From fb7feb9056751895e5f90f22b3cf37e963092706 Mon Sep 17 00:00:00 2001 From: Patricia Clement <41481345+patsycle@users.noreply.github.com> Date: Tue, 23 Feb 2021 16:23:12 +0100 Subject: [PATCH 1/3] updated TotalAcquiredVolumes into TotalACquiredPairs TotalAcquiredVolumes became TotalAcquiredPairs with the following changes: - required: it appears that this should be required as it is crucial information for quantitative analysis - small changes in description --- .../01-magnetic-resonance-imaging-data.md | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md index aa7f3cee75..1fe990c7c5 100644 --- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md +++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @@ -748,24 +748,24 @@ Additionally, some common metadata fields are REQUIRED for the `*_asl.json`: See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#summary-image-of-the-most-common-asl-sequences) for more information on the most common ASL sequences. #### Common metadata fields applicable to both (P)CASL and PASL -| **Key name** | **Requirement level** | **Data type** | **Description** | -|-----------------------------------|-------------------------------------------------------------------------------|----------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| ArterialSpinLabelingType | REQUIRED | [string][] | `CASL`, `PCASL`, `PASL`. | -| PostLabelingDelay | REQUIRED | [number][] or [array][] of [numbers][] | This is the postlabeling delay (PLD) time, in seconds, after the end of the labeling (for `(P)CASL`) or middle of the labeling pulse (for `PASL`) until the middle of the excitation pulse applied to the imaging slab (for 3D acquisition) or first slice (for 2D acquisition). Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker). In the latter case, the array of numbers contains the PLD of each volume, namely each `control` and `label`, in the acquisition order. Any image within the time-series without a PLD, for example an `m0scan`, is indicated by a zero. Based on DICOM Tags 0018,9079 `Inversion Times` and 0018,0082 `InversionTime`. | -| BackgroundSuppression | REQUIRED | [boolean][] | Boolean indicating if background suppression is used. | -| M0Type | REQUIRED | [string][] | Describes the presence of M0 information, as either: `Separate` when a separate `*_m0scan.nii[.gz]` is present, `Included` when an m0scan volume is contained within the current `*_asl.nii[.gz]`, `Estimate` when a single whole-brain M0 value is provided, or `Absent` when no specific M0 information is present. | -| VascularCrushing | RECOMMENDED | [boolean][] | Boolean indicating if Vascular Crushing is used. Corresponds to DICOM Tag 0018,9259 `ASL Crusher Flag`. | -| AcquisitionVoxelSize | RECOMMENDED | [array][] of [numbers][] | An array of numbers with a length of 3, in millimeters. This parameter denotes the original acquisition voxel size, excluding any inter-slice gaps and before any interpolation or resampling within reconstruction or image processing. Any point spread function effects, for example due to T2-blurring, that would decrease the effective resolution are not considered here. | -| M0Estimate | OPTIONAL, but REQUIRED when `M0Type` is defined as `Estimate` | [number][] | A single numerical whole-brain M0 value (referring to the M0 of blood), only if obtained externally (for example retrieved from CSF in a separate measurement). | -| TotalAcquiredVolumes | OPTIONAL, but RECOMMENDED when not all 3D volumes are provided by the scanner | [array][] of [numbers][] | The original number of 3D volumes acquired for each volume defined in the `*_aslcontext.tsv`. | -| BackgroundSuppressionNumberPulses | OPTIONAL, RECOMMENDED if `BackgroundSuppression` is `true` | [number][] | The number of background suppression pulses used. Note that this excludes any effect of background suppression pulses applied before the labeling. | -| BackgroundSuppressionPulseTime | OPTIONAL, RECOMMENDED if `BackgroundSuppression` is `true` | [array][] of [numbers][] | Array of numbers containing timing, in seconds, of the background suppression pulses with respect to the start of the labeling. In case of multi-PLD with different background suppression pulse times, only the pulse time of the first PLD should be defined. | -| VascularCrushingVENC | OPTIONAL, RECOMMENDED if `VascularCrushing` is `true` | [number][] or [array][] of [numbers][] | The crusher gradient strength, in centimeters per second. Specify either one number for the total time-series, or provide an array of numbers, for example when using QUASAR, using the value zero to identify volumes for which `VascularCrushing` was turned off. Corresponds to DICOM Tag 0018,925A `ASL Crusher Flow Limit`. | -| LabelingOrientation | RECOMMENDED | [array][] of [numbers][] | Orientation of the labeling plane (`(P)CASL`) or slab (`PASL`). The direction cosines of a normal vector perpendicular to the ASL labeling slab or plane with respect to the patient. Corresponds to DICOM Tag 0018,9255 `ASL Slab Orientation`. | -| LabelingDistance | RECOMMENDED | [number][] | Distance from the center of the imaging slab to the center of the labeling plane (`(P)CASL`) or the leading edge of the labeling slab (`PASL`), in millimeters. If the labeling is performed inferior to the isocenter, this number should be negative. Based on DICOM macro C.8.13.5.14. | -| LabelingLocationDescription | RECOMMENDED | [string][] | Description of the location of the labeling plane (`(P)CASL`) or the labeling slab (`PASL`) that cannot be captured by fields ‘LabelingOrientation’ or ‘LabelingDistance’. May include a link to an anonymized screenshot of the planning of the labeling slab/plane with respect to the imaging slab or slices `*_asllabeling.jpg`. Based on DICOM macro C.8.13.5.14. | -| LookLocker | OPTIONAL | [boolean][] | Boolean indicating if a Look-Locker readout is used. | -| LabelingEfficiency | OPTIONAL | [number][] | Labeling efficiency, specified as a number between zero and one, only if obtained externally (for example phase-contrast based). | +| **Key name** | **Requirement level** | **Data type** | **Description** | +|-----------------------------------|---------------------------------------------------------------|----------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| ArterialSpinLabelingType | REQUIRED | [string][] | `CASL`, `PCASL`, `PASL`. | +| PostLabelingDelay | REQUIRED | [number][] or [array][] of [numbers][] | This is the postlabeling delay (PLD) time, in seconds, after the end of the labeling (for `(P)CASL`) or middle of the labeling pulse (for `PASL`) until the middle of the excitation pulse applied to the imaging slab (for 3D acquisition) or first slice (for 2D acquisition). Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker). In the latter case, the array of numbers contains the PLD of each volume, namely each `control` and `label`, in the acquisition order. Any image within the time-series without a PLD, for example an `m0scan`, is indicated by a zero. Based on DICOM Tags 0018,9079 `Inversion Times` and 0018,0082 `InversionTime`. | +| BackgroundSuppression | REQUIRED | [boolean][] | Boolean indicating if background suppression is used. | +| M0Type | REQUIRED | [string][] | Describes the presence of M0 information, as either: `Separate` when a separate `*_m0scan.nii[.gz]` is present, `Included` when an m0scan volume is contained within the current `*_asl.nii[.gz]`, `Estimate` when a single whole-brain M0 value is provided, or `Absent` when no specific M0 information is present. | +| TotalAcquiredPairs | REQUIRED | [array][] of [numbers][] | The total number of acquired `control`-`label` pairs. A single pair consists of a single `control` and a single `label` image. | +| VascularCrushing | RECOMMENDED | [boolean][] | Boolean indicating if Vascular Crushing is used. Corresponds to DICOM Tag 0018,9259 `ASL Crusher Flag`. | +| AcquisitionVoxelSize | RECOMMENDED | [array][] of [numbers][] | An array of numbers with a length of 3, in millimeters. This parameter denotes the original acquisition voxel size, excluding any inter-slice gaps and before any interpolation or resampling within reconstruction or image processing. Any point spread function effects, for example due to T2-blurring, that would decrease the effective resolution are not considered here. | +| M0Estimate | OPTIONAL, but REQUIRED when `M0Type` is defined as `Estimate` | [number][] | A single numerical whole-brain M0 value (referring to the M0 of blood), only if obtained externally (for example retrieved from CSF in a separate measurement). | +| BackgroundSuppressionNumberPulses | OPTIONAL, RECOMMENDED if `BackgroundSuppression` is `true` | [number][] | The number of background suppression pulses used. Note that this excludes any effect of background suppression pulses applied before the labeling. | +| BackgroundSuppressionPulseTime | OPTIONAL, RECOMMENDED if `BackgroundSuppression` is `true` | [array][] of [numbers][] | Array of numbers containing timing, in seconds, of the background suppression pulses with respect to the start of the labeling. In case of multi-PLD with different background suppression pulse times, only the pulse time of the first PLD should be defined. | +| VascularCrushingVENC | OPTIONAL, RECOMMENDED if `VascularCrushing` is `true` | [number][] or [array][] of [numbers][] | The crusher gradient strength, in centimeters per second. Specify either one number for the total time-series, or provide an array of numbers, for example when using QUASAR, using the value zero to identify volumes for which `VascularCrushing` was turned off. Corresponds to DICOM Tag 0018,925A `ASL Crusher Flow Limit`. | +| LabelingOrientation | RECOMMENDED | [array][] of [numbers][] | Orientation of the labeling plane (`(P)CASL`) or slab (`PASL`). The direction cosines of a normal vector perpendicular to the ASL labeling slab or plane with respect to the patient. Corresponds to DICOM Tag 0018,9255 `ASL Slab Orientation`. | +| LabelingDistance | RECOMMENDED | [number][] | Distance from the center of the imaging slab to the center of the labeling plane (`(P)CASL`) or the leading edge of the labeling slab (`PASL`), in millimeters. If the labeling is performed inferior to the isocenter, this number should be negative. Based on DICOM macro C.8.13.5.14. | +| LabelingLocationDescription | RECOMMENDED | [string][] | Description of the location of the labeling plane (`(P)CASL`) or the labeling slab (`PASL`) that cannot be captured by fields ‘LabelingOrientation’ or ‘LabelingDistance’. May include a link to an anonymized screenshot of the planning of the labeling slab/plane with respect to the imaging slab or slices `*_asllabeling.jpg`. Based on DICOM macro C.8.13.5.14. | +| LookLocker | OPTIONAL | [boolean][] | Boolean indicating if a Look-Locker readout is used. | +| LabelingEfficiency | OPTIONAL | [number][] | Labeling efficiency, specified as a number between zero and one, only if obtained externally (for example phase-contrast based). | #### (P)CASL-specific metadata fields These fields can only be used when `ArterialSpinLabelingType` is `CASL` or `PCASL`. See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#pcasl-sequence) for more information on the (P)CASL sequence and the Labeling Pulse fields. From 7bf0d492c8ee22d753dc028f5e926cea0f3a567b Mon Sep 17 00:00:00 2001 From: Patricia Clement <41481345+patsycle@users.noreply.github.com> Date: Tue, 23 Feb 2021 16:28:52 +0100 Subject: [PATCH 2/3] update TotalAcquiredPairs changed array of numbers into number --- .../01-magnetic-resonance-imaging-data.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md index 1fe990c7c5..e64fd9320b 100644 --- a/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md +++ b/src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md @@ -754,7 +754,7 @@ See [Appendix XII - ASL](../99-appendices/12-arterial-spin-labeling.md#summary-i | PostLabelingDelay | REQUIRED | [number][] or [array][] of [numbers][] | This is the postlabeling delay (PLD) time, in seconds, after the end of the labeling (for `(P)CASL`) or middle of the labeling pulse (for `PASL`) until the middle of the excitation pulse applied to the imaging slab (for 3D acquisition) or first slice (for 2D acquisition). Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker). In the latter case, the array of numbers contains the PLD of each volume, namely each `control` and `label`, in the acquisition order. Any image within the time-series without a PLD, for example an `m0scan`, is indicated by a zero. Based on DICOM Tags 0018,9079 `Inversion Times` and 0018,0082 `InversionTime`. | | BackgroundSuppression | REQUIRED | [boolean][] | Boolean indicating if background suppression is used. | | M0Type | REQUIRED | [string][] | Describes the presence of M0 information, as either: `Separate` when a separate `*_m0scan.nii[.gz]` is present, `Included` when an m0scan volume is contained within the current `*_asl.nii[.gz]`, `Estimate` when a single whole-brain M0 value is provided, or `Absent` when no specific M0 information is present. | -| TotalAcquiredPairs | REQUIRED | [array][] of [numbers][] | The total number of acquired `control`-`label` pairs. A single pair consists of a single `control` and a single `label` image. | +| TotalAcquiredPairs | REQUIRED | [number][] | The total number of acquired `control`-`label` pairs. A single pair consists of a single `control` and a single `label` image. | | VascularCrushing | RECOMMENDED | [boolean][] | Boolean indicating if Vascular Crushing is used. Corresponds to DICOM Tag 0018,9259 `ASL Crusher Flag`. | | AcquisitionVoxelSize | RECOMMENDED | [array][] of [numbers][] | An array of numbers with a length of 3, in millimeters. This parameter denotes the original acquisition voxel size, excluding any inter-slice gaps and before any interpolation or resampling within reconstruction or image processing. Any point spread function effects, for example due to T2-blurring, that would decrease the effective resolution are not considered here. | | M0Estimate | OPTIONAL, but REQUIRED when `M0Type` is defined as `Estimate` | [number][] | A single numerical whole-brain M0 value (referring to the M0 of blood), only if obtained externally (for example retrieved from CSF in a separate measurement). | From d391a53393f58a2b0f01db3d8160abc76e217e1b Mon Sep 17 00:00:00 2001 From: bids-maintenance Date: Tue, 23 Feb 2021 18:48:04 +0000 Subject: [PATCH 3/3] [DOC] Auto-generate changelog entry for PR #742 --- src/CHANGES.md | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/src/CHANGES.md b/src/CHANGES.md index 5f33b4ab3b..fa2b3a7dd8 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -2,13 +2,15 @@ ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) -- FIX: Add deprecated anatomical MRI suffixes back into schema [#725](https://github.com/bids-standard/bids-specification/pull/725) ([tsalo](https://github.com/tsalo)) -- FIX: Correct schema irregularities for func datatype [#724](https://github.com/bids-standard/bids-specification/pull/724) ([tsalo](https://github.com/tsalo)) -- FIX: Make flip optional for MP2RAGE [#722](https://github.com/bids-standard/bids-specification/pull/722) ([tsalo](https://github.com/tsalo)) -- FIX: Correct entity names in YAML files [#720](https://github.com/bids-standard/bids-specification/pull/720) ([tsalo](https://github.com/tsalo)) -- ENH: Clarify run indexing information for MRI acquisitions [#719](https://github.com/bids-standard/bids-specification/pull/719) ([effigies](https://github.com/effigies)) -- ENH: Harmonize CoordinateSystem details for MRI, MEG, EEG, iEEG [#717](https://github.com/bids-standard/bids-specification/pull/717) ([sappelhoff](https://github.com/sappelhoff)) -- SCHEMA: Update entity YAML keys [#714](https://github.com/bids-standard/bids-specification/pull/714) ([effigies](https://github.com/effigies)) +- Updated TotalAcquiredVolumes into TotalAcquiredPairs [#742](https://github.com/bids-standard/bids-specification/pull/742) ([effigies](https://github.com/effigies)) +- \[SCHEMA] Update qMRI fieldmap schema [#728](https://github.com/bids-standard/bids-specification/pull/728) ([effigies](https://github.com/effigies)) +- \[FIX] Add deprecated anatomical MRI suffixes back into schema [#725](https://github.com/bids-standard/bids-specification/pull/725) ([tsalo](https://github.com/tsalo)) +- \[FIX] Correct schema irregularities for func datatype [#724](https://github.com/bids-standard/bids-specification/pull/724) ([tsalo](https://github.com/tsalo)) +- \[FIX] Make flip optional for MP2RAGE [#722](https://github.com/bids-standard/bids-specification/pull/722) ([tsalo](https://github.com/tsalo)) +- \[FIX] Correct entity names in YAML files [#720](https://github.com/bids-standard/bids-specification/pull/720) ([tsalo](https://github.com/tsalo)) +- \[ENH] Clarify run indexing information for MRI acquisitions [#719](https://github.com/bids-standard/bids-specification/pull/719) ([effigies](https://github.com/effigies)) +- \[ENH] Harmonize CoordinateSystem details for MRI, MEG, EEG, iEEG [#717](https://github.com/bids-standard/bids-specification/pull/717) ([sappelhoff](https://github.com/sappelhoff)) +- \[SCHEMA] Update entity YAML keys [#714](https://github.com/bids-standard/bids-specification/pull/714) ([effigies](https://github.com/effigies)) - \[MISC] Added full names for some contributors in .mailmap file [#705](https://github.com/bids-standard/bids-specification/pull/705) ([yarikoptic](https://github.com/yarikoptic)) - \[INFRA] Migrate md and yml checks from travis to GH actions [#693](https://github.com/bids-standard/bids-specification/pull/693) ([sappelhoff](https://github.com/sappelhoff)) - \[INFRA] Move part entity to before recording entity [#692](https://github.com/bids-standard/bids-specification/pull/692) ([tsalo](https://github.com/tsalo))