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[ENH] Update AcquisitionDuration definition to match DICOM, define FrameAcquisitionDuration for sparse sequences #1974

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[ENH] Update AcquisitionDuration definition to match DICOM, define FrameAcquisitionDuration for sparse sequences #1974

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10321ad
[ENH] Update definition of Acquisition Duration to match DICOM
effigies Oct 31, 2024
1a773b7
[ENH] Add FrameAcquisitionDuration
effigies Oct 31, 2024
32a7f80
Make AcquisitionDuration optional for all MRI images
effigies Nov 1, 2024
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14 changes: 7 additions & 7 deletions src/modality-specific-files/magnetic-resonance-imaging-data.md
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Expand Up @@ -600,13 +600,13 @@ to be populated for functional sequences. Note that all these options can be
used for non sparse sequences but that only options B, D and E are valid for
sparse sequences.

| | **`RepetitionTime`** | **`SliceTiming`** | **`AcquisitionDuration`** | **`DelayTime`** | **`VolumeTiming`** |
| -------- | -------------------- | ----------------- | ------------------------- | --------------- | ------------------ |
| option A | \[ X ] | | \[ ] | | \[ ] |
| option B | \[ ] | \[ X ] | | \[ ] | \[ X ] |
| option C | \[ ] | | \[ X ] | \[ ] | \[ X ] |
| option D | \[ X ] | \[ X ] | \[ ] | | \[ ] |
| option E | \[ X ] | | \[ ] | \[ X ] | \[ ] |
| | **`RepetitionTime`** | **`SliceTiming`** | **`FrameAcquisitionDuration`** | **`DelayTime`** | **`VolumeTiming`** |
| -------- | -------------------- | ----------------- | ------------------------------ | --------------- | ------------------ |
| option A | \[ X ] | | \[ ] | | \[ ] |
| option B | \[ ] | \[ X ] | | \[ ] | \[ X ] |
| option C | \[ ] | | \[ X ] | \[ ] | \[ X ] |
| option D | \[ X ] | \[ X ] | \[ ] | | \[ ] |
| option E | \[ X ] | | \[ ] | \[ X ] | \[ ] |

**Legend**

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12 changes: 10 additions & 2 deletions src/schema/objects/metadata.yaml
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Expand Up @@ -20,9 +20,8 @@ AcquisitionDuration:
name: AcquisitionDuration
display_name: Acquisition Duration
description: |
Duration (in seconds) of volume acquisition.
Duration (in seconds) of scan acquisition, including all volumes for multi-volume scans.
Corresponds to DICOM Tag 0018, 9073 `Acquisition Duration`.
This field is mutually exclusive with `"RepetitionTime"`.
type: number
exclusiveMinimum: 0
unit: s
Expand Down Expand Up @@ -1198,6 +1197,15 @@ FlipAngle:
unit: degree
exclusiveMinimum: 0
maximum: 360
FrameAcquisitionDuration:
name: AcquisitionDuration
display_name: Acquisition Duration
description: |
Duration (in seconds) of volume acquisition.
Corresponds to DICOM Tag 0018, 9220 `Frame Acquisition Duration`.
type: number
exclusiveMinimum: 0
unit: s
FrameDuration:
name: FrameDuration
display_name: Frame Duration
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16 changes: 8 additions & 8 deletions src/schema/rules/checks/func.yaml
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Expand Up @@ -94,18 +94,18 @@ VolumeTimingRepetitionTimeMutex:
checks:
- type(sidecar.RepetitionTime) == "null"

RepetitionTimeAcquisitionDurationMutex:
RepetitionTimeFrameAcquisitionDurationMutex:
issue:
code: REPETITION_TIME_AND_ACQUISITION_DURATION_MUTUALLY_EXCLUSIVE
message: |
The fields 'RepetitionTime' and 'AcquisitionDuration' for this file are mutually exclusive.
The fields 'RepetitionTime' and 'FrameAcquisitionDuration' for this file are mutually exclusive.
To specify acquisition duration, use 'SliceTiming' or 'DelayTime'
(RepetitionTime - AcquisitionDuration).
(RepetitionTime - FrameAcquisitionDuration).
level: error
selectors:
- type(nifti_header) != "null"
- intersects([suffix], ["asl", "bold"])
- type(sidecar.AcquisitionDuration) != "null"
- type(sidecar.FrameAcquisitionDuration) != "null"
checks:
- type(sidecar.RepetitionTime) == "null"

Expand All @@ -114,7 +114,7 @@ VolumeTimingDelayTimeMutex:
code: VOLUME_TIMING_AND_DELAY_TIME_MUTUALLY_EXCLUSIVE
message: |
The fields 'VolumeTiming' and 'DelayTime' for this file are mutually exclusive.
To specify acquisition duration, use 'AcquisitionDuration' or 'SliceTiming'.
To specify acquisition duration, use 'FrameAcquisitionDuration' or 'SliceTiming'.
level: error
selectors:
- type(nifti_header) != "null"
Expand All @@ -123,15 +123,15 @@ VolumeTimingDelayTimeMutex:
checks:
- type(sidecar.DelayTime) == "null"

VolumeTimingMissingAcquisitionDuration:
VolumeTimingMissingFrameAcquisitionDuration:
issue:
code: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
message: |
The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
The field 'VolumeTiming' requires 'FrameAcquisitionDuration' or 'SliceTiming' to be defined.
level: error
selectors:
- type(nifti_header) != "null"
- intersects([suffix], ["asl", "bold"])
- type(sidecar.VolumeTiming) != "null"
checks:
- '"SliceTiming" in sidecar || "AcquisitionDuration" in sidecar'
- '"SliceTiming" in sidecar || "FrameAcquisitionDuration" in sidecar'
4 changes: 2 additions & 2 deletions src/schema/rules/sidecars/func.yaml
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Expand Up @@ -44,7 +44,7 @@ MRIFuncVolumeTiming:
description_addendum: |
This field is mutually exclusive with `"DelayTime"`.
If defined, this requires acquisition time (TA) be defined via either
`"SliceTiming"` or `"AcquisitionDuration"`.
`"SliceTiming"` or `"FrameAcquisitionDuration"`.

# Timing Parameters
MRIFuncTimingParameters:
Expand All @@ -56,7 +56,7 @@ MRIFuncTimingParameters:
NumberOfVolumesDiscardedByScanner: recommended
NumberOfVolumesDiscardedByUser: recommended
DelayTime: recommended
AcquisitionDuration:
FrameAcquisitionDuration:
level: recommended
level_addendum: |
required for sequences that are described with the `VolumeTiming`
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1 change: 1 addition & 0 deletions src/schema/rules/sidecars/mri.yaml
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Expand Up @@ -232,6 +232,7 @@ MRITimingParameters:
or variable echo time fMRI sequences.
InversionTime: recommended
DwellTime: recommended
AcquisitionDuration: optional

EchoTimeRequiredASL:
selectors:
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