[ENH] Add metadata fields for DeIdentificationMethod/CodeSequence for MRI and PET

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.
+
+<!-- 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") }}
+
+
 ### Defacing masks
 
 If the structural images included in the dataset were defaced (to protect

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.
+
+<!-- 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") }}
+
+
+### 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-<label>`](../appendices/entities.md#mod)
+entity corresponds to modality suffix,
+such as `T1w` or `inplaneT1`, referenced by the defacemask image.
+For example, `sub-01_mod-T1w_defacemask.nii.gz`.
+
+<!--
+This block generates a filename templates.
+The inputs for this macro can be found in the directory
+  src/schema/rules/files/raw
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filename_template("raw", datatypes=["anat"], suffixes=[
+         "defacemask",
+      ])

src/schema/objects/metadata.yaml

@@ -561,6 +561,53 @@ 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 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

src/schema/rules/sidecars/mri.yaml

@@ -319,3 +319,14 @@ 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`.

src/schema/rules/sidecars/pet.yaml

@@ -276,3 +276,14 @@ PETTask:
     TaskDescription: recommended
     CogAtlasID: recommended
     CogPOID: recommended
+
+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`.