dcmodify (1) - Linux Manuals

dcmodify: Modify DICOM files

Command to display dcmodify manual in Linux: $ man 1 dcmodify

NAME

dcmodify - Modify DICOM files

SYNOPSIS

dcmodify [options] dcmfile-in...

DESCRIPTION

dcmodify 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 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 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.

WILDCARDS

dcmodify 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 HANDLING

dcmodify 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.