dcmodify(1) OFFIS DCMTK dcmodify(1)NAMEdcmodify - Modify DICOM files
SYNOPSISdcmodify [options] dcmfile-in...
DESCRIPTIONdcmodify is a tool that allows to modify, insert and delete tags and
items in DICOM files. Sequences and tags with a value multiplicity > 1
are also supported. Metaheader information and the tag's VR can not be
modified directly by dcmodify at this time. In addition to tag
modifications, dcmodify makes available some input options - forcing
dcmodify to handle its input files as the user specifies - and output
options to control the output format of the resulting files.
In case multiple modifications have to be performed, dcmodify does the
modifications in the same order as they appear on the command line.
Please note that dcmodify does not check whether a given value matches
its value representation (VR). Usually, an error message is printed but
generally the user should take care of the right VR usage.
If dcmodify doesn't know the tag it should insert, then the tag's VR is
set to UN and the value provided on commandline is interpreted as being
a series of hexadecimal numbers (like they are provided for VR=OB).
Please insert these tags into the dictionary to avoid this behaviour.
Also, specifying the -iun option, it is possible to force dcmodify to
leave UN values untouched. Using option -u lets dcmodify saving all
VR=UN attributes as OB.
dcmodify is able to work with so-called tag paths to access tags in
sequences. The (pseudo-formalized) syntax is
{sequence[item-no].}*element
where 'sequence' is a sequence tag like (0008,1111) or a dictionary
name for a tag. 'item-no' describes the item number to be accessed
(counting from zero). 'element' defines the target tag to work on. A
tag can either be specified directly as (0010,0010) or through the
corresponding dictionary name 'PatientName'. The '*' denotes that you
can repeat sequence statements to access deeper levels in DICOM files
(see EXAMPLES section). For 'item-no', also a wildcard character '*'
can be used selecting all items in surrounding sequence (see section
WILDCARDS below).
When inserting tag paths consisting of multiple nodes (i.e. not a
single element) using the -i option, any missing path elements (items,
sequences, leaf elements) are inserted automatically when missing. That
does not work for item wildcards: When no single item exists in the
surrounding sequence dcmodify of course can't decide, how many items
should be generated. However, if specifying an item number like '5',
all 6 items (counted from zero) can be (and are) automatically
generated in insert mode. If already 2 items would exist, the rest (4)
would be inserted.
Please note that there are some issues concerning the modification of
private tags (see PRIVATE TAGS section) and for changing UIDs (CHANGING
UIDs section).
PARAMETERS
dcmfile-in DICOM input filename(s) to be modified
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
-ie--ignore-errors
continue with file, if modify error occurs
-nb--no-backup
don't backup files (DANGEROUS)
input options
input file format:
+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 odd-length attributes:
+ao --accept-odd-length
accept odd length attributes (default)
+ae --assume-even-length
assume real length is one byte larger
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
insert mode:
-i--insert "[t]ag-path=[v]alue"
insert (or overwrite) path at position t with value v
-if--insert-from-file "[t]ag-path=[f]ilename"
insert (or overwrite) path at position t with value from file f
-nrc--no-reserv-check
do not check private reservations
modify mode:
-m--modify "[t]ag-path=[v]alue"
modify tag at position t to value v
-mf--modify-from-file "[t]ag-path=[f]ilename"
modify tag at position t to value from file f
-ma--modify-all "[t]ag=[v]alue"
modify ALL matching tags t in file to value v
erase mode:
-e--erase "[t]ag-path"
erase tag/item at position t
-ea--erase-all "[t]ag"
erase ALL matching tags t in file
-ep--erase-private
erase ALL private data from file
unique identifier:
-gst--gen-stud-uid
generate new Study Instance UID
-gse--gen-ser-uid
generate new Series Instance UID
-gin--gen-inst-uid
generate new SOP Instance UID
-nmu--no-meta-uid
do not update metaheader UIDs if related
UIDs in the dataset are modified
other processing options:
-imt--ignore-missing-tags
treat 'tag not found' as success
when modifying or erasing in files
-iun--ignore-un-values
do not try writing any values to
elements having VR of UN
output options
output file format:
+F --write-file
write file format (default)
-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
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:
+le --length-explicit
write with explicit lengths (default)
-le--length-undefined
write with undefined lengths
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
PRIVATE TAGS
There are some issues you have to consider when working with private
tags. However, the insertion or modification of a reservation tag
(gggg,00xx) should always work.
Insertions
If you wish to insert a private tag (not a reservation with gggg,00xx),
be sure, that you've listed it in your dictionary (see
<docdir>/datadict.txt for details). If it's not listed, dcmodify will
insert it with VR=UN. Also, for some cases insertion may even fail for
some values.
If you've got your private tag in the dictionary, dcmodify acts as
follows: When it finds a reservation in the tag's enclosing dataset,
whose private creator matches, insertion is done with the VR found in
the dictionary and the value given on command line. But if the private
creator doesn't match or none is set, dcmodify will return with an
error. If a private tag should be inserted regardless whether a
reservation does not exist, the option -nrc can be used, forcing an
insertion. However, the VR is set to UN then, because the tag then
cannot be found in the dictionary.
See description above how inserting values into elements with unknown
VR are handled.
Modifications
If you modify a private tags value, dcmodify won't check its VR against
the dictionary. So please be careful to enter only values that match
the tag's VR.
If you wish to change a private tags value and VR, because you just
added this tag to your dictionary, you can delete it with dcmodify and
re-insert it. Then dcmodify uses your dicitionary entry to determine
the right VR (also see subsection insertions).
Also, see description above how inserting values into elements with
unknown VR are handled.
Deletions
When you use dcmodify to delete a private reservation tag, please note
that dcmodify won't touch the private tags that are under this
reservation. The user is forced to handle the consistency between
reservations and their pending private tags.
For the deletion of private non-reservation tags there are no special
issues.
CHANGING UIDSdcmodify will automatically correct 'Media Storage SOP Class UID' and
'Media Storage SOP Instance UID' in the metaheader, if you make changes
to the related tags in the dataset ('SOP Class UID' and 'SOP Instance
UID') via insert or modify mode options. You can disable this behaviour
by using the -nmu option.
If you generate new UID's with -gst, -gse or -gin, this will only
affect the UID you choosed to generate. So if you use -gst to generate
a new 'Study Instance UID', then 'Series Instance UID' and 'SOP
Instance UID' will not be affected! This gives you the possibility to
generate each value separately. Normally, you would also modify the
'underlying' UIDs. As a disadvantage of this flexibility, the user has
to assure, that when creating 'new' DICOM files with new UIDs with
dcmodify, other UIDs have to be updated by the user as necessary.
When choosing the -gin option, the related metaheader tag ('Media
Storage SOP Instance UID') is updated automatically. This behaviour
cannot be disabled.
ELEMENT VALUES FROM FILE
In order to read the element value from a file instead of specifying it
on the command line, option -mf and -if can be used. Please note that
for OW elements, the data is expected to be little endian ordered and
will be swapped if necessary. The file size should always be an even
number of bytes, i.e. no automatic padding is performed.
WILDCARDSdcmodify also permits the usage of a wildcard character '*' for item
numbers in path expressions, e.g. 'ContentSequence[*].CodeValue'
selects all 'Code Value' attributes in all items of the
ContentSequence. Using a wildcard is possible for all basic operations,
i.e. modifying -m, inserting -i and -e options which makes it, together
with the automatic creation of intermediate path nodes a powerful tool
for construction and processing complex datasets.
The options -ma and -ea for modifying or deleting all occurences of a
DICOM element based on its tag do not accept any wildcards but only
work on single elements (i.e. a single dictionary name or tag key).
EXAMPLES-i --insert:
dcmodify-i "(0010,0010)=A Name" file.dcm
Inserts the PatientName tag into 'file.dcm' at 1st level.
If tag already exists, -i will overwrite it! If you want to
insert an element with value multiplicity > 1 (e.g. 4) you
can do this with: dcmodify-i "(0018,1310)=1\2\3\4"
dcmodify-i "(0008,1111)[0].PatientName=Another Name" *.dcm
Inserts PatientName tag into the first item of sequence
(0008,1111). Note that the use of wildcards for files is
possible. You can specify longer tag paths, too (e.g.
"(0008,1111)[0].(0008,1111)[1].(0010,0010)=A Third One").
If any part of the path, e.g. the sequence or the item "0"
does not exist, it is automatically inserted by dcmodify.
dcmodify-i "(0008,1111)[*].PatientName=Another Name" *.dcm
Inserts PatientName tag into _every_ item of sequence
(0008,1111). Note that the use of wildcards for files is
possible. You can specify longer tag paths, too (e.g.
"(0008,1111)[*].(0008,1111)[*].(0010,0010)=A Third One").
-if --insert-from-file:
dcmodify-if "PixelData=pixel.raw" file.dcm
Inserts the content of file 'pixel.raw' into the PixelData element
of 'file.dcm'. The contents of the file will be read as is.
OW data is expected to be little endian ordered and will be
swapped if necessary. No checks will be made to ensure that the
amount of data is reasonable in terms of other attributes such as
Rows or Columns.
-m --modify:
dcmodify-m "(0010,0010)=A Name" file.dcm
Changes tag (0010,0010) on 1st level to "A Name".
This option also permits longer tag paths as demonstrated
above for -i. If the leaf element or any intermediate
part of the path does not exist, it is not inserted as it
would be if using the '-i' option.
dcmodify-m "(0010,0010)=A Name" -imt file.dcm
Changes tag (0010,0010) on 1st level to "A Name". Due to the
given option '-imt', success is returned instead of "tag not found",
if the element/item (or any intermediate node in a longer path) does
not exist.
Note that for the '-m' option the last node in the path must be
a leaf element, i.e. not a sequence or an item.
-mf --modify-from-file:
dcmodify-mf "PixelData=pixel.raw" file.dcm
Does the same as -if in case there was already a PixelData element
in 'file.dcm'. Otherwise nothing is changed.
-ma --modify-all:
dcmodify-ma "(0010,0010)=New Name" file.dcm
Does the same as -m but works on all matching tags found in
'file.dcm'. Therefore, it searches the whole dataset including
sequences for tag (0010,0010) and changes them to "New Name"
-e --erase:
dcmodify-e "(0010,0010)" *.dcm
Erases tag (0010,0010) in all *.dcm files at 1st level.
This option also allows longer tag paths as demonstrated
above for -i.
dcmodify-e "(0010,0010)" -imt *.dcm
Erases tag (0010,0010) in all *.dcm files at 1st level. Due to the
given option '-imt', success is returned instead of "tag not found",
if the element/item (or any intermediate node in a longer path) does
not exist.
-ea --erase-all:
dcmodify-ea "(0010,0010)" *.dcm
Same as -e, but also searches in sequences and items.
-ep --erase-private:
dcmodify-ep *.dcm
Deletes all private tags (i.e. tags having an odd group number) from
all files matching *.dcm in the current directory.
-gst --gen-stud-uid:
dcmodify-gst file.dcm
This generates a new value for the StudyInstanceUID
(0020,000d). Other UIDs are not modified!
-gse --gen-ser-uid:
dcmodify-gse file.dcm
This generates a new value for the SeriesInstanceUID
(0020,000e). Other UIDs are not modified!
-gin --gen-inst-uid:
dcmodify-gin file.dcm
This command generates a new value for the SOPInstanceUID
(0008,0018). The corresponding MediaStorageSOPInstanceUID
(0002,0003) is adjusted to the new value automatically.
Please note that it's not possible to avoid this metaheader
update via the -nmu option.
-nmu --no-meta-uid:
dcmodify-m "SOPInstanceUID=[UID]" -nmu *.dcm
This will modify the SOPInstanceUID to the given [UID],
but -nmu avoids, that dcmodify adjusts the
MediaStorageSOPInstanceUID in the metaheader, too.
ERROR HANDLINGdcmodify tries executing each modify operation given on command line:
If one returns an error, the others are being performed anyway. However
in case of any error, the modified file is not saved, unless the
--ignore-errors option is specified. If that option is selected,
dcmodify also continues modifying further files specified on
commandline; otherwise dcmodify exits after the first file that had
modification errors.
If the --ignore-missing-tags option is enabled, any modify or erase
operations (i.e. not --insert) that fails because of a non-existing tag
is treated as being successful. That does make sense if someone wants
to be sure that specific tags are not present in the file or that - if
they exist - that they are set to a specific value.
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
behaviour 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 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 dcmodify 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 behaviour 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.
COPYRIGHT
Copyright (C) 2003-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg,
Germany.
Version 3.6.0 6 Jan 2011 dcmodify(1)
