Provided by: dcmtk_3.6.7-9.1build4_amd64 
NAME
img2dcm - Convert standard image formats into DICOM format
SYNOPSIS
img2dcm [options] imgfile-in... dcmfile-out
DESCRIPTION
The img2dcm tool serves as a conversion tool from a standard image format like JPEG or BMP to DICOM.
Different output SOP Classes can be selected. The additional information (regarding patients, series,
etc.) stored in the DICOM output file can be extracted from other DICOM files which serve as a 'template'
for the resulting DICOM object. img2dcm can also be configured to invent missing DICOM type 1 and type 2
attributes to work even without any template dataset.
PARAMETERS
imgfile-in image input filename
dcmfile-out DICOM output filename
OPTIONS
general options
-h --help
print this help text and exit
--version
print version information and exit
--arguments
print expanded command line arguments
-q --quiet
quiet mode, print no warnings and errors
-v --verbose
verbose mode, print processing details
-d --debug
debug mode, print debug information
-ll --log-level [l]evel: string constant
(fatal, error, warn, info, debug, trace)
use level l for the logger
-lc --log-config [f]ilename: string
use config file f for the logger
input options
general:
-i --input-format [i]nput file format: string
supported formats: JPEG (default), BMP
-df --dataset-from [f]ilename: string
use dataset from DICOM file f
-dx --dataset-from-xml [f]ilename: string
use dataset from XML file f
-stf --study-from [f]ilename: string
read patient/study from DICOM file f
-sef --series-from [f]ilename: string
read patient/study/series from DICOM file f
-ii --instance-inc
increase instance number read from DICOM file
JPEG format:
-dp --disable-progr
disable support for progressive JPEG
-de --disable-ext
disable support for extended sequential JPEG
-jf --insist-on-jfif
insist on JFIF header existence
-ka --keep-appn
keep APPn sections (except JFIF)
-rc --remove-com
remove COM segment
XML validation:
+Vd --validate-document
validate XML document against DTD
+Vn --check-namespace
check XML namespace in document root
processing options
attribute checking:
--do-checks
enable attribute validity checking (default)
--no-checks
disable attribute validity checking
+i2 --insert-type2
insert missing type 2 attributes (default)
(only with --do-checks)
-i2 --no-type2-insert
do not insert missing type 2 attributes
(only with --do-checks)
+i1 --invent-type1
invent missing type 1 attributes (default)
(only with --do-checks)
-i1 --no-type1-invent
do not invent missing type 1 attributes
(only with --do-checks)
character set conversion of study/series file:
-Ct --transliterate
try to approximate characters that cannot be
represented through similar looking characters
-Cd --discard-illegal
discard characters that cannot be represented
in destination character set
other processing options:
-k --key [k]ey: gggg,eeee='str', path or dictionary name='str'
add further attribute
output options
target SOP class:
-sc --sec-capture
write Secondary Capture SOP class (default)
-nsc --new-sc
write new Secondary Capture SOP classes
-vlp --vl-photo
write Visible Light Photographic SOP class
-oph --oph-photo
write Ophthalmic Photography SOP classes
output file format:
+F --write-file
write file format (default)
-F --write-dataset
write data set without file meta information
group length encoding:
+g= --group-length-recalc
recalculate group lengths if present (default)
+g --group-length-create
always write with group length elements
-g --group-length-remove
always write without group length elements
length encoding in sequences and items:
+e --length-explicit
write with explicit lengths (default)
-e --length-undefined
write with undefined lengths
data set trailing padding (not with --write-dataset):
-p --padding-off
no padding (implicit if --write-dataset)
+p --padding-create [f]ile-pad [i]tem-pad: integer
align file on multiple of f bytes
and items on multiple of i bytes
NOTES
Attribute Sources
For converting a general image format into DICOM format, the img2dcm application may be fed with some
additional input for filling mandatory (and optional) attributes in the new DICOM file like patient,
study and series information. This information can be collected using different approaches, which can be
combined and are applied to the result file in the following order:
•
Using the --dataset-from option img2dcm is forced to import attributes from an existing DICOM file. The
given DICOM file is fully imported and serves as the basis for all further export operations. As an
exception, the SOP Instance UID is not copied by this option. Also image related data like Rows, Columns
etc. is exchanged during conversion. Note that img2dcm does not check any other attribute values for
validity, e.g. it does not look into sequences to adapt any attributes to the new object (referenced
images etc.). Therefore, it is recommended to use the templates in the data directory for (old) SC and
VLP objects. See also section 'Input Templates'.
•
Using the --dataset-from-xml option img2dcm is also forced to import attributes from an existing file.
In this case, however, the file must contain XML data in the format as produced by dcm2xml.
•
The --study-from and --series-from options (mutually exclusive) can be used to import patient, study and
series information from an existing DICOM file. If --series-from is specified, then the given DICOM file
is opened by img2dcm and all mandatory information down to the series level is imported. Note that this
includes patient, study and series information. In case of --study-from, the series information is
excluded. The following attributes are taken over:
Patient Level:
Patient's Name
Patient ID
Patient's Sex
Patient's Birth Date
Specific Character Set
Study Level:
Study Instance UID
Study Date
Study Time
Referring Physician's Name
Study ID
Accession Number
Series Level (only in case of option --series-from):
Series Instance UID
Series Number
Manufacturer
•
With the --insert-type2 and --invent-type1 options (both enabled per default), missing attributes (type
2 attributes) and/or missing attribute values (for type 1 attributes) are automatically added and
invented by img2dcm. Please note that these options are only evaluated if option --do-checks is enabled
(default). If the --no-checks options is enabled, no automatic attribute insertion will take place.
•
The --key option can be used to add further attributes to the DICOM output file. It is also possible to
specify sequences, items and nested attributes using the --key option. In these cases, a special 'path'
notation has to be used. Details on this path notation can be found in the documentation of dcmodify.
The --key option can be present more than once. The value part (after the '=') may be absent causing the
attribute to be set with zero length. Please be advised that the --key option is applied at the very
end, just before saving the DICOM file, so there is no value checking whatsoever.
UIDs
New Study and Series Instance UIDs are generated if necessary after applying the --study-from and
--series options. If Study Instance UID or Series Instance UID are not present after these steps, they
are newly generated, independently from each other. A contrary behavior is chosen for the SOP Instance
UID that one could expect to be taken over when using the --dataset-from option. This is not the case,
the SOP Instance UID is not copied to the new object. This should be the desirable behavior for most use
cases. However, if a certain SOP Instance UID should be inserted into the new object, the --key option
should be used.
Input Templates
For supporting the conversion into DICOM, img2dcm comes with some pre-defined templates which can be used
for the --dataset-from option (see sample files SC.dump and VLP.dump). These templates should be filled
with the desired values and then must be dumped (converted) to a DICOM file before actually being used
with img2dcm. Use dump2dcm to convert the dump to DICOM. Example:
dump2dcm SC.dump SC.dcm
For Ophthalmic Photography images, XML templates are provided (see sample file OP_template_utf_8.xml and
OP_template_latin_1.xml).
It is possible to use any DICOM file as a template. Please note that the complete DICOM dataset is
imported; hence, it should be assured that only attributes are present which should be part of the
constructed DICOM object. The SOP Class UID and the Pixel Data attributes (including attributes like
Rows, Columns etc.) are not copied but replaced by img2dcm during conversion.
Character Sets
When an input template is loaded using --dataset-from or --dataset-from-xml, the specific character set
of that template is used for the generated DICOM file. If the --study-from or --series-from options are
used additionally, img2dcm will try to convert the character set of these attributes to that of the
template, and will report an error if that is not possible. If the --study-from or --series-from options
are used without a template, the specific character set of this source is used for the generated DICOM
file. Any keys specified on the command line with the --key option are treated as raw bytes and override
any attributes that may already be present due to a template or study/series file. Therefore, care should
be taken to not specify a specific character set on the command line if one might be loaded from another
file. It is also the user's responsibility to ensure that attribute values specified on the command line
use the correct encoding, as no conversion will take place before the values are stored in the DICOM
file.
Input Plugins
The img2dcm application currently supports the JPEG and the BMP image format as input.
JPEG Input Plugin
For JPEG, the original JPEG from the source file is not decoded but extracted and slightly transformed
(e.g. JFIF header is cut off) to allow fast conversion of even big JPEG files without the need of
decoding and re-encoding. The JPEG plugin chooses the necessary output transfer syntax automatically
depending on the actual encoding of the data inside the JPEG file. Therefore, the following Transfer
Syntaxes (and their corresponding JPEG encodings) are used by the JPEG plugin:
•
JPEG Coding Process 1 Baseline, Lossy, Non-Hierarchical, Sequential, DCT, Huffman, 8 Bit SOP Class =
1.2.840.10008.1.2.4.50
•
JPEG Coding Process 2 (8-bit) and 4 (12-bit) Extended, Lossy, Non-Hierarchical, Sequential, DCT,
Huffman, 8/12 Bit SOP Class = 1.2.840.10008.1.2.4.51
•
JPEG Coding Process 10 (8-bit) and 12 (12-bit) Full Progression, lossy, Non-Hierarch., Progressive, DCT,
Huffman, 8/12 Bit SOP Class = 1.2.840.10008.1.2.4.55
Color and grayscale images are supported.
The support for the Extended JPEG Transfer Syntax can be disabled (--disable-ext option) as well as the
support for the (retired) Progressive JPEG Transfer Syntax (--disable-progr option).
JPEG lossless encoding as well as any arithmetic or hierarchical JPEG encoding modes are not supported by
the plugin.
JFIF (JPEG File Interchange Format) information facilitates optional APPn markers in a JPEG file. Many
digital cameras do not integrate such JFIF information into the JPEG output they create. For example,
JFIF contains information about the pixel aspect ratio of the compressed image. If you want the img2dcm
application to insist on a JFIF header in the JPEG stream, you can use the option --insist-on-jfif which
will abort if no JFIF information can be found. By default, missing JFIF information is ignored.
For DICOM it is kind of a 'gray zone', whether the integration of JFIF (or any other APPn) data into the
DICOM object's internal JPEG stream is allowed or not. However, the most reliable approach is to cut
those markers and their information off the JPEG stream. This approach is also taken by the img2dcm
application. By default, all APPn markers are cut off from the original JPEG stream. However, if you want
to keep other APPn markers than JFIF (e.g. EXIF information) inside the DICOM stream, the option --keep-
appn does the trick. It should also be slightly faster than cutting off APPn information, because it is
not necessary to scan the whole JPEG stream for such data. As stated before, JFIF information is always
removed by img2dcm. However, when using this option, the APP2 marker is retained, but img2dcm does not
create an equivalent ICC Profile (0028,2000) attribute.
BMP Input Plugin
img2dcm supports BMP as input format. However, so far only the most common BMP images are supported. In
particular, BMP images which use bit fields or run length encoding will be rejected. Such images are
uncommon. Input images will either be converted into a DICOM image with RGB color model and a bit depth
of 24, or into an image with MONOCHROME2 color model an 8 bits per pixel. There are no specific options
for fine-tuning BMP format conversion.
Output Plugins
The desired output SOP Class can be selected on the command line. Currently, export plugins for the
Secondary Capture Image SOP class (default, option -sc), the Multiframe Secondary Capture Image SOP
classes (option -nsc), Visible Light Photographic Image SOP class (option -vl), and the Ophthalmic
Photography Image SOP Classes (option -oph) are available. Please note that the first one is deprecated
according to the DICOM standard but is selected as a default because it is widely supported. Future
versions of img2dcm might provide further output plugins for other SOP Classes.
For the new Secondary Capture SOP classes, it is not possible to specify which specific SOP class should
be used for output. That is because these new SOP classes are differentiated from each other by color
depth (1/8/16) and the fact whether the image is black/white or color. That is why img2dcm decides during
conversion, which output SOP class is suitable for a given source image.
EXAMPLES
Here are some examples that show how the img2dcm application can be used.
1. img2dcm image.jpg out.dcm
Read JPEG file 'image.jpg', convert to the old Secondary Capture SOP class and save the result to
DICOM file 'out.dcm'. This is the easiest way of using img2dcm. Any type 1 and type 2 attributes
required for writing valid objects of this SOP class are inserted automatically.
2. img2dcm -i BMP image.bmp out.dcm
Same as above but tells img2dcm to read a BMP file instead of JPEG.
3. img2dcm image.jpg out.dcm -vlp -k 'PatientName=Bond^James'
Same as first example, but writes Visible Light Photographic Image object to 'out.dcm' and sets
PatientName to 'Bond^James' which otherwise would be left empty.
4. img2dcm image.jpg out.dcm --series-from template.dcm -k 'PatientName=Bond^James'
Same as 1), but imports patient/study/series information from DICOM file 'template.dcm'. Please note
that attribute PatientName will contain 'Bond^James' at the end, any value from 'template.dcm' will
be overwritten. That is, because the -k option is applied at the very end of the conversion pipeline
(see above).
5. img2dcm image.jpg out.dcm --no-checks
Same as 1), but does not perform any attribute checking and no type 1 and type 2 attribute insertion!
So in this case, an invalid DICOM object would be generated. This can be interesting if the output
file is not meant to be completed but will undergo further transformations, e.g. adding attributes
using dcmodify. Only use option --no-checks if you know what you are doing!
6. img2dcm image.jpg out.dcm --no-type1-invent
Same as 1), but does not insert missing type 1 attributes and/or their values. Type 2 attributes will
be inserted. Note that in this case it must be assured that all type 1 attributes are provided by
other means, i. e. by adding them with the --key option. Otherwise, img2dcm will report an error and
will stop converting.
7. img2dcm image.jpg out.dcm --keep-appn --insist-on-jfif
Same as 1), but takes over APPn information like EXIF into the DICOM object's resulting JPEG stream.
Further, --insist-on-jfif will force img2dcm to abort if no JFIF information is existent in the
source file.
LOGGING
The level of logging output of the various command line tools and underlying libraries can be specified
by the user. By default, only errors and warnings are written to the standard error stream. Using option
--verbose also informational messages like processing details are reported. Option --debug can be used to
get more details on the internal activity, e.g. for debugging purposes. Other logging levels can be
selected using option --log-level. In --quiet mode only fatal errors are reported. In such very severe
error events, the application will usually terminate. For more details on the different logging levels,
see documentation of module 'oflog'.
In case the logging output should be written to file (optionally with logfile rotation), to syslog (Unix)
or the event log (Windows) option --log-config can be used. This configuration file also allows for
directing only certain messages to a particular output stream and for filtering certain messages based on
the module or application where they are generated. An example configuration file is provided in
<etcdir>/logger.cfg.
COMMAND LINE
All command line tools use the following notation for parameters: square brackets enclose optional values
(0-1), three trailing dots indicate that multiple values are allowed (1-n), a combination of both means 0
to n values.
Command line options are distinguished from parameters by a leading '+' or '-' sign, respectively.
Usually, order and position of command line options are arbitrary (i.e. they can appear anywhere).
However, if options are mutually exclusive the rightmost appearance is used. This behavior conforms to
the standard evaluation rules of common Unix shells.
In addition, one or more command files can be specified using an '@' sign as a prefix to the filename
(e.g. @command.txt). Such a command argument is replaced by the content of the corresponding text file
(multiple whitespaces are treated as a single separator unless they appear between two quotation marks)
prior to any further evaluation. Please note that a command file cannot contain another command file.
This simple but effective approach allows one to summarize common combinations of options/parameters and
avoids longish and confusing command lines (an example is provided in file <datadir>/dumppat.txt).
ENVIRONMENT
The img2dcm utility will attempt to load DICOM data dictionaries specified in the DCMDICTPATH environment
variable. By default, i.e. if the DCMDICTPATH environment variable is not set, the file
<datadir>/dicom.dic will be loaded unless the dictionary is built into the application (default for
Windows).
The default behavior should be preferred and the DCMDICTPATH environment variable only used when
alternative data dictionaries are required. The DCMDICTPATH environment variable has the same format as
the Unix shell PATH variable in that a colon (':') separates entries. On Windows systems, a semicolon
(';') is used as a separator. The data dictionary code will attempt to load each file specified in the
DCMDICTPATH environment variable. It is an error if no data dictionary can be loaded.
FILES
<datadir>/SC.dump - Sample dump file for Secondary Capture images
<datadir>/VLP.dump - Sample dump file for Visible Light Photographic images
<datadir>/OP_template.xml - Sample XML template for Ophthalmic Photography images
SEE ALSO
dcm2pnm(1), dcmj2pnm(1), dump2dcm(1), dcmconv(1), dcmodify(1), dcm2xml(1)
COPYRIGHT
Copyright (C) 2007-2022 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.
Version 3.6.7 Mon Apr 15 2024 18:40:35 img2dcm(1)