gdcmclean - Tool to clean a DICOM file.

MathieuMalaterre
           Main developer

       Copyright © 2006, 2011 Mathieu Malaterre

GDCM 3.0.24                                        03/08/2025                                       GDCMCLEAN(1)

       The gdcmclean tool is an cleaning tool.

       gdcmclean - Tool to clean a DICOM file.

       You need to :

   specificoptions
             -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.

   Editingmodeoptions
                --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...).

   generaloptions
             -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

           file-in   DICOM input filename

           file-out  DICOM output filename

       or

           file-in   DICOM input directory

           file-out  DICOM output directory

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

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

Editingmode
       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

   DICOMPath
       For ease of use on shell command 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"

   SafePrivateAttributes
       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