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sappelhoff committed Sep 15, 2020
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The following metadata JSON fields are defined for preprocessed images:

| **Key name** | **Description** |
| ------------- | -------------------------------------------------------------------------------------------------------------------------------------- |
| SkullStripped | REQUIRED. Boolean. Whether the volume was skull stripped (non-brain voxels set to zero) or not. |
| Resolution | REQUIRED if `res` is present. String, or [object][] mapping labels to strings. Specifies the interpretation of the resolution keyword. |
| Density | REQUIRED if `den` is present. String, or [object][] mapping labels to strings. Specifies the interpretation of the density keyword. |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| ------------- | ----------------------------- | -------------------------------------------------- | ---------------------------------------------------------------------------- |
| SkullStripped | REQUIRED | [boolean][] | Whether the volume was skull stripped (non-brain voxels set to zero) or not. |
| Resolution | REQUIRED if `res` is present. | [string][] or [object][] mapping labels to strings | Specifies the interpretation of the resolution keyword. |
| Density | REQUIRED if `den` is present. | [string][] or [object][] mapping labels to strings | Specifies the interpretation of the density keyword. |

Example JSON file corresponding to
`pipeline1/sub-001/func/sub-001_task-rest_run-1_space-MNI305_bold.json` above:
Expand Down Expand Up @@ -131,13 +131,13 @@ and the `Atlas` metadata SHOULD be defined.

JSON metadata fields:

| **Key name** | **Description** |
| ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------- |
| RawSources | Same as defined in [Introduction][intro], but elevated from OPTIONAL to REQUIRED |
| Type | RECOMMENDED. Short identifier of the mask. Reserved values: `Brain` - brain mask, `Lesion` - lesion mask, `Face` - face mask, `ROI` - ROI mask |
| Atlas | OPTIONAL. Which atlas (if any) was used to generate the mask. RECOMMENDED if `label` entity is defined. |
| Resolution | REQUIRED if `res` is present. String, or [object][] mapping labels to strings. Specifies the interpretation of the resolution keyword. |
| Density | REQUIRED if `den` is present. String, or [object][] mapping labels to strings. Specifies the interpretation of the density keyword. |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| ------------ | -------------------------------------------------- | -------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------- |
| RawSources | REQUIRED | [array][] of [strings][] | Same as defined in [Introduction][intro], but elevated from OPTIONAL to REQUIRED. |
| Type | RECOMMENDED | [string][] | Short identifier of the mask. Reserved values: `Brain` - brain mask, `Lesion` - lesion mask, `Face` - face mask, `ROI` - ROI mask |
| Atlas | OPTIONAL, RECOMMENDED if `label` entity is defined | [string][] | Which atlas (if any) was used to generate the mask. |
| Resolution | REQUIRED if `res` is present | [string][] or [object][] mapping labels to strings | Specifies the interpretation of the resolution keyword. |
| Density | REQUIRED if `den` is present | [string][] or [object][] mapping labels to strings | Specifies the interpretation of the density keyword. |

Examples:

Expand Down Expand Up @@ -181,12 +181,12 @@ Probabilistic segmentations of surfaces are currently [unspecified][].

The following metadata fields apply to all segmentation files:

| **Key name** | **Description** |
| ------------ | -------------------------------------------------------------------------------------------------------------------------------------- |
| Manual | OPTIONAL. Boolean. Indicates if the segmentation was performed manually or via an automated process |
| Atlas | OPTIONAL. Which atlas (if any) was used to derive the segmentation. |
| Resolution | REQUIRED if `res` is present. String, or [object][] mapping labels to strings. Specifies the interpretation of the resolution keyword. |
| Density | REQUIRED if `den` is present. String, or [object][] mapping labels to strings. Specifies the interpretation of the density keyword. |
| **Key name** | **Requirement level** | **Data type** | **Description** |
| ------------ | ---------------------------- | -------------------------------------------------- | --------------------------------------------------------------------------------- |
| Manual | OPTIONAL | [boolean][] | Indicates if the segmentation was performed manually or via an automated process. |
| Atlas | OPTIONAL | [string][] | Which atlas (if any) was used to derive the segmentation. |
| Resolution | REQUIRED if `res` is present | [string][] or [object][] mapping labels to strings | Specifies the interpretation of the resolution keyword. |
| Density | REQUIRED if `den` is present | [string][] or [object][] mapping labels to strings | Specifies the interpretation of the density keyword. |

### Discrete Segmentations

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[common_preproc]: 02-common-data-types.md#preprocessed-or-cleaned-data
[object]: https://www.json.org/json-en.html
[unspecified]: ../02-common-principles.md#unspecified-data

[string]: https://www.w3schools.com/js/js_json_syntax.asp
[strings]: https://www.w3schools.com/js/js_json_syntax.asp
[boolean]: https://www.w3schools.com/js/js_json_datatypes.asp
[array]: https://www.w3schools.com/js/js_json_arrays.asp

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