From a2357a42ae81dd3ffdf2d1c4116c3613b32a4732 Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 19 Dec 2024 12:13:30 -0500
Subject: [PATCH 1/2] feat(schema): Encode qMRI metadata requirements

---
 src/schema/rules/sidecars/qmri.yaml | 104 ++++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100644 src/schema/rules/sidecars/qmri.yaml

diff --git a/src/schema/rules/sidecars/qmri.yaml b/src/schema/rules/sidecars/qmri.yaml
new file mode 100644
index 0000000000..a3c18918a5
--- /dev/null
+++ b/src/schema/rules/sidecars/qmri.yaml
@@ -0,0 +1,104 @@
+---
+# Anatomical qMRI sequences
+VariableFlipAngleMetadata:
+  selectors:
+    - suffix == "VFA"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    PulseSequenceType: required
+    RepetitionTimeExcitation: required
+
+InversionRecoveryT1Metadata:
+  selectors:
+    - suffix == "IRT1"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    InversionTime: required
+
+MP2RAGEMetadata:
+  selectors:
+    - suffix == "MP2RAGE"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    InversionTime: required
+    RepetitionTimeExcitation: required
+    RepetitionTimePreparation: required
+    NumberShots: required
+    MagneticFieldStrength: required
+
+MESpinEchoMetadata:
+  selectors:
+    - suffix == "MESE"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    EchoTime: required
+
+MEGradientEchoMetadata:
+  selectors:
+    - suffix == "MEGRE"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    EchoTime: required
+
+MTRatioMetadata:
+  selectors:
+    - suffix == "MTR"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    MTState: required
+
+MTSaturationMetadata:
+  selectors:
+    - suffix == "MTS"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    MTState: required
+    RepetitionTimeExcitation: required
+
+MultiParametricMappingMetadata:
+  selectors:
+    - suffix == "MPM"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    MTState: required
+    RepetitionTimeExcitation: required
+
+# Field mapping qMRI sequences
+TB1DAMMetadata:
+  selectors:
+    - suffix == "TB1DAM"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+
+TB1EPIMetadata:
+  selectors:
+    - suffix == "TB1EPI"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    EchoTime: required
+    FlipAngle: required
+    TotalReadoutTime: required
+    MixingTime: required
+
+TB1AFIMetadata:
+  selectors:
+    - suffix == "TB1AFI"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    RepetitionTimeExcitation: required
+
+TB1SRGEMetadata:
+  selectors:
+    - suffix == "TB1SRGE"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    FlipAngle: required
+    InversionTime: required
+    RepetitionTimeExcitation: required
+    RepetitionTimePreparation: required
+    NumberShots: required

From 96e57482d1b101212586767a2afbef9826cae00b Mon Sep 17 00:00:00 2001
From: "Christopher J. Markiewicz" <markiewicz@stanford.edu>
Date: Thu, 19 Dec 2024 12:14:36 -0500
Subject: [PATCH 2/2] fix: Indicate RepetitionTimeExcitation for TB1AFI

---
 src/appendices/qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/appendices/qmri.md b/src/appendices/qmri.md
index d5367cfcdd..83247c119b 100644
--- a/src/appendices/qmri.md
+++ b/src/appendices/qmri.md
@@ -303,7 +303,7 @@ and a guide for using macros can be found at
 | -------------------- | ---------------------------------------------------------------------------------------------------- |
 | TB1DAM               | `FlipAngle`                                                                                          |
 | TB1EPI               | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime`                                            |
-| TB1AFI               | `RepetitionTime`                                                                                     |
+| TB1AFI               | `RepetitionTimeExcitation`                                                                           |
 | TB1TFL               |                                                                                                      |
 | TB1RFM               |                                                                                                      |
 | TB1SRGE<sup>\*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |