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[SCHEMA] Update qMRI fieldmap schema #728

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Feb 12, 2021
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[SCHEMA] Update qMRI fieldmap schema #728

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0ed5d04
Update qMRI fieldmap schema
effigies Feb 10, 2021
9672f91
FIX: TB1RFM -> TB1RMF
effigies Feb 10, 2021
ab25456
SCHEMA: Move TB1map+RB1map to fmap datatype
effigies Feb 11, 2021
3bfeabb
TB1RMF -> TB1RFM
effigies Feb 12, 2021
6aad805
FIX: _fa- -> _flip-
effigies Feb 12, 2021
99c1eab
FA -> flip angle
effigies Feb 12, 2021
f6947c3
Escape superscripted asterisks
effigies Feb 12, 2021
a5d257a
Echo before flip
effigies Feb 12, 2021
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2 changes: 1 addition & 1 deletion src/99-appendices/10-file-collections.md
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Expand Up @@ -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). |
82 changes: 41 additions & 41 deletions src/99-appendices/11-qmri.md
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Expand Up @@ -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_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.
Expand Down Expand Up @@ -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:
Expand All @@ -154,17 +154,17 @@ Explanation of the table:

#### Field maps

| **File collection** | **REQUIRED metadata** |
|-------------------------|------------------------------------------------------------------------------------------------------|
| TB1DAM | `FlipAngle` |
| TB1EPI | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime` |
| TB1AFI | `RepetitionTime` |
| TB1TFL | |
| TB1RMF | |
| TB1SRGE<sup>*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreperation`, `NumberShots` |
| RB1COR | |
| **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`.
<sup>\*</sup> Please see TB1SRGE-specific notes for the calculation of `NumberShots`.

### Metadata requirements for qMRI maps

Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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

Expand Down Expand Up @@ -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.
Expand All @@ -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/
Expand Down
2 changes: 0 additions & 2 deletions src/schema/datatypes/anat.yaml
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Expand Up @@ -42,8 +42,6 @@
- MTVmap
- PDT2map
- Chimap
- TB1map
- RB1map
- S0map
- M0map
extensions:
Expand Down
64 changes: 60 additions & 4 deletions src/schema/datatypes/fmap.yaml
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@@ -1,5 +1,5 @@
---
# First group
# Fieldmaps
- suffixes:
- phasediff
- phase1
Expand All @@ -17,7 +17,7 @@
session: optional
acquisition: optional
run: optional
# Second group
# PEPolar
- suffixes:
- epi
- m0scan
Expand All @@ -32,7 +32,7 @@
ceagent: optional
direction: required
run: optional
# Third group
# TB1DAM
- suffixes:
- TB1DAM
extensions:
Expand All @@ -47,8 +47,9 @@
ceagent: optional
reconstruction: optional
flip: required
inversion: optional
part: optional
# Fourth group
# TB1EPI
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- suffixes:
- TB1EPI
extensions:
Expand All @@ -64,4 +65,59 @@
reconstruction: optional
echo: required
flip: required
inversion: optional
part: optional
# RFFieldMaps
- suffixes:
- TB1AFI
- TB1TFL
- TB1RFM
- 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
# Parametric
- suffixes:
- TB1map
- RB1map
extensions:
- .nii.gz
- .nii
- .json
entities:
subject: required
session: optional
run: optional
acquisition: optional
ceagent: optional
reconstruction: optional