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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.

COPYRIGHT

       Copyright (C) 2003-2010 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.