From d794736823d8d4f5005ab503905685c83446ccf9 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Fri, 15 Jan 2021 10:18:55 +0100 Subject: [PATCH] [ENH] Bep 005: Arterial Spin Labeling (#669) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * [ENH] Bep 005: Arterial Spin Labeling (#652) Co-authored-by: Patricia Clement <41481345+patsycle@users.noreply.github.com> Co-authored-by: Stefan Appelhoff Co-authored-by: Chris Markiewicz Co-authored-by: Julia Guiomar Niso GalΓ‘n Co-authored-by: Remi Gau * Update table errors * correction for table issues 'common metadata for PCASL/PASL' * correction latin phrases * Corrections tables * correction tables Cases * added link pepolar * deleted 'don't discriminate between types of labeling based on comment Thijs Van Osch * Moved MagneticFieldStrenght asl requirement to common * removed scaling factor info based on comment gllmflndn Removed: all ancillary scaling factors should be taken into account in the conversion to BIDS, which is why BIDS does not provide a separate scaling factor field other than the NIfTI header. * added MRAcquisitionType added in the common - sequence specifics table Reason: for ASL, defining 2D and 3D is required. This used to be added in the PulseSequenceType field, but this should stay a free text field. Therefore, the MRAcquisitionType field is added (based on DicomTag). * removed PulseSequenceType from the ASL part The 2D/3D information needed for ASL, is now moved to the new MRAcquisitionType field. * added required common fields sentence Some Common fields are required for ASL. To stress this out, we added a sentence for the *_as.json and the *_m0scan.json. * adaptation requirements for m0scan.json * adapted requirement level common fields for m0scan * update sentence required common fields for asl.json * Update common field EchoTime * Removed EchoTime from ASL-table * update FlipAngle in common RF and Contrasts * remove FlipAngle from ASL fields * update Dependency table ASL for MRAcquisitionType * update SliceTiming in common fields * remove SliceTiming from ASL tables * added (FA) for FlipAngle * update common RF and Contrast for table check * LabelingPulseDuration and LabelingPulseInterval in ms instead of s * required common metadatafields update RepetitionTime or VolumeTiming to RepetitionTimePreparation * update flipangle for timeseries versus file collections * update echotime for timeseries * update timing table (fence) * update definition BackgroundSuppressionPulseTime * removed common metadata fields from asl table MagneticFieldStrenght, EchoTime, SliceTiming, VolumeTiming, RepetitionTime, FlipAngle, PulseSequenceType * update scaling of asl and m0 files - update scaling description for nifti files - created separate scaling section (to highlight this important quantification factor), and M0 section - moved scaling section and M0 section after aslcontext section * update broken link in EchoTime (Timing Parameters) * update broken link (2) EchoTime * Update broken links FlipAngle * LabelingType changed to ArterialSpinLabelingType - changed in fields - Changed in dependency table - Dependency table: additionally removed repetitiontime/volumetiming parts * Update dependency table based on new M0Type and M0Estimate fields * Update new M0 field strategy M0 field becomes M0Type, with addition field M0Estimate. Also corrected IntendedFor description in m0 specific fields * TEMPORARY: disable 'strict' docs build this allows the build to proceed despite broken links * changed fail_on_warning to true Intermediate solution to get BEP005 build untill the missing link is available * see previous commit * update bep005 with latest master + resolve conflict (#689) * [DOC] Auto-generate changelog entry for PR #677 * [ENH] BEP001 - New entities: inv & mt (#681) * add entity inv * add mt: * add MT specific metadata * Generate entity.md * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Stefan Appelhoff * Update src/schema/entities.yaml Co-authored-by: Stefan Appelhoff * table fix by @sappelhoff * Conditional requirement Co-authored-by: Stefan Appelhoff * [ENH] BEP001 - Entity-linked file collections (#688) * Squashed commit of the following: commit 8e1ac5fe358691f34ca1c2b57b5812d2dc602173 Author: Stefan Appelhoff Date: Fri Nov 27 11:09:24 2020 +0100 fix links and latin commit 27c9b41b1d1cedc38654db39b3fd5e573b8ce660 Author: Stefan Appelhoff Date: Fri Nov 27 10:03:51 2020 +0100 remove latin Co-authored-by: Chris Markiewicz commit 7d87070ecb6eb3636d5b15e304b8e65de2b8c93b Author: Agah Date: Mon Nov 23 08:46:47 2020 -0500 Update src/99-appendices/10-file-collections.md Co-authored-by: Chris Markiewicz commit b137a9e3cd2bce7cfe7853909684267d4689b692 Author: Agah Date: Mon Nov 23 08:45:19 2020 -0500 Update src/02-common-principles.md Co-authored-by: Chris Markiewicz commit d7897b8259213dd1cfb6e1db4ec835116491bfb1 Author: Agah Date: Mon Nov 23 08:44:40 2020 -0500 Update src/02-common-principles.md Co-authored-by: Chris Markiewicz commit 09e9d32b033a076a8eeb8408d5e62798bb3629ed Author: Agah Date: Mon Nov 23 08:44:15 2020 -0500 Commit suggestion Co-authored-by: Chris Markiewicz commit 009a9ab1563020c130553253480ef76467d894c2 Author: Agah Karakuzu Date: Mon Nov 23 08:43:00 2020 -0500 Add file-collecitons appendix to the TOC commit 8f6c4dfbe7f79232cadca72f0fd22b693a238c52 Author: Agah Karakuzu Date: Mon Nov 23 08:41:13 2020 -0500 Address suggestion by @tsalo commit 45210a9d167a7532c1ab8463c62dbbc519969c95 Author: Agah Karakuzu Date: Wed Nov 11 14:32:20 2020 -0500 Wording commit 66ba5a5313d4951c826063de13da2d60363b6edd Author: Agah Karakuzu Date: Wed Nov 11 14:31:40 2020 -0500 RECOMMENDED --> MUST for adding an application def to the appdx commit 5611fac6a365eef07acf36290cbf12f22a1d4751 Author: Agah Karakuzu Date: Wed Nov 11 14:29:21 2020 -0500 Improve the appendix commit 6d3bbeadc464ec4a93f97d96d3cffdad8f920f29 Author: Agah Karakuzu Date: Mon Nov 2 16:12:04 2020 -0500 Address suggestions by @tsalo commit bcb02232ca769f14a11eb8b056bb963591901012 Author: Agah Karakuzu Date: Tue Oct 27 21:37:26 2020 -0400 [ADD] Link to the appendix commit 44e760f69163eb11bec74be58279bd260aad963c Author: Agah Karakuzu Date: Tue Oct 27 21:28:38 2020 -0400 [ADD] Appendix - File collections - For parametrically linked file collections commit 523b1c163df4b5a1d46f25156d1b0ea0d06ac7bb Author: Agah Karakuzu Date: Tue Oct 27 21:27:52 2020 -0400 [ADD] Parametrically linked file collections - Description * ENH: Link to all BEP-001 entities * STY: Escape asterisk, adjust table widths * Add suggestions by @sappelhoff * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz * Update src/99-appendices/10-file-collections.md Co-authored-by: Chris Markiewicz * Update src/02-common-principles.md Thank you @effigies! Co-authored-by: Chris Markiewicz * Update src/02-common-principles.md Co-authored-by: Chris Markiewicz Co-authored-by: Agah Karakuzu * [ENH] BEP001 - RepetitionTimeExcitation and RepetitionTimePreparation (#671) * [ENH] Improve TR definitions - Include RepetitionTimePreparation - Include RepetitionTimeExcitation - Add explanation on the former RepetitionTime field. * Typo * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * ENH: Allow for variable RTE/P * STY: Update table widths * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md * Change ref to DOI @Remi-Gau * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz Co-authored-by: Chris Markiewicz Co-authored-by: Chris Markiewicz * Update config.yml * Update readthedocs.yml Co-authored-by: bids-maintenance Co-authored-by: Agah Co-authored-by: Chris Markiewicz Co-authored-by: Chris Markiewicz * update required common fields for m0scan.json added EchoTime and FlipAngle in case LookLocker is true * update dependency table if PCASL : LabelingDuration is required if PCASL: LabelingDuration should not be filled in * update depedency table removed 'PASL' LAbelingDuration should not be filled in * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * update description aslcontext Co-authored-by: Chris Markiewicz * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * update PCASLType and CASLType Co-authored-by: Chris Markiewicz * updated required into REQUIRED for asl.json and m0scan.json (common fields * Added SummaryImages Added images: asl_pasl_boluscutoff_false.png asl_pasl_boluscutoff_true_q2tips.png asl_pasl_boluscutoff_true_quipssII.png asl_pcasl_labeling_pulses.png asl_pcasl_sequence.png * create Appendix 11 for ASL * Added asl_flowchart.png * added subtitles for linking from main specification * Added appendix link for control and label * added appendix for asl sequences in general * added appendix for (P)CASL * added appendix for PASL * added appendix for dependency table (flowcharts) * MNT: Add ASL appendix to TOC * TYPO: correct ASL appendix entry in tocwq * fix md style * Update src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md Co-authored-by: Chris Markiewicz * update table RF and Contrast * update link Appendix XI to Appendix XI - ASL * corrected link to appendix for PASL * Update aslcontext cases Case 1: changed asl.json to asl.nii[.gz`] Removed: The optional deltam or cbf volumes should be stored and specified as derivative. Case 2: Removed: The optional cbf volumes should be stored and specified as derivative. * Added aslcontext.tsv cases this is moved from main spec bep005 to appendix XI - ASL * Update aslcontext cases - moved three cases to appendix XI - ASL - added link to appendix XI - added: Note that the raw images, including the m0scan, may also be used for quality control. * corrected subtitles cases * improve linebreaks in ASL appendix * fix VascularCrushingVENC link Based on comment of Stefan Appelhof, the Data Type for VascularChrushingVENC was fixed: [number][] or \[array][] of [numbers][] to [number][] or [array][] of [numbers][] * added single column requirement for aslcontext.tsv based on comment of Stefan Appelhof, the need for a single column was added in the introductory text for aslcontext.tsv, before the 3 cases. * Changed VascularCrushingVENC to VascularCrushingVenc * [SCHEMA] Add ASL to schema (#703) * Add ASL to schema files and regenerate entity table. * Fix style issue. * Add fmap-format m0scan to schema. * update M0Estimate fields Added 'Referring to the M0 of blood' * update LabelingDuration Added additional information for LabelingDuration * update labeling.jpg into *_asllabeling.jpg * Change labeling to asllabeling. (#709) * RF: Renumber ASL appendix to XII Co-authored-by: Henk Mutsaerts Co-authored-by: Patricia Clement <41481345+patsycle@users.noreply.github.com> Co-authored-by: Chris Markiewicz Co-authored-by: Julia Guiomar Niso GalΓ‘n Co-authored-by: Remi Gau Co-authored-by: bids-maintenance Co-authored-by: Agah Co-authored-by: Chris Markiewicz Co-authored-by: Taylor Salo --- mkdocs.yml | 1 + .../01-magnetic-resonance-imaging-data.md | 200 +++++++++++++++--- .../images/asl_flowchart.png | Bin 0 -> 86206 bytes .../images/asl_pasl_boluscutoff_false.png | Bin 0 -> 6234 bytes .../asl_pasl_boluscutoff_true_q2tips.png | Bin 0 -> 42827 bytes .../asl_pasl_boluscutoff_true_quipssII.png | Bin 0 -> 34943 bytes .../images/asl_pcasl_labeling_pulses.png | Bin 0 -> 58418 bytes .../images/asl_pcasl_sequence.png | Bin 0 -> 10322 bytes src/99-appendices/01-contributors.md | 25 ++- src/99-appendices/04-entity-table.md | 4 +- .../12-arterial-spin-labeling.md | 130 ++++++++++++ src/schema/datatypes/fmap.yaml | 1 + src/schema/datatypes/perf.yaml | 40 ++++ src/schema/modalities.yaml | 1 + tools/bids_schema.py | 2 +- 15 files changed, 374 insertions(+), 30 deletions(-) create mode 100644 src/04-modality-specific-files/images/asl_flowchart.png create mode 100644 src/04-modality-specific-files/images/asl_pasl_boluscutoff_false.png create mode 100644 src/04-modality-specific-files/images/asl_pasl_boluscutoff_true_q2tips.png create mode 100644 src/04-modality-specific-files/images/asl_pasl_boluscutoff_true_quipssII.png create mode 100644 src/04-modality-specific-files/images/asl_pcasl_labeling_pulses.png create mode 100644 src/04-modality-specific-files/images/asl_pcasl_sequence.png create mode 100644 src/99-appendices/12-arterial-spin-labeling.md create mode 100644 src/schema/datatypes/perf.yaml diff --git a/mkdocs.yml b/mkdocs.yml index 5219216eeb..d773db36a5 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -51,6 +51,7 @@ nav: - Entities: 99-appendices/09-entities.md - File collections: 99-appendices/10-file-collections.md - Quantitative MRI: 99-appendices/11-qmri.md + - Arterial Spin Labeling: 99-appendices/12-arterial-spin-labeling.md - Changelog: CHANGES.md - The BIDS Starter Kit: - GitHub repository: https://github.com/bids-standard/bids-starter-kit 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 f876857dd4..aa7f3cee75 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 @@ -10,21 +10,21 @@ by Ben Inglis: ### Scanner Hardware -| **Key name** | **Requirement level** | **Data type** | **Description** | -|-------------------------------|-----------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| Manufacturer | RECOMMENDED | [string][] | Manufacturer of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0070 `Manufacturer` | -| ManufacturersModelName | RECOMMENDED | [string][] | Manufacturer's model name of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name` | -| DeviceSerialNumber | RECOMMENDED | [string][] | The serial number of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset | -| StationName | RECOMMENDED | [string][] | Institution defined name of the machine that produced the composite instances. Corresponds to DICOM Tag 0008, 1010 `Station Name` | -| SoftwareVersions | RECOMMENDED | [string][] | Manufacturer's designation of software version of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1020 `Software Versions` | -| HardcopyDeviceSoftwareVersion | [DEPRECATED][] | [string][] | Manufacturer's designation of the software of the device that created this Hardcopy Image (the printer). Corresponds to DICOM Tag 0018, 101A `Hardcopy Device Software Version` | -| MagneticFieldStrength | RECOMMENDED | [number][] | Nominal field strength of MR magnet in Tesla. Corresponds to DICOM Tag 0018,0087 `Magnetic Field Strength` | -| ReceiveCoilName | RECOMMENDED | [string][] | Information describing the receiver coil. Corresponds to DICOM Tag 0018, 1250 `Receive Coil Name`, although not all vendors populate that DICOM Tag, in which case this field can be derived from an appropriate private DICOM field | -| ReceiveCoilActiveElements | RECOMMENDED | [string][] | Information describing the active/selected elements of the receiver coil. This doesn't correspond to a tag in the DICOM ontology. The vendor-defined terminology for active coil elements can go in this field. See an example below the table. | -| GradientSetType | RECOMMENDED | [string][] | It should be possible to infer the gradient coil from the scanner model. If not, for example because of a custom upgrade or use of a gradient insert set, then the specifications of the actual gradient coil should be reported independently | -| MRTransmitCoilSequence | RECOMMENDED | [string][] | This is a relevant field if a non-standard transmit coil is used. Corresponds to DICOM Tag 0018, 9049 `MR Transmit Coil Sequence` | -| MatrixCoilMode | RECOMMENDED | [string][] | (If used) A method for reducing the number of independent channels by combining in analog the signals from multiple coil elements. There are typically different default modes when using un-accelerated or accelerated (for example, GRAPPA, SENSE) imaging | -| CoilCombinationMethod | RECOMMENDED | [string][] | Almost all fMRI studies using phased-array coils use root-sum-of-squares (rSOS) combination, but other methods exist. The image reconstruction is changed by the coil combination method (as for the matrix coil mode above), so anything non-standard should be reported | +| **Key name** | **Requirement level** | **Data type** | **Description** | +|-------------------------------|------------------------------------------------------|---------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Manufacturer | RECOMMENDED | [string][] | Manufacturer of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0070 `Manufacturer` | +| ManufacturersModelName | RECOMMENDED | [string][] | Manufacturer's model name of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name` | +| DeviceSerialNumber | RECOMMENDED | [string][] | The serial number of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset | +| StationName | RECOMMENDED | [string][] | Institution defined name of the machine that produced the composite instances. Corresponds to DICOM Tag 0008, 1010 `Station Name` | +| SoftwareVersions | RECOMMENDED | [string][] | Manufacturer's designation of software version of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1020 `Software Versions` | +| HardcopyDeviceSoftwareVersion | [DEPRECATED][] | [string][] | Manufacturer's designation of the software of the device that created this Hardcopy Image (the printer). Corresponds to DICOM Tag 0018, 101A `Hardcopy Device Software Version` | +| MagneticFieldStrength | RECOMMENDED, but REQUIRED for Arterial Spin Labeling | [number][] | Nominal field strength of MR magnet in Tesla. Corresponds to DICOM Tag 0018,0087 `Magnetic Field Strength` | +| ReceiveCoilName | RECOMMENDED | [string][] | Information describing the receiver coil. Corresponds to DICOM Tag 0018, 1250 `Receive Coil Name`, although not all vendors populate that DICOM Tag, in which case this field can be derived from an appropriate private DICOM field | +| ReceiveCoilActiveElements | RECOMMENDED | [string][] | Information describing the active/selected elements of the receiver coil. This doesn't correspond to a tag in the DICOM ontology. The vendor-defined terminology for active coil elements can go in this field. See an example below the table. | +| GradientSetType | RECOMMENDED | [string][] | It should be possible to infer the gradient coil from the scanner model. If not, for example because of a custom upgrade or use of a gradient insert set, then the specifications of the actual gradient coil should be reported independently | +| MRTransmitCoilSequence | RECOMMENDED | [string][] | This is a relevant field if a non-standard transmit coil is used. Corresponds to DICOM Tag 0018, 9049 `MR Transmit Coil Sequence` | +| MatrixCoilMode | RECOMMENDED | [string][] | (If used) A method for reducing the number of independent channels by combining in analog the signals from multiple coil elements. There are typically different default modes when using un-accelerated or accelerated (for example, GRAPPA, SENSE) imaging | +| CoilCombinationMethod | RECOMMENDED | [string][] | Almost all fMRI studies using phased-array coils use root-sum-of-squares (rSOS) combination, but other methods exist. The image reconstruction is changed by the coil combination method (as for the matrix coil mode above), so anything non-standard should be reported | Example for `ReceiveCoilActiveElements`: @@ -52,6 +52,7 @@ that a given scan was collected with the intended coil elements selected | 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. | +| MRAcquisitionType | RECOMMENDED, but REQUIRED for Arterial Spin Labeling | [string][] | Possible values: `2D` or `3D`. Type of sequence readout. Corresponds to DICOM Tag 0018,0023 `MR Acquisition Type`. | | 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). | @@ -90,20 +91,20 @@ and the center of the last "effective" echo, sometimes called the "FSL definitio ### Timing Parameters -| **Key name** | **Requirement level** | **Data type** | **Description** | -|------------------------|------------------------------------------------------------------------------------------------------------------|--------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| EchoTime | RECOMMENDED, but REQUIRED if corresponding fieldmap data is present or the data comes from a multi echo sequence | [number][] | The echo time (TE) for the acquisition, specified in seconds. Corresponds to DICOM Tag 0018, 0081 `Echo Time` (please note that the DICOM term is in milliseconds not seconds). | -| InversionTime | RECOMMENDED | [number][] | The inversion time (TI) for the acquisition, specified in seconds. Inversion time is the time after the middle of inverting RF pulse to middle of excitation pulse to detect the amount of longitudinal magnetization. Corresponds to DICOM Tag 0018, 0082 `Inversion Time` (please note that the DICOM term is in milliseconds not seconds). | -| SliceTiming | RECOMMENDED, but REQUIRED for sparse sequences that do not have the `DelayTime` field set | [array][] of [numbers][] | The time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the `SliceTiming` field, it is important to check if the OPTIONAL `SliceEncodingDirection` exists. In particular, if `SliceEncodingDirection` is negative, the entries in `SliceTiming` are defined in reverse order with respect to the slice axis, such that the final entry in the `SliceTiming` list is the time of acquisition of slice 0. Without this parameter slice time correction will not be possible. | -| SliceEncodingDirection | RECOMMENDED | [string][] | Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-` (the axis of the NIfTI data along which slices were acquired, and the direction in which `SliceTiming` is defined with respect to). `i`, `j`, `k` identifiers correspond to the first, second and third axis of the data in the NIfTI file. A `-` sign indicates that the contents of `SliceTiming` are defined in reverse order - that is, the first entry corresponds to the slice with the largest index, and the final entry corresponds to slice index zero. When present, the axis defined by `SliceEncodingDirection` needs to be consistent with the β€˜slice_dim' field in the NIfTI header. When absent, the entries in `SliceTiming` must be in the order of increasing slice index as defined by the NIfTI header. | -| DwellTime | RECOMMENDED | [number][] | Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling. For Siemens, this corresponds to DICOM field (0019,1018) (in ns). This value is necessary for the optional readout distortion correction of anatomicals in the HCP Pipelines. It also usefully provides a handle on the readout bandwidth, which isn't captured in the other metadata tags. Not to be confused with `EffectiveEchoSpacing`, and the frequent mislabeling of echo spacing (which is spacing in the phase encoding direction) as "dwell time" (which is spacing in the readout direction). | +| **Key name** | **Requirement level** | **Data type** | **Description** | +|------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| EchoTime | RECOMMENDED, but REQUIRED if corresponding fieldmap data is present, or the data comes from a multi echo sequence or Arterial Spin Labeling | [number][] or [array][] of [numbers][] | The echo time (TE) for the acquisition, specified in seconds. Corresponds to DICOM Tag 0018, 0081 Echo Time (please note that the DICOM term is in milliseconds not seconds). The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a [file collection](../99-appendices/10-file-collections.md) where the value of this field is iterated using the [echo entity](../99-appendices/09-entities.md#echo). The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in [ASL](#arterial-spin-labeling-perfusion-data) or variable echo time fMRI sequences. | +| InversionTime | RECOMMENDED | [number][] | The inversion time (TI) for the acquisition, specified in seconds. Inversion time is the time after the middle of inverting RF pulse to middle of excitation pulse to detect the amount of longitudinal magnetization. Corresponds to DICOM Tag 0018, 0082 `Inversion Time` (please note that the DICOM term is in milliseconds not seconds). | +| SliceTiming | RECOMMENDED, but REQUIRED for sparse sequences that do not have the `DelayTime` field set, and Arterial Spin Labeling with `MRAcquisitionType` set on `2D`. | [array][] of [numbers][] | The time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the `SliceTiming` field, it is important to check if the OPTIONAL `SliceEncodingDirection` exists. In particular, if `SliceEncodingDirection` is negative, the entries in `SliceTiming` are defined in reverse order with respect to the slice axis, such that the final entry in the `SliceTiming` list is the time of acquisition of slice 0. Without this parameter slice time correction will not be possible. | +| SliceEncodingDirection | RECOMMENDED | [string][] | Possible values: `i`, `j`, `k`, `i-`, `j-`, `k-` (the axis of the NIfTI data along which slices were acquired, and the direction in which `SliceTiming` is defined with respect to). `i`, `j`, `k` identifiers correspond to the first, second and third axis of the data in the NIfTI file. A `-` sign indicates that the contents of `SliceTiming` are defined in reverse order - that is, the first entry corresponds to the slice with the largest index, and the final entry corresponds to slice index zero. When present, the axis defined by `SliceEncodingDirection` needs to be consistent with the β€˜slice_dim' field in the NIfTI header. When absent, the entries in `SliceTiming` must be in the order of increasing slice index as defined by the NIfTI header. | +| DwellTime | RECOMMENDED | [number][] | Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling. For Siemens, this corresponds to DICOM field (0019,1018) (in ns). This value is necessary for the optional readout distortion correction of anatomicals in the HCP Pipelines. It also usefully provides a handle on the readout bandwidth, which isn't captured in the other metadata tags. Not to be confused with `EffectiveEchoSpacing`, and the frequent mislabeling of echo spacing (which is spacing in the phase encoding direction) as "dwell time" (which is spacing in the readout direction). | ### RF & Contrast -| **Key name** | **Requirement level** | **Data type** | **Description** | -| --------------------------- | --------------------- | ------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| FlipAngle | RECOMMENDED | [number][] | Flip angle for the acquisition, specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. | -| NegativeContrast | OPTIONAL | [boolean][] | `true` or `false` value specifying whether increasing voxel intensity (within sample voxels) denotes a decreased value with respect to the contrast suffix. This is commonly the case when Cerebral Blood Volume is estimated via usage of a contrast agent in conjunction with a T2\* weighted acquisition protocol. | +| **Key name** | **Requirement level** | **Data type** | **Description** | +|------------------|---------------------------------------------------------|----------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| FlipAngle | RECOMMENDED, but REQUIRED if `LookLocker` is set `true` | [number][] or [array][] of [numbers][] | Flip angle (FA) for the acquisition, specified in degrees. Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a [file collection](../99-appendices/10-file-collections.md) where the value of this field is iterated using the [flip entity](../99-appendices/09-entities.md#flip). The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in [ASL](#arterial-spin-labeling-perfusion-data) or variable flip angle fMRI sequences. | +| NegativeContrast | OPTIONAL | [boolean][] | `true` or `false` value specifying whether increasing voxel intensity (within sample voxels) denotes a decreased value with respect to the contrast suffix. This is commonly the case when Cerebral Blood Volume is estimated via usage of a contrast agent in conjunction with a T2\* weighted acquisition protocol. | ### Slice Acceleration @@ -680,6 +681,149 @@ JSON example: } ``` +## Arterial Spin Labeling perfusion data + +Template: + +```Text +sub-