From 62d2244a9967b781a6c6444767be3170850d16c8 Mon Sep 17 00:00:00 2001 From: "Christopher G. Schwarz" Date: Fri, 12 Apr 2024 09:30:16 -0500 Subject: [PATCH 01/11] Add tags for DeIdentificationMethod and DeIdentificationMethodCodeSequence, corresponding to the same-named DICOM tags. These record info on de-identification, including metadata and image content (e.g. de-facing or removing burned-in text) --- src/schema/objects/metadata.yaml | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index 57515dd6f0..3cabf06002 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -561,6 +561,36 @@ DecayCorrectionFactor: type: array items: type: number +DeIdentificationMethod: + name: DeIdentificationMethod + display_name: DeIdentification Method + description: | + A description of the mechanism or method used to remove the Patient's identity. + Corresponds to DICOM Tag 0012, 0063 `De-identification Method`. + type: string +DeIdentificationMethodCodeSequence: + name: DeIdentificationMethodCodeSequence + display_name: DeIdentification Method Code Sequence + description: | + A description of the mechanism or method used to remove the Patient's identity. + Corresponds to DICOM Tag 0012, 0064 `De-identification Method Code Sequence`. + type: array + items: + type: object + recommended_fields: + - CodeValue + - CodeMeaning + - CodingSchemeDesignator + - CodingSchemeVersion + properties: + CodeValue: + type: string + CodeMeaning: + type: string + CodingSchemeDesignator: + type: string + CodingSchemeVersion: + type: string DelayAfterTrigger: name: DelayAfterTrigger display_name: Delay After Trigger From c5a7e5c089f5212d0dc253ccfb6d78ed4588b0c0 Mon Sep 17 00:00:00 2001 From: "Christopher G. Schwarz" Date: Tue, 16 Apr 2024 10:45:16 -0500 Subject: [PATCH 02/11] Correct capitalization on DeIdentificationMethod to DeidentificationMethod, to match DICOM --- src/schema/objects/metadata.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index 3cabf06002..3fc1c143c6 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -561,16 +561,16 @@ DecayCorrectionFactor: type: array items: type: number -DeIdentificationMethod: - name: DeIdentificationMethod - display_name: DeIdentification Method +DeidentificationMethod: + name: DeidentificationMethod + display_name: Deidentification Method description: | A description of the mechanism or method used to remove the Patient's identity. Corresponds to DICOM Tag 0012, 0063 `De-identification Method`. type: string -DeIdentificationMethodCodeSequence: - name: DeIdentificationMethodCodeSequence - display_name: DeIdentification Method Code Sequence +DeidentificationMethodCodeSequence: + name: DeidentificationMethodCodeSequence + display_name: Deidentification Method Code Sequence description: | A description of the mechanism or method used to remove the Patient's identity. Corresponds to DICOM Tag 0012, 0064 `De-identification Method Code Sequence`. From a53ab038abc5d237f6f3cc6231d79be01601e2a8 Mon Sep 17 00:00:00 2001 From: "Christopher G. Schwarz" Date: Tue, 23 Apr 2024 08:35:08 -0500 Subject: [PATCH 03/11] Apply suggestions from code review Co-authored-by: Chris Markiewicz --- src/schema/objects/metadata.yaml | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index 3fc1c143c6..1e2664fbea 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -572,7 +572,7 @@ DeidentificationMethodCodeSequence: name: DeidentificationMethodCodeSequence display_name: Deidentification Method Code Sequence description: | - A description of the mechanism or method used to remove the Patient's identity. + A sequence of code objects describing the mechanism or method use to remove the Patient's identity. Corresponds to DICOM Tag 0012, 0064 `De-identification Method Code Sequence`. type: array items: @@ -584,13 +584,30 @@ DeidentificationMethodCodeSequence: - CodingSchemeVersion properties: CodeValue: + name: CodeValue type: string + description: | + An identifier that is unambiguous within the Coding Scheme + denoted by Coding Scheme Designator and Coding Scheme Version. + Corresponds to DICOM Tag 0008, 0100 `Code Value`. CodeMeaning: + name: CodeMeaning type: string + description: | + Text that has meaning to a human and conveys the meaning of the term + Corresponds to DICOM Tag 0008, 0104 `Code Meaning`. CodingSchemeDesignator: + name: CodingSchemeDesignator type: string + description: | + The identifier of the coding scheme in which the coded entry is defined. + Corresponds to DICOM Tag 0008, 0102 `Coding Scheme Designator`. CodingSchemeVersion: + name: CodingSchemeVersion type: string + description: | + An identifier of the version of the coding scheme if necessary to resolve ambiguity. + Corresponds to DICOM Tag 0008, 0103 `Coding Scheme Version`. DelayAfterTrigger: name: DelayAfterTrigger display_name: Delay After Trigger From 4327bc71221f4eacf1e6fdb6333f14c168a2d8d0 Mon Sep 17 00:00:00 2001 From: "Christopher G. Schwarz" Date: Tue, 23 Apr 2024 09:24:33 -0500 Subject: [PATCH 04/11] Add modality-specific-files and sidecars for DeidentificationMethod tags Co-authored-by: Chris Markiewicz --- .../magnetic-resonance-imaging-data.md | 26 ++++++++++ .../positron-emission-tomography.md | 47 +++++++++++++++++++ src/schema/rules/sidecars/mri.yaml | 13 +++++ src/schema/rules/sidecars/pet.yaml | 12 +++++ 4 files changed, 98 insertions(+) diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md index 072410f528..a195b58018 100644 --- a/src/modality-specific-files/magnetic-resonance-imaging-data.md +++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md @@ -356,6 +356,32 @@ recommended metadata fields, and the application specific entity or metadata requirement levels of [file collections](../appendices/file-collections.md) that can generate them, visit the [qMRI appendix](../appendices/qmri.md). +### Deidentification information + +Describes the mechanism or method used to modify or remove metadata +and/or pixel data to protect the patient or participant's identity. + + +{{ MACROS___make_sidecar_table("mri.DeidentificationMethod") }} + +Each object in the `DeidentificationMethodCodeSequence` array includes the following RECOMMENDED keys: + + +{{ MACROS___make_subobject_table("metadata.DeidentificationMethodCodeSequence.items") }} + + ### Defacing masks If the structural images included in the dataset were defaced (to protect diff --git a/src/modality-specific-files/positron-emission-tomography.md b/src/modality-specific-files/positron-emission-tomography.md index 5ea5f8bbcb..4073710232 100644 --- a/src/modality-specific-files/positron-emission-tomography.md +++ b/src/modality-specific-files/positron-emission-tomography.md @@ -433,3 +433,50 @@ time plasma_radioactivity whole_blood_radioactivity metabolite_parent_fraction m 5407 22.70 19.49 0.032 0.523 7193 19.71 15.70 0.02 0.559 ``` + +### Deidentification information + +Describes the mechanism or method used to modify or remove metadata +and/or pixel data to protect the patient or participant's identity. + + +{{ MACROS___make_sidecar_table("mri.DeidentificationMethod") }} + +Each object in the `DeidentificationMethodCodeSequence` array includes the following RECOMMENDED keys: + + +{{ MACROS___make_subobject_table("metadata.DeidentificationMethodCodeSequence.items") }} + + +### Defacing masks + +If the structural images included in the dataset were defaced (to protect +identity of participants) one MAY provide the binary mask that was used to +remove facial features in the form of `_defacemask` files. +In such cases, the OPTIONAL [`mod-