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Merge pull request #1772 from CGSchwarzMayo/DeIdentificationMethod
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[ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET
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effigies authored Sep 3, 2024
2 parents 183499c + 982bc7d commit b2798b0
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27 changes: 26 additions & 1 deletion src/modality-specific-files/magnetic-resonance-imaging-data.md
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Expand Up @@ -166,7 +166,7 @@ A guide for using macros can be found at
])
}}

#### Tissue description
### Tissue description

<!-- This block generates a metadata table.
These tables are defined in
Expand All @@ -178,6 +178,31 @@ A guide for using macros can be found at
-->
{{ MACROS___make_sidecar_table("mri.MRISample") }}

### 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.

<!-- This block generates a metadata table.
These tables are defined in
src/schema/rules/sidecars
The definitions of the fields specified in these tables may be found in
src/schema/objects/metadata.yaml
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("mri.DeidentificationMethod") }}

Each object in the `DeidentificationMethodCodeSequence` array includes the following RECOMMENDED keys:

<!-- This block generates a table describing subfields within a metadata field.
The definitions of these fields can be found in
src/schema/objects/metadata.yaml
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_subobject_table("metadata.DeidentificationMethodCodeSequence.items") }}

## Anatomy imaging data

Anatomy MRI sequences measure static, structural features of the brain.
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25 changes: 25 additions & 0 deletions src/modality-specific-files/positron-emission-tomography.md
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Expand Up @@ -230,6 +230,31 @@ A guide for using macros can be found at
-->
{{ MACROS___make_sidecar_table("pet.PETSample") }}

#### 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.

<!-- This block generates a metadata table.
These tables are defined in
src/schema/rules/sidecars
The definitions of the fields specified in these tables may be found in
src/schema/objects/metadata.yaml
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("mri.DeidentificationMethod") }}

Each object in the `DeidentificationMethodCodeSequence` array includes the following RECOMMENDED keys:

<!-- This block generates a table describing subfields within a metadata field.
The definitions of these fields can be found in
src/schema/objects/metadata.yaml
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_subobject_table("metadata.DeidentificationMethodCodeSequence.items") }}

#### Task

If the OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used,
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49 changes: 49 additions & 0 deletions src/schema/objects/metadata.yaml
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Expand Up @@ -591,6 +591,55 @@ 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: array
items:
type: string
DeidentificationMethodCodeSequence:
name: DeidentificationMethodCodeSequence
display_name: Deidentification Method Code Sequence
description: |
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:
type: object
recommended_fields:
- CodeValue
- CodeMeaning
- CodingSchemeDesignator
- 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
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11 changes: 11 additions & 0 deletions src/schema/rules/sidecars/mri.yaml
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Expand Up @@ -373,3 +373,14 @@ MRIInstitutionInformation:
InstitutionalDepartmentName:
level: recommended
description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.

DeidentificationMethod:
selectors:
- intersects([modality], ["mri", "pet"])
fields:
DeidentificationMethod:
level: optional
description_addendum: Corresponds to DICOM Tag 0012, 0063 `De-identification Method`.
DeidentificationMethodCodeSequence:
level: optional
description_addendum: Corresponds to DICOM Tag 0012, 0064 `De-identification Method Code Sequence`.

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