dicognito

Dicognito is a Python module and command-line utility that anonymizes DICOM files.

Use it to anonymize one or more DICOM files belonging to one or any number of patients. Objects will remain grouped in their original patients, studies, and series.

Anonymization causes significant elements, such as identifiers, names, and addresses, to be replaced by new values. Dates and times will be shifted into the past, but their order will remain consistent within and across the files.

The package is available on pypi and can be installed from the command line by typing

pip install dicognito

Anonymizing from the command line

Once installed, a dicognito command will be added to your Python scripts directory. You can run it on entire filesystem trees or a collection of files specified by glob like so:

# Recurse down the filesystem, anonymizing all found DICOM files.
# Anonymized files will be placed in out-dir, named by new SOP
# instance UID.
dicognito --output-directory out-dir .

# Anonymize all files in the current directory with the dcm extension
# (-o is an alias for --output-directory).
dicognito -o out-dir *.dcm

# Anonymize all files in the current directory with the dcm extension
# but overwrite the original files.
# Note: repeatedly anonymizing the same files will cause date elements
# to  move farther into the past.
dicognito --in-place *.dcm

Get more help via dicognito --help.

Anonymizing from within Python

To anonymize a bunch of DICOM objects from within a Python program, import the objects using pydicom and use the Anonymizer class:

import pydicom
import dicognito.anonymizer

anonymizer = dicognito.anonymizer.Anonymizer()

for original_filename in ("original1.dcm", "original2.dcm"):
    with pydicom.dcmread(original_filename) as dataset:
        anonymizer.anonymize(dataset)
        dataset.save_as("clean-" + original_filename)

Use a single Anonymizer on datasets that might be part of the same series, or the identifiers will not be consistent across objects.

Additional (even custom) element handlers can be added to the Anonymizer via add_element_handler to augment or override builtin behavior.

Exactly what does dicognito do?

Using the default settings, dicognito will

• Add "DICOGNITO" to DeidentificationMethod
• Remove BranchOfService
• Remove MedicalRecordLocator
• Remove MilitaryRank
• Remove Occupation
• Remove PatientInsurancePlanCodeSequence
• Remove PatientReligiousPreference
• Remove PatientTelecomInformation
• Remove PatientTelephoneNumbers
• Remove ReferencedPatientPhotoSequence
• Remove ResponsibleOrganization
• Replace AccessionNumber with anonymized values
• Replace CountryOfResidence with anonymized values
• Replace CurrentPatientLocation with ""
• Replace FillerOrderNumberImagingServiceRequest with anonymized values
• Replace FillerOrderNumberImagingServiceRequestRetired with anonymized values
• Replace FillerOrderNumberProcedure with anonymized values
• Replace InstitutionAddress with anonymized values (only if replacing matching InstitutionName element)
• Replace InstitutionName with anonymized values
• Replace InstitutionalDepartmentName with "RADIOLOGY"
• Replace IssuerOfPatientID with "DICOGNITO"
• Replace OtherPatientIDs with anonymized values
• Replace PatientAddress with anonymized values
• Replace PatientID with anonymized values
• Replace PerformedProcedureStepID with anonymized values
• Replace PlacerOrderNumberImagingServiceRequest with anonymized values
• Replace PlacerOrderNumberImagingServiceRequestRetired with anonymized values
• Replace PlacerOrderNumberProcedure with anonymized values
• Replace RegionOfResidence with anonymized values
• Replace RequestedProcedureID with anonymized values
• Replace RequestingService with ""
• Replace ScheduledProcedureStepID with anonymized values
• Replace StationName with anonymized values
• Replace StudyID with anonymized values
• Replace all DA elements with anonymized values that precede the originals
• Replace all DT elements with anonymized values that precede the originals
• Replace all PN elements with anonymized values
• Replace all TM elements with anonymized values that precede the originals (only if replacing matching DA element)
• Replace all UI elements with anonymized values
• Replace private "MITRA LINKED ATTRIBUTES 1.0" element "Global Patient ID" with anonymized values
• Set PatientIdentityRemoved to "YES" if BurnedInAnnotation is "NO"

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Logo: Remixed from Radiology by priyanka and Incognito by d͡ʒɛrmi Good from the Noun Project.