From e3ce5ffe7439477744ff41d862bd269f367aa9f1 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 10 Aug 2023 17:32:30 -0400
Subject: [PATCH 1/2] Move from atlas- to seg- in derivatives

---
 src/derivatives/imaging.md | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/derivatives/imaging.md b/src/derivatives/imaging.md
index b802d6c309..bcd653da08 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -153,8 +153,8 @@ 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
+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)),
 and the `Atlas` metadata SHOULD be defined.
 
@@ -229,10 +229,10 @@ 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#atlas) 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.
@@ -268,7 +268,7 @@ 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 +296,7 @@ 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#atlas) SHOULD be defined.
 
 For example:
 
@@ -310,8 +309,8 @@ 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 +332,7 @@ 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 +406,7 @@ 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

From 9c7ca6d5cc690f829b15f8c2e4851ca58fa2aba8 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 10 Aug 2023 17:33:25 -0400
Subject: [PATCH 2/2] Remove Atlas metadata object/rule

---
 src/schema/objects/metadata.yaml                       |  6 ------
 .../rules/sidecars/derivatives/common_derivatives.yaml | 10 ----------
 2 files changed, 16 deletions(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 0e1fe96916..7171581ad3 100644
--- a/src/schema/objects/metadata.yaml
+++ b/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
diff --git a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
index 5982b2e01d..301dac44ea 100644
--- a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
@@ -55,16 +55,6 @@ SegmentationCommon:
   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: