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[ENH] BEP001 - RepetitionTimeExcitation and RepetitionTimePreparation #671

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Dec 1, 2020
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[ENH] BEP001 - RepetitionTimeExcitation and RepetitionTimePreparation #671

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b7b01ae
Merge pull request #3 from bids-standard/master
agahkarakuzu Nov 11, 2020
02916ca
[ENH] Improve TR definitions
agahkarakuzu Nov 16, 2020
3ed7755
Typo
agahkarakuzu Nov 16, 2020
f684efd
Update src/04-modality-specific-files/01-magnetic-resonance-imaging-d…
agahkarakuzu Nov 16, 2020
1b459a0
ENH: Allow for variable RTE/P
effigies Nov 22, 2020
9bc528b
STY: Update table widths
effigies Nov 22, 2020
81ac117
Update src/04-modality-specific-files/01-magnetic-resonance-imaging-d…
agahkarakuzu Nov 24, 2020
d314835
Update src/04-modality-specific-files/01-magnetic-resonance-imaging-d…
agahkarakuzu Nov 24, 2020
e9ce8cd
Merge pull request #5 from effigies/TR-enhancement
agahkarakuzu Nov 24, 2020
1a9412c
Change ref to DOI @Remi-Gau
agahkarakuzu Nov 24, 2020
356966b
Update src/04-modality-specific-files/01-magnetic-resonance-imaging-d…
agahkarakuzu Dec 1, 2020
1bf9b27
Update src/04-modality-specific-files/01-magnetic-resonance-imaging-d…
agahkarakuzu Dec 1, 2020
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18 changes: 10 additions & 8 deletions src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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Expand Up @@ -191,9 +191,11 @@ 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:

| **Key name** | **Requirement level** | **Data type** | **Description** |
| ----------------------- | --------------------- | ------------- | ---------------------------------------------------------------------------------------------------------------------------------------- |
| ContrastBolusIngredient | OPTIONAL | [string][] | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| ----------------------- | --------------------- | -------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| ContrastBolusIngredient | OPTIONAL | [string][] | Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048. |
| RepetitionTimeExcitation | OPTIONAL | [number][] | The interval, in seconds, between two successive excitations. The DICOM tag that best refers to this parameter is [(0018, 0080)](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)). This field may be used together with the `RepetitionTimePreparation` for certain use cases, such as [MP2RAGE](https://doi.org/10.1016/j.neuroimage.2009.10.002). Use `RepetitionTimeExcitation` (in combination with `RepetitionTimePreparation` if needed) for anatomy imaging data rather than `RepetitionTime` as it is already defined as the amount of time that it takes to acquire a single volume in the [task imaging data](#task-including-resting-state-imaging-data) section. |
| RepetitionTimePreparation | OPTIONAL | [number][] or [array][] of [numbers][] | The interval, in seconds, that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. The data type number may apply to files from any MRI modality concerned with a single value for this field. 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). |

Similarly, the OPTIONAL [`rec-<label>`](../99-appendices/09-entities.md#rec)
key/value can be used to distinguish
Expand Down Expand Up @@ -288,11 +290,11 @@ JSON file.

### Required fields

| **Key name** | **Requirement level** | **Data type** | **Description** |
| -------------- | --------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| RepetitionTime | REQUIRED | [number][] | The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). Please note that this definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value needs to be consistent with the `pixdim[4]` field (after accounting for units stored in `xyzt_units` field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming` and is derived from DICOM Tag 0018, 0080 and converted to seconds. |
| VolumeTiming | REQUIRED | [array][] of [numbers][] | The time at which each volume was acquired during the acquisition. It is described using a list of times referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined. |
| TaskName | REQUIRED | [string][] | Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`. |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| -------------- | --------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| RepetitionTime | REQUIRED | [number][] | The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). When used in the context of functional acquisitions this parameter best corresponds to [DICOM Tag 0020,0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)): the "time delta between images in a dynamic of functional set of images" but may also be found in [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)): "the period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence". This definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value MUST be consistent with the '`pixdim[4]`' field (after accounting for units stored in '`xyzt_units`' field) in the NIfTI header. This field is mutually exclusive with `VolumeTiming`. |
| VolumeTiming | REQUIRED | [array][] of [numbers][] | The time at which each volume was acquired during the acquisition. It is described using a list of times referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with `RepetitionTime` and `DelayTime`. If defined, this requires acquisition time (TA) be defined via either `SliceTiming` or `AcquisitionDuration` be defined. |
| TaskName | REQUIRED | [string][] | Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this TaskName field by removing all non-alphanumeric (`[a-zA-Z0-9]`) characters. For example TaskName `faces n-back` will correspond to task label `facesnback`. A RECOMMENDED convention is to name resting state task using labels beginning with `rest`. |

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
Expand Down