From 42925e061e6dd5e1a9197a1601f4cfc8096a88c2 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 5 Feb 2023 16:15:06 +0100
Subject: [PATCH 1/7] ENH: Add sample metadata to MRI and PET

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 .../magnetic-resonance-imaging-data.md               | 12 ++++++++++++
 .../positron-emission-tomography.md                  | 12 ++++++++++++
 src/schema/rules/sidecars/mri.yaml                   |  8 ++++++++
 src/schema/rules/sidecars/pet.yaml                   | 11 +++++++++++
 4 files changed, 43 insertions(+)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 7099836c40..0015df6d13 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -162,6 +162,18 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table("mri.MRIEchoPlanarImagingAndB0Mapping") }}
 
+#### Tissue description
+
+<!-- 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.MRISample") }}
+
 ## Anatomy imaging data
 
 Anatomy MRI sequences measure static, structural features of the brain.
diff --git a/src/modality-specific-files/positron-emission-tomography.md b/src/modality-specific-files/positron-emission-tomography.md
index c16d144b4f..b63007ba10 100644
--- a/src/modality-specific-files/positron-emission-tomography.md
+++ b/src/modality-specific-files/positron-emission-tomography.md
@@ -216,6 +216,18 @@ A guide for using macros can be found at
 
 {{ MACROS___make_sidecar_table("pet.PETInstitutionInformation") }}
 
+#### Tissue description
+
+<!-- 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("pet.PETSample") }}
+
 #### Task
 
 If the OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used,
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 63e4a900df..cb67a1bbcb 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -35,6 +35,14 @@ MRIHardware:
     MatrixCoilMode: recommended
     CoilCombinationMethod: recommended
 
+MRISample:
+  selectors:
+    - modality == "mri"
+  fields:
+    BodyPart: optional
+    BodyPartDetails: optional
+    BodyPartDetailsOntology: optional
+
 MRIScannerHardwareASL:
   selectors:
     - datatype == "perf"
diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml
index 353389de71..bf2095b1ed 100644
--- a/src/schema/rules/sidecars/pet.yaml
+++ b/src/schema/rules/sidecars/pet.yaml
@@ -35,6 +35,17 @@ PETInstitutionInformation:
       level: recommended
       description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
 
+PETSample:
+  selectors:
+    - modality == "pet"
+    - suffix == "pet"
+  fields:
+    BodyPart:
+      level: recommended
+      description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
+    BodyPartDetails: optional
+    BodyPartDetailsOntology: optional
+
 PETRadioChemistry:
   selectors:
     - modality == "pet"

From 36644038930a51811d03365904d061ec103b1de0 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 5 Feb 2023 16:15:06 +0100
Subject: [PATCH 2/7] ENH: Add generic metadata from BEP22 to MRI

---
 src/schema/objects/metadata.yaml   | 36 ++++++++++++++++++++++++++++++
 src/schema/rules/sidecars/mri.yaml |  6 +++++
 2 files changed, 42 insertions(+)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 5347a5d5b5..241b0f7c9e 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -237,6 +237,18 @@ B0FieldSource:
     - type: array
       items:
         type: string
+B0ShimmingTechnique:
+  name: B0ShimmingTechnique
+  display_name: B0 Shimming Technique
+  description: |
+    The technique used to shim the *B<sub>0</sub>* field (for example, `"FASTMAP"`).
+  type: string
+B1ShimmingTechnique:
+  name: B1ShimmingTechnique
+  display_name: B1 Shimming Technique
+  description: |
+    The technique used to shim the *B<sub>1</sub>* field (for example, `"Simple phase align"`).
+  type: string
 BIDSVersion:
   name: BIDSVersion
   display_name: BIDS Version
@@ -2197,6 +2209,12 @@ NumberOfVolumesDiscardedByUser:
     `"NumberOfVolumesDiscardedByUser"` field.
   type: integer
   minimum: 0
+NumberReceiveCoilActiveElements:
+  name: NumberReceiveCoilActiveElements
+  display_name: Number of Receive Coil Active Elements
+  description: |
+    The number of active RF elements used by the receive coil.
+  type: integer
 NumberShots:
   name: NumberShots
   display_name: Number Shots
@@ -2216,6 +2234,12 @@ NumberShots:
     - type: array
       items:
         type: number
+NumberTransmitCoilActiveElements:
+  name: NumberTransmitCoilActiveElements
+  display_name: Number of Transmit Coil Active Elements
+  description: |
+    The number of active RF elements used by the transmit coil.
+  type: integer
 NumericalAperture:
   name: NumericalAperture
   display_name: Numerical Aperture
@@ -3578,6 +3602,18 @@ VolumeTiming:
   items:
     type: number
     unit: s
+WaterSuppression:
+  name: WaterSuppression
+  display_name: Water Suppression
+  description: |
+    Boolean indicating whether water suppression was used prior to acquisition.
+  type: boolean
+WaterSuppressionTechnique:
+  name: WaterSuppressionTechnique
+  display_name: Water Suppression Technique
+  description: |
+    The name of the pulse sequence used for water suppression (for example, `"CHESS"`, `"VAPOR"`).
+  type: string
 WholeBloodAvail:
   name: WholeBloodAvail
   display_name: Whole Blood Avail
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index cb67a1bbcb..d557660832 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -30,10 +30,12 @@ MRIHardware:
       level: recommended, but required for Arterial Spin Labeling
     ReceiveCoilName: recommended
     ReceiveCoilActiveElements: recommended
+    NumberReceiveCoilActiveElements: optional
     GradientSetType: recommended
     MRTransmitCoilSequence: recommended
     MatrixCoilMode: recommended
     CoilCombinationMethod: recommended
+    NumberTransmitCoilActiveElements: optional
 
 MRISample:
   selectors:
@@ -75,6 +77,10 @@ MRISequenceSpecifics:
     SpoilingRFPhaseIncrement: optional
     SpoilingGradientMoment: optional
     SpoilingGradientDuration: optional
+    WaterSuppression: optional
+    WaterSuppressionTechnique: optional
+    B0ShimmingTechnique: optional
+    B1ShimmingTechnique: optional
 
 PETMRISequenceSpecifics:
   selectors:

From 22073a5ec7dc5be00ece98ee2554aa12642c488e Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 24 Aug 2023 15:31:11 -0400
Subject: [PATCH 3/7] rm sample

---
 src/schema/rules/sidecars/mri.yaml |  8 --------
 src/schema/rules/sidecars/pet.yaml | 11 -----------
 2 files changed, 19 deletions(-)

diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index d557660832..0aa865ebf1 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -37,14 +37,6 @@ MRIHardware:
     CoilCombinationMethod: recommended
     NumberTransmitCoilActiveElements: optional
 
-MRISample:
-  selectors:
-    - modality == "mri"
-  fields:
-    BodyPart: optional
-    BodyPartDetails: optional
-    BodyPartDetailsOntology: optional
-
 MRIScannerHardwareASL:
   selectors:
     - datatype == "perf"
diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml
index bf2095b1ed..353389de71 100644
--- a/src/schema/rules/sidecars/pet.yaml
+++ b/src/schema/rules/sidecars/pet.yaml
@@ -35,17 +35,6 @@ PETInstitutionInformation:
       level: recommended
       description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
 
-PETSample:
-  selectors:
-    - modality == "pet"
-    - suffix == "pet"
-  fields:
-    BodyPart:
-      level: recommended
-      description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
-    BodyPartDetails: optional
-    BodyPartDetailsOntology: optional
-
 PETRadioChemistry:
   selectors:
     - modality == "pet"

From a9126e47e62eff65282e97fd5f304384ba51b365 Mon Sep 17 00:00:00 2001
From: Mark Mikkelsen <mark.mikkelsen@gmail.com>
Date: Wed, 10 Apr 2024 16:47:26 -0400
Subject: [PATCH 4/7] Update src/schema/objects/metadata.yaml

---
 src/schema/objects/metadata.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 241b0f7c9e..01f076b531 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -241,7 +241,7 @@ B0ShimmingTechnique:
   name: B0ShimmingTechnique
   display_name: B0 Shimming Technique
   description: |
-    The technique used to shim the *B<sub>0</sub>* field (for example, `"FASTMAP"`).
+    The technique used to shim the *B<sub>0</sub>* field (for example, `"Dynamic shim updating"` or `"FASTMAP"`).
   type: string
 B1ShimmingTechnique:
   name: B1ShimmingTechnique

From f5f554b6d81de469b4112db7cf16410c12c2023a Mon Sep 17 00:00:00 2001
From: Mark Mikkelsen <mark.mikkelsen@gmail.com>
Date: Wed, 10 Apr 2024 18:28:10 -0400
Subject: [PATCH 5/7] Update src/schema/objects/metadata.yaml

---
 src/schema/objects/metadata.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 01f076b531..2cf6edec95 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -247,7 +247,8 @@ B1ShimmingTechnique:
   name: B1ShimmingTechnique
   display_name: B1 Shimming Technique
   description: |
-    The technique used to shim the *B<sub>1</sub>* field (for example, `"Simple phase align"`).
+    The technique used to shim the *B<sub>1</sub>* field (for example, `"Simple phase align"`
+    or `"Pre-saturated TurboFLASH"`).
   type: string
 BIDSVersion:
   name: BIDSVersion

From bfc116d5cb0c65d9573f148d076580eb484d9d27 Mon Sep 17 00:00:00 2001
From: Mark Mikkelsen <mark.mikkelsen@gmail.com>
Date: Wed, 10 Apr 2024 18:30:59 -0400
Subject: [PATCH 6/7] Update src/schema/objects/metadata.yaml

---
 src/schema/objects/metadata.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 2cf6edec95..30f145aa96 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -241,7 +241,8 @@ B0ShimmingTechnique:
   name: B0ShimmingTechnique
   display_name: B0 Shimming Technique
   description: |
-    The technique used to shim the *B<sub>0</sub>* field (for example, `"Dynamic shim updating"` or `"FASTMAP"`).
+    The technique used to shim the *B<sub>0</sub>* field (for example, `"Dynamic shim updating"`
+    or `"FASTMAP"`).
   type: string
 B1ShimmingTechnique:
   name: B1ShimmingTechnique

From f93416064cd8458fa0764df95b4dc3a3356a6c58 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 11 Apr 2024 13:45:36 +0200
Subject: [PATCH 7/7] rm macros with missing metadata

---
 .../magnetic-resonance-imaging-data.md               | 12 ------------
 .../positron-emission-tomography.md                  | 12 ------------
 2 files changed, 24 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 0015df6d13..7099836c40 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -162,18 +162,6 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table("mri.MRIEchoPlanarImagingAndB0Mapping") }}
 
-#### Tissue description
-
-<!-- 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.MRISample") }}
-
 ## Anatomy imaging data
 
 Anatomy MRI sequences measure static, structural features of the brain.
diff --git a/src/modality-specific-files/positron-emission-tomography.md b/src/modality-specific-files/positron-emission-tomography.md
index b63007ba10..c16d144b4f 100644
--- a/src/modality-specific-files/positron-emission-tomography.md
+++ b/src/modality-specific-files/positron-emission-tomography.md
@@ -216,18 +216,6 @@ A guide for using macros can be found at
 
 {{ MACROS___make_sidecar_table("pet.PETInstitutionInformation") }}
 
-#### Tissue description
-
-<!-- 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("pet.PETSample") }}
-
 #### Task
 
 If the OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used,