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Merged
merged 11 commits into from
Dec 1, 2020
Merged

[ENH] BEP001 - New entities: inv & mt #681

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b7b01ae
Merge pull request #3 from bids-standard/master
agahkarakuzu Nov 11, 2020
436791d
Merge pull request #6 from bids-standard/master
agahkarakuzu Nov 23, 2020
6ab9640
add entity inv
agahkarakuzu Nov 23, 2020
dca0455
add mt:
agahkarakuzu Nov 23, 2020
0c70b56
add MT specific metadata
agahkarakuzu Nov 23, 2020
0a6c067
Generate entity.md
agahkarakuzu Nov 23, 2020
380fd3d
Update src/04-modality-specific-files/01-magnetic-resonance-imaging-d…
agahkarakuzu Nov 24, 2020
d34ac6f
Update src/schema/entities.yaml
agahkarakuzu Nov 24, 2020
a684410
table fix by @sappelhoff
agahkarakuzu Nov 25, 2020
f6f173a
Merge remote-tracking branch 'origin/entity-inv-mt' into entity-inv-mt
agahkarakuzu Nov 25, 2020
fe8ea37
Conditional requirement
agahkarakuzu Nov 26, 2020
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20 changes: 13 additions & 7 deletions src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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Expand Up @@ -45,13 +45,19 @@ that a given scan was collected with the intended coil elements selected

| **Key name** | **Requirement level** | **Data type** | **Description** |
|-----------------------------|-----------------------|----------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| PulseSequenceType | RECOMMENDED | [string][] | A general description of the pulse sequence used for the scan (for example, MPRAGE, Gradient Echo EPI, Spin Echo EPI, Multiband gradient echo EPI). |
| ScanningSequence | RECOMMENDED | [string][] or [array][] of [strings][] | Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 `Scanning Sequence`. |
| SequenceVariant | RECOMMENDED | [string][] or [array][] of [strings][] | Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 `Sequence Variant`. |
| ScanOptions | RECOMMENDED | [string][] or [array][] of [strings][] | Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 `Scan Options`. |
| SequenceName | RECOMMENDED | [string][] | Manufacturer's designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 `Sequence Name`. |
| PulseSequenceDetails | RECOMMENDED | [string][] | Information beyond pulse sequence type that identifies the specific pulse sequence used (for example, "Standard Siemens Sequence distributed with the VB17 software," "Siemens WIP ### version #.##," or "Sequence written by X using a version compiled on MM/DD/YYYY"). |
| NonlinearGradientCorrection | RECOMMENDED | [boolean][] | Boolean stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence. |
| PulseSequenceType | RECOMMENDED | [string][] | A general description of the pulse sequence used for the scan (for example, MPRAGE, Gradient Echo EPI, Spin Echo EPI, Multiband gradient echo EPI). |
| ScanningSequence | RECOMMENDED | [string][] or [array][] of [strings][] | Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 `Scanning Sequence`. |
| SequenceVariant | RECOMMENDED | [string][] or [array][] of [strings][] | Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 `Sequence Variant`. |
| ScanOptions | RECOMMENDED | [string][] or [array][] of [strings][] | Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 `Scan Options`. |
| SequenceName | RECOMMENDED | [string][] | Manufacturer's designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 `Sequence Name`. |
| PulseSequenceDetails | RECOMMENDED | [string][] | Information beyond pulse sequence type that identifies the specific pulse sequence used (for example, "Standard Siemens Sequence distributed with the VB17 software," "Siemens WIP ### version #.##," or "Sequence written by X using a version compiled on MM/DD/YYYY"). |
| NonlinearGradientCorrection | RECOMMENDED | [boolean][] | Boolean stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence. |
| MTState | RECOMMENDED | [boolean][] | Boolean stating whether the magnetization transfer pulse is applied. Corresponds to DICOM tag (0018, 9020) `Magnetization Transfer`. |
| MTOffsetFrequency | RECOMMENDED if the MTstate is `True`. | [number][] | The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz). |
| MTPulseBandwidth | RECOMMENDED if the MTstate is `True`. | [number][] | The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz). |
| MTNumberOfPulses | RECOMMENDED if the MTstate is `True`. | [number][] | The number of magnetization transfer RF pulses applied before the readout. |
| MTPulseShape | RECOMMENDED if the MTstate is `True`. | [string][] | Shape of the magnetization transfer RF pulse waveform. Accepted values: `HARD`, `GAUSSIAN`, `GAUSSHANN` (gaussian pulse with Hanning window), `SINC`, `SINCHANN` (sinc pulse with Hanning window), `SINCGAUSS` (sinc pulse with Gaussian window), `FERMI`. |
| MTPulseDuration | RECOMMENDED if the MTstate is `True`. | [number][] | Duration of the magnetization transfer RF pulse in seconds. |

### In-Plane Spatial Encoding
| **Key name** | **Requirement level** | **Data type** | **Description** |
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26 changes: 26 additions & 0 deletions src/99-appendices/09-entities.md
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Expand Up @@ -157,6 +157,32 @@ This entity represents the `FlipAngle` metadata field. Please note that the `<in
denotes the number/index (in the form of a nonnegative integer), not the `FlipAngle`
value which needs to be stored in the field `FlipAngle` of the separate JSON file.

## inv

Full name: Inversion Time

Format: `inv-<index>`

Definition: If files belonging to an entity-linked file collection are acquired at different
inversion times, the `_inv-<index>` key/value pair MUST be used to distinguish
individual files.
This entity represents the `InversionTime` metadata field. Please note that the `<index>`
denotes the number/index (in the form of a nonnegative integer), not the `InversionTime`
value which needs to be stored in the field `InversionTime` of the separate JSON file.

## mt

Full name: Magnetization Transfer

Format: `mt-<label>`

Definition: If files belonging to an entity-linked file collection are acquired at different
magnetization transfer (MT) states, the `_mt-<label>` key/value pair MUST be used to
distinguish individual files.
This entity represents the `MTState` metadata field. Allowed label values for this
entity are `on` and `off`, for images acquired in presence and absence of an MT pulse,
respectively.

## recording

Full name: Recording
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22 changes: 22 additions & 0 deletions src/schema/entities.yaml
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Expand Up @@ -121,6 +121,28 @@ flip:
denotes the number/index (in the form of a nonnegative integer), not the `FlipAngle`
value which needs to be stored in the field `FlipAngle` of the separate JSON file.
format: index
inv:
name: Inversion Time
entity: inv
description: |
If files belonging to an entity-linked file collection are acquired at different
inversion times, the `_inv-<index>` key/value pair MUST be used to distinguish
individual files.
This entity represents the `InversionTime` metadata field. Please note that the `<index>`
denotes the number/index (in the form of a nonnegative integer), not the `InversionTime`
value which needs to be stored in the field `InversionTime` of the separate JSON file.
format: index
mt:
name: Magnetization Transfer
entity: mt
description: |
If files belonging to an entity-linked file collection are acquired at different
magnetization transfer (MT) states, the `_mt-<label>` key/value pair MUST be used to
distinguish individual files.
This entity represents the `MTState` metadata field. Allowed label values for this
entity are `on` and `off`, for images acquired in presence and absence of an MT pulse,
respectively.
format: label
recording:
name: Recording
entity: recording
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