dcm2dir

Dcm2dir recursively scans a given root folder for DICOM files, extracts relevant metadata, and organizes the files into a structured output folder.

Description

This Python script recursively scans a given root folder for DICOM files, extracts relevant metadata, and organizes the files into a structured output folder. The folder structure is customizable using placeholders for different DICOM tags. Additionally, a CSV report is generated with details of all processed DICOM series. The tool also supports anonymizing DICOM files with a default anonymization configuration and allows providing custom anonymization actions.

Features

• Recursively scans and organizes DICOM files.
• Supports customizable folder structures.
• Utilizes multi-threading for faster processing.
• Generates a CSV report listing all series metadata.
• Handles missing DICOM tags gracefully.
• Anonymizes DICOM files based on a default anonymization configuration.

Installation

From PyPI

Install the package directly from PyPI using pip:

pip install dcm2dir

From Source Code

Clone the repository and install the dependencies manually:

git clone https://github.com/HoenikkerPerez/dcm2dir.git
cd dcm2dir
pip install -e .

Usage

Run dcm2dir with the following command-line arguments:

dcm2dir -i <input_folder> -o <output_folder> [-r <csv_report>] [-f <folder_structure>] [-a]

Arguments:

• -i, --input (required): Path to the root folder containing DICOM files.
• -o, --output (required): Path to the destination folder where organized files will be stored.
• -r, --report (optional): Path to save the generated CSV report.
• -f, --folder-structure (optional): Custom folder structure using placeholders. See "Folder Structure" section.
• -a, --anonymize (optional): Enable anonymization of DICOMs.
• -c, --custom_anon_config (optional): Path to the JSON file specifying anonymization rules.

Example Usage:

dcm2dir -i ./dicoms -o ./organized -r report.csv -f "%i/%x_%t/%s_%d"

Folder Structure:

The folder structure can be customized using placeholders for different DICOM tags. The following placeholders are available:

• %a: Antenna (coil) name
• %b: Basename
• %c: Comments
• %d: Description
• %e: Echo number
• %f: Folder name
• %g: Accession number
• %i: ID of patient
• %j: SeriesInstanceUID
• %k: StudyInstanceUID
• %m: Manufacturer
• %n: Name of patient
• %o: MediaObjectInstanceUID
• %p: Protocol
• %r: Instance number
• %s: Series number
• %t: Exam date
• %u: Acquisition number
• %v: Vendor
• %x: Study ID
• %z: Sequence name

If -f is not provided, the default structure is used:

"-f %i/%x_%t/%s_%d"

which corresponds to:

/path/to/output/
├── PatientID1/
│   ├── StudyID1_20250101/
│   │   ├── SeriesNumber1_SeriesDescription/
│   │   │   └── file1.dcm
│   │   │   └── file2.dcm
├── PatientID2/
│   ├── StudyID2_20250102/
│   │   ├── SeriesNumber2_SeriesDescription/
│   │   │   └── file3.dcm

Anonymization

The -a or --anonymize flag enables anonymization of DICOM files. When this flag is provided, the tool uses a default anonymization configuration to process the DICOM files. The configuration specifies how to handle sensitive DICOM tags, such as removing or replacing their values.

Default Anonymization Configuration

The default anonymization configuration is embedded in the tool and includes rules for handling sensitive DICOM tags. For example:

• Replace patient names and IDs with anonymized values.
• Remove sensitive metadata such as institution names and addresses.
• Retain essential metadata such as study and series UIDs.

For a detailed list of anonymization actions for specific DICOM tags, see the Anonymization Actions Table.

Custom Anonymization Configuration

Providing a custom anonymization configuration ("-c <custom_anon_file.json>") allows you to specify how to handle sensitive DICOM tags. The configuration is a JSON file that maps DICOM tags to anonymization actions. For example:

{
    "(0010,0010)": "C:ANONYMOUS^ANONYMOUS",
    "(0010,0020)": "C:ANONYMOUS_ID",
    "(0008,0020)": "K",
    "(0008,0021)": "K",
    "(0008,0022)": "K",
    "(0008,0023)": "Z",
    "(0008,0024)": "X",
    "(0008,0025)": "X"
}

Legend for Actions:

• U: Keep the tag but ensure it is unique.
• X: Remove the tag entirely.
• Z: Replace the tag value with anonymized data.
• D: Clean the tag value (e.g., remove sensitive information but keep the tag).
• C:VALUE: Replace the tag value with a custom value.

Example Usage with DEFAULT anonymization:

dcm2dir -i ./dicoms -o ./organized -r report.csv -f "%i/%x_%t/%s_%d" -a

Example Usage with CUSTOM anonymization:

dcm2dir -i ./dicoms -o ./organized -r report.csv -f "%i/%x_%t/%s_%d" -a -c custom_anonymization_file.json

This command will anonymize the DICOM files and organize them into the specified folder structure.

Output

The tool organizes DICOM files into the specified output folder following the given structure. A CSV report is saved, containing the following columns:

• SubjectID
• ExamDate
• ExamID
• SeriesID
• SeriesDescription

Notes

• Non-alphanumeric characters in metadata are replaced with underscores.
• If a DICOM tag is missing, a default placeholder na is used.
• The script uses multi-threading for better performance.
• Anonymization ensures sensitive patient data is removed or replaced.

License

This project is open-source and available under the MIT License.

Anonymization Actions Table

The following table lists the anonymization actions for specific DICOM tags:

Tag	Description	Action
(0002-0003)	MediaStorageSOPInstanceUID	U
(0008-0014)	InstanceCreatorUID	X
(0008-0015)	InstanceCoercionDateTime	X
(0008-0018)	SOPInstanceUID	U
(0008-0020)	StudyDate	K
(0008-0021)	SeriesDate	K
(0008-0022)	AcquisitionDate	K
(0008-0023)	ContentDate	Z
(0008-0024)	OverlayDate	X
(0008-0025)	CurveDate	X
(0008-0050)	AccessionNumber	Z
(0008-0054)	RetrieveAETitle	X
(0008-0058)	FailedSOPInstanceUIDList	U
(0008-0080)	InstitutionName	Z
(0008-0081)	InstitutionAddress	X
(0008-0090)	ReferringPhysicianName	Z
(0008-0092)	ReferringPhysicianAddress	X
(0008-0094)	ReferringPhysicianTelephoneNumbers	X
(0008-0096)	ReferringPhysicianIdentificationSequence	X
(0008-0201)	TimezoneOffsetFromUTC	X
(0008-1032)	ProcedureCodeSequence	X
(0008-1040)	InstitutionalDepartmentName	X
(0008-1048)	PhysiciansOfRecord	X
(0008-1049)	PhysiciansOfRecordIdentificationSequence	X
(0008-1050)	PerformingPhysicianName	X
(0008-1052)	PerformingPhysicianIdentificationSequence	X
(0008-1060)	NameOfPhysiciansReadingStudy	X
(0008-1062)	PhysiciansReadingStudyIdentificationSequence	X
(0008-1070)	OperatorsName	D
(0008-1072)	OperatorIdentificationSequence	D
(0008-1080)	AdmittingDiagnosesDescription	X
(0008-1084)	AdmittingDiagnosesCodeSequence	X
(0008-1090)	ManufacturerModelName	X
(0008-1110)	ReferencedStudySequence	X
(0008-1120)	ReferencedPatientSequence	X
(0008-1140)	ReferencedImageSequence	X
(0008-1155)	ReferencedSOPInstanceUID	U
(0008-1195)	TransactionUID	U
(0008-2111)	DerivationDescription	X
(0008-3010)	IrradiationEventUID	U
(0008-4000)	IdentifyingComments	X
(0010-0010)	PatientName	C:ANONYMOUS^ANONYMOUS
(0010-0020)	PatientID	C:ANONYMOUS_ID
(0010-0021)	IssuerOfPatientID	X
(0010-0030)	PatientBirthDate	Z
(0010-0032)	PatientBirthTime	X
(0010-0050)	PatientInsurancePlanCodeSequence	X
(0010-0101)	PatientPrimaryLanguageCodeSequence	X
(0010-0102)	PatientPrimaryLanguageModifierCodeSequence	X
(0010-1000)	OtherPatientIDs	X
(0010-1001)	OtherPatientNames	X
(0010-1002)	OtherPatientIDsSequence	X
(0010-1005)	PatientBirthName	X
(0010-1020)	PatientSize	X
(0010-1030)	PatientWeight	X
(0010-1040)	PatientAddress	X
(0010-1050)	InsurancePlanIdentification	X
(0010-1060)	PatientMotherBirthName	X
(0010-1080)	MilitaryRank	X
(0010-1081)	BranchOfService	X
(0010-1090)	MedicalRecordLocator	X
(0010-2000)	MedicalAlerts	X
(0010-2110)	Allergies	X
(0010-2150)	CountryOfResidence	X
(0010-2152)	RegionOfResidence	X
(0010-2154)	PatientTelephoneNumbers	X
(0010-2160)	EthnicGroup	X
(0010-2180)	Occupation	X
(0010-21A0)	SmokingStatus	X
(0010-21B0)	AdditionalPatientHistory	X
(0010-21C0)	PregnancyStatus	X
(0010-21D0)	LastMenstrualDate	X
(0010-21F0)	PatientReligiousPreference	X
(0010-2203)	PatientSexNeutered	X
(0010-2297)	ResponsiblePerson	X
(0010-2299)	ResponsibleOrganization	X
(0010-4000)	PatientComments	X
(0012-0010)	ClinicalTrialSponsorName	D
(0012-0020)	ClinicalTrialProtocolID	D
(0012-0021)	ClinicalTrialProtocolName	Z
(0012-0030)	ClinicalTrialSiteID	Z
(0012-0031)	ClinicalTrialSiteName	Z
(0012-0040)	ClinicalTrialSubjectID	D
(0012-0042)	ClinicalTrialSubjectReadingID	D
(0012-0050)	ClinicalTrialTimePointID	Z
(0012-0051)	ClinicalTrialTimePointDescription	X
(0012-0060)	ClinicalTrialCoordinatingCenterName	Z
(0018-1002)	DeviceUID	U
(0018-1004)	PlateID	X
(0018-1005)	GeneratorID	X
(0018-1007)	CassetteID	X
(0018-1008)	GantryID	X
(0018-1012)	DateOfSecondaryCapture	X
(0018-1014)	TimeOfSecondaryCapture	X
(0018-1020)	SoftwareVersions	X
(0018-1042)	ContrastBolusStartTime	X
(0018-1043)	ContrastBolusStopTime	X
(0018-1072)	RadiopharmaceuticalStartTime	X
(0018-1073)	RadiopharmaceuticalStopTime	X
(0018-1200)	DateOfLastCalibration	X
(0018-1201)	TimeOfLastCalibration	X
(0018-1400)	AcquisitionDeviceProcessingDescription	D
(0018-4000)	AcquisitionComments	X
(0018-700A)	DetectorID	X
(0018-700C)	DateOfLastDetectorCalibration	X
(0018-700E)	TimeOfLastDetectorCalibration	X
(0018-9424)	AcquisitionProtocolDescription	X
(0018-A003)	ContributionDescription	X
(0020-000D)	StudyInstanceUID	U
(0020-000E)	SeriesInstanceUID	U
(0020-0010)	StudyID	C:CUSTOM_EXAM_ID
(0020-0052)	FrameOfReferenceUID	U
(0020-3401)	ModifyingDeviceID	X
(0020-3404)	ModifyingDeviceManufacturer	X
(0020-3406)	ModifiedImageDescription	X
(0020-4000)	ImageComments	X
(0020-9158)	FrameComments	X
(0020-9161)	ConcatenationUID	U
(0020-9164)	DimensionOrganizationUID	U
(0028-1199)	PaletteColorLookupTableUID	U
(0028-1214)	LargePaletteColorLookupTableUID	U
(0032-0012)	StudyIDIssuer	X
(0032-0032)	StudyVerifiedDate	X
(0032-0033)	StudyVerifiedTime	X
(0032-0034)	StudyReadDate	X
(0032-0035)	StudyReadTime	X
(0032-1000)	ScheduledStudyStartDate	X
(0032-1001)	ScheduledStudyStartTime	X
(0032-1010)	ScheduledStudyStopDate	X
(0032-1011)	ScheduledStudyStopTime	X
(0032-1020)	ScheduledStudyLocation	X
(0032-1021)	ScheduledStudyLocationAETitle	X
(0032-1030)	ReasonForStudy	X
(0032-1032)	RequestingPhysician	X
(0032-1033)	RequestingService	X
(0032-1040)	StudyArrivalDate	X
(0032-1041)	StudyArrivalTime	X
(0032-1050)	StudyCompletionDate	X
(0032-1051)	StudyCompletionTime	X
(0032-1060)	RequestedProcedureDescription	X
(0032-1070)	RequestedContrastAgent	X
(0032-4000)	StudyComments	X
(0038-0004)	ReferencedPatientAliasSequence	X
(0038-0010)	AdmissionID	X
(0038-0011)	IssuerOfAdmissionID	X
(0038-001A)	ScheduledAdmissionDate	X
(0038-001B)	ScheduledAdmissionTime	X
(0038-001C)	ScheduledDischargeDate	X
(0038-001D)	ScheduledDischargeTime	X
(0038-001E)	ScheduledPatientInstitutionResidence	X
(0038-0020)	AdmittingDate	X
(0038-0021)	AdmittingTime	X
(0038-0030)	DischargeDate	X
(0038-0032)	DischargeTime	X
(0038-0040)	DischargeDiagnosisDescription	X
(0038-0050)	SpecialNeeds	X
(0038-0060)	ServiceEpisodeID	X
(0038-0061)	IssuerOfServiceEpisodeID	X
(0038-0062)	ServiceEpisodeDescription	X
(0038-0300)	CurrentPatientLocation	X
(0038-0400)	PatientInstitutionResidence	X
(0038-0500)	PatientState	X
(0038-4000)	VisitComments	X
(0040-0001)	ScheduledStationAETitle	X
(0040-0002)	ScheduledProcedureStepStartDate	X
(0040-0003)	ScheduledProcedureStepStartTime	X
(0040-0004)	ScheduledProcedureStepEndDate	X
(0040-0005)	ScheduledProcedureStepEndTime	X
(0040-0006)	ScheduledPerformingPhysicianName	X
(0040-0007)	ScheduledProcedureStepDescription	X
(0040-0009)	ScheduledProcedureStepID	X
(0040-000B)	ScheduledPerformingPhysicianIdentificationSequence	X
(0040-0010)	ScheduledStationName	X
(0040-0011)	ScheduledProcedureStepLocation	X
(0040-0012)	PreMedication	X
(0040-0241)	PerformedStationAETitle	X
(0040-0242)	PerformedStationName	X
(0040-0243)	PerformedLocation	X
(0040-0244)	PerformedProcedureStepStartDate	X
(0040-0245)	PerformedProcedureStepStartTime	X
(0040-0250)	PerformedProcedureStepEndDate	X
(0040-0251)	PerformedProcedureStepEndTime	X
(0040-0253)	PerformedProcedureStepID	X
(0040-0254)	PerformedProcedureStepDescription	X
(0040-0275)	RequestAttributesSequence	X
(0040-0280)	CommentsOnThePerformedProcedureStep	X
(0040-0281)	PerformedProcedureStepDiscontinuationReasonCodeSequence	X
(0040-0310)	CommentsOnRadiationDose	X
(0040-050A)	SpecimenAccessionNumber	X
(0040-0555)	AcquisitionContextSequence	X
(0040-06FA)	SlideIdentifier	X
(0040-1001)	RequestedProcedureID	X
(0040-1002)	ReasonForTheRequestedProcedure	X
(0040-1004)	PatientTransportArrangements	X
(0040-1005)	RequestedProcedureLocation	X
(0040-1010)	NamesOfIntendedRecipientsOfResults	X
(0040-1011)	IntendedRecipientsOfResultsIdentificationSequence	X
(0040-1102)	PersonAddress	X
(0040-1103)	PersonTelephoneNumbers	X
(0040-1400)	RequestedProcedureComments	X
(0040-2001)	ReasonForTheImagingServiceRequest	X
(0040-2004)	IssueDateOfImagingServiceRequest	X
(0040-2005)	IssueTimeOfImagingServiceRequest	X
(0040-2008)	OrderEnteredBy	X
(0040-2009)	OrderEntererLocation	X
(0040-2010)	OrderCallbackPhoneNumber	X
(0040-2016)	PlacerOrderNumberImagingServiceRequest	Z
(0040-2017)	FillerOrderNumberImagingServiceRequest	Z
(0040-2400)	ImagingServiceRequestComments	X
(0040-3001)	ConfidentialityConstraintOnPatientDataDescription	X
(0040-4023)	ReferencedGeneralPurposeScheduledProcedureStepTransactionUID	U
(0040-4025)	ScheduledStationNameCodeSequence	X
(0040-4027)	ScheduledStationGeographicLocationCodeSequence	X
(0040-4030)	PerformedStationGeographicLocationCodeSequence	X
(0040-4034)	ScheduledHumanPerformersSequence	X
(0040-4035)	ActualHumanPerformersSequence	X
(0040-4036)	HumanPerformerOrganization	X
(0040-4037)	HumanPerformerName	X
(0040-A073)	VerifyingObserverSequence	X
(0040-A075)	VerifyingObserverName	D
(0040-A078)	AuthorObserverSequence	X
(0040-A07A)	ParticipantSequence	X
(0040-A07C)	CustodialOrganizationSequence	X
(0040-A088)	VerifyingObserverIdentificationCodeSequence	Z
(0040-A122)	Time	X
(0040-A123)	PersonName	D
(0040-A124)	UID	U
(0040-A730)	ContentSequence	X
(0040-DB06)	TemplateVersion	X
(0040-DB07)	TemplateLocalVersion	X
(0040-DB0C)	TemplateExtensionOrganizationUID	U
(0040-DB0D)	TemplateExtensionCreatorUID	U
(0060-3000)	HistogramSequence	X
(0070-031A)	FiducialUID	U
(0088-0140)	StorageMediaFileSetUID	U
(0088-0200)	IconImageSequence	X
(0088-0906)	TopicSubject	X
(0088-0910)	TopicAuthor	X
(0088-0912)	TopicKeywords	X
(0400-0100)	DigitalSignatureUID	U
(2030-0010)	AnnotationPosition	Z
(2030-0020)	TextString	X
(2040-0010)	ReferencedOverlayPlaneSequence	Z
(2040-0011)	ReferencedOverlayPlaneGroups	Z
(2040-0020)	OverlayPixelDataSequence	Z
(2040-0060)	OverlayMagnificationType	Z
(2040-0070)	OverlaySmoothingType	Z
(2040-0072)	OverlayOrImageMagnification	Z
(2040-0074)	MagnifyToNumberOfColumns	Z
(2040-0080)	OverlayForegroundDensity	Z
(2040-0082)	OverlayBackgroundDensity	Z
(2040-0090)	OverlayMode	Z
(2040-0100)	ThresholdDensity	Z
(2040-0500)	ReferencedImageBoxSequenceRetired	Z
(2100-0020)	ExecutionStatus	Z
(2100-0030)	ExecutionStatusInfo	Z
(2100-0040)	CreationDate	X
(2100-0050)	CreationTime	X
(2100-0070)	Originator	X
(2110-0010)	PrinterStatus	Z
(2110-0020)	PrinterStatusInfo	Z
(2110-0030)	PrinterName	Z
(2110-0099)	PrintQueueID	Z
(3006-0024)	ReferencedFrameOfReferenceUID	U
(3006-00C2)	RelatedFrameOfReferenceUID	U
(300A-0013)	DoseReferenceUID	U
(4000-0010)	Arbitrary	X
(4000-4000)	TextComments	X
(4008-0042)	ResultsIDIssuer	X
(4008-0102)	InterpretationRecorder	X
(4008-010A)	InterpretationTranscriber	X
(4008-010B)	InterpretationText	X
(4008-010C)	InterpretationAuthor	X
(4008-0111)	InterpretationApproverSequence	X
(4008-0114)	PhysicianApprovingInterpretation	X
(4008-0115)	InterpretationDiagnosisDescription	X
(4008-0118)	ResultsDistributionListSequence	X
(4008-0119)	DistributionName	X
(4008-011A)	DistributionAddress	X
(4008-0202)	InterpretationIDIssuer	X
(4008-0300)	Impressions	X
(4008-4000)	ResultsComments	X

Legend for Actions:

• U: Keep the tag but ensure it is unique.
• X: Remove the tag entirely.
• Z: Replace the tag value with anonymized data.
• D: Clean the tag value (e.g., remove sensitive information but keep the tag).
• C:VALUE: Replace the tag value with a custom value.