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: