diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index a2a39b06c4..de45eb194a 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -2,16 +2,9 @@
## Common metadata fields
-MR Data described in the following sections share the following RECOMMENDED metadata
-fields (stored in sidecar JSON files).
-MRI acquisition parameters are divided into several categories based on
-"A checklist for fMRI acquisition methods reporting in the literature"
-([article](https://doi.org/10.15200/winn.143191.17127)) by Ben Inglis.
+MR Data described in the following sections share the following RECOMMENDED metadata fields (stored in sidecar JSON files). MRI acquisition parameters are divided into several categories based on "A checklist for fMRI acquisition methods reporting in the literature" ([article](https://doi.org/10.15200/winn.143191.17127)) by Ben Inglis.
-When adding additional metadata please use the CamelCase version of
-[DICOM ontology terms](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_d.html)
-whenever possible. See also
-[recommendations on JSON files](../common-principles.md#key-value-files-dictionaries).
+When adding additional metadata please use the CamelCase version of [DICOM ontology terms](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_d.html) whenever possible. See also [recommendations on JSON files](../common-principles.md#key-value-files-dictionaries).
### Hardware information
@@ -23,22 +16,12 @@ The definitions of the fields specified in these tables may be found in
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.MRIHardware") }}
Example for `ReceiveCoilActiveElements`:
-For Siemens, coil channels are typically not activated/selected individually,
-but rather in pre-defined selectable "groups" of individual channels,
-and the list of the "groups" of elements that are active/selected in any
-given scan populates the `Coil String` entry in Siemens' private DICOM fields
-(for example, `HEA;HEP` for the Siemens standard 32 ch coil
-when both the anterior and posterior groups are activated).
-This is a flexible field that can be used as most appropriate for a given
-vendor and coil to define the "active" coil elements.
-Since individual scans can sometimes not have the intended coil elements selected,
-it is preferable for this field to be populated directly from the DICOM
-for each individual scan, so that it can be used as a mechanism for checking
-that a given scan was collected with the intended coil elements selected.
+For Siemens, coil channels are typically not activated/selected individually, but rather in pre-defined selectable "groups" of individual channels, and the list of the "groups" of elements that are active/selected in any given scan populates the `Coil String` entry in Siemens' private DICOM fields (for example, `HEA;HEP` for the Siemens standard 32 ch coil when both the anterior and posterior groups are activated). This is a flexible field that can be used as most appropriate for a given vendor and coil to define the "active" coil elements. Since individual scans can sometimes not have the intended coil elements selected, it is preferable for this field to be populated directly from the DICOM for each individual scan, so that it can be used as a mechanism for checking that a given scan was collected with the intended coil elements selected.
### Institution information
@@ -50,6 +33,7 @@ The definitions of the fields specified in these tables may be found in
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.MRIInstitutionInformation") }}
### Sequence Specifics
@@ -62,6 +46,7 @@ The definitions of the fields specified in these tables may be found in
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.MRISequenceSpecifics") }}
### In- and Out-of-Plane Spatial Encoding
@@ -74,19 +59,12 @@ The definitions of the fields specified in these tables may be found in
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.MRISpatialEncoding", "mri.PhaseEncodingDirectionRec"]) }}
-2 Conveniently, for Siemens data, this value is easily obtained as
-`1 / (BWPPPE * ReconMatrixPE)`, where BWPPPE is the
-"BandwidthPerPixelPhaseEncode" in DICOM Tag 0019, 1028 and ReconMatrixPE is
-the size of the actual reconstructed data in the phase direction (which is NOT
-reflected in a single DICOM Tag for all possible aforementioned scan
-manipulations). See
-[Acquiring and using field maps - LCNI](https://lcni.uoregon.edu/wiki/acquiring-and-using-field-maps/)
-and [TotalReadoutTime - dcm\_qa](https://github.com/neurolabusc/dcm_qa/tree/master/In/TotalReadoutTime).
+2 Conveniently, for Siemens data, this value is easily obtained as `1 / (BWPPPE * ReconMatrixPE)`, where BWPPPE is the "BandwidthPerPixelPhaseEncode" in DICOM Tag 0019, 1028 and ReconMatrixPE is the size of the actual reconstructed data in the phase direction (which is NOT reflected in a single DICOM Tag for all possible aforementioned scan manipulations). See [Acquiring and using field maps - LCNI](https://lcni.uoregon.edu/wiki/acquiring-and-using-field-maps/) and [TotalReadoutTime - dcm_qa](https://github.com/neurolabusc/dcm_qa/tree/master/In/TotalReadoutTime).
-3 We use the time between the center of the first "effective" echo
-and the center of the last "effective" echo, sometimes called the "FSL definition".
+3 We use the time between the center of the first "effective" echo and the center of the last "effective" echo, sometimes called the "FSL definition".
### Timing Parameters
@@ -98,6 +76,7 @@ The definitions of the fields specified in these tables may be found in
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.MRITimingParameters", "mri.SliceTimingMRI"]) }}
### RF & Contrast
@@ -110,6 +89,7 @@ The definitions of the fields specified in these tables may be found in
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.MRIFlipAngleLookLockerFalse", "mri.MRIRFandContrast" ]) }}
### Slice Acceleration
@@ -122,6 +102,7 @@ The definitions of the fields specified in these tables may be found in
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.MRISliceAcceleration") }}
### Anatomical landmarks
@@ -136,21 +117,14 @@ The definitions of the fields specified in these tables may be found in
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.MRIAnatomicalLandmarks") }}
-### Echo-Planar Imaging and *B0 * mapping
+### Echo-Planar Imaging and _B0 _ mapping
-Echo-Planar Imaging (EPI) schemes typically used in the acquisition of
-diffusion and functional MRI may also be *intended for* estimating the
-*B0 * field nonuniformity inside the scanner (in other words,
-*mapping the field*) without the acquisition of additional MRI schemes
-such as gradient-recalled echo (GRE) sequences that are stored under the
-`fmap/` directory of the BIDS structure.
+Echo-Planar Imaging (EPI) schemes typically used in the acquisition of diffusion and functional MRI may also be _intended for_ estimating the _B0 _ field nonuniformity inside the scanner (in other words, _mapping the field_) without the acquisition of additional MRI schemes such as gradient-recalled echo (GRE) sequences that are stored under the `fmap/` directory of the BIDS structure.
-The modality labels `dwi` (under `dwi/`), `bold` (under `func/`),
-`asl` (under `perf/`), `sbref` (under `dwi/`, `func/` or `perf/`), and
-any modality under `fmap/` are allowed to encode the MR protocol intent for
-fieldmap estimation using the following metadata:
+The modality labels `dwi` (under `dwi/`), `bold` (under `func/`), `asl` (under `perf/`), `sbref` (under `dwi/`, `func/` or `perf/`), and any modality under `fmap/` are allowed to encode the MR protocol intent for fieldmap estimation using the following metadata:
+
{{ MACROS___make_sidecar_table([
"mri.MRIB0FieldIdentifier",
"mri.MRIEchoPlanarImagingAndB0FieldSource",
@@ -176,12 +151,12 @@ The definitions of the fields specified in these tables may be found in
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") }}
### Deidentification information
-Describes the mechanism or method used to modify or remove metadata
-and/or pixel data to protect the patient or participant's identity.
+Describes the mechanism or method used to modify or remove metadata and/or pixel data to protect the patient or participant's identity.
+
{{ MACROS___make_sidecar_table("mri.DeidentificationMethod") }}
Each object in the `DeidentificationMethodCodeSequence` array includes the following RECOMMENDED keys:
@@ -201,21 +177,18 @@ The definitions of these fields can be found in
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_subobject_table("metadata.DeidentificationMethodCodeSequence.items") }}
## Anatomy imaging data
Anatomy MRI sequences measure static, structural features of the brain.
-This datatype is divided into two groups:
-non-parametric and parametric.
+This datatype is divided into two groups: non-parametric and parametric.
-Non-parametric structural images have an arbitrary scale.
-For example, T1w data are T1-weighted,
-but the values do not correspond to actual T1 value estimates.
+Non-parametric structural images have an arbitrary scale. For example, T1w data are T1-weighted, but the values do not correspond to actual T1 value estimates.
-Parametric structural imaging, on the other hand, use a non-arbitrary scale.
-For example, a T1map file contains T1 value estimates, in seconds.
+Parametric structural imaging, on the other hand, use a non-arbitrary scale. For example, a T1map file contains T1 value estimates, in seconds.
### Non-parametric structural MR images
@@ -226,6 +199,7 @@ The inputs for this macro can be found in the directory
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_filename_template("raw", datatypes=["anat"], suffixes=[
"T1w",
"T2w",
@@ -249,6 +223,7 @@ The definitions of these fields can be found in
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_suffix_table(
[
"T1w",
@@ -265,19 +240,13 @@ and a guide for using macros can be found at
)
}}
-The [`part-`](../appendices/entities.md#part) entity is
-used to indicate which component of the complex representation of the MRI
-signal is represented in voxel data.
-This entity is associated with the DICOM Tag `0008, 9208`.
-Allowed label values for this entity are `phase`, `mag`, `real` and `imag`,
-which are typically used in `part-mag`/`part-phase` or `part-real`/`part-imag`
-pairs of files.
-For example:
+The [`part-`](../appendices/entities.md#part) entity is used to indicate which component of the complex representation of the MRI signal is represented in voxel data. This entity is associated with the DICOM Tag `0008, 9208`. Allowed label values for this entity are `phase`, `mag`, `real` and `imag`, which are typically used in `part-mag`/`part-phase` or `part-real`/`part-imag` pairs of files. For example:
+
{{ MACROS___make_filetree_example(
{
"sub-01": {
@@ -292,9 +261,7 @@ A guide for using macros can be found at
)
}}
-Phase images MAY be in radians or in arbitrary units.
-The sidecar JSON file MUST include the units of the `phase` image.
-The possible options are `rad` or `arbitrary`.
+Phase images MAY be in radians or in arbitrary units. The sidecar JSON file MUST include the units of the `phase` image. The possible options are `rad` or `arbitrary`.
For example, for `sub-01_part-phase_T1w.json`:
@@ -308,8 +275,7 @@ When there is only a magnitude image of a given type, the `part` entity MAY be o
### Parametric structural MR images
-Structural MR images whose intensity is represented in a non-arbitrary scale
-constitute parametric maps.
+Structural MR images whose intensity is represented in a non-arbitrary scale constitute parametric maps.
+
{{ MACROS___make_filename_template("raw", datatypes=["anat"], suffixes=[
"T1map",
"R1map",
@@ -339,14 +306,7 @@ and a guide for using macros can be found at
])
}}
-Parametric images listed in the table below are typically generated by
-processing a [file collection](../common-principles.md#entity-linked-file-collections).
-Please visit the [file collections appendix](../appendices/file-collections.md) to see the
-list of suffixes available for quantitative MRI (qMRI) applications associated
-with these maps
-(for example, [MPM](../glossary.md#mpm-suffixes),
-[MP2RAGE](../glossary.md#mp2rage-suffixes),
-and [MTR](../glossary.md#mtransfer-entities)).
+Parametric images listed in the table below are typically generated by processing a [file collection](../common-principles.md#entity-linked-file-collections). Please visit the [file collections appendix](../appendices/file-collections.md) to see the list of suffixes available for quantitative MRI (qMRI) applications associated with these maps (for example, [MPM](../glossary.md#mpm-suffixes), [MP2RAGE](../glossary.md#mp2rage-suffixes), and [MTR](../glossary.md#mtransfer-entities)).
Currently supported parametric maps include:
@@ -357,6 +317,7 @@ The definitions of these fields can be found in
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_suffix_table(
[
"T1map",
@@ -380,20 +341,11 @@ and a guide for using macros can be found at
)
}}
-For any other details on the organization of parametric maps, their
-recommended metadata fields, and the application specific entity or
-metadata requirement levels of [file collections](../appendices/file-collections.md) that can generate
-them, visit the [qMRI appendix](../appendices/qmri.md).
+For any other details on the organization of parametric maps, their recommended metadata fields, and the application specific entity or metadata requirement levels of [file collections](../appendices/file-collections.md) that can generate them, visit the [qMRI appendix](../appendices/qmri.md).
### Defacing masks
-If the structural images included in the dataset were defaced (to protect
-identity of participants) one MAY provide the binary mask that was used to
-remove facial features in the form of `_defacemask` files.
-In such cases, the OPTIONAL [`mod-`](../appendices/entities.md#mod)
-entity corresponds to modality suffix,
-such as `T1w` or `inplaneT1`, referenced by the defacemask image.
-For example, `sub-01_mod-T1w_defacemask.nii.gz`.
+If the structural images included in the dataset were defaced (to protect identity of participants) one MAY provide the binary mask that was used to remove facial features in the form of `_defacemask` files. In such cases, the OPTIONAL [`mod-`](../appendices/entities.md#mod) entity corresponds to modality suffix, such as `T1w` or `inplaneT1`, referenced by the defacemask image. For example, `sub-01_mod-T1w_defacemask.nii.gz`.
+
{{ MACROS___make_filename_template("raw", datatypes=["anat"], suffixes=[
"defacemask",
])
@@ -409,9 +362,7 @@ and a guide for using macros can be found at
### Task metadata for anatomical scans
-The OPTIONAL [`task-`](../appendices/entities.md#task) entity can be used
-in order to allow tasks during structural MR acquisitions,
-for example pre-described motion paradigms such as nodding, to be described.
+The OPTIONAL [`task-`](../appendices/entities.md#task) entity can be used in order to allow tasks during structural MR acquisitions, for example pre-described motion paradigms such as nodding, to be described.
+
{{ MACROS___make_sidecar_table("anat.TaskMetadata") }}
-Some meta information about the acquisition MAY be provided in an additional
-JSON file. See [Common metadata fields](#common-metadata-fields) for a
-list of terms and their definitions. There are also some OPTIONAL JSON
-fields specific to anatomical scans:
+Some meta information about the acquisition MAY be provided in an additional JSON file. See [Common metadata fields](#common-metadata-fields) for a list of terms and their definitions. There are also some OPTIONAL JSON fields specific to anatomical scans:
+
{{ MACROS___make_sidecar_table("anat.MRIAnatomyCommonMetadataFields") }}
### Deprecated suffixes
-Some suffixes that were available in versions of the specification prior to
-1.5.0 have been deprecated.
-These suffixes are ambiguous and have been superseded by more precise conventions.
-Therefore, they are not recommended for use in new datasets.
-They are, however, still valid suffixes, to maintain backwards compatibility.
+Some suffixes that were available in versions of the specification prior to 1.5.0 have been deprecated. These suffixes are ambiguous and have been superseded by more precise conventions. Therefore, they are not recommended for use in new datasets. They are, however, still valid suffixes, to maintain backwards compatibility.
-The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible
-datasets (created after version 1.5.0.):
+The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible datasets (created after version 1.5.0.):
+
{{ MACROS___make_suffix_table(
[
"T2star",
@@ -474,6 +420,7 @@ The definitions of these fields can be found in
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_suffix_table(
[
"bold",
@@ -490,22 +437,18 @@ The inputs for this macro can be found in the directory
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_filename_template("raw", datatypes=["func"]) }}
-Functional imaging consists of techniques that support rapid temporal repetition.
-This includes, but is not limited to, task based fMRI, as well as resting state fMRI, which is treated like any other task.
-For task based fMRI, a corresponding task events file (see below) MUST be provided
-(please note that this file is not necessary for resting state scans).
-For multiband acquisitions, one MAY also save the single-band reference image with the `sbref` suffix
-(for example, `sub-control01_task-nback_sbref.nii.gz`).
+Functional imaging consists of techniques that support rapid temporal repetition. This includes, but is not limited to, task based fMRI, as well as resting state fMRI, which is treated like any other task. For task based fMRI, a corresponding task events file (see below) MUST be provided (please note that this file is not necessary for resting state scans). For multiband acquisitions, one MAY also save the single-band reference image with the `sbref` suffix (for example, `sub-control01_task-nback_sbref.nii.gz`).
-Multi-echo data MUST be split into one file per echo using the
-[`echo-`](../appendices/entities.md#echo) entity. For example:
+Multi-echo data MUST be split into one file per echo using the [`echo-`](../appendices/entities.md#echo) entity. For example:
+
{{ MACROS___make_filetree_example(
{
"sub-01": {
@@ -521,18 +464,9 @@ A guide for using macros can be found at
}
) }}
-Please note that the `` denotes the number/index (in the form of a
-nonnegative integer) of the echo not the echo time value which needs to be stored in the
-field EchoTime of the separate JSON file.
+Please note that the `` denotes the number/index (in the form of a nonnegative integer) of the echo not the echo time value which needs to be stored in the field EchoTime of the separate JSON file.
-Complex-valued data MUST be split into one file for each data type.
-For BOLD data, there are separate suffixes for magnitude (`_bold`) and phase
-(`_phase`) data, but the `_phase` suffix is [deprecated](../common-principles.md#definitions).
-Newly generated datasets SHOULD NOT use the `_phase` suffix, and the suffix will be removed
-from the specification in the next major release.
-For backwards compatibility, `_phase` is considered equivalent to `_part-phase_bold`.
-When the `_phase` suffix is not used, each file shares the same
-name with the exception of the `part-` or `part-` entity.
+Complex-valued data MUST be split into one file for each data type. For BOLD data, there are separate suffixes for magnitude (`_bold`) and phase (`_phase`) data, but the `_phase` suffix is [deprecated](../common-principles.md#definitions). Newly generated datasets SHOULD NOT use the `_phase` suffix, and the suffix will be removed from the specification in the next major release. For backwards compatibility, `_phase` is considered equivalent to `_part-phase_bold`. When the `_phase` suffix is not used, each file shares the same name with the exception of the `part-` or `part-` entity.
For example:
@@ -540,6 +474,7 @@ For example:
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_filetree_example(
{
"sub-01": {
@@ -569,6 +504,7 @@ The definitions of the fields specified in these tables may be found in
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([
"func.MRIFuncRepetitionTime",
"func.MRIFuncVolumeTiming",
@@ -576,10 +512,7 @@ A guide for using macros can be found at
])
}}
-For the fields described above and in the following section, the term "Volume"
-refers to a reconstruction of the object being imaged (for example, brain or part of a
-brain). In case of multiple channels in a coil, the term "Volume" refers to a
-combined image rather than an image from each coil.
+For the fields described above and in the following section, the term "Volume" refers to a reconstruction of the object being imaged (for example, brain or part of a brain). In case of multiple channels in a coil, the term "Volume" refers to a combined image rather than an image from each coil.
### Other RECOMMENDED metadata
@@ -593,26 +526,24 @@ The definitions of the fields specified in these tables may be found in
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("func.MRIFuncTimingParameters") }}
-The following table recapitulates the different ways that specific fields have
-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.
+The following table recapitulates the different ways that specific fields have 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`** | **`AcquisitionDuration`** | **`DelayTime`** | **`VolumeTiming`** |
+| --- | --- | --- | --- | --- | --- |
+| option A | \[ X ] | | \[ ] | | \[ ] |
+| option B | \[ ] | \[ X ] | | \[ ] | \[ X ] |
+| option C | \[ ] | | \[ X ] | \[ ] | \[ X ] |
+| option D | \[ X ] | \[ X ] | \[ ] | | \[ ] |
+| option E | \[ X ] | | \[ ] | \[ X ] | \[ ] |
**Legend**
-- \[ X ] --> MUST be defined
-- \[ \] --> MUST NOT be defined
-- empty cell --> MAY be specified
+- \[ X ] --> MUST be defined
+- \[ \] --> MUST NOT be defined
+- empty cell --> MAY be specified
#### fMRI task information
@@ -624,10 +555,10 @@ The definitions of the fields specified in these tables may be found in
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("func.MRIFuncTaskInformation") }}
-See [Common metadata fields](#common-metadata-fields) for a list of
-additional terms and their definitions.
+See [Common metadata fields](#common-metadata-fields) for a list of additional terms and their definitions.
Example:
@@ -635,6 +566,7 @@ Example:
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_filetree_example(
{
"sub-01": {
@@ -675,8 +607,7 @@ A guide for using macros can be found at
- [`ds114`](https://github.com/bids-standard/bids-examples/tree/master/ds114)
- [`ds000117`](https://github.com/bids-standard/bids-examples/tree/master/ds000117)
-Diffusion-weighted imaging data acquired for a participant.
-Currently supported image types include:
+Diffusion-weighted imaging data acquired for a participant. Currently supported image types include:
+
{{ MACROS___make_suffix_table(["dwi", "sbref"]) }}
Additionally, the following suffixes are used for scanner-generated images:
@@ -696,6 +628,7 @@ The definitions of these fields can be found in
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_suffix_table(["ADC", "expADC", "trace", "FA", "colFA", "S0map"]) }}
+
{{ MACROS___make_filename_template("raw", datatypes=["dwi"]) }}
-The [`run-`](../appendices/entities.md#run) entity is RECOMMENDED
-to encode the splits of multipart DWI scans
-(see [below](#multipart-split-dwi-schemes) for more information on multipart DWI schemes).
-
-**Combining multi- and single-band acquisitions**.
-The single-band reference image MAY be stored with suffix `sbref` (for example,
-`dwi/sub-control01_sbref.nii[.gz]`) as long as the image has no corresponding
-[gradient information (`[*_]dwi.bval` and `[*_]dwi.bvec` sidecar files)](#required-gradient-orientation-information)
-to be stored.
-
-Otherwise, if some gradient information is associated to the single-band diffusion
-image and a multi-band diffusion image also exists, the `acq-` entity
-MUST be used to distinguish both images.
-In such a case, two files could have the following names:
-`sub-01_acq-singleband_dwi.nii.gz` and `sub-01_acq-multiband_dwi.nii.gz`.
-The user is free to choose any other label than `singleband` and
-`multiband`, as long as they are consistent across subjects and sessions.
-
-Scanner-generated derivative images,
-such as trace-weighted, ADC, exponentiated ADC,
-fractional anisotropy (FA and colFA), and estimated unweighted signal intensity,
-MAY be included using the `trace`, `ADC`, `expADC`, `FA`, `colFA` and `S0map` suffixes, respectively.
-If trace, ADC, expADC, FA, colFA, or S0 volume filenames match a diffusion series with all applicable entities,
-such volumes SHOULD have been computed from that series.
-Otherwise, some entity, such as [`acq-`](../appendices/entities.md#acq),
-SHOULD be used to indicate that the files are unrelated.
+The [`run-`](../appendices/entities.md#run) entity is RECOMMENDED to encode the splits of multipart DWI scans (see [below](#multipart-split-dwi-schemes) for more information on multipart DWI schemes).
+
+**Combining multi- and single-band acquisitions**. The single-band reference image MAY be stored with suffix `sbref` (for example, `dwi/sub-control01_sbref.nii[.gz]`) as long as the image has no corresponding [gradient information (`[*_]dwi.bval` and `[*_]dwi.bvec` sidecar files)](#required-gradient-orientation-information) to be stored.
+
+Otherwise, if some gradient information is associated to the single-band diffusion image and a multi-band diffusion image also exists, the `acq-` entity MUST be used to distinguish both images. In such a case, two files could have the following names: `sub-01_acq-singleband_dwi.nii.gz` and `sub-01_acq-multiband_dwi.nii.gz`. The user is free to choose any other label than `singleband` and `multiband`, as long as they are consistent across subjects and sessions.
+
+Scanner-generated derivative images, such as trace-weighted, ADC, exponentiated ADC, fractional anisotropy (FA and colFA), and estimated unweighted signal intensity, MAY be included using the `trace`, `ADC`, `expADC`, `FA`, `colFA` and `S0map` suffixes, respectively. If trace, ADC, expADC, FA, colFA, or S0 volume filenames match a diffusion series with all applicable entities, such volumes SHOULD have been computed from that series. Otherwise, some entity, such as [`acq-`](../appendices/entities.md#acq), SHOULD be used to indicate that the files are unrelated.
### REQUIRED gradient orientation information
-The REQUIRED gradient orientation information corresponding to a DWI acquisition
-MUST be stored using `[*_]dwi.bval` and `[*_]dwi.bvec` pairs of files.
-The `[*_]dwi.bval` and `[*_]dwi.bvec` files MAY be saved on any level of the directory structure
-and thus define those values for all sessions and/or subjects in one place (see
-[the inheritance principle](../common-principles.md#the-inheritance-principle)).
-
-As an exception to the [common principles](../common-principles.md#definitions)
-that parameters are constant across runs, the gradient table information (stored
-within the `[*_]dwi.bval` and `[*_]dwi.bvec` files) MAY change across DWI runs.
-
-**Gradient orientation file formats**.
-The `[*_]dwi.bval` and `[*_]dwi.bvec` files MUST follow the
-[FSL format](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/diffusion/index?id=diffusion-data-in-fsl).
-
-The `[*_]dwi.bvec` file contains 3 rows with *N* space-delimited floating-point numbers,
-corresponding to the *N* volumes in the corresponding NIfTI file.
-Across these three rows,
-each column encodes three elements of a 3-vector for the corresponding image volume;
-each vector MUST be either of unit norm,
-or optionally the vector `[0.0,0.0,0.0]`
-for *non-diffusion-weighted* (also called *b*=0 or *low-b*) volumes.
-These values are to be interpreted as cosine values with respect to the image axis orientations
-as defined by the corresponding NIfTI image header transformation;
-*unless* the image axes defined in the corresponding NIfTI image header
-form a right-handed coordinate system
-(that is, the 3x3 matrix of direction cosines has a positive determinant),
-in which case the sign of the first element of each 3-vector must be inverted
-for this interpretation to be valid.
-Note that this definition of orientations with respect to the NIfTI image axes
-is *not* equivalent to the DICOM convention,
-where orientations are instead defined with respect to the scanner device's coordinate system
-(see [Coordinate systems](../appendices/coordinate-systems.md)).
-
-The `[*_]dwi.bval` file contains the *b*-values (in s/mm2 )
-corresponding to the volumes in the relevant NIfTI file,
-with 0 designating *b*=0 volumes; space-delimited.
-
-Examples of `[*_]dwi.bvec` and `[*_]dwi.bval` files,
-corresponding to a NIfTI image with 6 volumes
-with the first two volumes having no diffusion sensitization:
-
-- `[*_]dwi.bvec`:
- ```Text
- 0 0 0.021828 -0.015425 -0.70918 -0.2465
- 0 0 0.80242 0.22098 -0.00063106 0.1043
- 0 0 -0.59636 0.97516 -0.70503 -0.96351
- ```
-
-- `[_]dwi.bval`:
- ```Text
- 0 0 2000 2000 1000 1000
- ```
+The REQUIRED gradient orientation information corresponding to a DWI acquisition MUST be stored using `[*_]dwi.bval` and `[*_]dwi.bvec` pairs of files. The `[*_]dwi.bval` and `[*_]dwi.bvec` files MAY be saved on any level of the directory structure and thus define those values for all sessions and/or subjects in one place (see [the inheritance principle](../common-principles.md#the-inheritance-principle)).
+
+As an exception to the [common principles](../common-principles.md#definitions) that parameters are constant across runs, the gradient table information (stored within the `[*_]dwi.bval` and `[*_]dwi.bvec` files) MAY change across DWI runs.
+
+**Gradient orientation file formats**. The `[*_]dwi.bval` and `[*_]dwi.bvec` files MUST follow the [FSL format](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/diffusion/index?id=diffusion-data-in-fsl).
+
+The `[*_]dwi.bvec` file contains 3 rows with _N_ space-delimited floating-point numbers, corresponding to the _N_ volumes in the corresponding NIfTI file. Across these three rows, each column encodes three elements of a 3-vector for the corresponding image volume; each vector MUST be either of unit norm, or optionally the vector `[0.0,0.0,0.0]` for _non-diffusion-weighted_ (also called _b_=0 or _low-b_) volumes. These values are to be interpreted as cosine values with respect to the image axis orientations as defined by the corresponding NIfTI image header transformation; _unless_ the image axes defined in the corresponding NIfTI image header form a right-handed coordinate system (that is, the 3x3 matrix of direction cosines has a positive determinant), in which case the sign of the first element of each 3-vector must be inverted for this interpretation to be valid. Note that this definition of orientations with respect to the NIfTI image axes is _not_ equivalent to the DICOM convention, where orientations are instead defined with respect to the scanner device's coordinate system (see [Coordinate systems](../appendices/coordinate-systems.md)).
+
+The `[*_]dwi.bval` file contains the _b_-values (in s/mm2 ) corresponding to the volumes in the relevant NIfTI file, with 0 designating _b_=0 volumes; space-delimited.
+
+Examples of `[*_]dwi.bvec` and `[*_]dwi.bval` files, corresponding to a NIfTI image with 6 volumes with the first two volumes having no diffusion sensitization:
+
+- `[*_]dwi.bvec`:
+
+ ```Text
+ 0 0 0.021828 -0.015425 -0.70918 -0.2465
+ 0 0 0.80242 0.22098 -0.00063106 0.1043
+ 0 0 -0.59636 0.97516 -0.70503 -0.96351
+ ```
+
+- `[_]dwi.bval`:
+ ```Text
+ 0 0 2000 2000 1000 1000
+ ```
### Multipart (split) DWI schemes
-Some MR schemes cannot be acquired directly by some scanner devices,
-requiring to generate several DWI runs that were originally meant to belong
-in a single one.
-For instance, some GE scanners cannot collect more than ≈160 volumes
-in a single run under fast-changing gradients, so acquiring *HCP-style*
-diffusion images will require splitting the DWI scheme in several runs.
-Because researchers will generally optimize the data splits, these will likely
-not be able to be directly concatenated.
-BIDS permits defining arbitrary groupings of these multipart scans with the
-following metadata:
+Some MR schemes cannot be acquired directly by some scanner devices, requiring to generate several DWI runs that were originally meant to belong in a single one. For instance, some GE scanners cannot collect more than ≈160 volumes in a single run under fast-changing gradients, so acquiring _HCP-style_ diffusion images will require splitting the DWI scheme in several runs. Because researchers will generally optimize the data splits, these will likely not be able to be directly concatenated. BIDS permits defining arbitrary groupings of these multipart scans with the following metadata:
+
{{ MACROS___make_sidecar_table("dwi.MRIDiffusionMultipart") }}
JSON example:
@@ -820,15 +699,13 @@ JSON example:
}
```
-For instance, if there are two phase-encoding directions (`AP`, `PA`), and
-two runs each, and the intent of the researcher is that all of them are
-part of a unique multipart scan, then they will tag all four runs with the
-same `MultipartID` (shown at the right-hand side of the file listing):
+For instance, if there are two phase-encoding directions (`AP`, `PA`), and two runs each, and the intent of the researcher is that all of them are part of a unique multipart scan, then they will tag all four runs with the same `MultipartID` (shown at the right-hand side of the file listing):
+
{{ MACROS___make_filetree_example(
{
"sub-1": {
@@ -842,13 +719,13 @@ A guide for using macros can be found at
}
) }}
-If, conversely, the researcher wanted to store two multipart scans, one possibility
-is to combine matching phase-encoding directions:
+If, conversely, the researcher wanted to store two multipart scans, one possibility is to combine matching phase-encoding directions:
+
{{ MACROS___make_filetree_example(
{
"sub-1": {
@@ -862,13 +739,13 @@ A guide for using macros can be found at
}
) }}
-Alternatively, the researcher's intent could be combining opposed phase-encoding
-runs instead:
+Alternatively, the researcher's intent could be combining opposed phase-encoding runs instead:
+
{{ MACROS___make_filetree_example(
{
"sub-1": {
@@ -882,13 +759,13 @@ A guide for using macros can be found at
}
) }}
-The `MultipartID` metadata MAY be used with the
-[`acq-`](../appendices/entities.md#acq) entity, for example:
+The `MultipartID` metadata MAY be used with the [`acq-`](../appendices/entities.md#acq) entity, for example:
+
{{ MACROS___make_filetree_example(
{
"sub-1": {
@@ -904,11 +781,7 @@ A guide for using macros can be found at
### Other RECOMMENDED metadata
-The `PhaseEncodingDirection` and `TotalReadoutTime` metadata
-fields are RECOMMENDED to enable the correction of geometrical distortions
-with [fieldmap information](#fieldmap-data).
-See [Common metadata fields](#common-metadata-fields) for a list of
-additional terms that can be included in the corresponding JSON file.
+The `PhaseEncodingDirection` and `TotalReadoutTime` metadata fields are RECOMMENDED to enable the correction of geometrical distortions with [fieldmap information](#fieldmap-data). See [Common metadata fields](#common-metadata-fields) for a list of additional terms that can be included in the corresponding JSON file.
JSON example:
@@ -935,76 +808,44 @@ The inputs for this macro can be found in the directory
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_filename_template("raw", datatypes=["perf"]) }}
-The complete ASL time series should be stored as a 4D NIfTI file in the original acquisition order,
-accompanied by two ancillary files: `*_asl.json` and `*_aslcontext.tsv`.
+The complete ASL time series should be stored as a 4D NIfTI file in the original acquisition order, accompanied by two ancillary files: `*_asl.json` and `*_aslcontext.tsv`.
### `*_aslcontext.tsv`
-The `*_aslcontext.tsv` table consists of a single column of labels identifying the
-`volume_type` of each volume in the corresponding `*_asl.nii[.gz]` file.
-Volume types are defined in the following table, based on DICOM Tag 0018, 9257 `ASL Context`.
-Note that the volume_types `control` and `label` within BIDS only serve
-to specify the magnetization state of the blood and thus the ASL subtraction order.
-See the [ASL Appendix](../appendices/arterial-spin-labeling.md#which-image-is-control-and-which-is-label)
-for more information on `control` and `label`.
-
-| **volume_type** | **Definition** |
-| --------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `control` | The control image is acquired in the exact same way as the label image, except that the magnetization of the blood flowing into the imaging region has not been inverted. |
-| `label` | The label image is acquired in the exact same way as the control image, except that the blood magnetization flowing into the imaging region has been inverted. |
-| `m0scan` | The M0 image is a calibration image, used to estimate the equilibrium magnetization of blood. |
-| `deltam` | The deltaM image is a perfusion-weighted image, obtained by the subtraction of `control` - `label`. |
-| `cbf` | The cerebral blood flow (CBF) image is produced by dividing the deltaM by the M0, quantified into `mL/100g/min` (See also [doi:10.1002/mrm.25197](https://doi.org/10.1002/mrm.25197)). |
-| `noRF` | No radio frequency excitation (noRF) images are produced by disabling the radio frequency excitation, while maintaining all other parameters from the associated scan. |
-| `n/a` | In some cases, there may be volume types that are not yet supported by BIDS, or which cannot be used by tools. |
-
-If the `control` and `label` images are not available,
-their derivative `deltam` should be stored within the `*_asl.nii[.gz]`
-and specified in the `*_aslcontext.tsv` instead.
-If the `deltam` is not available,
-`cbf` should be stored within the `*_asl.nii[.gz]` and specified in the `*_aslcontext.tsv`.
-When `cbf` is stored within the `*_asl.nii[.gz]`,
-its units need to be specified in the `*_asl.json` as well.
-Note that the raw images, including the `m0scan`, may also be used for quality control.
-See the [ASL Appendix](../appendices/arterial-spin-labeling.md#_aslcontexttsv-three-possible-cases)
-for examples of the three possible cases, in order of decreasing preference.
+The `*_aslcontext.tsv` table consists of a single column of labels identifying the `volume_type` of each volume in the corresponding `*_asl.nii[.gz]` file. Volume types are defined in the following table, based on DICOM Tag 0018, 9257 `ASL Context`. Note that the volume_types `control` and `label` within BIDS only serve to specify the magnetization state of the blood and thus the ASL subtraction order. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#which-image-is-control-and-which-is-label) for more information on `control` and `label`.
+
+| **volume_type** | **Definition** |
+| --- | --- |
+| `control` | The control image is acquired in the exact same way as the label image, except that the magnetization of the blood flowing into the imaging region has not been inverted. |
+| `label` | The label image is acquired in the exact same way as the control image, except that the blood magnetization flowing into the imaging region has been inverted. |
+| `m0scan` | The M0 image is a calibration image, used to estimate the equilibrium magnetization of blood. |
+| `deltam` | The deltaM image is a perfusion-weighted image, obtained by the subtraction of `control` - `label`. |
+| `cbf` | The cerebral blood flow (CBF) image is produced by dividing the deltaM by the M0, quantified into `mL/100g/min` (See also [doi:10.1002/mrm.25197](https://doi.org/10.1002/mrm.25197)). |
+| `noRF` | No radio frequency excitation (noRF) images are produced by disabling the radio frequency excitation, while maintaining all other parameters from the associated scan. |
+| `n/a` | In some cases, there may be volume types that are not yet supported by BIDS, or which cannot be used by tools. |
+
+If the `control` and `label` images are not available, their derivative `deltam` should be stored within the `*_asl.nii[.gz]` and specified in the `*_aslcontext.tsv` instead. If the `deltam` is not available, `cbf` should be stored within the `*_asl.nii[.gz]` and specified in the `*_aslcontext.tsv`. When `cbf` is stored within the `*_asl.nii[.gz]`, its units need to be specified in the `*_asl.json` as well. Note that the raw images, including the `m0scan`, may also be used for quality control. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#_aslcontexttsv-three-possible-cases) for examples of the three possible cases, in order of decreasing preference.
### Scaling
-The `*_asl.nii.gz` and `*_m0scan.nii.gz` should contain appropriately scaled data,
-and no additional scaling factors are allowed other than the scale slope in the respective
-NIfTI headers.
+The `*_asl.nii.gz` and `*_m0scan.nii.gz` should contain appropriately scaled data, and no additional scaling factors are allowed other than the scale slope in the respective NIfTI headers.
### `*_asllabeling.*`
-A deidentified screenshot of the planning of the labeling slab/plane
-with respect to the imaging slab or slices.
-This screenshot is based on DICOM macro C.8.13.5.14.
+A deidentified screenshot of the planning of the labeling slab/plane with respect to the imaging slab or slices. This screenshot is based on DICOM macro C.8.13.5.14.
See [`LabelingLocationDescription`](../glossary.md#labelinglocationdescription-metadata) for more details.
### M0
-The `m0scan` can either be stored inside the 4D ASL time-series NIfTI file
-or as a separate NIfTI file,
-depending on whether it was acquired within the ASL time-series or as a separate scan.
-These and other M0 options are specified in the REQUIRED `M0Type` field of the `*_asl.json` file.
-It can also be stored under
-`fmap/sub-[_ses-][_acq-][_ce-]_dir-[_run-]_m0scan.nii[.gz]`,
-when the [pepolar approach](#case-4-multiple-phase-encoded-directions-pepolar) is used.
+The `m0scan` can either be stored inside the 4D ASL time-series NIfTI file or as a separate NIfTI file, depending on whether it was acquired within the ASL time-series or as a separate scan. These and other M0 options are specified in the REQUIRED `M0Type` field of the `*_asl.json` file. It can also be stored under `fmap/sub-[_ses-][_acq-][_ce-]_dir-[_run-]_m0scan.nii[.gz]`, when the [pepolar approach](#case-4-multiple-phase-encoded-directions-pepolar) is used.
### `*_asl.json` file
-Depending on the method used for ASL acquisition ((P)CASL or PASL)
-different metadata fields are applicable.
-Additionally, some common metadata fields are REQUIRED for the `*_asl.json`:
-`MagneticFieldStrength`, `MRAcquisitionType`, `EchoTime`,
-`SliceTiming` in case `MRAcquisitionType` is defined as 2D,
-`RepetitionTimePreparation`, and `FlipAngle` in case `LookLocker` is `true`.
-See the [ASL Appendix](../appendices/arterial-spin-labeling.md#summary-image-of-the-most-common-asl-sequences)
-for more information on the most common ASL sequences.
+Depending on the method used for ASL acquisition ((P)CASL or PASL) different metadata fields are applicable. Additionally, some common metadata fields are REQUIRED for the `*_asl.json`: `MagneticFieldStrength`, `MRAcquisitionType`, `EchoTime`, `SliceTiming` in case `MRAcquisitionType` is defined as 2D, `RepetitionTimePreparation`, and `FlipAngle` in case `LookLocker` is `true`. See the [ASL Appendix](../appendices/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
@@ -1016,6 +857,7 @@ The definitions of the fields specified in these tables may be found in
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(["asl.MRIASLCommonMetadataFields", "asl.MRIASLCommonMetadataFieldsM0TypeRec", "asl.MRIASLCommonMetadataFieldsBackgroundSuppressionOpt", "asl.MRIASLCommonMetadataFieldsVascularCrushingOpt", ]) }}
#### (P)CASL-specific metadata fields
@@ -1030,6 +872,7 @@ The definitions of the fields specified in these tables may be found in
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([
"asl.MRIASLPcaslSpecific",
"asl.MRIASLCaslSpecific",
@@ -1038,9 +881,7 @@ A guide for using macros can be found at
#### PASL-specific metadata fields
-These fields can only be used when `ArterialSpinLabelingType` is `PASL`.
-See the [ASL Appendix](../appendices/arterial-spin-labeling.md#pasl-sequence)
-for more information on the PASL sequence and the BolusCutOff fields.
+These fields can only be used when `ArterialSpinLabelingType` is `PASL`. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#pasl-sequence) for more information on the PASL sequence and the BolusCutOff fields.
+
{{ MACROS___make_sidecar_table(["asl.MRIASLPaslSpecific", "asl.MRIASLPASLSpecificBolusCutOffFlagFalse"]) }}
### `m0scan` metadata fields
@@ -1064,42 +906,39 @@ The definitions of the fields specified in these tables may be found in
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("asl.MRIASLM0Scan") }}
-The following table recapitulates the ASL field dependencies. If Source field (column 1) contains the Value specified in column 2, then the Requirements in column 4 are
-imposed on the Dependent fields in column 3. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#flowchart-based-on-dependency-table) for this information in the
-form of flowcharts.
-
-| **Source field** | **Value** | **Dependent field** | **Requirements** |
-| ------------------------ | ------------ | -------------------- | ------------------------------------------------ |
-| MRAcquisitionType | 2D / 3D | SliceTiming | \[X\] / \[\] |
-| LookLocker | true | FlipAngle | \[X\] |
-| ArterialSpinLabelingType | PCASL | LabelingDuration | \[X\] |
-| ArterialSpinLabelingType | PASL | BolusCutOffFlag | \[X\] |
-| BolusCutOffFlag | true / false | BolusCutOffDelayTime | \[X\] / \[\] |
-| BolusCutOffFlag | true / false | BolusCutOffTechnique | \[X\] / \[\] |
-| M0Type | Separate | */perf/ | contains `*_m0scan.nii[.gz]` and `*_m0scan.json` |
-| M0Type | Included | *_aslcontext.tsv | contains m0scan |
-| M0Type | Estimate | M0Estimate | \[X\] |
-| `*_aslcontext.tsv` | cbf | Units | \[X\] |
+The following table recapitulates the ASL field dependencies. If Source field (column 1) contains the Value specified in column 2, then the Requirements in column 4 are imposed on the Dependent fields in column 3. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#flowchart-based-on-dependency-table) for this information in the form of flowcharts.
+
+| **Source field** | **Value** | **Dependent field** | **Requirements** |
+| --- | --- | --- | --- |
+| MRAcquisitionType | 2D / 3D | SliceTiming | \[X\] / \[\] |
+| LookLocker | true | FlipAngle | \[X\] |
+| ArterialSpinLabelingType | PCASL | LabelingDuration | \[X\] |
+| ArterialSpinLabelingType | PASL | BolusCutOffFlag | \[X\] |
+| BolusCutOffFlag | true / false | BolusCutOffDelayTime | \[X\] / \[\] |
+| BolusCutOffFlag | true / false | BolusCutOffTechnique | \[X\] / \[\] |
+| M0Type | Separate | \*/perf/ | contains `*_m0scan.nii[.gz]` and `*_m0scan.json` |
+| M0Type | Included | \*\_aslcontext.tsv | contains m0scan |
+| M0Type | Estimate | M0Estimate | \[X\] |
+| `*_aslcontext.tsv` | cbf | Units | \[X\] |
**Legend**
-- \[ X ] --> MUST be defined
-- \[ \] --> MUST NOT be defined
+- \[ X ] --> MUST be defined
+- \[ \] --> MUST NOT be defined
## Fieldmap data
-Data acquired to correct for *B0 * inhomogeneities can come in different forms.
-The current version of this standard considers four different scenarios:
+Data acquired to correct for _B0 _ inhomogeneities can come in different forms. The current version of this standard considers four different scenarios:
1. [Phase-difference map](#case-1-phase-difference-map-and-at-least-one-magnitude-image)
1. [Two phase maps](#case-2-two-phase-maps-and-two-magnitude-images)
-1. [Direct *field mapping*](#case-3-direct-field-mapping)
-1. ["*PEpolar*" fieldmaps](#case-4-multiple-phase-encoded-directions-pepolar)
+1. [Direct _field mapping_](#case-3-direct-field-mapping)
+1. ["_PEpolar_" fieldmaps](#case-4-multiple-phase-encoded-directions-pepolar)
-These four different types of field mapping strategies can be encoded
-using the following image types:
+These four different types of field mapping strategies can be encoded using the following image types:
+
{{ MACROS___make_suffix_table(
[
"magnitude",
@@ -1124,25 +964,15 @@ and a guide for using macros can be found at
### Expressing the MR protocol intent for fieldmaps
-Fieldmaps are typically acquired with the purpose of correcting one or more EPI
-scans under `dwi/`, `func/`, or `perf/` for distortions derived from *B0 *
-nonuniformity.
+Fieldmaps are typically acquired with the purpose of correcting one or more EPI scans under `dwi/`, `func/`, or `perf/` for distortions derived from _B0 _ nonuniformity.
#### Using `B0FieldIdentifier` metadata
-The general purpose [`B0FieldIdentifier` MRI metadata](#echo-planar-imaging-and-b0-mapping)
-is RECOMMENDED for the prescription of the *B0 * field estimation intent of the
-original acquisition protocol.
-`B0FieldIdentifier` and `B0FieldSource` duplicate the capabilities of
-the original `IntendedFor` approach (see below), while permitting more
-complex use cases.
-It is RECOMMENDED to use both approaches to maintain compatibility with
-tools that support older datasets.
+The general purpose [`B0FieldIdentifier` MRI metadata](#echo-planar-imaging-and-b0-mapping) is RECOMMENDED for the prescription of the _B0 _ field estimation intent of the original acquisition protocol. `B0FieldIdentifier` and `B0FieldSource` duplicate the capabilities of the original `IntendedFor` approach (see below), while permitting more complex use cases. It is RECOMMENDED to use both approaches to maintain compatibility with tools that support older datasets.
#### Using `IntendedFor` metadata
-Fieldmap data MAY be linked to the specific scan(s) it was acquired for by
-filling the `IntendedFor` field in the corresponding JSON file.
+Fieldmap data MAY be linked to the specific scan(s) it was acquired for by filling the `IntendedFor` field in the corresponding JSON file.
+
{{ MACROS___make_sidecar_table("fmap.MRIFieldmapIntendedFor") }}
For example:
@@ -1185,12 +1016,10 @@ The inputs for this macro can be found in the directory
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
+
{{ MACROS___make_filename_template("raw", datatypes=["fmap"], suffixes=["phasediff", "magnitude1", "magnitude2"]) }}
-where
-the REQUIRED `_phasediff` image corresponds to the phase-drift map between echo times,
-the REQUIRED `_magnitude1` image corresponds to the shorter echo time, and
-the OPTIONAL `_magnitude2` image to the longer echo time.
+where the REQUIRED `_phasediff` image corresponds to the phase-drift map between echo times, the REQUIRED `_magnitude1` image corresponds to the shorter echo time, and the OPTIONAL `_magnitude2` image to the longer echo time.
Required fields:
@@ -1202,13 +1031,10 @@ The definitions of the fields specified in these tables may be found in
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("fmap.MRIFieldmapPhaseDifferencePhasediff") }}
-In this particular case, the sidecar JSON file
-`sub-[_ses-][_acq-][_run-]_phasediff.json`
-MUST define the time of two echos used to map the phase and finally calculate
-the phase-difference map.
-For example:
+In this particular case, the sidecar JSON file `sub-[_ses-][_acq-][_run-]_phasediff.json` MUST define the time of two echos used to map the phase and finally calculate the phase-difference map. For example:
```JSON
{
@@ -1220,9 +1046,7 @@ For example:
#### Case 2: Two phase maps and two magnitude images
-Similar to case 1, but instead of a precomputed phase-difference map, two
-separate phase images and two magnitude images corresponding to first and
-second echos are available.
+Similar to case 1, but instead of a precomputed phase-difference map, two separate phase images and two magnitude images corresponding to first and second echos are available.
+
{{ MACROS___make_filename_template("raw", datatypes=["fmap"], suffixes=["phase1", "phase2", "magnitude1", "magnitude2"]) }}
Required fields:
@@ -1243,10 +1068,10 @@ The definitions of the fields specified in these tables may be found in
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("fmap.MRIFieldmapTwoPhase") }}
-Each phase map has a corresponding sidecar JSON file to specify its corresponding `EchoTime`.
-For example, `sub-[_ses-][_acq-][_run-]_phase2.json` may read:
+Each phase map has a corresponding sidecar JSON file to specify its corresponding `EchoTime`. For example, `sub-[_ses-][_acq-][_run-]_phase2.json` may read:
```JSON
{
@@ -1255,10 +1080,9 @@ For example, `sub-[_ses-][_acq-][_run-]_phase2.json`
}
```
-#### Case 3: Direct *field mapping*
+#### Case 3: Direct _field mapping_
-In some cases (for example GE), the scanner software will directly reconstruct a
-*B0 * field map along with a magnitude image used for anatomical reference.
+In some cases (for example GE), the scanner software will directly reconstruct a _B0 _ field map along with a magnitude image used for anatomical reference.
+
{{ MACROS___make_filename_template("raw", datatypes=["fmap"], suffixes=["fieldmap", "magnitude"]) }}
Required fields:
@@ -1279,6 +1104,7 @@ The definitions of the fields specified in these tables may be found in
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("fmap.MRIFieldmapDirectFieldMapping") }}
For example:
@@ -1291,8 +1117,7 @@ For example:
}
```
-See [Using `IntendedFor` metadata](#using-intendedfor-metadata)
-for details on the `IntendedFor` field.
+See [Using `IntendedFor` metadata](#using-intendedfor-metadata) for details on the `IntendedFor` field.
#### Case 4: Multiple phase encoded directions ("pepolar")
@@ -1303,14 +1128,7 @@ for details on the `IntendedFor` field.
- [`ieeg_visual_multimodal`](https://github.com/bids-standard/bids-examples/tree/master/ieeg_visual_multimodal)
-The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo
-EPI scans with different phase encoding directions to estimate the distortion
-map corresponding to the nonuniformities of the *B0 * field.
-These `*_epi.nii[.gz]` - or `*_m0scan.nii[.gz]` for arterial spin labeling perfusion data - files can be 3D or 4D --
-in the latter case, all timepoints share the same scanning parameters.
-Some 4D scans intended for correcting DWIs may have accompanying `*_epi.bval` and `*_epi.bvec` files.
-Examples of software tools using these kinds of images are FSL TOPUP and
-AFNI `3dqwarp`.
+The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo EPI scans with different phase encoding directions to estimate the distortion map corresponding to the nonuniformities of the _B0 _ field. These `*_epi.nii[.gz]` - or `*_m0scan.nii[.gz]` for arterial spin labeling perfusion data - files can be 3D or 4D -- in the latter case, all timepoints share the same scanning parameters. Some 4D scans intended for correcting DWIs may have accompanying `*_epi.bval` and `*_epi.bvec` files. Examples of software tools using these kinds of images are FSL TOPUP and AFNI `3dqwarp`.
+
{{ MACROS___make_filename_template("raw", datatypes=["fmap"], suffixes=["epi"]) }}
-The [`dir-`](../appendices/entities.md#dir) entity is REQUIRED
-for these files.
-This entity MUST be used in addition to
-the REQUIRED `PhaseEncodingDirection` metadata field
-(see [Filename structure](../common-principles.md#filenames)).
+The [`dir-`](../appendices/entities.md#dir) entity is REQUIRED for these files. This entity MUST be used in addition to the REQUIRED `PhaseEncodingDirection` metadata field (see [Filename structure](../common-principles.md#filenames)).
Required fields:
@@ -1337,6 +1152,7 @@ The definitions of the fields specified in these tables may be found in
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("fmap.MRIFieldmapPepolar") }}
For example:
@@ -1350,10 +1166,6 @@ For example:
}
```
-See [Using `IntendedFor` metadata](#using-intendedfor-metadata)
-for details on the `IntendedFor` field.
+See [Using `IntendedFor` metadata](#using-intendedfor-metadata) for details on the `IntendedFor` field.
-As for other EPI sequences, these field mapping sequences may have any of the
-[in-plane spatial encoding](#in-and-out-plane-spatial-encoding) metadata keys.
-However, please note that `PhaseEncodingDirection` and `TotalReadoutTime` keys
-are REQUIRED for these field mapping sequences.
+As for other EPI sequences, these field mapping sequences may have any of the [in-plane spatial encoding](#in-and-out-of-plane-spatial-encoding) metadata keys. However, please note that `PhaseEncodingDirection` and `TotalReadoutTime` keys are REQUIRED for these field mapping sequences.