From 2c0141781ad2d9e64eed15bf4ce6e9822a32fec6 Mon Sep 17 00:00:00 2001
From: "Christopher G. Schwarz" <schwarz.christopher@mayo.edu>
Date: Wed, 24 Apr 2024 15:07:15 -0500
Subject: [PATCH]     Apply additional suggestions from code review

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../magnetic-resonance-imaging-data.md        | 51 +++++++++----------
 .../positron-emission-tomography.md           | 24 +--------
 src/schema/rules/sidecars/pet.yaml            | 11 ----
 3 files changed, 26 insertions(+), 60 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index a195b58018..9ea9209166 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -174,6 +174,31 @@ 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.
@@ -356,32 +381,6 @@ 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
diff --git a/src/modality-specific-files/positron-emission-tomography.md b/src/modality-specific-files/positron-emission-tomography.md
index cfde9bf02d..3300c22127 100644
--- a/src/modality-specific-files/positron-emission-tomography.md
+++ b/src/modality-specific-files/positron-emission-tomography.md
@@ -434,7 +434,7 @@ time plasma_radioactivity whole_blood_radioactivity metabolite_parent_fraction m
 7193    19.71    15.70    0.02    0.559
 ```
 
-### Deidentification information
+## 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.
@@ -459,25 +459,3 @@ and a guide for using macros can be found at
 -->
 {{ 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",
-      ])
-}}
diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml
index dd12ee38dc..2b2264a59b 100644
--- a/src/schema/rules/sidecars/pet.yaml
+++ b/src/schema/rules/sidecars/pet.yaml
@@ -276,14 +276,3 @@ 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`.