diff --git a/src/atlas.md b/src/atlas.md
index 6a2297b97f..10a68845d5 100644
--- a/src/atlas.md
+++ b/src/atlas.md
@@ -1,183 +1,57 @@
-# BIDS-Atlas
+# Explanation
 
 In the following we describe how an [atlas](schema/objects/entities.yaml#atlas) can be shared within BIDS.
-We describe a broad set of atlases and use cases thereof.
+Broadly we define an atlas as a reference quantity sampled to a template.
+With this definition, an atlas can be a parcellation, a segmentation, or a quantitative map.
 
-More specifically, this entails providing and referring to existing atlas datasets,
-describing atlases that were newly derived within an analysis,
-and providing information for derivatives that were obtained through them.
-The first would comprise (publicly) available atlases, for example,
+We aim to cover three main use cases with the given definition:
+1. Generating/sharing atlas(es) to be published and used by others.
+2. Using a shared atlas and transforming/resampling it into new template spaces or subject spaces.
+3. Creating subject-specific atlases derived from the corresponding subject’s data.
+
+These three use cases cover the majority of scenarios where atlases are used in neuroimaging research.
+
+The first use case would comprise (publicly) available atlases, for example,
 Destrieux et al. ([doi.org/10.1016/j.neuroimage.2010.06.010](https://doi.org/10.1016/j.neuroimage.2010.06.010)),
 AAL ([doi.org/10.1006/nimg.2001.0978](https://doi.org/10.1006/nimg.2001.0978)),
 Yeo ([doi.org/10.1152/jn.00338.2011](https://doi.org/10.1152/jn.00338.2011))
 and JHU DTI-based white-matter atlases
 ([eBook ISBN: 9780080456164](https://shop.elsevier.com/books/mri-atlas-of-human-white-matter/mori/978-0-444-51741-8)
-and [doi.org/10.1016/j.neuroimage.2007.07.053](https://doi.org/10.1016/j.neuroimage.2007.07.053)),
-while the second would include atlases obtained through analyses within a dataset at hand,
+and [doi.org/10.1016/j.neuroimage.2007.07.053](https://doi.org/10.1016/j.neuroimage.2007.07.053)).
+The second use case would comprise transforming/resampling the publicly available atlases into new template spaces or subject spaces for further analysis.
+For example, resampling the AAL atlas from MNI152NLin6Asym space to a subject’s native T1w space.
+The third use case would include atlases obtained through analyses within a dataset at hand,
 for example, resting-state networks and functional localizers.
-Importantly, the latter can also be utilized as existing atlases if made available.
-The third would entail referencing an atlas and its properties used to derive,
-for example, a parcellated time series or a connectivity matrix.
-
-## Atlas as new DatasetType
-Here we introduce an additional value to the `DatasetType field` of `dataset_description.json`.
-If a dataset declares its DatasetType to be [atlas](schema/objects/entities.yaml#atlas),
-the top-level directories MUST be `atlas-` instead of `sub-`.
-This will allow sharing existing atlases as stand-alone datasets,
-validating them via the [BIDS validator](https://github.com/bids-standard/bids-validator) and enabling their integration as sub-datasets of other BIDS datasets.
-
-## File formats for the raw data
-BIDS-Atlas aims to describe brain atlases via three REQUIRED files.
-They entail the atlas itself (for example, in .nii, .nii.gz, .gii, or .tsv),
-a file indexing/labeling each node in the atlas (in .tsv) and a file containing exhaustive meta-data about the atlas (in .json).
-
-The usage of [_desc-](schema/objects/entities.yaml#desc) is generally discouraged but should be evaluated on a case by case basis in order to keep this identifier available for necessary cases.
-Specifically, this refers to the atlas at hand and potential different versions thereof.
-As a rule of thumb, BIDS-Atlas proposed to evaluate and consider how many versions across how many levels of versions an atlas is (commonly) provided and used in.
-If there is only one version, as in "release", of an atlas
-and no sub-versions, as in "different parcel numbers" (or comparable),
-[_desc-](schema/objects/entities.yaml#desc) is most likely not expected and/or required.
-An example for [_desc-](schema/objects/entities.yaml#desc) in such a use case would be
-to indicate a subset of parcels and would entail the addition of
-the [_mask-](schema/objects/entities.yaml#mask) extension,
-for example, providing/using the "postcentral gyrus" region of the [Destrieux atlas](doi:10.1093/cercor/bhg087.) would result in the following file name:
-`atlas-Destrieux_space-MNI152NLin6Asym_res-2_desc-PostCentralGyrus_mask.nii.gz`.
-Similar to the above case, if there are multiple versions, as in "release",
-of an atlas and no sub-versions, as in "different parcel numbers" (or comparable),
-[_desc-](schema/objects/entities.yaml#desc) is also most likely not expected and/or required,
-as the version(s) (release(s)) should be indicated via `atlas-`.
-For example, the different versions of the [AAL parcellation](http://www.gin.cnrs.fr/AAL-217?lang=en)
-would result in the following file names:
-`atlas-AAL1_space-MNI152NLin6Asym_res-2.nii.gz`, `atlas-AAL2_space-MNI152NLin6Asym_res-2.nii.gz` and `atlas-AAL3_space-MNI152NLin6Asym_res-2.nii.gz`.
-Given an atlas has only one version, as in "release", and multiple sub-versions
-as in "different parcel numbers" (or comparable)
-[_desc-](schema/objects/entities.yaml#desc) is considered appropriate.
-For example, when indicating information pertaining to the probabilistic nature of an atlas
-such as the [_probseg](schema/objects/entities.yaml#probseg) version of
-the [Harvard-Oxford parcellation](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases):
-`atlas-HarvardOxford_res-2_desc-th25_probseg.nii.gz`.
-In cases where an atlas has multiple versions, as in "release", and sub-versions,
-as in "different parcel numbers" (or comparable),
-the version(s) (release(s)) should be indicated via `atlas-` as outlined above and the sub-versions should be indicated via [_desc-](schema/objects/entities.yaml#desc).
-For example, different versions and sub-versions of the [Schaefer parcellation](https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/Updates/Update_20190916_README.md) would be denoted as follows:
-`atlas-Schaefer2018_space-MNI152NLin6Asym_res-2_desc-400Parcels7Networks.nii.gz`,
-`atlas-Schaefer2018_space-MNI152NLin6Asym_res-2_desc-400Parcels17Networks.nii.gz`,
-`atlas-Schaefer2022_space-MNI152NLin6Asym_res-2_desc-800Parcels7Networks.nii.gz`
-and `atlas-Schaefer2022_space-MNI152NLin6Asym_res-2_desc-800Parcels17Networks.nii.gz`.
-
-Importantly, already existing BIDS entities should be used to indicate certain aspects of an atlas,
-instead of [_desc-](schema/objects/entities.yaml#desc), for example,
-[hemi](schema/objects/entities.yaml#hemi) to denote a given hemisphere
-and [_dseg](schema/objects/entities.yaml#dseg)/[_probseg](schema/objects/entities.yaml#probseg)
-to denote deterministic and probabilistic atlases respectively.
-
-However, as mentioned above, these are general guidelines and the exact implementation should be evaluated on a case by case basis, with deviations following common BIDS principles being permitted.
-
-## Directory Structure
-BIDS-Atlas focuses on the utilization of atlases while also allowing their sharing.
-Thus, atlases are either stored within a dedicated `atlas` directory at the BIDS root directory
-(comparable to the `code` directory),
-such files are the non-altered/original atlases or within a given directory under `derivatives`.
-In the second case, atlases are altered,
-derived or applied and thus multiple use cases have to be distinguished as indicated further below.
-
-### Representing an atlas as a dataset
-
-The first option refers to atlases that were not altered, for example,
-via spatial transformations and/or resampling or applied to data
-and thus their initial inclusion/utilization in a given dataset.
-If there is only this form of atlases (that is, the tool used),
-they are always shared at the root directory and everything else is under derivatives.
-This allows validating any
-
-```Text
-<dataset>/atlas/
-```
-
-using the  [BIDS validator](https://github.com/bids-standard/bids-validator).
-Importantly, only this case follows the same directory structure as
-[sub](schema/objects/entities.yaml#sub), that is, one dedicated directory for each atlas within a given dataset.
-The default way of storage of the non-altered atlas at the root directory looks like this:
-
-```Text
-<dataset>/atlas/atlas-<label>/
-  atlas-<label>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
-  atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
-  atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].json
-```
-
-### Representing an atlas within a dataset
-
-Besides this default and required storage of the non-altered atlas at the root directory, the second use case provides three sub-cases to store atlases that were either altered, applied, or derived within a given dataset.
-While case 1 uses the [atlas](schema/objects/entities.yaml#atlas) identifier, case 2 and 3 use the [seg](schema/objects/entities.yaml#seg) identifier.
-The difference between the use of [atlas](schema/objects/entities.yaml#atlas) and [seg](schema/objects/entities.yaml#seg) identifier is that in the first case an existing atlas is changed, for example, transformed, but still remains an atlas.
-In the other case, the atlas is used to define a segmentation, for example, the AAL atlas is used to define a cortical parcellation, that then is applied to a subjects other content, for example, a cortical thickness or binding potential map.
 
-#### Case 1
+## Definitions and Terminology
 
-First, a given atlas underwent modifications before its utilization,
-specifically spatial transformations to a template space and is used in this form within a given pipeline.
-In this case, the respective BIDS-Atlas files will be stored at both the BIDS root level and the given pipeline directory under `derivatives`.
-Files stored at the BIDS root level will follow the structure outlined in option 1,
-while files stored at the pipeline level will follow the respective naming conventions.
-For example, if an atlas was spatially transformed to a certain MNI template,
-then the BIDS-Atlas files will be stored within the respective pipeline directory and the corresponding [space](schema/objects/entities.yaml#space)-<label> identifier will be adapted accordingly.
+Template - a canonical anatomical reference in a particular space; while two templates may be in the same space, the template matters for the association of coordinates with structures, so when something is said to be resampled into a space, the template used is the more useful name.
 
-```Text
-<dataset>/atlas/atlas-<label>/
-  atlas-<label>_desc-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
-  atlas-<label>_desc-<label>_[dseg|probseg|mask].tsv
-  atlas-<label>_desc-<label>_[dseg|probseg|mask].json
-
-<dataset>/derivatives/<pipeline>/
-  atlas-<label>_space-<label>_res-<label>_desc-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii|.tsv][.gz]
-  atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
-  atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].json
-```
-
-#### Case 2
+Space - A common coordinate frame with an origin, axis orientations and spatial units;
+in practice this definition is too abstract to be directly usable.
+Within the BIDS filename structure, the keyword `space-` is an application of a template onto a subject space.
 
-Second, a given atlas underwent modifications before its utilization,
-specifically spatial transformations to an individual subject space and is used in this form.
-In this case, the respective BIDS-Atlas files will be stored at both the BIDS root level and at the given subject level under `derivatives`.
-Files stored at the BIDS root level will follow the structure outlined in option 1.
-Files stored at the subject level now use the [seg](schema/objects/entities.yaml#seg) entity with it's value referring to the atlas use on a given file.
+Atlas - A reference quantity sampled to a template. In many contexts this is a parcellation, but it in some communities (notably PET) it is more common to publish absolute quantities and leave it to end-users to discretize the quantities into segmentations. It is also common to publish reference data sampled to one or more public templates, rather than publishing yet another atlas.
 
-```Text
-<dataset>/atlas/atlas-<label>/
-  atlas-<label>_desc-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
-  atlas-<label>_desc-<label>_[dseg|probseg|mask].tsv
-  atlas-<label>_desc-<label>_[dseg|probseg|mask].json
-
-<dataset>/derivatives/
-  sub-01/
-    func/
-      sub-01_space-<label>_seg-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii|tsv][.gz]
-      sub-01_space-<label>_seg-<label>_desc-<label>_[dseg|probseg|mask].tsv
-      sub-01_space-<label>_seg-<label>_desc-<label>_[dseg|probseg|mask].json
-```
+Segmentation - A partition of an image into multiple segments or regions based on certain criteria, such as intensity, texture, or anatomical features.
+Both atlases and segmentations provide spatial information about the brain,
+however, they serve distinct purposes: atlases provide a common spatial framework and
+delineate predefined regions of interest, while segmentations partition brain images into distinct tissue types for quantitative analysis and anatomical characterization
+for individual subjects or groups of subjects.
+Within the BIDS filenaming structure, the keyword `seg` is used to indicate
+an application of an atlas to a subject.
 
-#### Case 3
+## File formats for the data
 
-Third, a given atlas was derived from the corresponding subject’s data and thus is subject-specific.
-In this case, the `atlas` directory at the root of the dataset does not exist.
-The subject specific atlas filenames are the same as in case 2 at the subject level within the modality directory of the data the atlas was derived from.
-Optionally, a `*_coordsystem.json` file that specifies the
-[Image-based Coordinate System](/appendices/coordinate-systems.md) of the subject-specific atlas can be used for,
-for example, an histological atlas/segmentation.
-Unlike as in the prior use case, the [atlas](schema/objects/entities.yaml#atlas) identifier will be replaced with the [seg](schema/objects/entities.yaml#seg) identifier.
+BIDS-Atlas aims to describe brain atlases via four REQUIRED files.
+They entail the atlas itself (for example, in .nii, .nii.gz, .gii, or .tsv),
+a file indexing/labeling each node in the atlas (in .tsv), a sidecar json file containing
+spatial meta-data about the atlas, and an exhaustive meta-data `_description.json`
+file containing information about how the atlas was generated.
 
-```Text
-<dataset>/derivatives/
-  sub-01/
-    anat/
-      sub-01_atlas-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii|tsv][.gz][.ome-tiff|.png]
-      sub-01_atlas-<label>_desc-<label>_[dseg|probseg|mask].tsv
-      sub-01_atlas-<label>_desc-<label>_[dseg|probseg|mask].json
-      sub-01_atlas-<label>_desc-<label>_coordsystem.json
-```
+{{ MACROS___make_filename_template("atlas", suffixes=["dseg", "probseg", "mask"]) }}
 
-### Representing locations in an atlas file
+## Atlas file formats
 
 The `[probseg|dseg|mask].[nii|dlabel.nii|label.gii][.gz]` file represents the location and extent of the nodes/parcels/regions within the atlas.
 Different file types are supported based on the modality and atlas at hand.
@@ -205,96 +79,25 @@ then excluding the space entity at the top level is a good way to ensure the fil
 Additionally, the [desc](schema/objects/entities.yaml#desc) label should be avoided as an inherited file.
 One may need to use the [desc](schema/objects/entities.yaml#desc) label to contain information related or unrelated to the atlas.
 
-The `[probseg|dseg|mask|channels].tsv` file indexes and labels each node/parcel/region within the atlas.
-This file resembles the typical Look Up Table (LUT) often shared with atlases.
-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.
-Additional fields can be added with their respective definition/description in the sidecar json file.
+## Directory Structure
 
-<table>
-  <tr>
-   <td>index (or placeholder in fragment in reference)
-   </td>
-   <td>REQUIRED. (Integer) The number associated with the node/parcel/region (right/left hemispheres may be different).
-   </td>
-  </tr>
-  <tr>
-   <td>label
-   </td>
-   <td>RECOMMENDED. The node name
-   </td>
-  </tr>
-  <tr>
-   <td>network_id
-   </td>
-   <td>OPTIONAL. Network ID the node/parcel belongs to
-   </td>
-  </tr>
-  <tr>
-   <td>network_label
-   </td>
-   <td>OPTIONAL. Label of Network (for example, Dorsal Attention Network)
-   </td>
-  </tr>
-  <tr>
-   <td>coordinate_report_strategy
-   </td>
-   <td>OPTIONAL (RECOMMENDED if x, y, z keys are specified).  The strategy used to assess and report x, y and z coordinates of a given node/parcel/region. For example, "CenterOfMass".
-   </td>
-  </tr>
-  <tr>
-   <td>x
-   </td>
-   <td>OPTIONAL. The x-coordinate of the node in the spatial reference space (See SpatialReference in the .json file)
-   </td>
-  </tr>
-  <tr>
-   <td>y
-   </td>
-   <td>OPTIONAL. The y-coordinate of the node in the spatial reference space (See SpatialReference in the .json file)
-   </td>
-  </tr>
-  <tr>
-   <td>z
-   </td>
-   <td>OPTIONAL. The z-coordinate of the node in the spatial reference space (See SpatialReference in the .json file)
-   </td>
-  </tr>
-  <tr>
-   <td>hemisphere
-   </td>
-   <td>OPTIONAL. MUST BE ONE OF: "left", "right", "bilateral". Indicate whether the node/parcel/region is in the left or right hemispheres, or is available bilaterally.
-   </td>
-  </tr>
-  <tr>
-   <td>color
-   </td>
-   <td>OPTIONAL. RGB color to use for the node.
-   </td>
-  </tr>
-  <tr>
-   <td>seed
-   </td>
-   <td>OPTIONAL. Seed vertex/channel of the node/region
-   </td>
-  </tr>
-  <tr>
-   <td>region
-   </td>
-   <td>OPTIONAL. "XY", where X can be L:left, R:right, B:bilateral, and Y can be F:frontal, T:temporal, P:parietal, O:occipital
-   </td>
-  </tr>
-</table>
+An atlas can be conceptualized with three use cases in mind.
+1. Generating/Sharing an atlas to be published and used by others.
+2. Using a shared atlas and transforming it into new template spaces or subject spaces.
+3. Creating subject-specific atlases derived from the corresponding subject’s data.
 
-Example:
-```Text
-index	label	network_label	hemisphere
-1	Heschl's Gyrus	Somatomotor	left
-2	Heschl's Gyrus	Somatomotor	right
-```
+For all three use cases, a compatible directory structure is proposed that is modular
+and extensible for representing atlases in BIDS derivative datasets.
+
+
+# Reference
+
+## Files
+
+### atlas-\<label>_description.json
+
+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.
 
-The `[probseg|dseg|mask].json` file provides metadata to uniquely identify, describe and characterize the atlas, as well as give proper attribution to the creators.
-Additionally, SpatialReference serves the important purpose of unambiguously identifying the space the atlas is labeled in.
 
 <table>
   <tr>
@@ -309,18 +112,6 @@ Additionally, SpatialReference serves the important purpose of unambiguously ide
    <td>RECOMMENDED. Longform description of the atlas
    </td>
   </tr>
-  <tr>
-   <td>SpatialReference
-   </td>
-   <td>RECOMMENDED. Point to an existing atlas in a template space (URL or relative file path where this file is located).
-   </td>
-  </tr>
-  <tr>
-   <td>Resolution
-   </td>
-   <td>RECOMMENDED. Resolution atlas is provided in.
-   </td>
-  </tr>
   <tr>
    <td>Dimensions
    </td>
@@ -389,13 +180,11 @@ Additionally, SpatialReference serves the important purpose of unambiguously ide
   </tr>
 </table>
 
-
-
-Example:
+#### Example:
 
 ```JSON
 {
-  "Name": "FSL's MNI ICBM 152 non-linear 6th Generation Asymmetric Average Brain Stereotaxic Registration Model",
+  "Name": "HarvardOxford cort maxprob thr25 2mm",
   "Authors": [
     "David Kennedy",
     "Christian Haselgrove",
@@ -407,9 +196,6 @@ Example:
   ],
   "BIDSVersion": "1.1.0",
   "Curators": "FSL team",
-  "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz",
-  "Space": "MNI152NLin6Asym",
-  "Resolution": "Matched with original template resolution (2x2x3 mm^3)",
   "License": "See LICENSE file",
   "RRID": "SCR_002823",
   "ReferencesAndLinks": [
@@ -420,143 +206,343 @@ Example:
 }
 ```
 
-# BIDS-Atlas Example datasets
-Within the following, multiple examples showcasing the proposed extension are provided.
-They include BEP-specific as well as other/general BIDS files.
-
-## Atlas as dataset - single existing atlas in template space
-
-The example below illustrates how a single existing atlas in template space is represented as a dataset according to the atlas BEP.
-Specifically, the example refers to the Harvard-Oxford atlas in MN152NLin6Asym space with a resolution of 2 mm3,
-used without modifications (for example, transformations, subsetting, etc.)
-for all subjects to which the pipeline was applied.
+### atlas-\<label>_[dseg|probseg|mask].json
 
-```Text
-my_dataset/atlas-HarvardOxford/
-  atlas-HarvardOxford_res-2_dseg.json
-  atlas-HarvardOxford_res-2_dseg.nii.gz
-  atlas-HarvardOxford_res-2_dseg.tsv
-```
+This sidecar json file contains the spatial meta-data about the atlas, including the spatial reference and resolution of the atlas projected onto a template space.
 
-The content of each file is further outlined in the following,
-starting with the .json sidecar file containing meta-data about the atlas at hand.
 
-Example content of the `atlas-HarvardOxford_res-2_dseg.json` file:
+|       Name       | Description                                                                                                         |
+|:----------------:|---------------------------------------------------------------------------------------------------------------------|
+| SpatialReference | RECOMMENDED. Point to an existing atlas in a template space (url or bids URI where file is located). |
+| Resolution       | RECOMMENDED. Resolution atlas is provided in.                                                                       |
 
+#### Example:
 ```JSON
 {
-  "Authors": [
-    "David Kennedy",
-    "Christian Haselgrove",
-    "Bruce Fischl",
-    "Janis Breeze",
-    "Jean Frazie",
-    "Larry Seidman",
-    "Jill Goldstein"
-  ],
-  "BIDSVersion": "1.1.0",
-  "Curators": "FSL team",
   "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz",
-  "Space": "MNI152NLin6Asym",
-  "Resolution": "Matched with original template resolution (2x2x3 mm^3)",
-  "License": "See LICENSE file",
-    "Name": "FSL's MNI ICBM 152 non-linear 6th Generation Asymmetric Average Brain Stereotaxic Registration Model",
-  "RRID": "SCR_002823",
-  "ReferencesAndLinks": [
-    "https://doi.org/10.1016/j.neuroimage.2012.01.024",
-    "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases"
-  ],
-  "Species": "Human"
+  "Resolution": "Matched with original template resolution (2x2x3 mm^3)"
 }
 ```
 
-Next, the content of the tsv files describing the indices and corresponding labels present in the atlas at hand.
-
-Example content of the `atlas-HarvardOxford_res-2_dseg.tsv` file:
-
-```Text
-index	label	hemisphere
-0	Background	bilateral
-1	Frontal Pole	bilateral
-2
-Insular Cortex	bilateral
-3	Superior Frontal Gyrus	bilateral
-4	Middle Frontal Gyrus	bilateral
-5	Inferior Frontal Gyrus, pars triangularis	bilateral
-6	Inferior Frontal Gyrus, pars opercularis	bilateral
-```
-
-## Multiple existing atlases in template space
-The example below illustrates how multiple existing atlases in the same template space are represented according to the atlas BEP.
-Specifically, the example refers to the Harvard-Oxford, Schaefer, Yeo and MSDL atlases,
-all in MN152NLin6Asym space and with a resolution of 2 mm3,
-were utilized without modifications (for example, transformations, subsetting, etc.)
-for all subjects to which the pipeline was applied.
-Importantly, all atlas-related information is indicated via the value of the atlas- key and not via desc- to help prevent inheritance problems in subsequent steps.
-Here, this was used to indicate that the Harvard-Oxford atlas in its version with a maximum probability of 50,
-the Schaefer atlas in its 400 parcel version and the Yeo atlas in its 17 networks version were used.
-The respective information found in each file follows the example outlined in 4.1 as atlases were used independently from one another.
-
-
-```Text
-bids/atlases/
-  atlas-HarvardOxford/
-    atlas-HarvardOxford_dseg.nii.gz
-    atlas-HarvardOxford_dseg.json
-    atlas-HarvardOxford_dseg.tsv
-  atlas-Schaefer400/
-    atlas-Schaefer400_dseg.nii.gz
-    atlas-Schaefer400_dseg.json
-    atlas-Schaefer400_dseg.tsv
-  atlas-Yeo17/
-    atlas-Yeo17_dseg.nii.gz
-    atlas-Yeo17_dseg.json
-    atlas-Yeo17_dseg.tsv
-  atlas-msdl/
-    atlas-msdl_probseg.nii.gz
-    atlas-msdl_probseg.json
-    atlas-msdl_probseg.tsv
-```
- 
-## Single existing atlas transformed to subject space
-The example below illustrates how a single existing atlas transformed into a subject’s native space space is represented according to the atlas BEP.
-Specifically, the example refers to the Harvard-Oxford atlas with a resolution of 2 mm3 that was transformed from the MN152NLin6Asym template space to a given subject’s native T1w space.
-While the original atlas-related files remain as outlined in the use case in template space,
-the spatially transformed version of the nii.gz atlas file will be placed within a given subjects directory.
-The precise location within the latter depends on the modality space to which the atlas was transformed to,
-for example, anat, func or dwi.
-The same location furthermore entails a corresponding json file outlining further information on the source atlas and applied transformation(s).
+### atlas-\<label>_[dseg|probseg|mask].tsv
 
+The `[probseg|dseg|mask|channels].tsv` file indexes and labels each node/parcel/region within the atlas.
+This file resembles the typical Look Up Table (LUT) often shared with atlases.
+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.
+Additional fields can be added with their respective definition/description in the sidecar json file.
+This file is not applicable for quantitative maps.
 
-```Text
-bids/atlases/atlas-HarvardOxford/
-  atlas-HarvardOxford_dseg.json
-  atlas-HarvardOxford_dseg.tsv
-  atlas-HavardOxford2_dseg.nii.gz
-bids/derivatives/pipeline-<name>/
+<table>
+  <tr>
+   <td>index (or placeholder in fragment in reference)
+   </td>
+   <td>REQUIRED. (Integer) The number associated with the node/parcel/region (right/left hemispheres may be different).
+   </td>
+  </tr>
+  <tr>
+   <td>label
+   </td>
+   <td>RECOMMENDED. The node name
+   </td>
+  </tr>
+  <tr>
+   <td>network_id
+   </td>
+   <td>OPTIONAL. Network ID the node/parcel belongs to
+   </td>
+  </tr>
+  <tr>
+   <td>network_label
+   </td>
+   <td>OPTIONAL. Label of Network (for example, Dorsal Attention Network)
+   </td>
+  </tr>
+  <tr>
+   <td>coordinate_report_strategy
+   </td>
+   <td>OPTIONAL (RECOMMENDED if x, y, z keys are specified).  The strategy used to assess and report x, y and z coordinates of a given node/parcel/region. For example, "CenterOfMass".
+   </td>
+  </tr>
+  <tr>
+   <td>x
+   </td>
+   <td>OPTIONAL. The x-coordinate of the node in the spatial reference space (See SpatialReference in the sidecar json file)
+   </td>
+  </tr>
+  <tr>
+   <td>y
+   </td>
+   <td>OPTIONAL. The y-coordinate of the node in the spatial reference space (See SpatialReference in the sidecar json file)
+   </td>
+  </tr>
+  <tr>
+   <td>z
+   </td>
+   <td>OPTIONAL. The z-coordinate of the node in the spatial reference space (See SpatialReference in the sidecar json file)
+   </td>
+  </tr>
+  <tr>
+   <td>hemisphere
+   </td>
+   <td>OPTIONAL. MUST BE ONE OF: "left", "right", "bilateral". Indicate whether the node/parcel/region is in the left or right hemispheres, or is available bilaterally.
+   </td>
+  </tr>
+  <tr>
+   <td>color
+   </td>
+   <td>OPTIONAL. RGB color to use for the node.
+   </td>
+  </tr>
+  <tr>
+   <td>seed
+   </td>
+   <td>OPTIONAL. Seed vertex/channel of the node/region
+   </td>
+  </tr>
+  <tr>
+   <td>region
+   </td>
+   <td>OPTIONAL. "XY", where X can be L:left, R:right, B:bilateral, and Y can be F:frontal, T:temporal, P:parietal, O:occipital
+   </td>
+  </tr>
+</table>
+
+#### Example:
+```Text
+index	label	network_label	hemisphere
+1	Heschl's Gyrus	Somatomotor	left
+2	Heschl's Gyrus	Somatomotor	right
+```
+
+## Directory Structure
+
+```Text
+<dataset>/derivatives/atlas-<label>
+  atlas-<label>_description.json
+  atlas-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+  atlas-<label>_[dseg|probseg|mask].tsv
+  atlas-<label>_[dseg|probseg|mask].json
+  sub-<label>/...
+    sub-<label>_space-<label>_seg-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+    sub-<label>_space-<label>_seg-<label>_[dseg|probseg|mask].tsv
+    sub-<label>_space-<label>_seg-<label>_[dseg|probseg|mask].json
+```
+
+# How to use BIDS-Atlas
+
+Below are a collection of exemplary use cases that illustrate how to use the BIDS-Atlas extension.
+
+## Sharing an atlas
+
+The example below illustrates how a single existing atlas in template space is represented as a dataset according to the atlas BEP.
+Specifically, the example refers to the Harvard-Oxford atlas in MN152NLin6Asym space with a resolution of 2 mm3,
+used without modifications (for example, transformations, subsetting, etc.)
+for all subjects to which the pipeline was applied.
+
+```Text
+my_dataset/derivatives/atlas-HarvardOxford/
+  atlas-HarvardOxford_description.json
+  atlas-HarvardOxford_res-2_dseg.json
+  atlas-HarvardOxford_res-2_dseg.nii.gz
+  atlas-HarvardOxford_res-2_dseg.tsv
+```
+
+The content of each file is further outlined in the following,
+starting with the .json sidecar file containing meta-data about the atlas at hand.
+
+Example content of the `atlas-HarvardOxford_description.json` file:
+
+```JSON
+{
+  "Name": "HarvardOxford cort maxprob thr25 2mm",,
+  "Authors": [
+    "David Kennedy",
+    "Christian Haselgrove",
+    "Bruce Fischl",
+    "Janis Breeze",
+    "Jean Frazie",
+    "Larry Seidman",
+    "Jill Goldstein"
+  ],
+  "BIDSVersion": "1.1.0",
+  "Curators": "FSL team",
+  "License": "See LICENSE file",
+  "RRID": "SCR_002823",
+  "ReferencesAndLinks": [
+    "https://doi.org/10.1016/j.neuroimage.2012.01.024",
+    "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases"
+  ],
+  "Species": "Human"
+}
+```
+
+Example content of the `atlas-HarvardOxford_res-2_dseg.json` file:
+
+```JSON
+{
+  "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz",
+  "Resolution": "Matched with original template resolution (2x2x3 mm^3)"
+}
+```
+
+Next, the content of the tsv files describing the indices and corresponding labels present in the atlas at hand.
+
+Example content of the `atlas-HarvardOxford_res-2_dseg.tsv` file:
+
+```Text
+index	label	hemisphere
+0	Background	bilateral
+1	Frontal Pole	bilateral
+2 Insular Cortex	bilateral
+3	Superior Frontal Gyrus	bilateral
+4	Middle Frontal Gyrus	bilateral
+5	Inferior Frontal Gyrus, pars triangularis	bilateral
+6	Inferior Frontal Gyrus, pars opercularis	bilateral
+```
+
+If the atlas was projected into multiple resolutions, for example, 1 mm3, 2 mm3, and 3 mm3, this could be described with a sidecar and nifti file for each resolution.
+
+
+```Text
+my_dataset/derivatives/atlas-HarvardOxford/
+  atlas-HarvardOxford_description.json
+  atlas-HarvardOxford_dseg.tsv
+  atlas-HarvardOxford_res-1_dseg.json
+  atlas-HarvardOxford_res-2_dseg.nii.gz
+  atlas-HarvardOxford_res-2_dseg.json
+  atlas-HarvardOxford_res-2_dseg.nii.gz
+  atlas-HarvardOxford_res-3_dseg.json
+  atlas-HarvardOxford_res-3_dseg.nii.gz
+```
+
+Here the tsv file would be applicable to all resolutions, while the json and nii.gz files would be specific to each resolution.
+For certain atlases, the resolution may be coarse enough such that certain nodes are not present in the atlas.
+In such cases, a unique tsv could be defined for each resolution, removing the rows
+that are not present in the atlas at that resolution.
+
+```Text
+my_dataset/derivatives/atlas-HarvardOxford/
+  atlas-HarvardOxford_description.json
+  atlas-HarvardOxford_res-1_dseg.tsv
+  atlas-HarvardOxford_res-1_dseg.json
+  atlas-HarvardOxford_res-2_dseg.nii.gz
+  atlas-HarvardOxford_res-1_dseg.tsv
+  atlas-HarvardOxford_res-2_dseg.json
+  atlas-HarvardOxford_res-2_dseg.nii.gz
+  atlas-HarvardOxford_res-1_dseg.tsv
+  atlas-HarvardOxford_res-3_dseg.json
+  atlas-HarvardOxford_res-3_dseg.nii.gz
+```
+
+## Same Atlas projected into multiple Template spaces
+
+```Text
+bids/
+  derivatives/
+    atlas-AAL/
+      dataset_description.json
+      atlas-AAL_description.json
+      atlas-AAL_dseg.tsv
+      atlas-AAL_space-MNI152NLin6Asym_dseg.json
+      atlas-AAL_space-MNI152NLin6Asym_dseg.nii.gz
+      atlas-AAL_space-MNI305Lin_dseg.json
+      atlas-AAL_space-MNI305Lin_dseg.nii.gz
+```
+
+## Transforming an Atlas to subject space
+
+The example below illustrates how a single existing atlas transformed into a subject’s native space space is represented according to the atlas BEP.
+Specifically, the example refers to the Harvard-Oxford atlas with a resolution of 2 mm3 that was transformed from the MN152NLin6Asym template space to a given subject’s native T1w space.
+While the original atlas-related files remain as outlined in the use case in template space,
+the spatially transformed version of the nii.gz atlas file will be placed within a given subjects directory.
+The precise location within the latter depends on the modality space to which the atlas was transformed to,
+for example, anat, func or dwi.
+The same location furthermore entails a corresponding json file outlining further information on the source atlas and applied transformation(s).
+
+
+```Text
+bids/derivatives/pipeline-test/
+  atlas-HarvardOxfordThr50_description.json
+  atlas-HarvardOxfordThr50_dseg.json
+  atlas-HarvardOxfordThr50_dseg.tsv
+  atlas-HavardOxfordThr50_dseg.nii.gz
   sub-01/
     anat/
       sub-01_T1w.nii.gz
-      sub-01_space-T1w_seg-HarvardOxfordThr50_res-2_dseg.nii.gz
-      sub-01_space-T1w_seg-HarvardOxfordThr50_res-2_dseg.json
-      sub-01_space-T1w_seg-HarvardOxfordThr50_res-2_dseg.tsv
+      sub-01_space-T1w_res-1_seg-HarvardOxfordThr50_dseg.nii.gz
+      sub-01_space-T1w_res-1_seg-HarvardOxfordThr50_dseg.json
+      sub-01_space-T1w_res-1_seg-HarvardOxfordThr50_dseg.tsv
 ```
 
 The json file accompanying the transformed atlas should include the following information.
 
-Example content of the `sub-01_space-T1w_seg-HarvardOxford_res-2_dseg.json` file:
+Example content of the `sub-01_space-T1w_res-1_seg-HarvardOxford_dseg.json` file:
 
 ```JSON
 {
-  "BIDSVersion": "1.1.0",
   "SpatialReference": "sub-01/anat/sub-01_T1w.nii.gz",
-  "Space": "T1w",
   "Resolution": "Matched with original resolution in subject T1w space (1x1x1 mm^3)",
-  "Sources": [],
-  "transformation":
 }
 ```
 
+## Multiple Atlases in the same space
+
+The example below illustrates how multiple existing atlases in the same template space are represented according to the atlas BEP.
+Specifically, the example refers to the Harvard-Oxford, Schaefer, Yeo and MSDL atlases,
+all in MN152NLin6Asym space and with a resolution of 2 mm3, and this information
+is represented in the sidecar `_dseg.json` file.
+Importantly, all atlas-related information is indicated via the value of the atlas- key and not via desc- to help prevent inheritance problems in subsequent steps.
+Here, the `atlas` entity was used to indicate that the Harvard-Oxford atlas in its version with a maximum probability of 50,
+the Schaefer atlas in its 400 parcel version and the Yeo atlas in its 17 networks version were used.
+Below, each of the atlases are given their own derivative dataset.
+
+```Text
+bids/derivatives/
+  atlas-HarvardOxford50thr/
+    atlas-HarvardOxford50thr_description.json
+    atlas-HarvardOxford50thr_dseg.nii.gz
+    atlas-HarvardOxford50thr_dseg.json
+    atlas-HarvardOxford50thr_dseg.tsv
+  atlas-Schaefer400/
+    atlas-Schaefer400_description.json
+    atlas-Schaefer400_dseg.nii.gz
+    atlas-Schaefer400_dseg.json
+    atlas-Schaefer400_dseg.tsv
+  atlas-Yeo17/
+    atlas-Yeo17_description.json
+    atlas-Yeo17_dseg.nii.gz
+    atlas-Yeo17_dseg.json
+    atlas-Yeo17_dseg.tsv
+  atlas-msdl/
+    atlas-msdl_description.json
+    atlas-msdl_probseg.nii.gz
+    atlas-msdl_probseg.json
+    atlas-msdl_probseg.tsv
+```
+
+Or they could all be represented in the same directory:
+
+```Text
+bids/derivatives/
+  atlas-HarvardOxford50thr_description.json
+  atlas-HarvardOxford50thr_dseg.nii.gz
+  atlas-HarvardOxford50thr_dseg.json
+  atlas-HarvardOxford50thr_dseg.tsv
+  atlas-Schaefer400_description.json
+  atlas-Schaefer400_dseg.nii.gz
+  atlas-Schaefer400_dseg.json
+  atlas-Schaefer400_dseg.tsv
+  atlas-Yeo17_description.json
+  atlas-Yeo17_dseg.nii.gz
+  atlas-Yeo17_dseg.json
+  atlas-Yeo17_dseg.tsv
+  atlas-msdl_description.json
+  atlas-msdl_probseg.nii.gz
+  atlas-msdl_probseg.json
+  atlas-msdl_probseg.tsv
+```
+
 ##  MyConnectome example
 
 The example below illustrates how two atlases,
@@ -569,42 +555,67 @@ the individual parcellation in FS_lr space will be placed only within a given su
 The same location furthermore entails a corresponding json file outlining further information on the atlas and applied analysis to obtain it.
 
 ```Text
-bids/atlases/atlas-FreeSurferASEG/
-  atlas-FreeSurferASEG_dseg.json
-  atlas-FreeSurferASEG_dseg.tsv
-  atlas-FreeSurferASEG_dseg.nii.gz
+bids/
+  sub-01/
+    anat/
+      sub-01_T1w.nii.gz
 
 bids/derivatives/pipeline-<name>/
+  atlas-Russome_description.json
+  atlas-FreeSurferASEG_description.json
   sub-01/
     anat/
-      sub-01_space-T1w_seg-FreeSurferASEG_res-2_dseg.nii.gz
-      sub-01_space-T1w_seg-FreeSurferASEG_res-2_dseg.json
-      sub-01_space-T1w_seg-FreeSurferASEG_res-2_dseg.tsv
+      sub-01_T1w.nii.gz
+      sub-01_space-T1w_res-2_seg-FreeSurferASEG_dseg.nii.gz
+      sub-01_space-T1w_res-2_seg-FreeSurferASEG_dseg.json
+      sub-01_space-T1w_res-2_seg-FreeSurferASEG_dseg.tsv
     func/
-      sub-01_space-FSlr_seg-Russome_res-2_dseg.nii.gz
-      sub-01_space-FSlr_seg-Russome_res-2_dseg.json
-      sub-01_space-FSlr_seg-Russome_res-2_dseg.tsv
+      sub-01_space-FSLr_res-2_seg-Russome_dseg.nii.gz
+      sub-01_space-FSLr_res-2_seg-Russome_dseg.json
+      sub-01_space-FSLr_res-2_seg-Russome_dseg.tsv
 ```
 
 The json file accompanying the functionally derived atlas should include the following information.
 
-Example content of the `sub-01_task-rest_atlas.json` file contains top-level metadata about the atlas:
+Example content of the `atlas-FreeSurferASEG_description.json` file contains top-level metadata about the atlas:
 
 ```JSON
 
-"Atlas":
 {
-  "Russome":
-  {
-    "Atlasfile": "/link/to/russome/file",
-    "Extra": "individualized surface parcellation"
-  },
-  "FS_aseg": {
-    "Atlasfile": "/link/to/aseg/file",
-    "Extra": "freesurfer aseg"
-  }
+  "Name": "FreeSurferASEG",,
+  "Authors": [
+    "Bruce Fischl",
+    "David H. Salat",
+    "Evelina Busa",
+    "Marilyn Albert",
+    "Megan Dieterich",
+    "Christian Haselgrove",
+    "Andre van der Kouwe",
+    "Ron Killiany",
+    "David Kennedy",
+    "Shuna Klaveness",
+    "Albert Montillo",
+    "Nikos Makris",
+    "Bruce Rosen",
+    "Anders M. Dale",
+  ],
+  "BIDSVersion": "1.1.0",
+  "License": "See LICENSE file",
+  "ReferencesAndLinks": [
+    "https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferVersion3",
+    "https://surfer.nmr.mgh.harvard.edu/ftp/articles/fischl02-labeling.pdf",
+  ],
+  "Species": "Human"
 }
+```
 
+This is what is contained in the `sub-01_space-T1w_res-2_seg-FreeSurferASEG_dseg.json` file:
+
+```JSON
+{
+  "SpatialReference": "bids:sub-01/anat/sub-01_T1w.nii.gz",
+  "Resolution": "Matched with original template resolution (2x2x3 mm^3)",
+}
 ```
 
 ## Quantitative atlas examples
@@ -626,7 +637,8 @@ The dataset can be found [here](https://openneuro.org/datasets/ds004401/versions
 Example directory content for a quantitative atlas that provides values at all voxels and/or vertices:
 
 ```Text
-bids/atlas/atlas-ps13/
+bids/derivatives/atlas-ps13/
+    atlas-ps13_description.json
     atlas-ps13_space-fsaverage_hemi-L_stat-mean_meas-VT_mimap.json
     atlas-ps13_space-fsaverage_hemi-L_stat-mean_meas-VT_mimap.nii.gz
     atlas-ps13_space-fsaverage_hemi-R_stat-mean_meas-VT_mimap.json
@@ -647,26 +659,459 @@ Example directory content for a quantitative atlas that provides values for cert
 in this case defined by the AAL atlas:
 
 ```Text
-bids/atlas/
-  atlas-mni305/
-    atlas-aparc.DKTatlas+aseg.mgz
-    atlas-aparc.DKTatlas+aseg.tsv
-    atlas-RB_all_2008-03-26.probseg.gca
-    atlas-RB_all_2008-03-26.probseg.tsv
-  atlas-ps13/
-    atlas-ps13_space-fsaverage_hemi-L_stat-mean_meas-VT_seg-AAL_mimap.json
-    atlas-ps13_space-fsaverage-hemi-L_stat-mean_meas-VT_seg-AAL_mimap.tsv
-    atlas-ps13_space-fsaverage-hemi-L_stat-std_meas-VT_seg-AAL_mimap.json
-    atlas-ps13_space-fsaverage-hemi-L_stat-std_meas-VT_seg-AAL_mimap.tsv
-    atlas-ps13_space-fsaverage-hemi-R_stat-mean_meas-VT_seg-AAL_mimap.json
-    atlas-ps13_space-fsaverage-hemi-R_stat-mean_meas-VT_seg-AAL_mimap.tsv
-    atlas-ps13_space-fsaverage-hemi-R_stat-std_meas-VT_seg-AAL_mimap.json
-    atlas-ps13_space-fsaverage-hemi-R_stat-std_meas-VT_seg-AAL_mimap.tsv
-    atlas-ps13_space-MNI305Lin_res-2_stat-mean_meas-VT_seg-AAL_mimap.json
-    atlas-ps13_space-MNI305Lin_res-2_stat-mean_meas-VT_seg-AAL_mimap.tsv
-    atlas-ps13_space-MNI305Lin_res-2_stat-std_meas-VT_seg-AAL_mimap.json
-    atlas-ps13_space-MNI305Lin_res-2_stat-std_meas-VT_seg-AAL_mimap.tsv
+bids/derivatives/atlas/
+  atlas-aparc.DKTatlas+aseg.mgz  # need to figure out how to represent this
+  atlas-aparc.DKTatlas+aseg.tsv   # need to figure out how to represent this
+  atlas-RB_all_2008-03-26.probseg.gca   # need to figure out how to represent this
+  atlas-RB_all_2008-03-26.probseg.tsv   # need to figure out how to represent this
+  atlas-ps13_description.json
+  atlas-ps13_space-fsaverage_hemi-L_stat-mean_meas-VT_seg-AAL_mimap.json # should not have seg and atlas in the same filename
+  atlas-ps13_space-fsaverage-hemi-L_stat-mean_meas-VT_seg-AAL_mimap.tsv
+  atlas-ps13_space-fsaverage-hemi-L_stat-std_meas-VT_seg-AAL_mimap.json
+  atlas-ps13_space-fsaverage-hemi-L_stat-std_meas-VT_seg-AAL_mimap.tsv
+  atlas-ps13_space-fsaverage-hemi-R_stat-mean_meas-VT_seg-AAL_mimap.json
+  atlas-ps13_space-fsaverage-hemi-R_stat-mean_meas-VT_seg-AAL_mimap.tsv
+  atlas-ps13_space-fsaverage-hemi-R_stat-std_meas-VT_seg-AAL_mimap.json
+  atlas-ps13_space-fsaverage-hemi-R_stat-std_meas-VT_seg-AAL_mimap.tsv
+  atlas-ps13_space-MNI305Lin_res-2_stat-mean_meas-VT_seg-AAL_mimap.json
+  atlas-ps13_space-MNI305Lin_res-2_stat-mean_meas-VT_seg-AAL_mimap.tsv
+  atlas-ps13_space-MNI305Lin_res-2_stat-std_meas-VT_seg-AAL_mimap.json
+  atlas-ps13_space-MNI305Lin_res-2_stat-std_meas-VT_seg-AAL_mimap.tsv
 ```
 
 Note that there is no image file present in a regional quantitative atlas.
-The json file accompanying the quantitative atlas should include the information as in [Single existing atlas in template space](#_Single_existing_atlas_in_template_space).
+The `atlas-<label>_description.json` file accompanying the quantitative atlas should include the information as in [Single existing atlas in template space](#_Single_existing_atlas_in_template_space).
+
+
+## FAQ
+
+### How should I use the _desc- entity?
+
+The usage of [_desc-](schema/objects/entities.yaml#desc) is generally discouraged but should be evaluated on a case by case basis in order to keep this identifier available for necessary cases.
+Specifically, this refers to the atlas at hand and potential different versions thereof.
+As a rule of thumb, BIDS-Atlas proposed to evaluate and consider how many versions across how many levels of versions an atlas is (commonly) provided and used in.
+If there is only one version, as in "release", of an atlas
+and no sub-versions, as in "different parcel numbers" (or comparable),
+[_desc-](schema/objects/entities.yaml#desc) is most likely not expected and/or required.
+An example for [_desc-](schema/objects/entities.yaml#desc) in such a use case would be
+to indicate a subset of parcels and would entail the addition of
+the [_mask-](schema/objects/entities.yaml#mask) extension,
+for example, providing/using the "postcentral gyrus" region of the [Destrieux atlas](doi:10.1093/cercor/bhg087.) would result in the following file name:
+`atlas-Destrieux_space-MNI152NLin6Asym_res-2_desc-PostCentralGyrus_mask.nii.gz`.
+Similar to the above case, if there are multiple versions, as in "release",
+of an atlas and no sub-versions, as in "different parcel numbers" (or comparable),
+[_desc-](schema/objects/entities.yaml#desc) is also most likely not expected and/or required,
+as the version(s) (release(s)) should be indicated via `atlas-`.
+For example, the different versions of the [AAL parcellation](http://www.gin.cnrs.fr/AAL-217?lang=en)
+would result in the following file names:
+`atlas-AAL1_space-MNI152NLin6Asym_res-2.nii.gz`, `atlas-AAL2_space-MNI152NLin6Asym_res-2.nii.gz` and `atlas-AAL3_space-MNI152NLin6Asym_res-2.nii.gz`.
+Given an atlas has only one version, as in "release", and multiple sub-versions
+as in "different parcel numbers" (or comparable)
+[_desc-](schema/objects/entities.yaml#desc) is considered appropriate.
+For example, when indicating information pertaining to the probabilistic nature of an atlas
+such as the [_probseg](schema/objects/entities.yaml#probseg) version of
+the [Harvard-Oxford parcellation](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases):
+`atlas-HarvardOxford_res-2_desc-th25_probseg.nii.gz`.
+In cases where an atlas has multiple versions, as in "release", and sub-versions,
+as in "different parcel numbers" (or comparable),
+the version(s) (release(s)) should be indicated via `atlas-` as outlined above and the sub-versions should be indicated via [_desc-](schema/objects/entities.yaml#desc).
+For example, different versions and sub-versions of the [Schaefer parcellation](https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Parcellations/Updates/Update_20190916_README.md) would be denoted as follows:
+`atlas-Schaefer2018_space-MNI152NLin6Asym_res-2_desc-400Parcels7Networks.nii.gz`,
+`atlas-Schaefer2018_space-MNI152NLin6Asym_res-2_desc-400Parcels17Networks.nii.gz`,
+`atlas-Schaefer2022_space-MNI152NLin6Asym_res-2_desc-800Parcels7Networks.nii.gz`
+and `atlas-Schaefer2022_space-MNI152NLin6Asym_res-2_desc-800Parcels17Networks.nii.gz`.
+
+Importantly, already existing BIDS entities should be used to indicate certain aspects of an atlas,
+instead of [_desc-](schema/objects/entities.yaml#desc), for example,
+[hemi](schema/objects/entities.yaml#hemi) to denote a given hemisphere
+and [_dseg](schema/objects/entities.yaml#dseg)/[_probseg](schema/objects/entities.yaml#probseg)
+to denote deterministic and probabilistic atlases respectively.
+
+However, as mentioned above, these are general guidelines and the exact implementation should be evaluated on a case by case basis, with deviations following common BIDS principles being permitted.
+
+
+# TO BE DELETED
+
+### Each atlas gets its own derivative directory
+```Text
+bids/
+  derivatives/
+    atlas-AAL/
+      dataset_description.json
+      atlas-AAL_description.json
+      atlas-AAL_dseg.tsv
+      atlas-AAL_dseg.json
+      atlas-AAL_dseg.nii.gz
+    atlas-Destrieux/
+      dataset_description.json
+      atlas-Destrieux_description.json
+      atlas-Destrieux_dseg.tsv
+      atlas-Destrieux_dseg.json
+      atlas-Destrieux_dseg.nii.gz
+```
+
+### Multiple atlases in the same directory
+
+```Text
+bids/
+  derivatives/
+    atlasRepository/
+      dataset_description.json
+      atlas-AAL_description.json
+      atlas-AAL_dseg.tsv
+      atlas-AAL_dseg.json
+      atlas-AAL_dseg.nii.gz
+      atlas-Destrieux_description.json
+      atlas-Destrieux_dseg.tsv
+      atlas-Destrieux_dseg.json
+      atlas-Destrieux_dseg.nii.gz
+```
+
+### Multiple atlases in subdirectories in the same derivative dataset
+
+```Text
+bids/
+  derivatives/
+    AtlasRepository/
+      dataset_description.json
+      atlas-AAL/
+        atlas-AAL_description.json
+        atlas-AAL_dseg.tsv
+        atlas-AAL_dseg.json
+        atlas-AAL_dseg.nii.gz
+      atlas-Destrieux/
+        atlas-Destrieux_description.json
+        atlas-Destrieux_dseg.tsv
+        atlas-Destrieux_dseg.json
+        atlas-Destrieux_dseg.nii.gz
+```
+
+
+## I want to transform/resample a public atlas onto subject specific space(s)
+
+This is a use case where a publicly available/previously generated atlas is transformed/resampled into subject spaces.
+In this example, the referenced atlas is also in derivatives, but it could
+also be an external link.
+
+### Filesystem
+
+```Text
+bids/
+  sub-01/
+    anat/
+      sub-01_T1w.nii.gz
+  derivatives/
+    atlas-MyNewAtlas/
+      atlas-MyNewAtlas_description.json
+      atlas-MyNewAtlas_dseg.tsv
+      atlas-MyNewAtlas_dseg.json
+      atlas-MyNewAtlas_dseg.nii.gz
+    resampleAtlasToSubjects/
+      seg-MyNewAtlas_dseg.json  # recommended
+      seg-MyNewAtlas_dseg.tsv  # optional
+      sub-01/
+        func/
+          sub-01_space-T1w_seg-MyNewAtlas_dseg.nii.gz
+          sub-01_space-T1w_seg-MyNewAtlas_dseg.tsv  # optional
+          sub-01_space-T1w_seg-MyNewAtlas_dseg.json  # optional
+```
+
+### atlas-MyNewAtlas/atlas-MyNewAtlas_description.json (Required)
+
+```JSON
+{
+  "Name": "MyNewAtlas",
+  "Authors": [
+    "John Doe",
+    "Jane Doe"
+  ]
+}
+```
+
+### atlas-MyNewAtlas/atlas-MyNewAtlas_dseg.tsv (Required)
+
+In the original atlas, the index/label information is stored in a tsv file.
+
+| Index | Label       |
+|:-----:|-------------|
+| 1     | amygdala    |
+| 2     | hippocampus |
+
+### atlas-MyNewAtlas/atlas-MyNewAtlas_dseg.json (Required)
+
+```JSON
+{
+  "SpatialReference": "https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym_res-02_T1w.nii.gz",
+  "Resolution": "Matched with original template resolution (2x2x2 mm^3)"
+}
+```
+
+### atlas-MyNewAtlas/atlas-MyNewAtlas_dseg.nii.gz (Required)
+
+The actual atlas that contains the value 1 for voxels
+in the amygdala and 2 for voxel in the hippocampus.
+
+### resampleAtlasToSubjects/seg-MyNewAtlas_dseg.json (Recommended)
+
+Having sources here helps to keep track of the original atlas used to generate the subject-specific atlases.
+This could be defined in the subject directories, but it is more efficient to define it at the top level.
+
+```JSON
+{
+  "Sources": [
+     "atlas-MyNewAtlas:atlas-MyNewAtlas_dseg.nii.gz",
+  ]
+}
+```
+
+### resampleAtlasToSubjects/seg-MyNewAtlas_dseg.tsv (Optional)
+
+In the applied the index/label information is stored in a tsv file,
+this could differ from the original atlas, but will generally be the same.
+
+| Index | Label       |
+|:-----:|-------------|
+| 1     | amygdala    |
+| 2     | hippocampus |
+
+### resampleAtlasToSubjects/sub-01/func/sub-01_space-T1w_seg-MyNewAtlas_dseg.tsv (Optional)
+
+For this subject, the resampling/transformation result in the elimination of the
+hippocampus, either because of a lesion or from the resolution of the space
+being resampled into.
+
+| Index | Label       |
+|:-----:|-------------|
+| 1     | amygdala    |
+
+
+### resampleAtlasToSubjects/sub-01/func/sub-01_space-T1w_seg-MyNewAtlas_dseg.json (Recommended)
+
+This defines the spatial reference of the atlas in subject space.
+This is important for understanding the spatial relationship between the atlas and the subject data.
+
+```JSON
+  {
+    "SpatialReference": "bids:sub-01/anat/sub-01_T1w.nii.gz",
+    "Resolution": "Matched with original anat resolution (1x1x1 mm^3)"
+  }
+```
+## Case N/A: Using a public atlas with my subject data resampled into the atlas template space
+
+The same file from the public atlas can already be applied to the subject data, no need to transform/resample the atlas into subject specific directories.
+
+## I want to transform/resample a shared/public atlas into new template space
+
+When you are extending an atlas to include other spaces and you are not the
+owner/curator of the atlas and cannot modify the original atlas,
+you will likely copy the `.tsv` and `_description.json` files
+from the original atlas for re-use.
+
+### FileSystem
+
+```Text
+  derivatives/
+    atlas-ExtendedAtlas/
+      atlas-ExtendedAtlas_description.json
+      atlas-ExtendedAtlas_dseg.tsv
+      atlas-ExtendedAtlas_space-Tal_dseg.json
+      atlas-ExtendedAtlas_space-Tal_dseg.nii.gz
+      atlas-ExtendedAtlas_space-MNINew_dseg.json
+      atlas-ExtendedAtlas_space-MNINew_dseg.nii.gz
+```
+
+### atlas-ExtendedAtlas/atlas-ExtendedAtlas_description.json (Required)
+
+```JSON
+{
+  "Name": "ExtendedAtlas",
+  "Authors": [
+    "John Doe",
+    "Jane Doe"
+  ]
+}
+```
+
+### atlas-ExtendedAtlas_dseg.tsv (Required)
+
+| Index | Label       |
+|:-----:|-------------|
+| 1     | amygdala    |
+| 2     | hippocampus |
+
+### atlas-ExtendedAtlas_space-Tal_dseg.json (Required)
+
+```JSON
+{
+  "SpatialReference": "URI/URL to Talairach space",
+  "Resolution": "Matched with original template resolution (2x2x2 mm^3)",
+  "Sources": [
+    "URI/URL to original atlas in original space"
+  ]
+}
+```
+
+### atlas-ExtendedAtlas_space-Tal_dseg.nii.gz (Required)
+
+The actual atlas transformed into Talairach space.
+
+
+### atlas-ExtendedAtlas_space-MNINew_dseg.json (Required)
+
+```JSON
+{
+  "SpatialReference": "URI to MNI1New space",
+  "Resolution": "Matched with original template resolution (2x2x2 mm^3)",
+  "Sources": [
+    "URI/URL to original atlas in original space"
+  ]
+}
+```
+
+### atlas-ExtendedAtlas_space-MNINew_dseg.nii.gz (Required)
+
+The actual atlas transformed into MNINew space.
+
+## I want to create subject specific atlases derived from subject specific data
+
+The `seg-individualConnectome.json` will typically be the same for all subjects if the
+process for generating the atlas is the same for all subjects.
+
+```Text
+bids/
+  derivatives/
+    subjectAtlases/
+      seg-individualConnectome_dseg.json # recommended
+      seg-individualConnectome_dseg.tsv
+  sub-01/
+    func/
+      sub-01_space-orig_seg-individualConnectome_dseg.nii.gz
+      sub-01_space-orig_seg-individualConnectome_dseg.tsv
+      sub-01_space-orig_seg-individualConnectome_dseg.json
+  sub-02/
+    func/
+      sub-02_space-orig_seg-individualConnectome_dseg.nii.gz
+      sub-02_space-orig_seg-individualConnectome_dseg.tsv
+      sub-02_space-orig_seg-individualConnectome_dseg.json
+
+```
+
+### Case 1: sharing atlas(es) to be used by others
+
+In the simplest case, there are four files for each atlas.
+`atlas-<label>_description.json` contains metadata about the atlas, `atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv` contains the index/label information for the atlas, and `atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].json` contains spatial information about the atlas file
+projected/transformed into a template space.
+If the atlas is projected/transformed into multiple spaces, generally the same `atlas-<label>_description.json` file is used for all spaces, but the sidecar
+.json files are specific to each space.
+If there are a number of atlases to share that cannot be differentiated by the available entities (`space`, `res`, `desc`, etc.) and suffixes/extensions then
+each atlas may have its own directory, or be represented in a single directory with a unique identifier for each atlas.
+
+#### Each atlas gets its own derivative directory
+```Text
+<dataset>/
+  derivatives/
+    <pipeline1>/
+      atlas-<label>_description.json
+      atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
+      atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].json
+      atlas-<label>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+    <pipeline2>/
+      atlas-<label>_description.json
+      atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
+      atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].json
+      atlas-<label>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+```
+
+#### Multiple atlases in the same directory
+```Text
+<dataset>/
+  derivatives/
+    <pipeline1>/
+      atlas-<label1>_description.json
+      atlas-<label1>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
+      atlas-<label1>_space-<label>_desc-<label>_[dseg|probseg|mask].json
+      atlas-<label1>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+      atlas-<label2>_description.json
+      atlas-<label2>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
+      atlas-<label2>_space-<label>_desc-<label>_[dseg|probseg|mask].json
+      atlas-<label2>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+```
+
+#### Multiple atlases in subdirectories in the same derivative dataset
+
+```Text
+<dataset>/
+  derivatives/
+    <pipeline1>/
+      atlas-<label1>/
+        atlas-<label1>_description.json
+        atlas-<label1>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
+        atlas-<label1>_space-<label>_desc-<label>_[dseg|probseg|mask].json
+        atlas-<label1>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+      atlas-<label2>/
+        atlas-<label2>_description.json
+        atlas-<label2>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
+        atlas-<label2>_space-<label>_desc-<label>_[dseg|probseg|mask].json
+        atlas-<label2>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+```
+
+#### Same atlas projected into multiple template spaces
+
+```Text
+<dataset>/
+  derivatives/
+    <pipeline1>/
+      atlas-<label>_description.json
+      atlas-<label>_space-<space1label>_desc-<label>_[dseg|probseg|mask].tsv
+      atlas-<label>_space-<space1label1>_desc-<label>_[dseg|probseg|mask].json
+      atlas-<label>_space-<space1label1>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+      atlas-<label>_space-<space2label>_desc-<label>_[dseg|probseg|mask].tsv
+      atlas-<label>_space-<space2label>_desc-<label>_[dseg|probseg|mask].json
+      atlas-<label>_space-<space2label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+```
+
+### Case 2: using a shared atlas to transform/resample into subject spaces
+
+This is a typical use case where a publicly available/previously generated atlas is transformed/resampled into subject spaces.
+
+
+```Text
+<dataset>/
+  derivatives/
+    <pipeline1>/
+      atlas-<label>_description.json
+      atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].tsv
+      atlas-<label>_space-<label>_desc-<label>_[dseg|probseg|mask].json
+      atlas-<label>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]
+    <pipeline2>/
+      seg-<label>_[dseg|probseg|mask].json # {"Sources": ["derivatives/pipeline1:atlas-<label>_space-<label>[_desc-<label>]_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii][.gz]"]}
+      seg-<label>_[dseg|probseg|mask].tsv
+      sub-01/
+        func/
+          sub-01_space-<label>_seg-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii|tsv][.gz]
+          sub-01_space-<label>_seg-<label>_desc-<label>_[dseg|probseg|mask].tsv
+          sub-01_space-<label>_seg-<label>_desc-<label>_[dseg|probseg|mask].json
+```
+
+With this structure, the atlas is projected into subject space and/or resampled into
+subject space.
+As with use case 1, the top level directory contains the four atlas files.
+Then the atlas is resampled/transformed into each individual subject space.
+
+## Case 3: using a shared atlas to transform/resample it into new template space
+
+## Case 4: representing subject-specific atlases derived from the corresponding subject’s data
+
+```Text
+<dataset>/derivatives/<pipleline>
+  atlas-<label>_description.json
+  sub-01/
+    anat/
+      sub-01_atlas-<label>_[dseg|probseg|mask].[nii|dscalar.nii|dlabel.nii|label.gii|tsv][.gz][.ome-tiff|.png]
+      sub-01_atlas-<label>_desc-<label>_[dseg|probseg|mask].tsv
+      sub-01_atlas-<label>_desc-<label>_[dseg|probseg|mask].json
+      sub-01_atlas-<label>_desc-<label>_coordsystem.json
+```
+
+The `atlas-<label>_description.json` will typically be the same for all subjects if the
+process for generating the atlas is the same for all subjects.
diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index d46bc6b084..f5b1cfb507 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -41,6 +41,8 @@ atlas:
     myelination, cytoarchitecture), functional features (e.g. resting-state networks, localizers) and such based on
     multimodal data integration (e.g. gene expression, receptors). Furthermore, it covers both volume/voxel and
     surface/vertex data, as well as gray and white matter atlases.
+  type: string
+  format: label
 ceagent:
   name: ce
   display_name: Contrast Enhancing Agent
diff --git a/src/schema/objects/extensions.yaml b/src/schema/objects/extensions.yaml
index 96056e497d..23a661dabd 100644
--- a/src/schema/objects/extensions.yaml
+++ b/src/schema/objects/extensions.yaml
@@ -73,6 +73,13 @@ CTF:
   display_name: CTF MEG Dataset Directory
   description: |
     A directory for MEG data, typically containing a `.meg4` file for the data and a `.res4` file for the resources.
+dscalarnii:
+  value: .dscalar.nii
+  display_name: CIFTI-2 Dense Scalar File
+  description: |
+    A CIFTI-2 dense scalar file.
+
+    This extension may only be used in derivative datasets.
 dlabelnii:
   value: .dlabel.nii
   display_name: CIFTI-2 Dense Label File
diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index 2194a61a92..4fec1550df 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -2,6 +2,7 @@
 # This file simply defines the order in which entities should appear within filenames.
 # Entity definitions appear in the `objects/entities.yaml` file.
 - subject
+- atlas
 - session
 - sample
 - task
diff --git a/src/schema/rules/files/deriv/atlas.yaml b/src/schema/rules/files/deriv/atlas.yaml
new file mode 100644
index 0000000000..f7e9efca3d
--- /dev/null
+++ b/src/schema/rules/files/deriv/atlas.yaml
@@ -0,0 +1,65 @@
+---
+volumetric:
+  suffixes:
+    - dseg
+    - probseg
+    - mask
+  extensions:
+    - .nii
+    - .nii.gz
+    - .tsv
+    - .json
+  datatypes: []
+  entities:
+    atlas: required
+    space: optional
+    resolution: optional
+    description: optional
+
+surface:
+  suffixes:
+    - dseg
+    - probseg
+    - mask
+  extensions:
+    - .label.gii
+    - .gii
+    - .tsv
+    - .json
+  datatypes: []
+  entities:
+    atlas: required
+    space: optional
+    density: optional
+    description: optional
+
+cifti_probseg:
+  suffixes:
+    - probseg
+  extensions:
+    - .dscalar.nii
+    - .tsv
+    - .json
+  datatypes: []
+  entities:
+    atlas: required
+    space: optional
+    resolution: optional
+    density: optional
+    description: optional
+
+cifti_dseg:
+  suffixes:
+    - dseg
+    - mask
+  extensions:
+    - .dlabel.nii
+    - .tsv
+    - .json
+  datatypes: []
+  entities:
+    atlas: required
+    space: optional
+    resolution: optional
+    density: optional
+    description: optional