From 0ed5d041b3d300ab701f7f80c3fcc3a0600056ac Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Wed, 10 Feb 2021 08:50:15 -0500
Subject: [PATCH 1/8] Update qMRI fieldmap schema

---
 src/schema/datatypes/fmap.yaml | 49 +++++++++++++++++++++++++++++++---
 1 file changed, 45 insertions(+), 4 deletions(-)

diff --git a/src/schema/datatypes/fmap.yaml b/src/schema/datatypes/fmap.yaml
index 1eb84f7e59..f4ed147f57 100644
--- a/src/schema/datatypes/fmap.yaml
+++ b/src/schema/datatypes/fmap.yaml
@@ -1,5 +1,5 @@
 ---
-# First group
+# Fieldmaps
 - suffixes:
     - phasediff
     - phase1
@@ -17,7 +17,7 @@
     session: optional
     acquisition: optional
     run: optional
-# Second group
+# PEPolar
 - suffixes:
     - epi
     - m0scan
@@ -32,7 +32,7 @@
     ceagent: optional
     direction: required
     run: optional
-# Third group
+# TB1DAM
 - suffixes:
     - TB1DAM
   extensions:
@@ -47,8 +47,9 @@
     ceagent: optional
     reconstruction: optional
     flip: required
+    inversion: optional
     part: optional
-# Fourth group
+# TB1EPI
 - suffixes:
     - TB1EPI
   extensions:
@@ -64,4 +65,44 @@
     reconstruction: optional
     echo: required
     flip: required
+    inversion: optional
+    part: optional
+# RFFieldMaps
+- suffixes:
+    - TB1AFI
+    - TB1TFL
+    - TB1RMF
+    - RB1COR
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    subject: required
+    session: optional
+    run: optional
+    acquisition: optional
+    ceagent: optional
+    reconstruction: optional
+    echo: optional
+    flip: optional
+    inversion: optional
+    part: optional
+# TB1SRGE
+- suffixes:
+    - TB1SRGE
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    subject: required
+    session: optional
+    run: optional
+    acquisition: optional
+    ceagent: optional
+    reconstruction: optional
+    echo: optional
+    flip: required
+    inversion: required
     part: optional

From 9672f911a4cec302e25fdbc558ad59c8ed37dc90 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Wed, 10 Feb 2021 09:39:39 -0500
Subject: [PATCH 2/8] FIX: TB1RFM -> TB1RMF

Normalizing to the most common. Cannot find a canonical reference outside of BIDS, so it may be backward.
---
 src/99-appendices/11-qmri.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index c83013b409..0ee3768f73 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -529,7 +529,7 @@ values of the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be
          └── sub-01_acq-famp_TB1TFL.json
 ```
 
-The example above applies to the `TB1RFM` suffix as well.
+The example above applies to the `TB1RMF` suffix as well.
 
 #### `RB1COR` specific notes
 

From ab25456da9549ca8fd99128a83ec0c20ffbbd019 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 11 Feb 2021 13:44:06 -0500
Subject: [PATCH 3/8] SCHEMA: Move TB1map+RB1map to fmap datatype

---
 src/schema/datatypes/anat.yaml |  2 --
 src/schema/datatypes/fmap.yaml | 15 +++++++++++++++
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/src/schema/datatypes/anat.yaml b/src/schema/datatypes/anat.yaml
index 3c5018569a..5ae49feda3 100644
--- a/src/schema/datatypes/anat.yaml
+++ b/src/schema/datatypes/anat.yaml
@@ -42,8 +42,6 @@
     - MTVmap
     - PDT2map
     - Chimap
-    - TB1map
-    - RB1map
     - S0map
     - M0map
   extensions:
diff --git a/src/schema/datatypes/fmap.yaml b/src/schema/datatypes/fmap.yaml
index f4ed147f57..0efb368406 100644
--- a/src/schema/datatypes/fmap.yaml
+++ b/src/schema/datatypes/fmap.yaml
@@ -106,3 +106,18 @@
     flip: required
     inversion: required
     part: optional
+# Parametric
+- suffixes:
+    - TB1map
+    - RB1map
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  entities:
+    subject: required
+    session: optional
+    run: optional
+    acquisition: optional
+    ceagent: optional
+    reconstruction: optional

From 3bfeabbf57da2f6408f0f5384b804cc7c55166c8 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 12 Feb 2021 14:57:19 -0500
Subject: [PATCH 4/8] TB1RMF -> TB1RFM

---
 src/99-appendices/10-file-collections.md | 2 +-
 src/99-appendices/11-qmri.md             | 8 ++++----
 src/schema/datatypes/fmap.yaml           | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/99-appendices/10-file-collections.md b/src/99-appendices/10-file-collections.md
index eb260f0e56..df0f0783b5 100644
--- a/src/99-appendices/10-file-collections.md
+++ b/src/99-appendices/10-file-collections.md
@@ -55,6 +55,6 @@ sub-<label>/[ses-<label>/]
 | TB1EPI  | flip, echo                                                   | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                       |
 | TB1AFI  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.                                                                                                                                                                                                                                               |
 | TB1TFL  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `tfl_b1_map`               | B1<sup>+</sup> data acquired using `tfl_b1_map` product sequence by Siemens based on the method by [Chung et al. (2010)](https://doi.org/10.1002/mrm.22423). The sequence generates one anatomical image and one scaled flip angle map.                                                                                                                                                                                                                 |
-| TB1RMF  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens.                                                                                                                                                                                                                                                                                                                                                                                |
+| TB1RFM  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | Siemens `rf_map`                   | B1<sup>+</sup> data acquired using `rf_map` product sequence by Siemens.                                                                                                                                                                                                                                                                                                                                                                                |
 | TB1SRGE | `flip`, `inv`                                                | SA2RAGE                            | Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ ([Eggenschwiler et al. 2011](https://doi.org/10.1002/mrm.23145)). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation ([Marques & Gruetter 2013](https://doi.org/10.1371/journal.pone.0069294)). |
 | RB1COR  | Please see the [qMRI appendix](../99-appendices/11-qmri.md). | B1<sup>-</sup> field correction    | Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in [Papp et al. (2016)](https://doi.org/10.1002/mrm.26058).                                                                                                                                                                                                 |
diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 0ee3768f73..4a8f692020 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -160,7 +160,7 @@ Explanation of the table:
 | TB1EPI                  | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime`                                            |
 | TB1AFI                  | `RepetitionTime`                                                                                     |
 | TB1TFL                  |                                                                                                      |
-| TB1RMF                  |                                                                                                      |
+| TB1RFM                  |                                                                                                      |
 | TB1SRGE<sup>*</sup>     | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |
 | RB1COR                  |                                                                                                      |
 
@@ -433,7 +433,7 @@ by entities that can generalize to other applications.
 Instead of introducing an entity that is exclusive to a single application,
 method developers who commonly use these file collections for the `MPM` application reached
 the consensus on the use of `acq` entity to distinguish individual files.
-These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RMF`, and `RB1COR`.
+These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RFM`, and `RB1COR`.
 
 #### `TB1EPI` specific notes
 
@@ -505,7 +505,7 @@ and MAY be followed by freeform entries:
          └── sub-01_acq-tr2_TB1AFI.json
 ```
 
-#### `TB1TFL` and `TB1RMF` specific notes
+#### `TB1TFL` and `TB1RFM` specific notes
 
 These suffixes describe two outputs generated by Siemens `tfl_b1_map` and `rf_map` product sequences, respectively.
 Both sequences output two images.
@@ -529,7 +529,7 @@ values of the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be
          └── sub-01_acq-famp_TB1TFL.json
 ```
 
-The example above applies to the `TB1RMF` suffix as well.
+The example above applies to the `TB1RFM` suffix as well.
 
 #### `RB1COR` specific notes
 
diff --git a/src/schema/datatypes/fmap.yaml b/src/schema/datatypes/fmap.yaml
index 0efb368406..6192757a5d 100644
--- a/src/schema/datatypes/fmap.yaml
+++ b/src/schema/datatypes/fmap.yaml
@@ -71,7 +71,7 @@
 - suffixes:
     - TB1AFI
     - TB1TFL
-    - TB1RMF
+    - TB1RFM
     - RB1COR
   extensions:
     - .nii.gz

From 6aad8051fe19b59af72d96ef99ece8e2ee6cc1a1 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 12 Feb 2021 15:12:02 -0500
Subject: [PATCH 5/8] FIX: _fa- -> _flip-

---
 src/99-appendices/11-qmri.md | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 4a8f692020..3264c00615 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -62,14 +62,14 @@ Below is an example file collection for RF transmit field map `TB1EPI`:
 ```text
 └── sub-01/
      └── fmap/
-         ├── sub-01_fa-1_echo-1_TB1EPI.nii.gz
-         ├── sub-01_fa-1_echo-1_TB1EPI.json
-         ├── sub-01_fa-1_echo-2_TB1EPI.nii.gz
-         ├── sub-01_fa-1_echo-2_TB1EPI.json
-         ├── sub-01_fa-2_echo-1_TB1EPI.nii.gz
-         ├── sub-01_fa-2_echo-1_TB1EPI.json
-         ├── sub-01_fa-2_echo-2_TB1EPI.nii.gz
-         └── sub-01_fa-2_echo-2_TB1EPI.json
+         ├── sub-01_flip-1_echo-1_TB1EPI.nii.gz
+         ├── sub-01_flip-1_echo-1_TB1EPI.json
+         ├── sub-01_flip-1_echo-2_TB1EPI.nii.gz
+         ├── sub-01_flip-1_echo-2_TB1EPI.json
+         ├── sub-01_flip-2_echo-1_TB1EPI.nii.gz
+         ├── sub-01_flip-2_echo-1_TB1EPI.json
+         ├── sub-01_flip-2_echo-2_TB1EPI.nii.gz
+         └── sub-01_flip-2_echo-2_TB1EPI.json
 ```
 
 Please visit the [file collections appendix](./10-file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.
@@ -253,10 +253,10 @@ sub-01_T1map.json:
 
 <<Parameter injected by the software/pipeline>>
 
-"BasedOn":["anat/sub-01_fa-1_VFA.nii.gz",
-           "anat/sub-01_fa-2_VFA.nii.gz",
-           "anat/sub-01_fa-3_VFA.nii.gz",
-           "anat/sub-01_fa-4_VFA.nii.gz",
+"BasedOn":["anat/sub-01_flip-1_VFA.nii.gz",
+           "anat/sub-01_flip-2_VFA.nii.gz",
+           "anat/sub-01_flip-3_VFA.nii.gz",
+           "anat/sub-01_flip-4_VFA.nii.gz",
            "fmap/sub-01_TB1map.nii.gz"],
 "EstimationPaper":"Deoni et. al.MRM, 2015",
 "EstimationAlgorithm":"Linear",

From 99c1eabc43dd0dc589fa20436840b5dd1b50ba4d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 12 Feb 2021 15:15:43 -0500
Subject: [PATCH 6/8] FA -> flip angle

---
 src/99-appendices/11-qmri.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 3264c00615..d15e7324bb 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -514,11 +514,11 @@ The first image appears like an anatomical image and the second output is a scal
 To properly identify files of this particular file collection,
 values of the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be followed by freeform entries:
 
-| Anatomical (like) image | Scaled FA map     | Use case             |
-| ----------------------- | ----------------- | -------------------- |
-| `_acq-anat`             | `_acq-famp`       | Single acquisition   |
-| `_acq-anatTest`         | `_acq-fampTest`   | Acquisition `Test`   |
-| `_acq-anatRetest`       | `_acq-fampRetest` | Acquisition `Retest` |
+| Anatomical (like) image | Scaled flip angle map     | Use case             |
+| ----------------------- | ------------------------- | -------------------- |
+| `_acq-anat`             | `_acq-famp`               | Single acquisition   |
+| `_acq-anatTest`         | `_acq-fampTest`           | Acquisition `Test`   |
+| `_acq-anatRetest`       | `_acq-fampRetest`         | Acquisition `Retest` |
 
 ```text
 └── sub-01/

From f6947c37828ebcf2489ea603ba2213285bc26488 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 12 Feb 2021 15:16:10 -0500
Subject: [PATCH 7/8] Escape superscripted asterisks

---
 src/99-appendices/11-qmri.md | 46 ++++++++++++++++++------------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index d15e7324bb..2643d486e9 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -125,18 +125,18 @@ but also by which metadata fields are provided in accompanying json files.
 
 #### Anatomy imaging data
 
-| **File collection**  | **REQUIRED metadata**                                                                                                        | **OPTIONAL metadata**      |
-|----------------------|------------------------------------------------------------------------------------------------------------------------------|----------------------------|
-| VFA                  | `FlipAngle`, `PulseSequenceType`, `RepetitionTimeExcitation`                                                                 | `SpoilingRFPhaseIncrement` |
-| IRT1                 | `InversionTime`                                                                                                              |                            |
-| MP2RAGE<sup>*</sup>  | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots`,`MagneticFieldStrength` | `EchoTime`                 |
-| MESE                 | `EchoTime`                                                                                                                   |                            |
-| MEGRE                | `EchoTime`                                                                                                                   |                            |
-| MTR                  | `MTState`                                                                                                                    |                            |
-| MTS                  | `FlipAngle`, `MTState`, `RepetitionTimeExcitation`                                                                           |                            |
-| MPM                  | `FlipAngle`, `MTState`, `RepetitionTimeExcitation`                                                                           | `EchoTime`                 |
-
-<sup>*</sup> Please see MP2RAGE-specific notes for the calculation of `NumberShots` and regarding the
+| **File collection**   | **REQUIRED metadata**                                                                                                        | **OPTIONAL metadata**      |
+|-----------------------|------------------------------------------------------------------------------------------------------------------------------|----------------------------|
+| VFA                   | `FlipAngle`, `PulseSequenceType`, `RepetitionTimeExcitation`                                                                 | `SpoilingRFPhaseIncrement` |
+| IRT1                  | `InversionTime`                                                                                                              |                            |
+| MP2RAGE<sup>\*</sup>  | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots`,`MagneticFieldStrength` | `EchoTime`                 |
+| MESE                  | `EchoTime`                                                                                                                   |                            |
+| MEGRE                 | `EchoTime`                                                                                                                   |                            |
+| MTR                   | `MTState`                                                                                                                    |                            |
+| MTS                   | `FlipAngle`, `MTState`, `RepetitionTimeExcitation`                                                                           |                            |
+| MPM                   | `FlipAngle`, `MTState`, `RepetitionTimeExcitation`                                                                           | `EchoTime`                 |
+
+<sup>\*</sup> Please see MP2RAGE-specific notes for the calculation of `NumberShots` and regarding the
 organization of `UNIT1` image.
 
 Explanation of the table:
@@ -154,17 +154,17 @@ Explanation of the table:
 
 #### Field maps
 
-| **File collection**     | **REQUIRED metadata**                                                                                |
-|-------------------------|------------------------------------------------------------------------------------------------------|
-| TB1DAM                  | `FlipAngle`                                                                                          |
-| TB1EPI                  | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime`                                            |
-| TB1AFI                  | `RepetitionTime`                                                                                     |
-| TB1TFL                  |                                                                                                      |
-| TB1RFM                  |                                                                                                      |
-| TB1SRGE<sup>*</sup>     | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |
-| RB1COR                  |                                                                                                      |
-
-<sup>*</sup> Please see TB1SRGE-specific notes for the calculation of `NumberShots`.
+| **File collection**  | **REQUIRED metadata**                                                                                |
+|----------------------|------------------------------------------------------------------------------------------------------|
+| TB1DAM               | `FlipAngle`                                                                                          |
+| TB1EPI               | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime`                                            |
+| TB1AFI               | `RepetitionTime`                                                                                     |
+| TB1TFL               |                                                                                                      |
+| TB1RFM               |                                                                                                      |
+| TB1SRGE<sup>\*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |
+| RB1COR               |                                                                                                      |
+
+<sup>\*</sup> Please see TB1SRGE-specific notes for the calculation of `NumberShots`.
 
 ### Metadata requirements for qMRI maps
 

From a5d257ad6eabe72547e5a79482137ee432599630 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 12 Feb 2021 15:18:00 -0500
Subject: [PATCH 8/8] Echo before flip

---
 src/99-appendices/11-qmri.md | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/99-appendices/11-qmri.md b/src/99-appendices/11-qmri.md
index 2643d486e9..f37ac3e341 100644
--- a/src/99-appendices/11-qmri.md
+++ b/src/99-appendices/11-qmri.md
@@ -62,14 +62,14 @@ Below is an example file collection for RF transmit field map `TB1EPI`:
 ```text
 └── sub-01/
      └── fmap/
-         ├── sub-01_flip-1_echo-1_TB1EPI.nii.gz
-         ├── sub-01_flip-1_echo-1_TB1EPI.json
-         ├── sub-01_flip-1_echo-2_TB1EPI.nii.gz
-         ├── sub-01_flip-1_echo-2_TB1EPI.json
-         ├── sub-01_flip-2_echo-1_TB1EPI.nii.gz
-         ├── sub-01_flip-2_echo-1_TB1EPI.json
-         ├── sub-01_flip-2_echo-2_TB1EPI.nii.gz
-         └── sub-01_flip-2_echo-2_TB1EPI.json
+         ├── sub-01_echo-1_flip-1_TB1EPI.nii.gz
+         ├── sub-01_echo-1_flip-1_TB1EPI.json
+         ├── sub-01_echo-2_flip-1_TB1EPI.nii.gz
+         ├── sub-01_echo-2_flip-1_TB1EPI.json
+         ├── sub-01_echo-1_flip-2_TB1EPI.nii.gz
+         ├── sub-01_echo-1_flip-2_TB1EPI.json
+         ├── sub-01_echo-2_flip-2_TB1EPI.nii.gz
+         └── sub-01_echo-2_flip-2_TB1EPI.json
 ```
 
 Please visit the [file collections appendix](./10-file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.