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[ENH] Make explicit that "task" metadata applies to "beh" modality #804

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Aug 2, 2021
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[ENH] Make explicit that "task" metadata applies to "beh" modality #804

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fbdc70e
Add metadata to JSON files in beh folder
Remi-Gau May 22, 2021
a092b57
add task metadata to PET
Remi-Gau May 22, 2021
00d0f6d
style fix
Remi-Gau May 22, 2021
6fc7ae8
Revert PET task change
Remi-Gau May 30, 2021
c44c96c
Apply suggestions from code review
Remi-Gau Jul 26, 2021
cd7b47b
Apply suggestions from code review
Remi-Gau Jul 26, 2021
d629e66
STY: Table fences
effigies Jul 26, 2021
1c10b4e
Merge remote-tracking branch 'upstream/master' into remi-task_standar…
Remi-Gau Jul 28, 2021
a05fcfe
replace hard coded table with macro call
Remi-Gau Jul 28, 2021
944baf0
lint fix
Remi-Gau Jul 28, 2021
3961f1b
update taskname definition
Remi-Gau Jul 29, 2021
1c810a5
update instruction definition
Remi-Gau Jul 29, 2021
1352662
remove extra info about task from iEEG as non specific to iEEG
Remi-Gau Jul 29, 2021
74526c3
Revert "remove extra info about task from iEEG as non specific to iEEG"
Remi-Gau Jul 29, 2021
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21 changes: 21 additions & 0 deletions src/04-modality-specific-files/07-behavioral-experiments.md
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Expand Up @@ -14,8 +14,29 @@ Additionally, events files that do not include the mandatory `onset` and
`duration` columns can still be included, but should be labeled `_beh.tsv`
rather than `_events.tsv`.

Each task has a unique label that MUST only consist of letters and/or numbers
(other characters, including spaces and underscores, are not allowed) with the
[`task-<label>`](../99-appendices/09-entities.md#task) key/value pair.
Those labels MUST be consistent across subjects and sessions.

The OPTIONAL [`acq-<label>`](../99-appendices/09-entities.md#acq) key/value pair corresponds to a custom label to
distinguish different conditions present during multiple runs of the same task.
For example, if a study includes runs of an n-back task, with deep brain
stimulation turned on or off, the data files may be labelled
`sub-01_task-nback_acq-dbson_beh.tsv` and `sub-01_task-nback_acq-dbsoff_beh.tsv`.

## RECOMMENDED metadata

In addition of the metadata REQUIRED for some data that can be found in the `beh` folder
(for example `SamplingFrequency` and `StartTime` for `*_<physio|stim>.tsv.gz` files),
it is RECOMMENDED to add the following metadata to the JSON files of this folder.

| **Key name** | **Requirement level** | **Data type** | **Description** |
| ------------------ | --------------------- | ------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| TaskName | RECOMMENDED | [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`. |
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| TaskDescription | RECOMMENDED | [string][] | Description of the task. |
| Instructions | RECOMMENDED | [string][] | Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (for example, to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [Cognitive Atlas](https://www.cognitiveatlas.org/) term that describes the task (for example, Resting State with eyes closed "<https://www.cognitiveatlas.org/task/id/trm_54e69c642d89b>"). |
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| CogPOID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (for example, Rest "<http://wiki.cogpo.org/index.php?title=Rest>") . |
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| InstitutionName | RECOMMENDED | [string][] | The name of the institution in charge of the equipment that produced the composite instances. |
| InstitutionAddress | RECOMMENDED | [string][] | The address of the institution in charge of the equipment that produced the composite instances. |
10 changes: 10 additions & 0 deletions src/04-modality-specific-files/09-positron-emission-tomography.md
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Expand Up @@ -219,6 +219,16 @@ We refer to the common principles for the standards for describing dates and tim

All reconstruction-specific parameters that are not specified, but one wants to include, should go into the `ReconMethodParameterValues` field.

#### Task related metadata

| **Key name** | **Requirement level** | **Data type** | **Description** |
| ----------------| --------------------- | ------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| TaskName | RECOMMENDED | [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`. |
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| TaskDescription | RECOMMENDED | [string][] | Description of the task. |
| Instructions | RECOMMENDED | [string][] | Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (for example, to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [Cognitive Atlas](https://www.cognitiveatlas.org/) term that describes the task (for example, Resting State with eyes closed "<https://www.cognitiveatlas.org/task/id/trm_54e69c642d89b>"). |
| CogPOID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (for example, Rest "<http://wiki.cogpo.org/index.php?title=Rest>") . |

#### Example (`*_pet.json`)

```JSON
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