Merge pull request #1579 from melanieganz/master

[SCHEMA][ENH] Remove atlas entity and replace it with seg in prep of BEP038

src/derivatives/imaging.md

@@ -153,10 +153,9 @@ Template:
 
 A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` entity](../appendices/entities.md#space).
 If no transformation has taken place, the value of `space` SHOULD be set to `orig`.
-If the mask is an ROI mask derived from an atlas, then the [`label` entity](../appendices/entities.md#label)) SHOULD
-be used to specify the masked structure
-(see [Common image-derived labels](#common-image-derived-labels)),
-and the `Atlas` metadata SHOULD be defined.
+If the mask is an ROI mask derived from an atlas segmentation,
+then the [`label` entity](../appendices/entities.md#label) SHOULD be used to specify the masked structure
+(see [Common image-derived labels](#common-image-derived-labels)).
 
 JSON metadata fields:
 
@@ -170,7 +169,6 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table([
  "derivatives.common_derivatives.MaskDerivatives",
- "derivatives.common_derivatives.MaskDerivativesAtlas",
  "derivatives.common_derivatives.ImageDerivativeResEntity",
  "derivatives.common_derivatives.ImageDerivativeDenEntity",
  ]) }}
@@ -229,10 +227,10 @@ structure may be concatenated in a single file.
 Segmentations may be defined in a volume (labeled voxels), a surface (labeled
 vertices) or a combined volume/surface space.
 
-If the segmentation can be derived from different atlases,
-the [`atlas` entity](../appendices/entities.md#atlas) MAY be used to
-distinguish the different segmentations.
-If so, the `Atlas` metadata SHOULD also be defined.
+If the segmentation can be generated in different ways,
+for example, following an atlas segmentation,
+the [`seg` entity](../appendices/entities.md#segmentation) MAY be used to
+distinguish the name of the segmentation used.
 
 The following section describes discrete and probabilistic segmentations of
 volumes, followed by discrete segmentations of surface/combined spaces.
@@ -250,7 +248,6 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table([
  "derivatives.common_derivatives.SegmentationCommon",
- "derivatives.common_derivatives.SegmentationCommonAtlas",
  "derivatives.common_derivatives.ImageDerivativeResEntity",
  "derivatives.common_derivatives.ImageDerivativeDenEntity",
  ]) }}
@@ -268,7 +265,7 @@ Template:
 <pipeline_name>/
  sub-<label>/
  anat|func|dwi/
- <source_entities>[_space-<space>][_atlas-<label>][_res-<label>][_den-<label>]_dseg.nii.gz
+ <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.nii.gz
 ```
 
 Example:
@@ -296,8 +293,7 @@ In this case, the mask suffix MUST be used,
 the [`label` entity](../appendices/entities.md#label)) SHOULD be used
 to specify the masked structure
 (see [Common image-derived labels](#common-image-derived-labels)),
-the [`atlas` entity](../appendices/entities.md#atlas) and the
-`Atlas` metadata SHOULD be defined.
+and the [`seg` entity](../appendices/entities.md#segmentation) SHOULD be defined.
 
 For example:
 
@@ -310,8 +306,8 @@ A guide for using macros can be found at
  "pipeline": {
  "sub-001": {
  "anat": {
- "sub-001_space-orig_atlas-Desikan_label-GM_mask.nii.gz": "",
- "sub-001_space-orig_atlas-Desikan_label-GM_mask.json": "",
+ "sub-001_space-orig_seg-Desikan_label-GM_mask.nii.gz": "",
+ "sub-001_space-orig_seg-Desikan_label-GM_mask.json": "",
  },
  },
  }
@@ -333,7 +329,7 @@ Template:
 <pipeline_name>/
  sub-<label>/
  func|anat|dwi/
- <source_entities>[_space-<space>][_atlas-<label>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
+ <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
 ```
 
 Example:
@@ -407,7 +403,7 @@ Template:
 <pipeline_name>/
  sub-<label>/
  anat/
- <source_entities>[_hemi-{L|R}][_space-<space>][_atlas-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
+ <source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
 ```
 
 The [`hemi-<label>`](../appendices/entities.md#hemi) entity is REQUIRED for GIFTI files storing information about

src/schema/objects/entities.yaml

@@ -25,16 +25,6 @@ acquisition:
  remains at the discretion of the researcher.
  type: string
  format: label
-atlas:
- name: atlas
- display_name: Atlas
- description: |
- The `atlas-<label>` key/value pair corresponds to a custom label the user
- MAY use to distinguish a different atlas used for similar type of data.
-
- This entity is only applicable to derivative data.
- type: string
- format: label
 ceagent:
  name: ce
  display_name: Contrast Enhancing Agent
@@ -286,6 +276,16 @@ sample:
  The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
  type: string
  format: label
+segmentation:
+ name: seg
+ display_name: Segmentation
+ description: |
+ The `seg-<label>` key/value pair corresponds to a custom label the user
+ MAY use to distinguish different segmentations.
+
+ This entity is only applicable to derivative data.
+ type: string
+ format: label
 session:
  name: ses
  display_name: Session

src/schema/objects/metadata.yaml

@@ -177,12 +177,6 @@ AssociatedEmptyRoom:
  format: dataset_relative
  - type: string
  format: bids_uri
-Atlas:
- name: Atlas
- display_name: Atlas
- description: |
- Which atlas (if any) was used to generate the mask.
- type: string
 AttenuationCorrection:
  name: AttenuationCorrection
  display_name: Attenuation Correction

src/schema/rules/entities.yaml

@@ -25,7 +25,7 @@
 - split
 - recording
 - chunk
-- atlas
+- segmentation
 - resolution
 - density
 - label

src/schema/rules/sidecars/derivatives/common_derivatives.yaml

@@ -38,33 +38,13 @@ MaskDerivatives:
  Sources: recommended
  RawSources: deprecated
 
-MaskDerivativesAtlas:
- selectors:
- - dataset.dataset_description.DatasetType == "derivative"
- - suffix == "mask"
- - '"label" in entities'
- fields:
- Atlas:
- level: recommended
- level_addendum: if `label` entity is defined
-
 SegmentationCommon:
  selectors:
  - dataset.dataset_description.DatasetType == "derivative"
  - 'intersects([suffix], ["dseg", "probseg"])'
  fields:
  Manual: optional
 
-SegmentationCommonAtlas:
- selectors:
- - dataset.dataset_description.DatasetType == "derivative"
- - 'intersects([suffix], ["dseg", "probseg"])'
- - '"atlas" in entities'
- fields:
- Atlas:
- level: recommended
- level_addendum: if `atlas` is present
-
 # Derivatives -> Imaging data types
 ImageDerivatives:
  selectors: