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NAME

       dcmodify - Modify DICOM files

SYNOPSIS

       dcmodify [options] dcmfile-in...

DESCRIPTION

       dcmodify  is  a  tool that allows one 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 command line 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 behavior. 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

   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

         +fc   --create-file
                 create file format if file does not exist

       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
       backup input files:

               --backup
                 backup files before modifying (default)

         -nb   --no-backup
                 don't backup files (DANGEROUS)

       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

       error handling:

         -ie   --ignore-errors
                 continue with file, if modify error occurs

         -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 a 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
       dictionary 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 associated 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 behavior by using the -nmu option.

       If you generate new UID's with -gst, -gse or -gin, this will only affect the UID you chose
       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 behavior cannot be disabled.

CREATING NEW FILES

       Option  --create-file  lets  dcmodify  create a file if it does not already exist on disk.
       This can be used  in  order  to  create  files  from  scratch  by  performing  consecutive
       insertions  with  options  like --insert. This might especially become handy when creating
       query files for tools like findscu or movescu. In case no specific output transfer  syntax
       is  defined,  dcmodify  chooses Little Endian Explicit Uncompressed for output. Files that
       are newly created are always written as DICOM file format, i.e. option --write-dataset  is
       not  permitted together with --create. This way, at least the metaheader is written and no
       file with zero byte length is created in a case where no insertions are performed  in  the
       dcmodify call.

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 occurrences 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..fi

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  command  line;
       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 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 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  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.

COPYRIGHT

       Copyright (C) 2003-2014 by OFFIS e.V., Escherweg 2, 26121 Oldenburg, Germany.