually being used with img2dcm. Use dump2dcm to convert
246 the dump to DICOM. Example:
247 dump2dcm SC.dump SC.dcm
248 It is possible to use any DICOM file as a template. Please note that
250 the complete DICOM dataset is imported; hence, it should be assured
251 that only attributes are present which should be part of the
252 constructed DICOM object. The SOP Class UID and the Pixel Data
253 attributes (including attributes like Rows, Columns etc.) are not
254 copied but replaced by img2dcm during conversion.
255 Input Plugins
256 The img2dcm application currently supports the JPEG and the BMP image
257 format as input.
258 JPEG Input Plugin
259 For JPEG, the original JPEG from the source file is not decoded but
260 extracted and slightly transformed (e. g. JFIF header is cut off) to
261 allow fast conversion of even big JPEG files without the need of
262 decoding and re-encoding. The JPEG plugin chooses the necessary output
263 transfer syntax automatically depending on the actual encoding of the
264 data inside the JPEG file. Therefore, the following Transfer Syntaxes
265 (and their corresponding JPEG encodings) are used by the JPEG plugin:
266 · JPEG Coding Process 1 Baseline, Lossy, Non-Hierarchical, Sequential,
267 DCT, Huffman, 8 Bit SOP Class = 1.2.840.10008.1.2.4.50
268 · JPEG Coding Process 2 (8-bit) and 4 (12-bit) Extended, Lossy, Non-
269 Hierarchical, Sequential, DCT, Huffman, 8/12 Bit SOP Class =
270 1.2.840.10008.1.2.4.51
271 · JPEG Coding Process 10 (8-bit) and 12 (12-bit) Full Progression,
272 lossy, Non-Hierarch., Progressive, DCT, Huffman, 8/12 Bit SOP Class =
273 1.2.840.10008.1.2.4.55
274 Color and grayscale images are supported.
275 The support for the Extended JPEG Transfer Syntax can be disabled
276 (--disable-ext option) as well as the support for the (retired)
277 Progressive JPEG Transfer Syntax (--disable-progr option).
278 JPEG lossless encoding as well as any arithmethic or hierarchical JPEG
279 encoding modes are not supported by the plugin.
280 JFIF (JPEG File Interchange Format) information facilitates optional
281 APPn markers in a JPEG file. Many digital cameras do not integrate such
282 JFIF information into the JPEG output they create. For example, JFIF
283 contains information about the pixel aspect ratio of the compressed
284 image. If you want the img2dcm application to insist on a JFIF header
285 in the JPEG stream, you can use the option --insist-on-jfif which will
286 abort if no JFIF information can be found. By default, missing JFIF
287 information is ignored.
288 For DICOM it is kind of a 'gray zone', whether the integration of JFIF
289 (or any other APPn) data into the DICOM object's internal JPEG stream
290 is allowed or not. However, the most reliable approach is to cut those
291 markers and their information off the JPEG stream. This approach is
292 also taken by the img2dcm application. By default, all APPn markers are
293 cut off from the original JPEG stream. However, if you want to keep
294 other APPn markers than JFIF (e. g. EXIF information) inside the DICOM
295 stream, the option --keep-appn does the trick. It should also be
296 slightly faster than cutting off APPn information, because it is not
297 necessary to scan the whole JPEG stream for such data. JFIF information
298 is always removed by img2dcm.
299 BMP Input Plugin
300 img2dcm supports BMP as input format. However, so far only the most
301 commmon BMP images are supported. In particular, BMP images which use
302 bitfields or run length encoding will be rejected. Such images are
303 uncommon. All input images will be converted into a DICOM image with
304 RGB color model and a bit depth of 24. There are no specific options
305 for fine-tuning BMP format conversion.
306 Output Plugins
307 The desired output SOP Class can be selected on the command line.
308 Currently, an export plugin for the Secondary Capture Image SOP class
309 (default, option -sc), the new Secondary Capture Image SOP classes
310 (option -nsc) and Visible Light Photographic Image SOP class (option
311 -vl) are available. Please note that the first one is deprecated
312 according to the DICOM standard but is selected as a default because it
313 is widely supported. Future versions of img2dcm might provide further
314 output plugins for other SOP Classes.
315 For the new Secondary Capture SOP classes, it is not possible to
316 specifiy which specific SOP class should be used for output. That is
317 because these new SOP classes are differentiated from each other by
318 colour depth (1/8/16) and the fact whether the image is black/white or
319 colour. That is why img2dcm decides during conversion, which output SOP
320 class is suitable for a given source image.
322 Here are some examples that show how the img2dcm application can be
323 used.
324 1. img2dcm image.jpg out.dcm
325 Read JPEG file 'image.jpg', convert to the old Secondary Capture
326 SOP class and save the result to DICOM file 'out.dcm'. This is the
327 easiest way of using img2dcm. Any type 1 and type 2 attributes
328 required for writing valid objects of this SOP class are inserted
329 automatically.
330 2. img2dcm -i BMP image.bmp out.dcm
331 Same as above but tells img2dcm to read a BMP file instead of JPEG.
332 3. img2dcm image.jpg out.dcm -vlp -k 'PatientName=Bond^James'
333 Same as first example, but writes Visible Light Photographic Image
334 object to 'out.dcm' and sets PatientName to 'Bond^James' which
335 otherwise would be left empty.
336 4. img2dcm image.jpg out.dcm --series-from template.dcm -k
337 'PatientName=Bond^James'
338 Same as 1), but imports patient/study/series infomation from DICOM
339 file 'template.dcm'. Please note that attribute PatientName will
340 contain 'Bond^James' at the end, any value from 'template.dcm' will
341 be overwritten. That is, because the -k option is applied at the
342 very end of the conversion pipeline (see above).
343 5. img2dcm image.jpg out.dcm --no-checks
344 Same as 1), but does not perform any attribute checking and no type
345 1 and type 2 attribute insertion! So in this case, an invalid DICOM
346 object would be generated. This can be interesting if the output
347 file is not meant to be completed but will undergo further
348 transformations, e. g. adding attributes using dcmodify. Only use
349 option --no-checks if you know what you are doing!
350 6. img2dcm image.jpg out.dcm --no-type1-invent
351 Same as 1), but does not insert missing type 1 attributes and/or
352 their values. Type 2 attributes will be inserted. Note that in this
353 case it must be assured that all type 1 attributes are provided by
354 other means, i. e. by adding them with the --key option. Otherwise,
355 img2dcm will report an error and will stop converting.
356 7. img2dcm image.jpg out.dcm --keep-appn --insist-on-jfif
357 Same as 1), but takes over APPn information like EXIF into the
358 DICOM object's resulting JPEG stream. Further, --insist-on-jfif
359 will force img2dcm to abort if no JFIF information is existent in
360 the source file.
362 The level of logging output of the various command line tools and
363 underlying libraries can be specified by the user. By default, only
364 errors and warnings are written to the standard error stream. Using
365 option --verbose also informational messages like processing details
366 are reported. Option --debug can be used to get more details on the
367 internal activity, e.g. for debugging purposes. Other logging levels
368 can be selected using option --log-level. In --quiet mode only fatal
369 errors are reported. In such very severe error events, the application
370 will usually terminate. For more details on the different logging
371 levels, see documentation of module 'oflog'.
372 In case the logging output should be written to file (optionally with
373 logfile rotation), to syslog (Unix) or the event log (Windows) option
374 --log-config can be used. This configuration file also allows for
375 directing only certain messages to a particular output stream and for
376 filtering certain messages based on the module or application where
377 they are generated. An example configuration file is provided in
378 <etcdir>/logger.cfg).
380 All command line tools use the following notation for parameters:
381 square brackets enclose optional values (0-1), three trailing dots
382 indicate that multiple values are allowed (1-n), a combination of both
383 means 0 to n values.
384 Command line options are distinguished from parameters by a leading '+'
385 or '-' sign, respectively. Usually, order and position of command line
386 options are arbitrary (i.e. they can appear anywhere). However, if
387 options are mutually exclusive the rightmost appearance is used. This
388 behaviour conforms to the standard evaluation rules of common Unix
389 shells.
390 In addition, one or more command files can be specified using an '@'
391 sign as a prefix to the filename (e.g. @command.txt). Such a command
392 argument is replaced by the content of the corresponding text file
393 (multiple whitespaces are treated as a single separator unless they
394 appear between two quotation marks) prior to any further evaluation.
395 Please note that a command file cannot contain another command file.
396 This simple but effective approach allows to summarize common
397 combinations of options/parameters and avoids longish and confusing
398 command lines (an example is provided in file <datadir>/dumppat.txt).
400 The img2dcm utility will attempt to load DICOM data dictionaries
401 specified in the DCMDICTPATH environment variable. By default, i.e. if
402 the DCMDICTPATH environment variable is not set, the file
403 <datadir>/dicom.dic will be loaded unless the dictionary is built into
404 the application (default for Windows).
405 The default behaviour should be preferred and the DCMDICTPATH
406 environment variable only used when alternative data dictionaries are
407 required. The DCMDICTPATH environment variable has the same format as
408 the Unix shell PATH variable in that a colon (':') separates entries.
409 On Windows systems, a semicolon (';') is used as a separator. The data
410 dictionary code will attempt to load each file specified in the
411 DCMDICTPATH environment variable. It is an error if no data dictionary
412 can be loaded.
414 <datadir>/SC.dump - Sample dump file for Secondary Capture images
415 <datadir>/VLP.dump - Sample dump file for Visible Light Photographic
416 images
418 dcm2pnm(1), dcmj2pnm(1), dump2dcm(1), dcmconv(1), dcmodify(1)
420 Copyright (C) 2007-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
421 Germany.
422Version 3.6.0 6 Jan 2011 img2dcm(1)