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[ENH] Add generic metadata from BEP22 to MRI #1396

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Apr 11, 2024
Merged

[ENH] Add generic metadata from BEP22 to MRI #1396

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42925e0
ENH: Add sample metadata to MRI and PET
Remi-Gau Feb 5, 2023
3664403
ENH: Add generic metadata from BEP22 to MRI
Remi-Gau Feb 5, 2023
fb1f5cc
Merge remote-tracking branch 'upstream/master' into extra_mri_metadata
Remi-Gau Aug 24, 2023
22073a5
rm sample
Remi-Gau Aug 24, 2023
a9126e4
Update src/schema/objects/metadata.yaml
markmikkelsen Apr 10, 2024
f5f554b
Update src/schema/objects/metadata.yaml
markmikkelsen Apr 10, 2024
bfc116d
Update src/schema/objects/metadata.yaml
markmikkelsen Apr 10, 2024
f934160
rm macros with missing metadata
Remi-Gau Apr 11, 2024
f3dd861
Merge remote-tracking branch 'upstream/master' into extra_mri_metadata
Remi-Gau Apr 11, 2024
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12 changes: 12 additions & 0 deletions src/modality-specific-files/magnetic-resonance-imaging-data.md
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Expand Up @@ -162,6 +162,18 @@ A guide for using macros can be found at
-->
{{ MACROS___make_sidecar_table("mri.MRIEchoPlanarImagingAndB0Mapping") }}

#### Tissue description

<!-- This block generates a metadata table.
These tables are defined in
src/schema/rules/sidecars
The definitions of the fields specified in these tables may be found in
src/schema/objects/metadata.yaml
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("mri.MRISample") }}

## Anatomy imaging data

Anatomy MRI sequences measure static, structural features of the brain.
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12 changes: 12 additions & 0 deletions src/modality-specific-files/positron-emission-tomography.md
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Expand Up @@ -216,6 +216,18 @@ A guide for using macros can be found at

{{ MACROS___make_sidecar_table("pet.PETInstitutionInformation") }}

#### Tissue description

<!-- This block generates a metadata table.
These tables are defined in
src/schema/rules/sidecars
The definitions of the fields specified in these tables may be found in
src/schema/objects/metadata.yaml
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("pet.PETSample") }}

#### Task

If the OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used,
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36 changes: 36 additions & 0 deletions src/schema/objects/metadata.yaml
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Expand Up @@ -237,6 +237,18 @@ B0FieldSource:
- type: array
items:
type: string
B0ShimmingTechnique:
name: B0ShimmingTechnique
display_name: B0 Shimming Technique
description: |
The technique used to shim the *B<sub>0</sub>* field (for example, `"FASTMAP"`).
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type: string
B1ShimmingTechnique:
name: B1ShimmingTechnique
display_name: B1 Shimming Technique
description: |
The technique used to shim the *B<sub>1</sub>* field (for example, `"Simple phase align"`).
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type: string
BIDSVersion:
name: BIDSVersion
display_name: BIDS Version
Expand Down Expand Up @@ -2197,6 +2209,12 @@ NumberOfVolumesDiscardedByUser:
`"NumberOfVolumesDiscardedByUser"` field.
type: integer
minimum: 0
NumberReceiveCoilActiveElements:
name: NumberReceiveCoilActiveElements
display_name: Number of Receive Coil Active Elements
description: |
The number of active RF elements used by the receive coil.
type: integer
NumberShots:
name: NumberShots
display_name: Number Shots
Expand All @@ -2216,6 +2234,12 @@ NumberShots:
- type: array
items:
type: number
NumberTransmitCoilActiveElements:
name: NumberTransmitCoilActiveElements
display_name: Number of Transmit Coil Active Elements
description: |
The number of active RF elements used by the transmit coil.
type: integer
NumericalAperture:
name: NumericalAperture
display_name: Numerical Aperture
Expand Down Expand Up @@ -3578,6 +3602,18 @@ VolumeTiming:
items:
type: number
unit: s
WaterSuppression:
name: WaterSuppression
display_name: Water Suppression
description: |
Boolean indicating whether water suppression was used prior to acquisition.
type: boolean
WaterSuppressionTechnique:
name: WaterSuppressionTechnique
display_name: Water Suppression Technique
description: |
The name of the pulse sequence used for water suppression (for example, `"CHESS"`, `"VAPOR"`).
type: string
WholeBloodAvail:
name: WholeBloodAvail
display_name: Whole Blood Avail
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6 changes: 6 additions & 0 deletions src/schema/rules/sidecars/mri.yaml
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Expand Up @@ -30,10 +30,12 @@ MRIHardware:
level: recommended, but required for Arterial Spin Labeling
ReceiveCoilName: recommended
ReceiveCoilActiveElements: recommended
NumberReceiveCoilActiveElements: optional
GradientSetType: recommended
MRTransmitCoilSequence: recommended
MatrixCoilMode: recommended
CoilCombinationMethod: recommended
NumberTransmitCoilActiveElements: optional

MRIScannerHardwareASL:
selectors:
Expand Down Expand Up @@ -67,6 +69,10 @@ MRISequenceSpecifics:
SpoilingRFPhaseIncrement: optional
SpoilingGradientMoment: optional
SpoilingGradientDuration: optional
WaterSuppression: optional
WaterSuppressionTechnique: optional
Comment on lines +82 to +83
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@markmikkelsen markmikkelsen Feb 29, 2024 •
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@effigies DICOM tag (0018,9025) fits these, but the value is not boolean as is proposed in #1377. The DICOM tag also covers OuterVolumeSuppression that the MRS BEP includes (which would be the FAT value in DICOM).

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So do we want to add something like the following to WaterSuppression:

Corresponds to DICOM Tag 0018, 9025 SpectrallySelectedSuppression.
If present and not NONE, then this value SHOULD be True, otherwise False.

And the following to WaterSuppressionTechnique?

Corresponds to DICOM Tag 0018, 9025 SpectrallySelectedSuppression.
May be omitted if the value is NONE.

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Makes sense to me! And the same would be the case for OuterVolumeSuppression.

B0ShimmingTechnique: optional
B1ShimmingTechnique: optional

PETMRISequenceSpecifics:
selectors:
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