This is the command gdcmanon that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
gdcmanon - Tool to anonymize a DICOM file.
gdcmanon [options] file-in file-out
gdcmanon [options] dir-in dir-out
The gdcmanon tool is an implementation of PS 3.15 / E.1 / Basic Application Level
Confidentiality Profile (Implementation of E.1.1 De-identify & E.1.2 Re-identify)
This tool is split into two very different operating mode:
· An implementation of PS 3.15, see -e and -d flags
· A dumb mode, see –dumb
Dumb mode and PS 3.15 do not work well together, you should really only use one type of
anonymization. In case of doubt, avoid using –dumb.
In order to use the PS 3.15 implementation (-d & -e flag), you'll need a certificate to do
de-identification operations, and the associated private key to do the re-identification
operation. If you are only doing a one-shot anonymization and do not need to properly
re-identify the DICOM file, you can safely discard the private key and only keep the
certificate. See OpenSSL refsection below for an example on how to generate the private
gdcmanon will exit early if OpenSSL was not configured/build properly into the library
(see GDCM_USE_SYSTEM_OPENSSL in cmake).
file-in DICOM input filename
file-out DICOM output filename
file-in DICOM input directory
file-out DICOM output directory
You need to specify at least one operating mode, from the following list (and only one):
-e --de-identify De-identify DICOM (default)
-d --re-identify Re-identify DICOM
--dumb Dumb mode anonymizer
Warning when operating in dumb mode, you need to also specify an operation to do, such as
'remove' or 'empty' a tag, see below the dumb mode 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.
--root-uid Root UID.
--resources-path Resources path.
-k --key Path to RSA Private Key.
-c --certificate Path to Certificate.
--des3 Triple DES.
--aes128 AES 128.
--aes192 AES 192.
--aes256 AES 256.
dumb mode options
--empty %d,%d DICOM tag(s) to empty
--remove %d,%d DICOM tag(s) to remove
--replace %d,%d,%s DICOM tag(s) to replace
print this help text and exit
print version information and exit
verbose mode (warning+error).
warning mode, print warning information
error mode, print error information
debug mode, print debug information
GDCM_ROOT_UID Root UID
GDCM_RESOURCES_PATH path pointing to resources files (Part3.xml, ...)
De-identification (anonymization, encrypt)
The only thing required for this operation is a certificate file (in PEM format).
$ gdcmanon --certificate certificate.pem -e original.dcm original_anonymized.dcm
You can use –asn1 option from gdcmdump to dump the generated DataSet as ASN1 structure
(see gdcmdump(1) for example).
The only thing required for this operation is a private key (in PEM format). It is
required that the private key used for the re-identification process, was the actual
private key used to generate the certificate file (certificate.pem) used during the
$ gdcmanon --key privatekey.pem -d original_anonymized.dcm original_copy.dcm
You can then check that original.dcm and original_copy.dcm are identical.
Multiple files caveat
It is very important to understand the following refsection, when anonymizing more than
one single file. When anonymizing multiple DICOM files, you are required to use the
directory input. You cannot call multiple time the gdcmanon command line tool. Indeed the
tool stores in memory during the process only a hash table of conversion so that each time
a particular value is found it get always replaced by the same de-identified value (think:
consistent Series Instance UID).
This functionality is not described in the DICOM standard. Users are advised that improper
use of that mode is not recommended, meaning that important tag can be
emptied/removed/replaced resulting in illegal/invalid DICOM file. Only use when you know
what you are doing. If you delete a Type 1 attribute, chance is that your DICOM file will
be not accepted in most DICOM third party viewer. Unfortunately this is often this mode
that is implemented in popular DICOM Viewer, always prefer what the DICOM standard
describes, and avoid the dumb mode.
The following example shows how to use dumb mode and achieve 5 operations at the same
· Empty the tag (0010,0010) Patient's Name,
· Empty the tag (0010,0020) Patient ID,
· Remove the tag (0010,0040) Patient's Sex
· Remove the tag (0010,1010) Patient's Age
· Replace the tag (0010,1030) Patient's Weight with the value '10'
You are required to check which DICOM attribute is Type 1 and Type 1C, before trying to
'Empty' or 'Remove' a particular DICOM attribute. For the same reason, you are required to
check what are valid value in a replace operation.
$ gdcmanon --dumb --empty 10,10 --empty 10,20 --remove 10,40 --remove 10,1010 --replace 10,1030,10 012345.002.050.dcm out.dcm
Multiple operation of –dumb mode can take place, just reuse the output of the previous
operation. Always use gdcmdump on the input and output file to check what was actually
achieved. You can use a diff program to check only what changed (see gdcmdiff(1) for
In some very rare cases, one would want to anonymize using the PS 3.15 mode so as to
take benefit of the automatic conversion of all content that could contain Patient
In the end all Patient related information has been removed and has been secretly
stored in the 0400,0500 DICOM attribute. However to make sure that no-one ever try to
break that security using brute-force algorithm, one want want to remove completely
this DICOM attribute. This will make the DICOM:
· Completely free of any Patient related information (as per PS 3.15 specification)
· Remove any mean of people to brute force attack the file to find out the identity
of the Patient
In this case one could simply do, as a first step execute the reversible anonymizer:
$ gdcmanon -c certificate.pem input.dcm anonymized_reversible.dcm
and now completely remove the DICOM attribute containing the secretly encrypted
Patient related information:
$ gdcmanon --dumb --remove 400,500 --remove 12,62 --remove 12,63 anonymized_reversible.dcm anonymized_irreversible.dcm
On most system you can have access to OpenSSL to generate the Private Key/Certificate
Generating a Private Key
Command line to generate a rsa key (512bit)
$ openssl genrsa -out CA_key.pem
Command line to generate a rsa key (2048bit)
$ openssl genrsa -out CA_key.pem 2048
Command line to generate a rsa key (2048bit) + passphrase
$ openssl genrsa -des3 -out CA_key.pem 2048
Generating a Certificate
From your previously generated Private Key, you can now generate a certificate in PEM (DER
format is currently not supported).
$ openssl req -new -key CA_key.pem -x509 -days 365 -out CA_cert.cer
Page to the DICOM Standard:
The DICOM Standard at the time of releasing gdcmanon is:
Direct link to PS 3.15-2008:
Certain attributes may still contains Protected Health Information (PHI) after an
anonymization step. This is typically the case for Patient's Address (0010,1040). The
reason is that this particular attribute is not supposed to be in the composite IODs in
the first place. DICOM Supp 142 includes it (however gdcmanon does not implement it).
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