GDCMCLEAN(1)

NAME
gdcmclean - Tool to clean a DICOM file.

SYNOPSIS

    gdcmclean [options] file-in file-out
    gdcmclean [options] dir-in  dir-out

DESCRIPTION

The gdcmclean tool is an cleaning tool.

PARAMETERS

    file-in   DICOM input filename

    file-out  DICOM output filename

or

    file-in   DICOM input directory

    file-out  DICOM output directory

OPTIONS

You need to :

  specific options

      -i --input                  DICOM filename / directory
      -o --output                 DICOM filename / directory
      -r --recursive              recursively process (sub-)directories.
         --continue               Do not stop when file found is not DICOM.

  Editing mode options

         --empty    %d,%d         DICOM tag(s) to empty
                    %d,%d,%s      DICOM private tag(s) to empty
                    %s            DICOM keyword/path(s) to empty
         --remove   %d,%d         DICOM tag(s) to remove
                    %d,%d,%s      DICOM private tag(s) to remove
                    %s            DICOM keyword/path(s) to remove
         --scrub    %d,%d         DICOM tag(s) to scrub
                    %d,%d,%s      DICOM private tag(s) to scrub
                    %s            DICOM keyword/path(s) to scrub
         --preserve %s            DICOM path(s) to preserve
         --preserve-missing-private-creator             Whether or not preserve private attributes with missing private creator.
         --preserve-group-length                        Whether or not preserve deprecated group length attributes (will not be re-computed).
         --preserve-illegal                             Whether or not preserve illegal attributes (eg. group 0003...).

  general options

      -h   --help
             print this help text and exit

      -v   --version
             print version information and exit

      -V   --verbose
             verbose mode (warning+error).

      -W   --warning
             warning mode, print warning information

      -E   --error
             error mode, print error information

      -D   --debug
             debug mode, print debug information

TYPICAL USAGE

  Editing mode

This functionality is not described in the DICOM standard.

The following example shows how to use editing mode and achieve multiple operations at the same time:

    • Preserve illegal attributes (removed by default),

    • Empty any 'PN' attributes anywhere in the hierarchy tree, but preserve the DICOM attribute value only at location "0010,0010",

    • Empty the tag (0010,0020) Patient ID, (only if keyword is know internally),

    • Empty the tag (0070,0084),

    • Remove the private attributes: (0029,20, SIEMENS MEDCOM HEADER) / (0033,02,MITRA OBJECT UTF8 ATTRIBUTES 1.0) / (0043,2a,GEMS_PARM_01). Since (0033,02,MITRA OBJECT UTF8 ATTRIBUTES 1.0) is defined internally in the private dictionary with Value Representation = PN, this attribute will be skipped (since redundant).

    • Scrub the private attributes: (0029,10,SIEMENS CSA HEADER) / (0029,20,SIEMENS CSA HEADER) / (700d,08,TOSHIBA_MEC_MR3) / (0029,90,PMTF INFORMATION DATA)

    $ gdcmclean \
        --recursive --continue \
        --preserve-illegal \
        --empty PN --preserve /0010,0010 \
        --empty PatientID --empty "0070,0084" \
        --remove "0029,20,SIEMENS MEDCOM HEADER" --remove "0033,02,MITRA OBJECT UTF8 ATTRIBUTES 1.0" --remove "0043,2a,GEMS_PARM_01" \
    	--scrub "0029,10,SIEMENS CSA HEADER" --scrub "0029,20,SIEMENS CSA HEADER" \
    	--scrub "700d,08,TOSHIBA_MEC_MR3" \
    	--scrub "0029,90,PMTF INFORMATION DATA" --scrub "0029,90,TOSHIBA_MEC_MR3" \
        input_folder output_folder

  DICOM Path

For ease of use on shell cmmand the syntax allow for the '/' separator in the DICOM Path notation. So the following is valid

    "/0040,0100/1/0040,0006"

However Private Creator can use all of Value Representation LO definition. So in some case you will be required to use backslash as separator (since illegal in VR:LO):

    "\\4109,2,Applicare/Centricity Radiology Web/Version 1.0"

  Safe Private Attributes

It is currently not possible to empty/remove any private attribute listed in the Safe Private Attributes table at:

https://dicom.nema.org/medical/dicom/current/output/chtml/part15/sect_E.3.10.html#table_E.3.10-1

SEE ALSO

gdcmanon(1), gdcmdump(1), gdcmdiff(1)

AUTHOR

Mathieu Malaterre
    Main developer

COPYRIGHT
Copyright © 2006, 2011 Mathieu Malaterre