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Update qMRI fieldmap schema (#728)
* Update qMRI fieldmap schema * FIX: TB1RFM -> TB1RMF Normalizing to the most common. Cannot find a canonical reference outside of BIDS, so it may be backward. * SCHEMA: Move TB1map+RB1map to fmap datatype * TB1RMF -> TB1RFM * FIX: _fa- -> _flip- * FA -> flip angle * Escape superscripted asterisks * Echo before flip
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‎src/99-appendices/10-file-collections.md‎

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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| 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. |
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| 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)). |
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| 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). |

‎src/99-appendices/11-qmri.md‎

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@@ -62,14 +62,14 @@ Below is an example file collection for RF transmit field map `TB1EPI`:
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```text
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└── sub-01/
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└── fmap/
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├── sub-01_fa-1_echo-1_TB1EPI.nii.gz
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├── sub-01_fa-1_echo-1_TB1EPI.json
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├── sub-01_fa-1_echo-2_TB1EPI.nii.gz
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├── sub-01_fa-1_echo-2_TB1EPI.json
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├── sub-01_fa-2_echo-1_TB1EPI.nii.gz
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├── sub-01_fa-2_echo-1_TB1EPI.json
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├── sub-01_fa-2_echo-2_TB1EPI.nii.gz
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└── sub-01_fa-2_echo-2_TB1EPI.json
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├── sub-01_echo-1_flip-1_TB1EPI.nii.gz
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├── sub-01_echo-1_flip-1_TB1EPI.json
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├── sub-01_echo-2_flip-1_TB1EPI.nii.gz
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├── sub-01_echo-2_flip-1_TB1EPI.json
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├── sub-01_echo-1_flip-2_TB1EPI.nii.gz
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├── sub-01_echo-1_flip-2_TB1EPI.json
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├── sub-01_echo-2_flip-2_TB1EPI.nii.gz
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└── sub-01_echo-2_flip-2_TB1EPI.json
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```
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Please visit the [file collections appendix](./10-file-collections.md#magnetic-resonance-imaging) to see the list of currently supported qMRI applications.
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#### Anatomy imaging data
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| **File collection** | **REQUIRED metadata** | **OPTIONAL metadata** |
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|----------------------|------------------------------------------------------------------------------------------------------------------------------|----------------------------|
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| VFA | `FlipAngle`, `PulseSequenceType`, `RepetitionTimeExcitation` | `SpoilingRFPhaseIncrement` |
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| IRT1 | `InversionTime` | |
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| MP2RAGE<sup>*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots`,`MagneticFieldStrength` | `EchoTime` |
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| MESE | `EchoTime` | |
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| MEGRE | `EchoTime` | |
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| MTR | `MTState` | |
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| MTS | `FlipAngle`, `MTState`, `RepetitionTimeExcitation` | |
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| MPM | `FlipAngle`, `MTState`, `RepetitionTimeExcitation` | `EchoTime` |
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<sup>*</sup> Please see MP2RAGE-specific notes for the calculation of `NumberShots` and regarding the
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| **File collection** | **REQUIRED metadata** | **OPTIONAL metadata** |
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|-----------------------|------------------------------------------------------------------------------------------------------------------------------|----------------------------|
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| VFA | `FlipAngle`, `PulseSequenceType`, `RepetitionTimeExcitation` | `SpoilingRFPhaseIncrement` |
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| IRT1 | `InversionTime` | |
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| MP2RAGE<sup>\*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots`,`MagneticFieldStrength` | `EchoTime` |
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| MESE | `EchoTime` | |
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| MEGRE | `EchoTime` | |
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| MTR | `MTState` | |
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| MTS | `FlipAngle`, `MTState`, `RepetitionTimeExcitation` | |
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| MPM | `FlipAngle`, `MTState`, `RepetitionTimeExcitation` | `EchoTime` |
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<sup>\*</sup> Please see MP2RAGE-specific notes for the calculation of `NumberShots` and regarding the
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organization of `UNIT1` image.
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Explanation of the table:
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#### Field maps
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| **File collection** | **REQUIRED metadata** |
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|-------------------------|------------------------------------------------------------------------------------------------------|
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| TB1DAM | `FlipAngle` |
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| TB1EPI | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime` |
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| TB1AFI | `RepetitionTime` |
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| TB1TFL | |
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| TB1RMF | |
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| TB1SRGE<sup>*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |
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| RB1COR | |
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| **File collection** | **REQUIRED metadata** |
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|----------------------|------------------------------------------------------------------------------------------------------|
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| TB1DAM | `FlipAngle` |
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| TB1EPI | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime` |
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| TB1AFI | `RepetitionTime` |
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| TB1TFL | |
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| TB1RFM | |
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| TB1SRGE<sup>\*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |
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| RB1COR | |
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<sup>*</sup> Please see TB1SRGE-specific notes for the calculation of `NumberShots`.
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<sup>\*</sup> Please see TB1SRGE-specific notes for the calculation of `NumberShots`.
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### Metadata requirements for qMRI maps
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<<Parameter injected by the software/pipeline>>
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"BasedOn":["anat/sub-01_fa-1_VFA.nii.gz",
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"anat/sub-01_fa-2_VFA.nii.gz",
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"anat/sub-01_fa-3_VFA.nii.gz",
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"anat/sub-01_fa-4_VFA.nii.gz",
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"BasedOn":["anat/sub-01_flip-1_VFA.nii.gz",
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"anat/sub-01_flip-2_VFA.nii.gz",
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"anat/sub-01_flip-3_VFA.nii.gz",
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"anat/sub-01_flip-4_VFA.nii.gz",
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"fmap/sub-01_TB1map.nii.gz"],
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"EstimationPaper":"Deoni et. al.MRM, 2015",
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"EstimationAlgorithm":"Linear",
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Instead of introducing an entity that is exclusive to a single application,
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method developers who commonly use these file collections for the `MPM` application reached
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the consensus on the use of `acq` entity to distinguish individual files.
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These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RMF`, and `RB1COR`.
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These suffixes include: `TB1AFI`, `TB1TFL`, `TB1RFM`, and `RB1COR`.
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#### `TB1EPI` specific notes
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└── sub-01_acq-tr2_TB1AFI.json
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```
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#### `TB1TFL` and `TB1RMF` specific notes
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#### `TB1TFL` and `TB1RFM` specific notes
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These suffixes describe two outputs generated by Siemens `tfl_b1_map` and `rf_map` product sequences, respectively.
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Both sequences output two images.
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To properly identify files of this particular file collection,
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values of the `acq` entity SHOULD begin with either `anat` or `famp` and MAY be followed by freeform entries:
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| Anatomical (like) image | Scaled FA map | Use case |
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| ----------------------- | ----------------- | -------------------- |
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| `_acq-anat` | `_acq-famp` | Single acquisition |
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| `_acq-anatTest` | `_acq-fampTest` | Acquisition `Test` |
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| `_acq-anatRetest` | `_acq-fampRetest` | Acquisition `Retest` |
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| Anatomical (like) image | Scaled flip angle map | Use case |
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| ----------------------- | ------------------------- | -------------------- |
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| `_acq-anat` | `_acq-famp` | Single acquisition |
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| `_acq-anatTest` | `_acq-fampTest` | Acquisition `Test` |
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| `_acq-anatRetest` | `_acq-fampRetest` | Acquisition `Retest` |
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```text
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└── sub-01/

‎src/schema/datatypes/anat.yaml‎

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- MTVmap
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- PDT2map
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- Chimap
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- TB1map
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- RB1map
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- S0map
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- M0map
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extensions:

‎src/schema/datatypes/fmap.yaml‎

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---
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# First group
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# Fieldmaps
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- suffixes:
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- phasediff
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- phase1
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session: optional
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acquisition: optional
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run: optional
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# Second group
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# PEPolar
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- suffixes:
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- epi
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- m0scan
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ceagent: optional
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direction: required
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run: optional
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# Third group
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# TB1DAM
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- suffixes:
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- TB1DAM
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extensions:
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ceagent: optional
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reconstruction: optional
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flip: required
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inversion: optional
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part: optional
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# Fourth group
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# TB1EPI
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- suffixes:
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- TB1EPI
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extensions:
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reconstruction: optional
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echo: required
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flip: required
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inversion: optional
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part: optional
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# RFFieldMaps
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- suffixes:
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- TB1AFI
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- TB1TFL
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- TB1RFM
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- RB1COR
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extensions:
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- .nii.gz
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- .nii
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- .json
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entities:
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subject: required
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session: optional
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run: optional
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acquisition: optional
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ceagent: optional
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reconstruction: optional
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echo: optional
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flip: optional
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inversion: optional
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part: optional
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# TB1SRGE
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- suffixes:
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- TB1SRGE
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extensions:
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- .nii.gz
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- .nii
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- .json
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entities:
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subject: required
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session: optional
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run: optional
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acquisition: optional
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ceagent: optional
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reconstruction: optional
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echo: optional
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flip: required
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inversion: required
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part: optional
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# Parametric
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- suffixes:
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- TB1map
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- RB1map
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extensions:
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- .nii.gz
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- .nii
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- .json
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entities:
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subject: required
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session: optional
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run: optional
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acquisition: optional
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ceagent: optional
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reconstruction: optional

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