dcmconv: Convert DICOM file encoding

SYNOPSIS

dcmconv [options] dcmfile-in dcmfile-out

DESCRIPTION

The dcmconv utility reads a DICOM file (dcmfile-in), performs an encoding conversion and writes the converted data to an output file (dcmfile-out).

PARAMETERS

dcmfile-in   DICOM input filename to be converted ("-" for stdin)

dcmfile-out  DICOM output filename to write to ("-" for stdout)

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
-l --log-level [l]evel: string constant: (fatal, error, warn, info, debug, trace) use level l for the logger
-l --log-config [f]ilename: string: use config file f for the logger

input options

+f --read-file: read file format or data set (default)
+fo --read-file-only: read file format only
-f --read-dataset: read data set without file meta information input transfer syntax:
-t= --read-xfer-auto: use TS recognition (default)
-td --read-xfer-detect: ignore TS specified in the file meta header
-te --read-xfer-little: read with explicit VR little endian TS
-tb --read-xfer-big: read with explicit VR big endian TS
-ti --read-xfer-implicit: read with implicit VR little endian TS parsing of file meta information:
+ml --use-meta-length: use file meta information group length (default)
-ml --ignore-meta-length: ignore file meta information group length parsing of odd-length attributes:
+ao --accept-odd-length: accept odd length attributes (default)
+ae --assume-even-length: assume real length is one byte larger handling of explicit VR:
+ev --use-explicit-vr: use explicit VR from dataset (default)
-ev --ignore-explicit-vr: ignore explicit VR (prefer data dictionary) handling of non-standard VR:
+vr --treat-as-unknown: treat non-standard VR as unknown (default)
-vr --assume-implicit: try to read with implicit VR little endian TS handling of undefined length UN elements:
+ui --enable-cp246: read undefined len UN as implicit VR (default)
-ui --disable-cp246: read undefined len UN as explicit VR handling of defined length UN elements:
-uc --retain-un: retain elements as UN (default)
+uc --convert-un: convert to real VR if known handling of private max-length elements (implicit VR):
-sq --maxlength-dict: read as defined in dictionary (default)
+sq --maxlength-seq: read as sequence with undefined length handling of wrong delimitation items:
-rd --use-delim-items: use delimitation items from dataset (default)
+rd --replace-wrong-delim: replace wrong sequence/item delimitation items handling of illegal undefined length OB/OW elements:
-oi --illegal-obow-rej: reject dataset with illegal element (default)
+oi --illegal-obow-conv: convert undefined length OB/OW element to SQ handling of VOI LUT Sequence with OW VR and explicit length:
-vi --illegal-voi-rej: reject dataset with illegal VOI LUT (default)
+vi --illegal-voi-conv: convert illegal VOI LUT to SQ handling of explicit length pixel data for encaps. transfer syntaxes:
-pe --abort-expl-pixdata: abort on explicit length pixel data (default)
+pe --use-expl-pixdata: use explicit length pixel data general handling of parser errors:
+Ep --ignore-parse-errors: try to recover from parse errors
-Ep --handle-parse-errors: handle parse errors and stop parsing (default) other parsing options:
+st --stop-after-elem [t]ag: "gggg,eeee" or dictionary name: stop parsing after element specified by t automatic data correction:
+dc --enable-correction: enable automatic data correction (default)
-dc --disable-correction: disable automatic data correction bitstream format of deflated input:
+bd --bitstream-deflated: expect deflated bitstream (default)
+bz --bitstream-zlib: expect deflated zlib bitstream

processing options

+U8 --convert-to-utf8: convert all element values that are affected by Specific Character Set (0008,0005) to UTF-8
+L1 --convert-to-latin1: convert affected element values to ISO 8859-1
+A7 --convert-to-ascii: convert affected element values to 7-bit ASCII
+C --convert-to-charset [c]harset: string: convert affected element values to the character set specified by the DICOM defined term c
-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:
-ig --no-invalid-groups: remove elements with invalid group number

output options

+Fm --write-new-meta-info: write file format with new meta information (default)
+F --write-file: write file format
-F --write-dataset: write data set without file meta information output transfer syntax:
+t= --write-xfer-same: write with same TS as input (default)
+te --write-xfer-little: write with explicit VR little endian TS
+tb --write-xfer-big: write with explicit VR big endian TS
+ti --write-xfer-implicit: write with implicit VR little endian TS
+td --write-xfer-deflated: write with deflated explicit VR little endian TS
+tg --write-xfer-ge: write private GE implicit VR little endian with big endian pixel data TS (non-standard) post-1993 value representations:
+u --enable-new-vr: enable support for new VRs (UN/UT) (default)
-u --disable-new-vr: disable support for new VRs, convert to OB 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
+eo --write-oversized: write oversized explicit length sequences and items with undefined length (default)
-eo --abort-oversized: abort on oversized explicit sequences/items data set trailing padding (not with --write-dataset):
-p= --padding-retain: do not change padding (default if not --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 deflate compression level (only with --write-xfer-deflated):
+cl --compression-level [l]evel: integer (default: 6): 0=uncompressed, 1=fastest, 9=best compression

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 dcmconv 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.

Depending on the command line options specified, the dcmconv utility will attempt to load character set mapping tables. This happens when DCMTK was compiled with the oficonv library (which is the default) and the mapping tables are not built into the library (default when DCMTK uses shared libraries).

The mapping table files are expected in DCMTK's < datadir>. The DCMICONVPATH environment variable can be used to specify a different location. If a different location is specified, those mapping tables also replace any built-in tables.