diff --git a/mkdocs.yml b/mkdocs.yml
index b860d6ca9e..85791e49bc 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -28,6 +28,7 @@ nav:
           - BIDS Derivatives: derivatives/introduction.md
           - Common data types and metadata: derivatives/common-data-types.md
           - Imaging data types: derivatives/imaging.md
+          - Templates and atlases: derivatives/atlas.md
       - Longitudinal and multi-site studies: longitudinal-and-multi-site-studies.md
       - Glossary: glossary.md
       - BIDS Extension Proposals: extensions.md
diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md
index 8cf00dc6b7..9c661b7b10 100644
--- a/src/appendices/coordinate-systems.md
+++ b/src/appendices/coordinate-systems.md
@@ -225,6 +225,13 @@ However, their use is [DEPRECATED][deprecated].
 | fsaverage\[3\|4\|5\|6\|sym\]        | Images were sampled to the FreeSurfer surface reconstructed from the subject's T1w image, and registered to an fsaverage template                        | fsaverage\[Sym\]                       |
 | UNCInfant\[0\|1\|2\]V\[21\|22\|23\] | Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | UNCInfant                              |
 
+!!! note "Important"
+
+    Please note that the template identifiers starting with `MNI` (for example `MNI305`)
+    are typically referred to with the umbrella term of *MNI Space*.
+    The [Common Principles](../common-principles.md#definitions) deliver a more precise definitions
+    of template, space, and atlas.
+
 ### Nonstandard coordinate system identifiers
 
 The following template identifiers are RECOMMENDED for individual- and study-specific reference
diff --git a/src/common-principles.md b/src/common-principles.md
index e5b7240361..13b95909b3 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -128,6 +128,12 @@ data type as defined above.
 A data type directory SHOULD NOT be defined if there are no files to be placed
 in that directory.
 
+**Specific structure of derived data**.
+In the case of [storing derived data (see below)](#source-vs-raw-vs-derived-data),
+template (`tpl-<label>`) directories may be found at the root of the dataset,
+and these may include cohort (`cohort-<label>`) subdirectories.
+These directories are described in [Templates and atlases](derivatives/atlas.md).
+
 ### Other top level directories
 
 In addition to the subject directories, the root directory of a BIDS dataset
@@ -297,6 +303,15 @@ However, in the case that these data are to be included:
     through the `sourcedata/` directory mechanism.
     In the case of source data, these aspects are likely more stringent.
 
+**Templates and atlases as derived data.**
+Templates and atlases are key neuroscientific tools to carry out group-level inferences
+and also employed in many atlas-based methodologies (such as atlas-based segmentation).
+Original templates and atlases employed as primary data to the analysis MAY be stored
+within the `sourcedata/atlases/` directory.
+Atlases and artifacts derived from atlases are considered derived data
+and MUST be stored as derivative datasets,
+as described in the next section.
+
 ### Storage of derived datasets
 
 Derivatives can be stored/distributed in two ways:
@@ -332,6 +347,15 @@ Derivatives can be stored/distributed in two ways:
     <dataset>/derivatives/spm-stats/sub-0001
     ```
 
+    Example of an atlas-generating pipeline, including outputs for individual subjects
+    prior to aggregation in the
+    [`MNI152NLin2009cAsym` standard space](appendices/coordinate-systems.md):
+
+    ```Plain
+    <dataset>/derivatives/atlas-generator/sub-0001
+    <dataset>/derivatives/atlas-generator/tpl-MNI152NLin2009cAsym
+    ```
+
     Example of a pipeline with nested derivative directories:
 
     ```Plain
@@ -386,11 +410,14 @@ Case 2.
 In both cases, every derivatives dataset is considered a BIDS dataset and must
 include a `dataset_description.json` file at the root level (see
 [Dataset description][dataset-description]).
-Consequently, files should be organized to comply with BIDS to the full extent
+Consequently, files SHOULD be organized to comply with BIDS to the full extent
 possible (that is, unless explicitly contradicted for derivatives).
-Any subject-specific derivatives should be housed within each subject's directory;
-if session-specific derivatives are generated, they should be deposited under a
+Any subject-specific derivatives SHOULD be housed within each subject's directory;
+if session-specific derivatives are generated, they SHOULD be deposited under a
 session subdirectory within the corresponding subject directory; and so on.
+Likewise, any template-specific derivatives SHOULD be housed within each template's directory;
+if cohort-specific derivatives are generated, they SHOULD be deposited under a
+cohort subdirectory within the corresponding template directory; and so on.
 
 ### Non-compliant derivatives
 
diff --git a/src/derivatives/atlas.md b/src/derivatives/atlas.md
new file mode 100644
index 0000000000..0a3e5b8b23
--- /dev/null
+++ b/src/derivatives/atlas.md
@@ -0,0 +1,553 @@
+# Templates and atlases
+
+In the following, we describe how the outcomes of analyses that produce
+[templates and atlases](../common-principles.md#definitions) are organized
+as BIDS-Derivatives.
+
+!!! note "Important"
+
+    For outcomes of analyses corresponding to individual subjects
+    that derive from atlases and may refer to spaces other than the original
+    subject's space, please refer to the
+    [Derivatives from atlases](imaging.md#derivatives-from-atlases) subsection.
+
+## Derived templates
+
+Many analyses include spatial standardization to pull individuals' data
+into a common spatial frame.
+For example, creating an atlas will most likely require the creation of a new template
+or the integration of existing ones to define a stereotactic space.
+
+For derivatives of template-generating pipelines, which typically aggregate
+several sessions and/or subjects, the derivatives-specific
+[`tpl-<label>` entity](../appendices/entities.md#tpl) indicates that the
+spatial frame of analysis is not defined by a single brain image but an
+aggregation thereof.
+
+!!! tip "Recommendation"
+
+    The selected `<label>` in the [`tpl-<label>` entity](../appendices/entities.md#tpl)
+    is RECOMMENDED for the [`space-<label>` entity](../appendices/entities.md#space)
+    in downstream derivatives from this particular template (see previous section
+    [Derivatives from atlases](imaging.md#derivatives-from-atlases)).
+
+Template:
+
+```Text
+<pipeline_name>/
+    tpl-<label>/
+        [cohort-<label>/]
+           [<datatype>/]
+               tpl-<label>[_cohort-<label>][_<entities>]_<suffix>.<extension>
+```
+
+where [`suffix`](../glossary.md#suffix-common_principles) is any valid BIDS suffix
+such as `T1w` or `PET`; and
+[`extension`](../glossary.md#extension-common_principles) is a valid BIDS extension
+such as `nii[.gz]`, `dscalar.nii[.gz]`, `dlabel.nii[.gz]`, `label.gii`, `tsv`, or `json`.
+Templates and atlases do not establish new suffixes or extensions,
+but any valid BIDS/BIDS Derivatives filename is permitted in a template directory,
+substituting `tpl` for `sub` and `cohort` for `ses`.
+
+The [`<datatype>/` directory](../glossary.md#data_type-common_principles) MAY be omitted in the case
+only one data type (such as `anat/`) is stored under the `tpl-<label>/` directory.
+
+The [`cohort-<label>` directory and entity](../appendices/entities.md#cohort) MUST be specified for templates
+with several cohorts.
+
+!!! note "Dataset structure"
+
+    In templates/atlases the [`tpl-<label>`](../appendices/entities.md#tpl) and
+    [`cohort-<label>`](../appendices/entities.md#cohort) entities are structurally
+    analogous to the [`sub-<label>`](../appendices/entities.md#sub)
+    and [`ses-<label>`](../appendices/entities.md#ses) entities,
+    appearing as both directories and entities.
+    The [`cohort-<label>`](../appendices/entities.md#cohort) entity is used
+    to track mappings of arbitrary subject/session pairs.
+
+In BIDS, a template is considered *any* aggregation of data and the `tpl-` entity
+replaces the subject-level `sub-` entity when aggregating data across subjects.
+The `tpl-` entity and `sub-` entity are mutually exclusive in a given file.
+When the `tpl-` entity is used without the `atlas-` entity, as in the following examples,
+the imaging data serves as an instantiation of a space.
+When the `tpl-` entity is used in conjunction with the `atlas-` entity,
+the intention is to describe aggregations of data in a particular space,
+as described in the [Derived atlases](#derived-atlases) section, below.
+For uses of the `atlas-` entity without the `tpl-` entity,
+see [Imaging derivatives - Derivatives from atlases](imaging.md#derivatives-from-atlases).
+
+### Example: Single-cohort template
+
+For the pipeline that generated [`MNI152NLin2009cAsym`](../appendices/coordinate-systems.md#standard-template-identifiers),
+the outputs could look like the following example:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "mni152nlin2009casym-pipeline": {
+      "tpl-MNI152NLin2009cAsym": {
+         "tpl-MNI152NLin2009cAsym_res-1_T1w.nii.gz": "",
+         "tpl-MNI152NLin2009cAsym_res-1_T1w.json": "",
+         "tpl-MNI152NLin2009cAsym_res-1_label-brain_mask.nii.gz": "",
+         "tpl-MNI152NLin2009cAsym_res-1_label-brain_mask.json": "",
+         "tpl-MNI152NLin2009cAsym_res-1_probseg.nii.gz": "",
+         "tpl-MNI152NLin2009cAsym_res-1_probseg.json": "",
+         "tpl-MNI152NLin2009cAsym_res-2_T1w.nii.gz": "",
+         "tpl-MNI152NLin2009cAsym_res-2_T1w.json": "",
+         "tpl-MNI152NLin2009cAsym_res-2_label-brain_mask.nii.gz": "",
+         "tpl-MNI152NLin2009cAsym_res-2_label-brain_mask.json": "",
+         "tpl-MNI152NLin2009cAsym_res-2_probseg.nii.gz": "",
+         "tpl-MNI152NLin2009cAsym_res-2_probseg.json": "",
+      },
+   }
+})
+}}
+
+### Example: Multi-cohort template
+
+In the case that the template-generating pipeline derives
+several cohorts, the file structure must employ the
+[`cohort-<label>` directory and entity](../appendices/entities.md#cohort).
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "mnipediatricasym-pipeline": {
+      "tpl-MNIPediatricAsym": {
+         "cohort-1": {
+            "tpl-MNIPediatricAsym_cohort-1_T1w.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-1_T2w.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-1_PDw.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-1_desc-brain_mask.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-1_probseg.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-1_probseg.json": "",
+         },
+         "...": "",
+         "cohort-6": {
+            "tpl-MNIPediatricAsym_cohort-6_T1w.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-6_T2w.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-6_PDw.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-6_desc-brain_mask.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-6_probseg.nii.gz": "",
+            "tpl-MNIPediatricAsym_cohort-6_probseg.json": "",
+         },
+      },
+   }
+})
+}}
+
+### Example: Subject-level and template derivatives
+
+Both subject-level and template-level results MAY coexist in a single derivatives dataset.
+For example, it is possible to share the subject-level results used to generate the template
+alongside the template:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "mni152nlin2009casym-pipeline": {
+      "sub-001": {
+         "anat": {
+            "sub-001_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5": "",
+            "sub-001_space-MNI152NLin2009cAsym_T1w.nii.gz": "",
+            "sub-001_T1w.nii.gz": "",
+         },
+      },
+      "...": "",
+      "sub-152": {
+         "anat": {
+            "sub-152_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5": "",
+            "sub-152_space-MNI152NLin2009cAsym_T1w.nii.gz": "",
+            "sub-152_T1w.nii.gz": "",
+         },
+      },
+      "tpl-MNI152NLin2009cAsym": {
+         "tpl-MNI152NLin2009cAsym_res-1_label-brain_mask.nii.gz": "",
+         "...": "",
+         "tpl-MNI152NLin2009cAsym_res-2_T1w.json": "",
+      },
+   }
+})
+}}
+
+!!! warning "Warning"
+
+    Please note that the specification for spatial transforms (BEP 014) is currently
+    under development, and therefore, the specification of transforms files (`xfm` suffix above)
+    may change in the future.
+
+## Derived atlases
+
+{{ MACROS___render_text('objects.common_principles.atlas.description') }}
+
+Template:
+
+```Text
+<pipeline_name>/
+    atlas-<label>_description.json
+    tpl-<label>/
+        [cohort-<label>/]
+           [<datatype>/]
+               tpl-<label>[_cohort-<label>][_<entities>]_<suffix>.<extension>
+```
+
+### Atlas identification and metadata
+
+The `atlas-<label>_description.json` file provides metadata to uniquely identify,
+describe and characterize the atlas, as well as give proper attribution to the creators.
+Atlases MUST include `atlas-<label>_description.json` files
+corresponding to the atlas or atlases in the structure.
+
+!!! tip "Recommendation"
+
+    The selected `<label>` in the `atlas-<label>_description.json` file is RECOMMENDED
+    for the [`atlas-<label>` entity](../appendices/entities.md#atlas)
+    in downstream derivatives from this particular atlas (see previous section
+    [Derivatives from atlases](imaging.md#derivatives-from-atlases)).
+
+Atlas metadata fields:
+
+<!-- This block generates a metadata table.
+The definitions of these fields can be found in
+  src/schema/objects/metadata.yaml
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_json_table('dataset_metadata.atlas_description') }}
+
+Example `atlas-MyAtlas2025_description.json`:
+
+```JSON
+{
+  "Name": "A new atlas of the human brain",
+  "Authors": [
+    "Jane Doe",
+    "John Doe"
+  ],
+  "License": "CC0",
+  "RRID": "SCR_002823",
+  "Species": "Human"
+}
+```
+
+### Atlas spatial reference
+
+Atlases are often aligned to a common spatial reference
+to allow for the ready application of atlas data.
+A file may indicate the spatial reference to which it has been aligned using the
+[`tpl` entity](../appendices/entities.md#template) and/or the `SpatialReference` metadata.
+
+The [`tpl` entity](../appendices/entities.md#template) may take any value in
+[Image-Based Coordinate Systems][coordsys].
+
+If the [`tpl` entity](../appendices/entities.md#template) is not in the
+[Standard template identifiers][templates] table,
+then the `SpatialReference` metadata is REQUIRED for files with that entity.
+
+### Example: Deriving templates and atlases
+
+A common use-case of brain templates is establishing stereotaxy for the creation
+of atlases.
+For example, the *Spatially Unbiased Infratentorial Template* (*SUIT*;
+[Diedrichsen, 2006](https://doi.org/10.1016/j.neuroimage.2006.05.056)),
+presents an *atlas template* of the human cerebellum and brainstem based
+on the anatomy of 20 young healthy individuals.
+
+The authors first developed a template of the cerebellum and brainstem,
+which is spatially standardized *in MNI space*.
+This could be the organization of the template part:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "suit-pipeline": {
+      "tpl-SUIT": {
+         "anat": {
+            "tpl-SUIT_T1w.nii.gz": "",
+            "tpl-SUIT_T1w.json": "",
+         },
+      },
+   }
+})
+}}
+
+Where `tpl-SUIT_T1w.json` contains (at minimum):
+
+```json
+{
+  "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz"
+}
+```
+
+Once the standard space of analysis was prepared, a first atlas was
+developed in 2009, integrating some segmentations and parcellations:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "suit-pipeline": {
+      "atlas-Diedrichsen2009_description.json": "",
+      "tpl-SUIT": {
+         "anat": {
+            "tpl-SUIT_T1w.nii.gz": "",
+            "tpl-SUIT_atlas-Diedrichsen2009_dseg.json": "",
+            "tpl-SUIT_atlas-Diedrichsen2009_dseg.nii.gz": "",
+            "tpl-SUIT_atlas-Diedrichsen2009_dseg.tsv": "",
+            "tpl-SUIT_atlas-Diedrichsen2009_probseg.nii.gz": "",
+         },
+      },
+   }
+})
+}}
+
+where `atlas-Diedrichsen2009_description.json` could contain:
+
+```JSON
+{
+  "Name": "A probabilistic MR atlas of the human cerebellum",
+  "Authors": [
+     "Jörn Diedrichsen",
+     "Joshua H Balsters",
+     "Jonathan Flavell",
+     "Emma Cussans",
+     "Narender Ramnani"
+  ],
+  "SampleSize": 20,
+  "License": "LICENSE file",
+  "ReferencesAndLinks": [
+     "https://doi.org/10.1016/j.neuroimage.2009.01.045",
+     "https://github.com/jdiedrichsen/suit"
+  ],
+  "Species": "Human"
+}
+```
+
+Later, in 2011 a second atlas was developed integrating new segmentations,
+so the template dataset can be updated to contain a second atlas:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "suit-pipeline": {
+      "atlas-Buckner2011_description.json": "",
+      "atlas-Diedrichsen2009_description.json": "",
+      "tpl-SUIT": {
+         "anat": {
+            "tpl-SUIT_T1w.nii.gz": "",
+            "tpl-SUIT_atlas-Buckner2011_dseg.json": "",
+            "tpl-SUIT_atlas-Buckner2011_seg-17n_dseg.nii.gz": "",
+            "tpl-SUIT_atlas-Buckner2011_seg-17n_dseg.tsv": "",
+            "tpl-SUIT_atlas-Buckner2011_seg-17n_desc-confidence_probseg.nii.gz": "",
+            "tpl-SUIT_atlas-Buckner2011_seg-7n_dseg.nii.gz": "",
+            "tpl-SUIT_atlas-Buckner2011_seg-7n_dseg.tsv": "",
+            "tpl-SUIT_atlas-Buckner2011_seg-7n_desc-confidence_probseg.nii.gz": "",
+            "tpl-SUIT_atlas-Diedrichsen2009_dseg.json": "",
+            "tpl-SUIT_atlas-Diedrichsen2009_dseg.nii.gz": "",
+            "tpl-SUIT_atlas-Diedrichsen2009_dseg.tsv": "",
+            "tpl-SUIT_atlas-Diedrichsen2009_probseg.nii.gz": "",
+         },
+      },
+   }
+})
+}}
+
+where `atlas-Diedrichsen2009_description.json` remains as above,
+and `atlas-Buckner2011_description.json` could contain:
+
+```JSON
+{
+  "Name": "Atlas of the human cerebellum estimated by intrinsic functional connectivity",
+  "Authors": [
+     "Randy L Buckner",
+     "Fenna M Krienen",
+     "Angela Castellanos",
+     "Julio C Diaz",
+     "B T Thomas Yeo"
+  ],
+  "SampleSize": 1000,
+  "License": "LICENSE file",
+  "ReferencesAndLinks": [
+     "https://doi.org/10.1152/jn.00339.2011",
+     "https://github.com/jdiedrichsen/suit"
+  ],
+  "Species": "Human"
+}
+```
+
+### Example: Deriving a new atlas referenced in an existing template
+
+For example, the `MIAL67ThalamicNuclei`
+([Najdenovska et al., 2018](https://doi.org/10.1038/sdata.2018.270))
+atlas-generation pipeline could display the following structure:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "mial67thalamicnuclei-pipeline": {
+      "atlas-MIAL67ThalamicNuclei_description.json": "",
+      "sub-01": {
+         "anat": {
+            "sub-01_seg-ThalamicNuclei_dseg.json": "",
+            "sub-01_seg-ThalamicNuclei_dseg.tsv": "",
+            "sub-01_seg-ThalamicNuclei_dseg.nii.gz": "",
+            "sub-01_space-MNI152NLin2009cAsym_T1w.nii.gz": "",
+            "sub-01_T1w.nii.gz": "",
+         },
+      },
+      "...": "",
+      "sub-67": {
+         "anat": {
+            "sub-67_seg-ThalamicNuclei_dseg.json": "",
+            "sub-67_seg-ThalamicNuclei_dseg.tsv": "",
+            "sub-67_seg-ThalamicNuclei_dseg.nii.gz": "",
+            "sub-67_space-MNI152NLin2009cAsym_T1w.nii.gz": "",
+            "sub-67_T1w.nii.gz": "",
+         },
+      },
+      "tpl-MNI152NLin2009cAsym": {
+         "anat": {
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_dseg.json": "",
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_dseg.tsv": "",
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz": "",
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz": "",
+         },
+      },
+   }
+})
+}}
+
+where the derivatives of anatomical processing of the 67 subjects that were
+employed to generate the atlas coexist with the template structure.
+
+The inheritance principle applies uniformly, allowing the segmentation
+metadata be stored only once at the root of the pipeline directory and
+apply to all the individual subject segmentations:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "mial67thalamicnuclei-pipeline": {
+      "atlas-MIAL67ThalamicNuclei_description.json": "",
+      "seg-ThalamicNuclei_dseg.json": "",
+      "seg-ThalamicNuclei_dseg.tsv": "",
+      "sub-01": {
+         "anat": {
+            "sub-01_seg-ThalamicNuclei_dseg.nii.gz": "",
+            "sub-01_space-MNI152NLin2009cAsym_T1w.nii.gz": "",
+            "sub-01_T1w.nii.gz": "",
+         },
+      },
+      "...": "",
+      "sub-67": {
+         "anat": {
+            "sub-67_seg-ThalamicNuclei_dseg.nii.gz": "",
+            "sub-67_space-MNI152NLin2009cAsym_T1w.nii.gz": "",
+            "sub-67_T1w.nii.gz": "",
+         },
+      },
+      "tpl-MNI152NLin2009cAsym": {
+         "anat": {
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_dseg.json": "",
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_dseg.tsv": "",
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz": "",
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz": "",
+         },
+      },
+   }
+})
+}}
+
+In the case the pipeline generated atlas-based segmentations of the original subjects in
+their native T1w space (for example, to compare with the original segmentation given by
+`seg-ThalamicNuclei`), the above example translates into:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "mial67thalamicnuclei-pipeline": {
+      "atlas-MIAL67ThalamicNuclei_description.json": "",
+      "atlas-MIAL67ThalamicNuclei_dseg.json": "",
+      "atlas-MIAL67ThalamicNuclei_dseg.tsv": "",
+      "seg-ThalamicNuclei_dseg.json": "",
+      "seg-ThalamicNuclei_dseg.tsv": "",
+      "sub-01": {
+         "anat": {
+            "sub-01_atlas-MIAL67ThalamicNuclei_dseg.nii.gz": "",
+            "sub-01_seg-ThalamicNuclei_dseg.nii.gz": "",
+            "sub-01_space-MNI152NLin2009cAsym_T1w.nii.gz": "",
+            "sub-01_T1w.nii.gz": "",
+         },
+      },
+      "...": "",
+      "sub-67": {
+         "anat": {
+            "sub-67_atlas-MIAL67ThalamicNuclei_dseg.nii.gz": "",
+            "sub-67_seg-ThalamicNuclei_dseg.nii.gz": "",
+            "sub-67_space-MNI152NLin2009cAsym_T1w.nii.gz": "",
+            "sub-67_T1w.nii.gz": "",
+         },
+      },
+      "tpl-MNI152NLin2009cAsym": {
+         "anat": {
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz": "",
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz": "",
+         },
+      },
+   }
+})
+}}
+
+### Example: Distributing one atlas aligned to two or more existing templates
+
+This directory structure can be generally applied when the atlas is derived into several
+template spaces, for example:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "mial67thalamicnuclei-pipeline": {
+      "atlas-MIAL67ThalamicNuclei_description.json": "",
+      "atlas-MIAL67ThalamicNuclei_dseg.json": "",
+      "atlas-MIAL67ThalamicNuclei_dseg.tsv": "",
+      "atlas-MIAL67ThalamicNuclei_probseg.json": "",
+      "tpl-MNI152NLin2009cAsym": {
+         "anat": {
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz": "",
+            "tpl-MNI152NLin2009cAsym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz": "",
+         },
+      },
+      "tpl-MNI152NLin6Asym": {
+         "anat": {
+            "tpl-MNI152NLin6Asym_atlas-MIAL67ThalamicNuclei_res-1_dseg.nii.gz": "",
+            "tpl-MNI152NLin6Asym_atlas-MIAL67ThalamicNuclei_res-1_probseg.nii.gz": "",
+         },
+      },
+   }
+})
+}}
+
+<!-- Link Definitions -->
+
+[coordsys]: ../appendices/coordinate-systems.md#image-based-coordinate-systems
+
+[templates]: ../appendices/coordinate-systems.md#standard-template-identifiers
diff --git a/src/derivatives/imaging.md b/src/derivatives/imaging.md
index 42073465e3..2aed096552 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -156,7 +156,7 @@ 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 segmentation,
+If the mask is an ROI mask derived from a discrete or probabilistic 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)).
 
@@ -187,8 +187,8 @@ A guide for using macros can be found at
     "func_loc": {
         "sub-001": {
             "func": {
-                "sub-001_task-rest_run-1_space-MNI305_desc-PFC_mask.nii.gz": "",
-                "sub-001_task-rest_run-1_space-MNI305_desc-PFC_mask.json": "",
+                "sub-001_task-rest_run-1_space-MNI305_label-PFC_mask.nii.gz": "",
+                "sub-001_task-rest_run-1_space-MNI305_label-PFC_mask.json": "",
                 },
             },
         }
@@ -204,8 +204,8 @@ A guide for using macros can be found at
     "manual_masks": {
         "sub-001": {
             "anat": {
-                "sub-001_desc-tumor_mask.nii.gz": "",
-                "sub-001_desc-tumor_mask.json": "",
+                "sub-001_label-tumor_mask.nii.gz": "",
+                "sub-001_label-tumor_mask.json": "",
                 },
             },
         }
@@ -214,12 +214,12 @@ A guide for using macros can be found at
 
 ## Segmentations
 
-A *segmentation* is a labeling of regions of an image such that each location
-(for example, a voxel or a surface vertex) is identified with a label or a
-combination of labels.
-Labeled regions may include anatomical structures (such as tissue class,
-Brodmann area or white matter tract), discontiguous, functionally-defined
-networks, tumors or lesions.
+A *segmentation* is a spatial partition of images and surfaces,
+such that each location (for example, a voxel or a surface vertex)
+is identified with one label (discrete) or a combination of labels (probabilistic).
+Labeled regions may include anatomical structures (for example, tissue classes,
+white matter tracts, Thalamic nuclei, cortical areas),
+functionally-defined networks, tumors or lesions.
 
 A *discrete segmentation* represents each region with a unique integer
 label.
@@ -230,10 +230,14 @@ 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 generated in different ways,
-for example, following an atlas segmentation,
-the [`seg` entity](../appendices/entities.md#seg) MAY be used to
-distinguish the name of the segmentation used.
+If different segmentations coexist within the same directory of the BIDS
+structure (for example, if they were generated with two alternative tools),
+the [`seg-<label>` entity](../appendices/entities.md#segmentation)
+SHOULD be used for disambiguation.
+
+The [`seg-<label>` entity](../appendices/entities.md#segmentation) MAY be used in combination
+with the [`atlas-<label>` entity](../appendices/entities.md#segmentation)
+as indicated by the [Templates and Atlases section](atlas.md).
 
 The following section describes discrete and probabilistic segmentations of
 volumes, followed by discrete segmentations of surface/combined spaces.
@@ -257,8 +261,7 @@ A guide for using macros can be found at
 
 ### Discrete Segmentations
 
-Discrete segmentations of brain tissue represent multiple anatomical structures
-(such as tissue class or Brodmann area) with a unique integer label in a 3D volume.
+Discrete segmentations of brain tissue represent regions with unique integer labels.
 See [Common image-derived labels](#common-image-derived-labels) for a description
 of how integer values map to anatomical structures.
 
@@ -268,13 +271,14 @@ Template:
 <pipeline-name>/
     sub-<label>/
         [ses-<label>/]
-            anat|func|dwi/
+            <data_type>/
                 <source-entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.json
                 <source-entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.nii[.gz]
                 <source-entities>[_space-<space>][_seg-<label>][_res-<label>][_desc-<label>]_dseg.tsv
 ```
 
-Example:
+For example, we can specify the results of a classic brain tissue segmentation algorithm
+of a T1w image based on a Gaussian mixture model as:
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -285,23 +289,19 @@ A guide for using macros can be found at
     "pipeline": {
         "sub-001": {
             "anat": {
-                "sub-001_space-orig_dseg.nii.gz": "",
-                "sub-001_space-orig_dseg.json": "",
+                "sub-001_dseg.nii.gz": "",
+                "sub-001_dseg.json": "",
                 },
             },
         }
    }
 ) }}
 
-A segmentation can be used to generate a binary mask that functions as a
-discrete "label" for a single structure.
-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)),
-and the [`seg` entity](../appendices/entities.md#seg) SHOULD be defined.
-
-For example:
+When several segmentations coexist at the same BIDS hierarchy point,
+[`seg-<label>` entity](../appendices/entities.md#segmentation) SHOULD
+be used for disambiguation.
+For example, if the brain tissue segmentation above will be stored next
+to segmentations of the eyes:
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -312,8 +312,10 @@ A guide for using macros can be found at
     "pipeline": {
         "sub-001": {
             "anat": {
-                "sub-001_space-orig_seg-Desikan_label-GM_mask.nii.gz": "",
-                "sub-001_space-orig_seg-Desikan_label-GM_mask.json": "",
+                "sub-001_seg-braintissues_dseg.nii.gz": "",
+                "sub-001_seg-braintissues_dseg.json": "",
+                "sub-001_seg-eyes_dseg.nii.gz": "",
+                "sub-001_seg-eyes_dseg.json": "",
                 },
             },
         }
@@ -387,11 +389,11 @@ for each volume:
 
 ```JSON
 {
-    "LabelMap": [
-        "BG",
-        "WM",
-        "GM"
-        ]
+  "LabelMap": [
+    "BG",
+    "WM",
+    "GM"
+  ]
 }
 ```
 
@@ -553,6 +555,255 @@ index	name	abbreviation
 139	pars orbitalis	IFGor
 ```
 
+## Derivatives from atlases
+
+Often, derivatives are *atlas-based*, meaning, a particular result has been
+derived from prior knowledge in the form of an [atlas](../common-principles.md).
+These derivatives follow the specifications above, with the addition of
+a set of entities that MAY be used to disambiguate the outputs.
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<label>/
+        <datatype>/
+            <source_entities>[_space-<space>][_atlas-<label>][_seg-<label>][_scale-<label>][_res-<label>][_den-<label>][_desc-<label>]_<suffix>.<extension>
+```
+
+-   [`space-<label>`](../appendices/entities.md#space) is REQUIRED to disambiguate derivatives defined with
+    respect to different [coordinate systems](../appendices/coordinate-systems.md), following the general
+    BIDS-Derivatives specifications.
+
+-   [`atlas-<label>`](../appendices/entities.md#atlas) is REQUIRED to encode files derived
+    from the atlas identified by the entity's label.
+
+-   [`seg-<label>`](../appendices/entities.md#seg) is REQUIRED when a single atlas has several different
+    realizations (for instance, segmentations and parcellations created with different criteria) that
+    need disambiguation.
+
+-   [`scale-<label>`](../appendices/entities.md#scale) is REQUIRED to disambiguate different atlas 'scales',
+    when the atlas has more than one 'brain unit' or 'areal resolution', typically relating to the
+    number of regions defined and the area they cover.
+
+For example, derivatives from a single subject segmented with the Automated Anatomical Labeling (AAL)
+atlas ([Tzourio-Mazoyer et al., 2002](https://doi.org/10.1006/nimg.2001.0978)).
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "aals-pipeline": {
+      "sub-01": {
+         "anat": {
+            "sub-01_atlas-AAL_dseg.json": "",
+            "sub-01_atlas-AAL_dseg.nii.gz": "",
+            "sub-01_atlas-AAL_dseg.tsv": "",
+            "sub-01_atlas-AAL_probseg.nii.gz": "",
+            "sub-01_label-brain_mask.nii.gz": "",
+            "sub-01_label-head_mask.nii.gz": "",
+            "sub-01_T1w.nii.gz": "",
+            "sub-01_T1w.json": "",
+         },
+      },
+   }
+})
+}}
+
+Because the AAL atlas was originally defined in the standardized space of MNI305,
+it would be unsurprising to find the anatomical reference resampled into the standard
+space for validation, as well as the spatial transformation file:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "aals-pipeline": {
+      "sub-001": {
+         "anat": {
+            "sub-001_atlas-AAL_dseg.json": "",
+            "sub-001_atlas-AAL_dseg.nii.gz": "",
+            "sub-001_atlas-AAL_dseg.tsv": "",
+            "sub-001_atlas-AAL_probseg.nii.gz": "",
+            "sub-001_from-T1w_to-MNI305_mode-image_xfm.h5": "",
+            "sub-001_label-brain_mask.nii.gz": "",
+            "sub-001_label-head_mask.nii.gz": "",
+            "sub-001_space-MNI305_T1w.nii.gz": "",
+            "sub-001_space-MNI305_T1w.json": "",
+            "sub-001_T1w.nii.gz": "",
+            "sub-001_T1w.json": "",
+         },
+      },
+   }
+})
+}}
+
+!!! warning "Warning"
+
+    Please note that the specification for spatial transforms (BEP 014) is currently under development,
+    and therefore, the specification of transforms files (`sub-01_from-T1w_to-MNI305_mode-image_xfm.h5`
+    in the example above) may change in the future.
+
+In the common case of multiple segmentations and parcellations derived from an atlas,
+[`seg-<label>`](../appendices/entities.md#segmentation) SHOULD be used in combination
+with the [`atlas-<label>` entity](../appendices/entities.md#atlas-entities).
+Extending on our previous example, when the brain tissue and the eye
+segmentations are stored next to the results of *FreeSurfer*'s automatic subcortical
+segmentation ("aseg") using the `Destrieux2009` atlas:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example(
+   {
+    "pipeline": {
+        "sub-001": {
+            "anat": {
+                "sub-001_atlas-Destrieux2009_seg-aseg_dseg.nii.gz": "",
+                "sub-001_atlas-Destrieux2009_seg-aseg_dseg.json": "",
+                "sub-001_atlas-Destrieux2009_seg-aseg+aparc_dseg.nii.gz": "",
+                "sub-001_atlas-Destrieux2009_seg-aseg+aparc_dseg.json": "",
+                "sub-001_seg-braintissues_dseg.nii.gz": "",
+                "sub-001_seg-braintissues_dseg.json": "",
+                "sub-001_seg-eyes_dseg.nii.gz": "",
+                "sub-001_seg-eyes_dseg.json": "",
+                },
+            },
+        }
+   }
+) }}
+
+Derivatives from several atlases can coexist in a single directory:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "aals-pipeline": {
+      "sub-001": {
+         "anat": {
+            "sub-001_atlas-AAL_dseg.json": "",
+            "sub-001_atlas-AAL_dseg.nii.gz": "",
+            "sub-001_atlas-AAL_dseg.tsv": "",
+            "sub-001_atlas-AAL_probseg.json": "",
+            "sub-001_atlas-AAL_probseg.nii.gz": "",
+            "sub-001_atlas-Destrieux2009_seg-aseg+aparc_dseg.json": "",
+            "sub-001_atlas-Destrieux2009_seg-aseg+aparc_dseg.nii.gz": "",
+            "sub-001_atlas-Destrieux2009_seg-aseg_dseg.json": "",
+            "sub-001_atlas-Destrieux2009_seg-aseg_dseg.nii.gz": "",
+            "sub-001_seg-braintissues_dseg.json": "",
+            "sub-001_seg-braintissues_dseg.nii.gz": "",
+         },
+      },
+   }
+})
+}}
+
+### Atlas tabular data
+
+Atlases are often distributed with a Look Up Table (LUT) that indexes and labels each
+node/parcel/region within the atlas.
+This file will be essential for downstream workflows that generate matrices or other derived files within
+which node/parcel/region information is required, as the index/label fields will be used to reference
+the original anatomy the index/labels are derived from.
+Atlas-derived results SHOULD encode this information with the `dseg.tsv` or `probseg.json` files
+following the prescriptions of the [Common image-derived labels](#common-image-derived-labels) section above.
+Additional fields can be added with their respective definition/description in the sidecar JSON file.
+
+Template:
+
+```Text
+<pipeline_name>/
+    sub-<label>/
+        <datatype>/
+            <source_entities>[_atlas-<label>][seg-<label>][_scale-<label>][_desc-<label>]_<suffix>.tsv
+```
+
+For example, the participant-level results using the Schaefer 2018 atlas
+could be structured as follows.
+Please note that, the `dseg.tsv` files have been moved to the root of the
+hierarchy following the common principles.
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+   "bold-pipeline": {
+      "atlas-Schaefer2018_dseg.json": "",
+      "atlas-Schaefer2018_seg-7n_scale-100_dseg.tsv": "",
+      "atlas-Schaefer2018_seg-7n_scale-200_dseg.tsv": "",
+      "atlas-Schaefer2018_seg-7n_scale-300_dseg.tsv": "",
+      "atlas-Schaefer2018_seg-17n_scale-100_dseg.tsv": "",
+      "atlas-Schaefer2018_seg-17n_scale-200_dseg.tsv": "",
+      "atlas-Schaefer2018_seg-17n_scale-300_dseg.tsv": "",
+      "atlas-Schaefer2018_seg-kong17n_scale-100_dseg.tsv": "",
+      "atlas-Schaefer2018_seg-kong17n_scale-200_dseg.tsv": "",
+      "atlas-Schaefer2018_seg-kong17n_scale-300_dseg.tsv": "",
+      "sub-01": {
+         "anat": {
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-7n_scale-100_den-164k_dseg.label.gii": "",
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-7n_scale-200_den-164k_dseg.label.gii": "",
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-7n_scale-300_den-164k_dseg.label.gii": "",
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-17n_scale-100_den-164k_dseg.label.gii": "",
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-17n_scale-200_den-164k_dseg.label.gii": "",
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-17n_scale-300_den-164k_dseg.label.gii": "",
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-kong17n_scale-100_den-164k_dseg.label.gii": "",
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-kong17n_scale-200_den-164k_dseg.label.gii": "",
+            "sub-01_hemi-L_atlas-Schaefer2018_seg-kong17n_scale-300_den-164k_dseg.label.gii": "",
+            "...": "",
+            "sub-01_hemi-R_atlas-Schaefer2018_seg-kong17n_scale-300_den-164k_dseg.label.gii": "",
+         },
+         "bold": {
+            "sub-01_task-rest_hemi-L_den-164k_bold.func.gii": "",
+            "sub-01_task-rest_hemi-R_den-164k_bold.func.gii": "",
+         }
+      },
+      "sub-02": {
+         "anat": {
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-7n_scale-100_den-164k_dseg.label.gii": "",
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-7n_scale-200_den-164k_dseg.label.gii": "",
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-7n_scale-300_den-164k_dseg.label.gii": "",
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-17n_scale-100_den-164k_dseg.label.gii": "",
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-17n_scale-200_den-164k_dseg.label.gii": "",
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-17n_scale-300_den-164k_dseg.label.gii": "",
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-kong17n_scale-100_den-164k_dseg.label.gii": "",
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-kong17n_scale-200_den-164k_dseg.label.gii": "",
+            "sub-02_hemi-L_atlas-Schaefer2018_seg-kong17n_scale-300_den-164k_dseg.label.gii": "",
+            "...": "",
+            "sub-02_hemi-R_atlas-Schaefer2018_seg-kong17n_scale-300_den-164k_dseg.label.gii": "",
+         },
+         "bold": {
+            "sub-02_task-rest_hemi-L_den-164k_bold.func.gii": "",
+            "sub-02_task-rest_hemi-R_den-164k_bold.func.gii": "",
+         }
+      },
+   }
+})
+}}
+
+**Example of contents**.
+For example, the file `atlas-Schaefer2018_seg-7n_scale-100_dseg.tsv` could look like:
+
+```tsv
+index	name	color
+1	17Networks_LH_VisCent_ExStr_1	#781180
+2	17Networks_LH_VisCent_ExStr_2	#781181
+3	17Networks_LH_VisCent_ExStr_3	#781182
+4	17Networks_LH_VisCent_ExStr_4	#781183
+5	17Networks_LH_VisCent_ExStr_5	#781184
+
+...
+
+998	17Networks_RH_TempPar_20	#0d2afb
+999	17Networks_RH_TempPar_21	#0d2afc
+1000	17Networks_RH_TempPar_22	#0d2afd
+```
+
 <!-- Link Definitions -->
 
 [common_preproc]: common-data-types.md#preprocessed-or-cleaned-data
diff --git a/src/metaschema.json b/src/metaschema.json
index 49d0f8cab7..7d5b83ebf5 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -419,9 +419,10 @@
             "^derivatives$": {
               "type": "object",
               "properties": {
+                "atlas": { "$ref": "#/definitions/json" },
                 "common_derivatives": { "$ref": "#/definitions/json" }
               },
-              "required": ["common_derivatives"],
+              "required": ["atlas", "common_derivatives"],
               "additionalProperties": false
             },
             "^(?!derivatives$)[a-z_]+$": {
diff --git a/src/schema/meta/associations.yaml b/src/schema/meta/associations.yaml
index 79ad8af6a2..9d68832e5e 100644
--- a/src/schema/meta/associations.yaml
+++ b/src/schema/meta/associations.yaml
@@ -100,3 +100,12 @@ electrodes:
     entities:
       - space
   inherit: true
+
+atlas_description:
+  selectors:
+    - entities.atlas
+    - extension != '.json'
+  target:
+    suffix: description
+    extension: .json
+  inherit: true
diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index bc61dd1cb2..a6c5f6e2e2 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -277,6 +277,15 @@ properties:
           path:
             description: 'Path to associated coordsystem file'
             type: string
+      atlas_description:
+        description: 'Atlas description file'
+        type: object
+        required: [path]
+        additionalProperties: false
+        properties:
+          path:
+            description: 'Path to associated atlas description file'
+            type: string
   # The following properties are populated if the current file is of an appropriate type
   columns:
     description: 'TSV columns, indexed by column header, values are arrays with column contents'
diff --git a/src/schema/meta/templates.yaml b/src/schema/meta/templates.yaml
index f9db50d33d..4e7aa668a0 100644
--- a/src/schema/meta/templates.yaml
+++ b/src/schema/meta/templates.yaml
@@ -119,7 +119,9 @@ deriv:
       - dseg
     entities:
       $ref: meta.templates.deriv.volumetric.entities
+      atlas: optional
       segmentation: optional
+      scale: optional
 
   probseg:
     $ref: meta.templates.deriv.volumetric
@@ -131,7 +133,9 @@ deriv:
       - probseg
     entities:
       $ref: meta.templates.deriv.volumetric.entities
+      atlas: optional
       segmentation: optional
+      scale: optional
       label: optional
 
   dseg_surface:
@@ -145,4 +149,18 @@ deriv:
       - dseg
     entities:
       $ref: meta.templates.deriv.surface.entities
+      atlas: optional
       segmentation: optional
+      scale: optional
+
+# Entities that apply to most atlas files
+# Include thus:
+#
+# filerule:
+#   entities:
+#     $ref: meta.templates.atlas.base.entities
+atlas:
+  base:
+    entities:
+      template: required
+      cohort: optional
diff --git a/src/schema/objects/common_principles.yaml b/src/schema/objects/common_principles.yaml
index 1ebfe3dfe7..10f77bf28b 100644
--- a/src/schema/objects/common_principles.yaml
+++ b/src/schema/objects/common_principles.yaml
@@ -3,6 +3,17 @@
 # WARNING: The terms are presented here in alphabetical order!
 # The order in which these terms are presented in the specification is defined in `rules/common_principles.yaml`,
 # rather than this file (`objects/common_principles.yaml`).
+atlas:
+  display_name: Atlas
+  description: |
+    An *atlas* is structured neuroanatomical or neurofunctional information expressed as spatial annotations,
+    such as anatomical landmarks, segmentations, parcellations, probabilistic maps, or feature maps,
+    typically defined in relation to a *space* engendered by a specific *template*.
+    Within BIDS, atlases provide standardized spatially-organized knowledge to label, localize,
+    and interpret data features.
+    Atlases often rely on or embed templates as their reference framework.
+    In BIDS, templates establish the spatial coordinate frames for atlases,
+    independently of whether or not they are considered part of specific atlases' outcomes.
 data_acquisition:
   display_name: Data acquisition
   description: |
@@ -143,6 +154,12 @@ session:
     often in the case of some intervention between sessions (for example, training).
     In the [PET](SPEC_ROOT/modality-specific-files/positron-emission-tomography.md) context,
     a session may also indicate a group of related scans, taken in one or more visits.
+space:
+  display_name: Space
+  description: |
+    A space in BIDS is a reference [coordinate system](SPEC_ROOT/appendices/coordinate-systems.md)
+    defined by neuroimaging data, which may originate from an individual participant (native space)
+    or a standardized reference derived from multiple participants (template space).
 suffix:
   display_name: suffix
   description: |
@@ -164,3 +181,11 @@ task:
     In the context of brain scanning, a task is always tied to one data acquisition.
     Therefore, even if during one acquisition the subject performed multiple conceptually different behaviors
     (with different sets of instructions) they will be considered one (combined) task.
+template:
+  display_name: Template
+  description: |
+    A template (sometimes called an *atlas template*) is any aggregation of data across subjects.
+    Templates MAY operationalize the notion of a common spatial frame of reference
+    (see *space*) beyond individual subjects.
+    In practical BIDS usage, templates can be recognized (via the `tpl-` entity) as
+    standard spaces that enable analyses of data from multiple individuals.
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index be94a5eb0a..8ea8237129 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -25,6 +25,13 @@ acquisition:
     remains at the discretion of the researcher.
   type: string
   format: label
+atlas:
+  name: atlas
+  display_name: Atlas
+  description: |
+    The `atlas-<label>` entity identifies files that are part of, or derived from, an atlas.
+  type: string
+  format: label
 ceagent:
   name: ce
   display_name: Contrast Enhancing Agent
@@ -37,6 +44,18 @@ ceagent:
     `"ContrastBolusIngredient"` MAY also be added in the JSON file, with the same label.
   type: string
   format: label
+cohort:
+  name: cohort
+  display_name: Cohort
+  description: |
+    A set of subjects sharing one or more common characteristics.
+
+    In the context of a template, the `cohort-<label>` entity identifies a subset of
+    subjects or sessions that were used to construct template variations.
+    For example, a developmental template may use scans from participants of different ages,
+    longitudinal sessions of the same participants, or a combination of the two.
+  type: string
+  format: label
 chunk:
   name: chunk
   display_name: Chunk
@@ -312,7 +331,41 @@ segmentation:
   display_name: Segmentation
   description: |
     The `seg-<label>` key/value pair corresponds to a custom label the user
-    MAY use to distinguish different segmentations.
+    MAY use to distinguish specific partitions of the data space
+    (segmentations or parcellations).
+
+    Segmentations and parcellations MAY or MAY NOT be associated with
+    [atlases](SPEC_ROOT/common-principles.md#definitions),
+    Therefore, `seg-<label>` SHOULD NOT be used to designate
+    [atlases](SPEC_ROOT/common-principles.md#definitions),
+    please refer to the [template and atlas section](SPEC_ROOT/derivatives/atlas.md)
+    for detailed specifications on their combined use.
+    When a segmentation *is a realization* of an atlas' segmentation or parcellation,
+    `seg-<label>` SHOULD be employed to distinguish them.
+    For example, the [Yeo 2011 atlas](https://doi.org/10.1152/jn.00338.2011)
+    is distributed within *FreeSurfer* with two different parcellations:
+    the *7 networks* MAY be described with `seg-7n`, for instance, and
+    the *17 networks* MAY correspondingly be described with `seg-17n`.
+
+    This entity is only applicable to derivative data.
+  type: string
+  format: label
+scale:
+  name: scale
+  display_name: Scale
+  description: |
+    The `scale-<label>` key/value pair corresponds to a custom label the user
+    MAY use to distinguish segmentations that entail different levels of
+    *regional resolution* (scales), often indicated by the number of ROIs.
+    See ([Bijsterbosch et al., 2020](https://doi.org/10.1038/s41593-020-00726-z))
+    for further details on *regional resolution* or, as defined by the authors of
+    the manuscript, the *brain units*.
+
+    For example, the [Schaefer 2018 atlas](https://doi.org/10.1093/cercor/bhx179)
+    is distributed within *FreeSurfer* with ten different scales
+    (100, 200, 300, 400, 500, 600, 700, 800, 900, and 1000 regions) for each of
+    its three different parcellations (*7 networks*, *17 networks*, and
+    *Kong's variation of 17 networks*).
 
     This entity is only applicable to derivative data.
   type: string
@@ -427,6 +480,16 @@ task:
     the `task` label for resting state files (for example, `task-rest`).
   type: string
   format: label
+template:
+  name: tpl
+  display_name: Template
+  description: |
+    A standardized space of analysis specified or generated by one or more averages of features
+    with respect to which group-level and atlas-derived results are provided.
+    The `<label>` SHOULD follow the modality-specific conventions listed in the
+    [Coordinate Systems Appendix](SPEC_ROOT/appendices/coordinate-systems.md).
+  type: string
+  format: label
 tracer:
   name: trc
   display_name: Tracer
diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml
index 19e0e30307..0e8808c819 100644
--- a/src/schema/objects/enums.yaml
+++ b/src/schema/objects/enums.yaml
@@ -44,7 +44,7 @@ _StandardTemplateCoordSys:
     - $ref: objects.enums.MNI152NLin2009bAsym.value
     - $ref: objects.enums.MNI152NLin2009cAsym.value
     - $ref: objects.enums.MNI152NLin6Sym.value
-    - $ref: objects.enums.MNI152NLin6ASym.value
+    - $ref: objects.enums.MNI152NLin6Asym.value
     - $ref: objects.enums.MNI305.value
     - $ref: objects.enums.NIHPD.value
     - $ref: objects.enums.OASIS30AntsOASISAnts.value
@@ -518,9 +518,9 @@ MNI152NLin6Sym:
     Also known as symmetric ICBM 6th generation (non-linear coregistration).
 
     Used by FSL.
-MNI152NLin6ASym:
-  value: MNI152NLin6ASym
-  display_name: MNI152NLin6ASym
+MNI152NLin6Asym:
+  value: MNI152NLin6Asym
+  display_name: MNI152NLin6Asym
   description: |
     A variation of `MNI152NLin6Sym` built by A. Janke that is released as the _MNI template_ of FSL.
     Volumetric templates included with
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index e6567a57f5..0fca7e5253 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -191,6 +191,20 @@ AssociatedEmptyRoom:
       format: dataset_relative
     - type: string
       format: bids_uri
+AtlasName:
+  name: Name
+  display_name: Name
+  description: |
+    Name of the atlas.
+  type: string
+AtlasSampleSize:
+  name: SampleSize
+  display_name: Atlas' sample size
+  description: |
+      Number of items (typically, independent participants,
+      although it could also refer, for example, to sessions)
+      that employed to create the corresponding atlas.
+  type: number
 AttenuationCorrection:
   name: AttenuationCorrection
   display_name: Attenuation Correction
@@ -615,6 +629,26 @@ ContrastBolusIngredient:
     # TODO: Add definitions for these values. (perhaps don't specify)
     - UNKNOWN
     - NONE
+CoordinateReportStrategy:
+  name: CoordinateReportStrategy
+  display_name: CoordinateReportStrategy
+  description: |
+    Indicate the method of coordinate reporting in statistically significant clusters.
+    Could be the "peak" statistical coordinate in the cluster or the
+    "center_of_mass" of the cluster.
+  enum:
+    - peak
+    - center_of_mass
+    - other
+  type: string
+Curators:
+  name: Curators
+  display_name: Curators
+  description: |
+    List of curators who helped make the atlas accessible in a database or dataset.
+  type: array
+  items:
+    type: string
 DCOffsetCorrection:
   name: DCOffsetCorrection
   display_name: DC Offset Correction
@@ -766,6 +800,12 @@ Derivative:
     from other columns (for example a summary score based on a subset of items in a
     questionnaire).
   type: boolean
+DerivedFrom:
+  name: DerivedFrom
+  display_name: DerivedFrom
+  description: |
+    Indicate what data modality the atlas was derived from, for example, "cytoarchitecture", "resting-state", "task".
+  type: string
 Description:
   name: Description
   display_name: Description
@@ -1985,6 +2025,12 @@ Levels:
             $ref: objects.metadata.TermURL
           Description:
             $ref: objects.metadata.Description
+LevelType:
+  name: LevelType
+  display_name: LevelType
+  description: |
+    Indicate what analysis level the atlas was derived from, for example, "group", "individual".
+  type: string
 License:
   name: License
   display_name: License
@@ -2873,6 +2919,14 @@ Purity:
   type: number
   minimum: 0
   maximum: 100
+RRID:
+  name: RRID
+  display_name: RRID
+  description: |
+    [Research Resource Identifier](https://rrid.site) of the file,
+    dataset or atlas being described.
+  type: string
+  format: rrid
 RandomRate:
   name: RandomRate
   display_name: Random Rate
@@ -3604,6 +3658,7 @@ SpatialReference:
   name: SpatialReference
   display_name: Spatial Reference
   description: |
+    String or object describing the reference image to which the current image is aligned.
     For images with a single reference, the value MUST be a single string.
     For images with multiple references, such as surface and volume references,
     a JSON object MUST be used.
@@ -3625,6 +3680,12 @@ SpatialReference:
             format: uri
           - type: string
             format: dataset_relative
+Species:
+  name: Species
+  display_name: Species
+  description: |
+    The species the atlas was derived from. For example, could be Human, Macaque, Rat, or Mouse.
+  type: string
 SpecificRadioactivity:
   name: SpecificRadioactivity
   display_name: Specific Radioactivity
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 1e2825ced2..0592acf140 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -578,6 +578,15 @@ defacemask:
   description: |
     A binary mask that was used to remove facial features from an anatomical MRI
     image.
+description:
+  value: description
+  display_name: Description file
+  description: |
+    A JSON file describing the entities that occur in the filename.
+
+    At present, this is used for atlas descriptions.
+
+    This file MUST be located at the root of the dataset.
 descriptions:
   value: descriptions
   display_name: Description Entity Definitions
diff --git a/src/schema/rules/checks/atlas.yaml b/src/schema/rules/checks/atlas.yaml
new file mode 100644
index 0000000000..66b127a99b
--- /dev/null
+++ b/src/schema/rules/checks/atlas.yaml
@@ -0,0 +1,27 @@
+AtlasDescriptionRequired:
+  issue:
+    code: ATLAS_DESCRIPTION_REQUIRED
+    message: |
+      No /atlas-{entities.atlas}_description.json could be found.
+    level: error
+  selectors:
+    - dataset.dataset_description.DatasetType == "derivative"
+    - entities.atlas
+    - entities.template
+    - extension != '.json'
+  checks:
+    - associations.atlas_description
+
+AtlasDescriptionRecommended:
+  issue:
+    code: ATLAS_DESCRIPTION_RECOMMENDED
+    message: |
+      No /atlas-{entities.atlas}_description.json could be found.
+    level: warning
+  selectors:
+    - dataset.dataset_description.DatasetType == "derivative"
+    - entities.atlas
+    - type(entities.template) == 'null'
+    - extension != '.json'
+  checks:
+    - associations.atlas_description
diff --git a/src/schema/rules/common_principles.yaml b/src/schema/rules/common_principles.yaml
index 8fac3a813d..2b403817f7 100644
--- a/src/schema/rules/common_principles.yaml
+++ b/src/schema/rules/common_principles.yaml
@@ -11,6 +11,9 @@
 - task
 - event
 - run
+- template
+- atlas
+- space
 - index
 - label
 - suffix
diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index b9c8e74761..679ce02e45 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -58,3 +58,22 @@ genetic_info:
     TissueOrigin: optional
     BrainLocation: optional
     CellType: optional
+
+atlas_description:
+  selectors:
+    - suffix == 'description'
+    - extension == '.json'
+    - entities.atlas
+  fields:
+    AtlasName: required
+    License: required
+    AtlasSampleSize: required
+    Description: recommended
+    Authors: recommended
+    Curators: optional
+    Funding: optional
+    ReferencesAndLinks: optional
+    Species: optional
+    DerivedFrom: optional
+    LevelType: optional
+    RRID: optional
diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
index e5415e8c14..3035be5c93 100644
--- a/src/schema/rules/directories.yaml
+++ b/src/schema/rules/directories.yaml
@@ -114,10 +114,17 @@ derivative:
       - sourcedata
       - stimuli
       - subject
+      - template
   code:
     name: code
     level: optional
     opaque: true
+  cohort:
+    entity: cohort
+    level: optional
+    opaque: false
+    subdirs:
+      - datatype
   docs:
     name: docs
     level: optional
@@ -155,6 +162,13 @@ derivative:
     opaque: false
     subdirs:
       - datatype
+  template:
+    entity: template
+    level: optional
+    opaque: false
+    subdirs:
+      - cohort
+      - datatype
   datatype:
     value: datatype
     level: optional
diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index 44174d333e..bad1a42744 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -2,7 +2,9 @@
 # This file simply defines the order in which entities should appear within filenames.
 # Entity definitions appear in the `objects/entities.yaml` file.
 - subject
+- template
 - session
+- cohort
 - sample
 - task
 - tracksys
@@ -27,7 +29,9 @@
 - split
 - recording
 - chunk
+- atlas
 - segmentation
+- scale
 - resolution
 - density
 - label
diff --git a/src/schema/rules/files/deriv/atlas.yaml b/src/schema/rules/files/deriv/atlas.yaml
new file mode 100644
index 0000000000..126dad7208
--- /dev/null
+++ b/src/schema/rules/files/deriv/atlas.yaml
@@ -0,0 +1,9 @@
+atlas_description:
+  selectors:
+    - dataset.dataset_description.DatasetType == 'derivative'
+  suffixes:
+    - description
+  extensions:
+    - .json
+  entities:
+    atlas: required
diff --git a/src/schema/rules/files/deriv/imaging.yaml b/src/schema/rules/files/deriv/imaging.yaml
index d2ce8a451d..d4fad4e68c 100644
--- a/src/schema/rules/files/deriv/imaging.yaml
+++ b/src/schema/rules/files/deriv/imaging.yaml
@@ -13,6 +13,13 @@ anat_parametric_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.parametric.entities
 
+anat_parametric_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_parametric_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_parametric_volumetric.entities
+
 anat_nonparametric_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -22,6 +29,13 @@ anat_nonparametric_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.nonparametric.entities
 
+anat_nonparametric_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_nonparametric_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_nonparametric_volumetric.entities
+
 anat_defacemask_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -31,6 +45,13 @@ anat_defacemask_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.defacemask.entities
 
+anat_defacemask_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_defacemask_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_defacemask_volumetric.entities
+
 anat_mese_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -40,6 +61,13 @@ anat_mese_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.mese.entities
 
+anat_mese_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_mese_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_mese_volumetric.entities
+
 anat_megre_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -49,6 +77,13 @@ anat_megre_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.megre.entities
 
+anat_megre_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_megre_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_megre_volumetric.entities
+
 anat_multiflip_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -58,6 +93,13 @@ anat_multiflip_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.multiflip.entities
 
+anat_multiflip_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_multiflip_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_multiflip_volumetric.entities
+
 anat_multiinversion_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -67,6 +109,13 @@ anat_multiinversion_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.multiinversion.entities
 
+anat_multiinversion_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_multiinversion_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_multiinversion_volumetric.entities
+
 anat_mp2rage_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -76,6 +125,13 @@ anat_mp2rage_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.mp2rage.entities
 
+anat_mp2rage_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_mp2rage_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_mp2rage_volumetric.entities
+
 anat_vfamt_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -85,6 +141,13 @@ anat_vfamt_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.vfamt.entities
 
+anat_vfamt_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_vfamt_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_vfamt_volumetric.entities
+
 anat_mtr_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -94,6 +157,13 @@ anat_mtr_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.anat.mtr.entities
 
+anat_mtr_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.anat_mtr_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_mtr_volumetric.entities
+
 dwi_dwi_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -103,6 +173,13 @@ dwi_dwi_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.dwi.dwi.entities
 
+dwi_dwi_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.dwi_dwi_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.dwi_dwi_volumetric.entities
+
 dwi_sbref_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -112,7 +189,14 @@ dwi_sbref_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.dwi.sbref.entities
 
-dwi_scannerderivatives:
+dwi_sbref_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.dwi_sbref_volumetric
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.deriv.imaging.dwi_sbref_volumetric.entities
+
+dwi_scannerderivatives_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
     - rules.files.raw.dwi.ScannerDerivatives
@@ -121,6 +205,13 @@ dwi_scannerderivatives:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.dwi.ScannerDerivatives.entities
 
+dwi_scannerderivatives_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.dwi_scannerderivatives_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.dwi_scannerderivatives_volumetric.entities
+
 func_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -130,6 +221,13 @@ func_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.func.func.entities
 
+func_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.func_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.func_volumetric.entities
+
 func_phase_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -139,6 +237,8 @@ func_phase_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.func.phase.entities
 
+# NB: Not permitting deprecated phase suffix for atlases
+
 fmap_fieldmaps_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -148,6 +248,13 @@ fmap_fieldmaps_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.fmap.fieldmaps.entities
 
+fmap_fieldmaps_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.fmap_fieldmaps_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.fmap_fieldmaps_volumetric.entities
+
 fmap_pepolar_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -157,7 +264,14 @@ fmap_pepolar_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.fmap.pepolar.entities
 
-fmap_pepolar_m0scan:
+fmap_pepolar_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.fmap_pepolar_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.fmap_pepolar_volumetric.entities
+
+fmap_pepolar_m0scan_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
     - rules.files.raw.fmap.pepolar_m0scan
@@ -166,6 +280,13 @@ fmap_pepolar_m0scan:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.fmap.pepolar.entities
 
+fmap_pepolar_m0scan_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.fmap_pepolar_m0scan_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.fmap_pepolar_m0scan_volumetric.entities
+
 fmap_TB1DAM_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -175,6 +296,13 @@ fmap_TB1DAM_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.fmap.TB1DAM.entities
 
+fmap_TB1DAM_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.fmap_TB1DAM_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.fmap_TB1DAM_volumetric.entities
+
 fmap_TB1EPI_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -184,6 +312,13 @@ fmap_TB1EPI_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.fmap.TB1EPI.entities
 
+fmap_TB1EPI_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.fmap_TB1EPI_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.fmap_TB1EPI_volumetric.entities
+
 fmap_RFFieldMaps_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -193,6 +328,13 @@ fmap_RFFieldMaps_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.fmap.RFFieldMaps.entities
 
+fmap_RFFieldMaps_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.fmap_RFFieldMaps_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.fmap_RFFieldMaps_volumetric.entities
+
 fmap_TB1SRGE_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -202,6 +344,13 @@ fmap_TB1SRGE_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.fmap.TB1SRGE.entities
 
+fmap_TB1SRGE_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.fmap_TB1SRGE_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.fmap_TB1SRGE_volumetric.entities
+
 fmap_parametric_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -211,6 +360,13 @@ fmap_parametric_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.fmap.parametric.entities
 
+fmap_parametric_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.fmap_parametric_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.fmap_parametric_volumetric.entities
+
 perf_asl_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -220,6 +376,13 @@ perf_asl_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.perf.asl.entities
 
+perf_asl_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.perf_asl_volumetric
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.perf_asl_volumetric.entities
+
 pet_pet_volumetric:
   $ref:
     - meta.templates.deriv.volumetric
@@ -229,6 +392,13 @@ pet_pet_volumetric:
       - meta.templates.deriv.volumetric.entities
       - rules.files.raw.pet.pet.entities
 
+pet_pet_volumetric_atlas:
+  $ref: rules.files.deriv.imaging.pet_pet_volumetric
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.deriv.imaging.pet_pet_volumetric.entities
+
 # Masks
 anat_mask:
   $ref:
@@ -241,6 +411,13 @@ anat_mask:
       - meta.templates.deriv.mask.entities
       - rules.files.raw.anat.nonparametric.entities
 
+anat_mask_atlas:
+  $ref: rules.files.deriv.imaging.anat_mask
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_mask.entities
+
 dwi_mask:
   $ref:
     - meta.templates.deriv.mask
@@ -250,6 +427,13 @@ dwi_mask:
       - meta.templates.deriv.mask.entities
       - rules.files.raw.dwi.dwi.entities
 
+dwi_mask_atlas:
+  $ref: rules.files.deriv.imaging.dwi_mask
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.dwi_mask.entities
+
 func_mask:
   $ref:
     - meta.templates.deriv.mask
@@ -259,6 +443,13 @@ func_mask:
       - meta.templates.deriv.mask.entities
       - rules.files.raw.func.func.entities
 
+func_mask_atlas:
+  $ref: rules.files.deriv.imaging.func_mask
+  entities:
+    $ref:
+      - meta.templates.deriv.volumetric.entities
+      - rules.files.deriv.imaging.func_mask.entities
+
 # Discrete and probabilistic segmentations
 anat_discrete_segmentation:
   $ref:
@@ -270,6 +461,13 @@ anat_discrete_segmentation:
       - meta.templates.deriv.dseg.entities
       - rules.files.raw.anat.nonparametric.entities
 
+anat_discrete_segmentation_atlas:
+  $ref: rules.files.deriv.imaging.anat_discrete_segmentation
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_discrete_segmentation.entities
+
 func_discrete_segmentation:
   $ref:
     - meta.templates.deriv.dseg
@@ -279,6 +477,13 @@ func_discrete_segmentation:
       - meta.templates.deriv.dseg.entities
       - rules.files.raw.func.func.entities
 
+func_discrete_segmentation_atlas:
+  $ref: rules.files.deriv.imaging.func_discrete_segmentation
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.func_discrete_segmentation.entities
+
 dwi_discrete_segmentation:
   $ref:
     - meta.templates.deriv.dseg
@@ -288,6 +493,13 @@ dwi_discrete_segmentation:
       - meta.templates.deriv.dseg.entities
       - rules.files.raw.dwi.dwi.entities
 
+dwi_discrete_segmentation_atlas:
+  $ref: rules.files.deriv.imaging.dwi_discrete_segmentation
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.dwi_discrete_segmentation.entities
+
 anat_probabilistic_segmentation:
   $ref:
     - meta.templates.deriv.probseg
@@ -298,6 +510,13 @@ anat_probabilistic_segmentation:
       - meta.templates.deriv.probseg.entities
       - rules.files.raw.anat.nonparametric.entities
 
+anat_probabilistic_segmentation_atlas:
+  $ref: rules.files.deriv.imaging.anat_probabilistic_segmentation
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_probabilistic_segmentation.entities
+
 func_probabilistic_segmentation:
   $ref:
     - meta.templates.deriv.probseg
@@ -307,6 +526,13 @@ func_probabilistic_segmentation:
       - meta.templates.deriv.probseg.entities
       - rules.files.raw.func.func.entities
 
+func_probabilistic_segmentation_atlas:
+  $ref: rules.files.deriv.imaging.func_probabilistic_segmentation
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.func_probabilistic_segmentation.entities
+
 dwi_probabilistic_segmentation:
   $ref:
     - meta.templates.deriv.probseg
@@ -316,6 +542,13 @@ dwi_probabilistic_segmentation:
       - meta.templates.deriv.probseg.entities
       - rules.files.raw.dwi.dwi.entities
 
+dwi_probabilistic_segmentation_atlas:
+  $ref: rules.files.deriv.imaging.dwi_probabilistic_segmentation
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.dwi_probabilistic_segmentation.entities
+
 anat_discrete_surface:
   $ref:
     - meta.templates.deriv.dseg_surface
@@ -325,3 +558,10 @@ anat_discrete_surface:
     $ref:
       - meta.templates.deriv.dseg_surface.entities
       - rules.files.raw.anat.nonparametric.entities
+
+anat_discrete_surface_atlas:
+  $ref: rules.files.deriv.imaging.anat_discrete_surface
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.imaging.anat_discrete_surface.entities
diff --git a/src/schema/rules/files/deriv/preprocessed_data.yaml b/src/schema/rules/files/deriv/preprocessed_data.yaml
index 0a1029b348..75c7f80aa3 100644
--- a/src/schema/rules/files/deriv/preprocessed_data.yaml
+++ b/src/schema/rules/files/deriv/preprocessed_data.yaml
@@ -156,6 +156,13 @@ micr_microscopy_common:
       - meta.templates.deriv.spatial.entities
       - rules.files.raw.micr.microscopy.entities
 
+micr_microscopy_atlas:
+  $ref: rules.files.deriv.preprocessed_data.micr_microscopy_common
+  entities:
+    $ref:
+      - meta.templates.atlas.base.entities
+      - rules.files.deriv.preprocessed_data.micr_microscopy_common.entities
+
 pet_blood_common:
   $ref:
     - meta.templates.deriv.spatial
@@ -165,7 +172,7 @@ pet_blood_common:
       - meta.templates.deriv.spatial.entities
       - rules.files.raw.pet.blood.entities
 
-task_events_common:
+events_common:
   $ref:
     - meta.templates.deriv.base
     - rules.files.raw.events.events
diff --git a/src/schema/rules/sidecars/derivatives/atlas.yaml b/src/schema/rules/sidecars/derivatives/atlas.yaml
new file mode 100644
index 0000000000..bc69a5bbc2
--- /dev/null
+++ b/src/schema/rules/sidecars/derivatives/atlas.yaml
@@ -0,0 +1,10 @@
+---
+TemplateNonStandard:
+  selectors:
+    - dataset.dataset_description.DatasetType == "derivative"
+    - '!intersects(schema.objects.enums._StandardTemplateCoordSys.enum, [entities.tpl])'
+    - >
+      type(entities.space) == 'null' ||
+      !intersects(schema.objects.enums._StandardTemplateCoordSys.enum, [entities.space])
+  fields:
+    SpatialReference: required
diff --git a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
index fbc05937bc..a1f2e12abe 100644
--- a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
@@ -23,7 +23,8 @@ SpatialReferenceEntity:
 SpatialReferenceNonStandard:
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"
-    - '!intersects(schema.objects.metadata._StandardTemplateCoordSys, [entities.space])'
+    - '!intersects(schema.objects.enums._StandardTemplateCoordSys.enum, [entities.space])'
+    - type(entities.tpl) == 'null' || !intersects(schema.objects.enums._StandardTemplateCoordSys.enum, [entities.tpl])
   fields:
     SpatialReference: required
 
@@ -41,9 +42,12 @@ MaskDerivatives:
 SegmentationCommon:
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"
-    - 'intersects([suffix], ["dseg", "probseg"])'
+    - 'intersects([suffix], ["dseg", "probseg", "mask"])'
   fields:
+    SpatialReference: recommended
     Manual: optional
+    CoordinateReportStrategy: optional
+
 
 # Derivatives -> Imaging data types
 ImageDerivatives:
diff --git a/tools/schemacode/src/bidsschematools/tests/test_render_text.py b/tools/schemacode/src/bidsschematools/tests/test_render_text.py
index 6f67567f1f..df9190f534 100644
--- a/tools/schemacode/src/bidsschematools/tests/test_render_text.py
+++ b/tools/schemacode/src/bidsschematools/tests/test_render_text.py
@@ -60,9 +60,9 @@ def test_make_glossary(schema_obj, schema_dir):
     for line in glossary.split("\n"):
         if line.startswith('<a name="objects.'):
             # Are all objects objects?
-            assert any([line.startswith(f'<a name="objects.{i}') for i in object_files])
+            assert any(line.startswith(f'<a name="objects.{i}.') for i in object_files)
             # Are rules loaded incorrectly?
-            assert not any([line.startswith(f'<a name="objects.{i}') for i in rules_only])
+            assert not any(line.startswith(f'<a name="objects.{i}.') for i in rules_only)
 
 
 @pytest.mark.parametrize("placeholders", [True, False])
diff --git a/tools/schemacode/uv.lock b/tools/schemacode/uv.lock
new file mode 100644
index 0000000000..fb1cb5e431
--- /dev/null
+++ b/tools/schemacode/uv.lock
@@ -0,0 +1,1353 @@
+version = 1
+revision = 2
+requires-python = ">=3.9"
+resolution-markers = [
+    "python_full_version >= '3.12'",
+    "python_full_version == '3.11.*'",
+    "python_full_version == '3.10.*'",
+    "python_full_version < '3.10'",
+]
+
+[[package]]
+name = "acres"
+version = "0.5.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "importlib-resources", marker = "python_full_version < '3.10'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/ec/ba/94b63a9af588fbf7bde25ce44d55456199654a92fb7b2337767198a824b0/acres-0.5.0.tar.gz", hash = "sha256:128b6447bf5df3b6210264feccbfa018b4ac5bd337358319aec6563f99db8f3a", size = 57750, upload-time = "2025-06-04T12:40:30.329Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/39/e8/806475fe4cdfd8635535d3fa11bd61d19b7cc94b61b9147ebdd2ab4cbbee/acres-0.5.0-py3-none-any.whl", hash = "sha256:fcc32b974b510897de0f041609b4234f9ff03e2e960aea088f63973fb106c772", size = 12703, upload-time = "2025-06-04T12:40:28.745Z" },
+]
+
+[[package]]
+name = "arrow"
+version = "1.3.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "python-dateutil" },
+    { name = "types-python-dateutil" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/2e/00/0f6e8fcdb23ea632c866620cc872729ff43ed91d284c866b515c6342b173/arrow-1.3.0.tar.gz", hash = "sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85", size = 131960, upload-time = "2023-09-30T22:11:18.25Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/f8/ed/e97229a566617f2ae958a6b13e7cc0f585470eac730a73e9e82c32a3cdd2/arrow-1.3.0-py3-none-any.whl", hash = "sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80", size = 66419, upload-time = "2023-09-30T22:11:16.072Z" },
+]
+
+[[package]]
+name = "attrs"
+version = "25.3.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/5a/b0/1367933a8532ee6ff8d63537de4f1177af4bff9f3e829baf7331f595bb24/attrs-25.3.0.tar.gz", hash = "sha256:75d7cefc7fb576747b2c81b4442d4d4a1ce0900973527c011d1030fd3bf4af1b", size = 812032, upload-time = "2025-03-13T11:10:22.779Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/77/06/bb80f5f86020c4551da315d78b3ab75e8228f89f0162f2c3a819e407941a/attrs-25.3.0-py3-none-any.whl", hash = "sha256:427318ce031701fea540783410126f03899a97ffc6f61596ad581ac2e40e3bc3", size = 63815, upload-time = "2025-03-13T11:10:21.14Z" },
+]
+
+[[package]]
+name = "bidsschematools"
+source = { editable = "." }
+dependencies = [
+    { name = "acres" },
+    { name = "click", version = "8.1.8", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
+    { name = "click", version = "8.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },
+    { name = "pyyaml" },
+]
+
+[package.optional-dependencies]
+all = [
+    { name = "check-jsonschema" },
+    { name = "codecov" },
+    { name = "coverage", extra = ["toml"] },
+    { name = "jsonschema", extra = ["format"] },
+    { name = "markdown-it-py" },
+    { name = "pandas" },
+    { name = "pyparsing" },
+    { name = "pytest" },
+    { name = "pytest-cov" },
+    { name = "tabulate" },
+]
+dev = [
+    { name = "check-jsonschema" },
+    { name = "codecov" },
+    { name = "coverage", extra = ["toml"] },
+    { name = "jsonschema", extra = ["format"] },
+    { name = "markdown-it-py" },
+    { name = "pandas" },
+    { name = "pyparsing" },
+    { name = "pytest" },
+    { name = "pytest-cov" },
+    { name = "ruff" },
+    { name = "tabulate" },
+]
+expressions = [
+    { name = "pyparsing" },
+]
+render = [
+    { name = "markdown-it-py" },
+    { name = "pandas" },
+    { name = "tabulate" },
+]
+tests = [
+    { name = "check-jsonschema" },
+    { name = "codecov" },
+    { name = "coverage", extra = ["toml"] },
+    { name = "jsonschema", extra = ["format"] },
+    { name = "markdown-it-py" },
+    { name = "pandas" },
+    { name = "pyparsing" },
+    { name = "pytest" },
+    { name = "pytest-cov" },
+    { name = "tabulate" },
+]
+validation = [
+    { name = "jsonschema", extra = ["format"] },
+]
+
+[package.metadata]
+requires-dist = [
+    { name = "acres" },
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