GDCMCLEAN(1)

💖 NAME 💖

okay so bestie, meet gdcmclean — the main character of this GDCMCLEAN(1) page, living under the DICOM Manipulation umbrella. It is literally the tool to clean a DICOM file. cleaning era ✨

🌸 SYNOPSIS 🌸

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

🧼 DESCRIPTION 🧼

the gdcmclean tool is a cleaning tool. That’s the whole vibe: DICOM goes in, cleaning happens. 🫧

🎀 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 — DICOM tag(s) to empty. the menu is:
  • %d,%d — DICOM tag(s) to empty
  • %d,%d,%s — DICOM private tag(s) to empty
  • %s — DICOM keyword/path(s) to empty
• --remove — DICOM tag(s) to remove. same little menu:
  • %d,%d — DICOM tag(s) to remove
  • %d,%d,%s — DICOM private tag(s) to remove
  • %s — DICOM keyword/path(s) to remove
• --scrub — DICOM tag(s) to scrub. yup, the menu again:
  • %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 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"

🌸 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

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this page is from GDCM 3.0.24, dated 12/25/2025 — go clean something cute, bestie 💅✨