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dcmodify

Langue: en

Version: 252540 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

NAME

dcmodify - Modify DICOM files

SYNOPSIS

 
 dcmodify [options] [dcmfile-in...]
 

DESCRIPTION

dcmodify is a tool that allows to modify, insert and delete tags in DICOM files. Sequences and tags with a value multiplicity > 1 are also supported. Currently dcmodify is not able to remove or insert single items. Metaheader information and a tags VR can't be modified directly through dcmodify, too. 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 tags VR is set to UN and an empty value. Please insert these tags into the dictionary to avoid this.

dcmodify is able to work with so-called tag paths to describe tags in sequences. The 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. You can either specify the tag directly as (0010,0010) or through the dictionary name PatientsName. The '*' denotes that you can repeat sequence statements to access deeper levels in DICOM files (see EXAMPLES section).

There are some issues concerning modifications 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
 
   -d   --debug
          debug mode, print debug information
 
   -v   --verbose
          verbose mode, print verbose output
 
   -ie  --ignore-errors
          continue with file, if modify error occurs
 

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 options:
 
   -i   --insert-tag  "tag-path=value"
          insert (or overwrite) tag at position t
          with value v
 
 modify mode options:
 
   -m   --modify-tag  "[t]ag-path=[v]alue"
          modify tag at position t to value v
 
   -ma  --modify-all-tags  "[t]ag=[v]value"
          modify ALL matching tags t in file to value v
 
 erase mode options:
 
   -e   --erase-tag  "[t]ag-path"
          erase tag at position t
 
   -ea  --erase-all-tags  "[t]ag"
          erase ALL matching tags t in file
 
 uid options:
 
   -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
           don't update metaheader UIDs
           UIDs in the metaheader won't be changed,
           if related UIDs in dataset are modified
           via options -m, -i or -ma
 

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 points you've got to consider when working with private tags. 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 dcmdata/docs/datadict.txt for details). If it's not listed, dcmodify will insert it with VR=UN and empty value. Please note, that the usage of option '-u' will change the VR from UN to OB when saving.

If you've got your private tag in the dictionary, dcmodify acts as follows: When it finds a reservation in the tags enclosing dataset, whose private creator matches, insertion is done with the VR found in dictionary and the value, you entered at commandline. But if the private creator doesn't match the one found in dictionary, dcmodify inserts the tag with VR Unknown (UN) and an empty value.

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 tags VR.

If you wish to change a private tags value and VR, because you just added this tag to your dictionary e.g., 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).

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 consistence between reservations and their pending private tags.

For deletion of private non-reservation tags there are no special issues.

CHANGING UIDs

dcmodify 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 seperately. 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 can not be disabled.

EXAMPLES

 
 -i  --insert-tag:
 
       dcmodify -i "(0010,0010)=A Name" file.dcm
       Inserts the PatientsName 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].PatientsName=Another Name" *.dcm
       Inserts PatientsName 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").
 
 -m  --modify-tag:
       dcmodify -m "(0010,0010)=A Name" file.dcm
       Changes tag (0010,0010) on 1st level to "A Name".
 
       This option also allows longer tag paths as demonstrated
       above for -i.
 
 -ma --modify-all-tags:
       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-tag:
       dcmodify -e "(0010,0010)" *.dcm
       Erases tag (0010,0010) in all *.dcm files at 1st level.
       Note: You can also erase whole sequences by using this
       option with a sequence tag, but in this version it's not
       possible to delete a single item in a sequence.
 
       This option also allows longer tag paths as demonstrated
       above for -i.
 
 -ea --erase-all-tags:
       dcmodify -ea "(0010,0010)" *.dcm
       Same as -e, but also searches in sequences and items.
 
 -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 adjustet 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.
 

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) 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 share/data/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 <PREFIX>/lib/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. 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 (C) 2003-2005 by Kuratorium OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.

TWELVE E, FIVE R,
SIX F, FIVE S,
THREE H, SIX T,
SEVEN I, THREE U,
TWO L, SIX V,
TWO N, FOUR W,
FIVE O, FOUR X.

-- Sallows, Lee