Remove cohort as an explicit entity

Author: effigies

src/common-principles.md

@@ -130,8 +130,7 @@ 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.
+template (`tpl-<label>`) directories may be found at the root of the dataset.
 These directories are described in [Templates and atlases](derivatives/atlas.md).
 
 ### Other top level directories
@@ -415,9 +414,7 @@ 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
 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.
+Likewise, any template-specific derivatives SHOULD be housed within each template's directory.
 
 ### Non-compliant derivatives
 

src/derivatives/atlas.md

@@ -36,9 +36,8 @@ Template:
 ```Text
 <pipeline_name>/
     tpl-<label>/
-        [cohort-<label>/]
-           [<datatype>/]
-               tpl-<label>[_cohort-<label>][_<entities>]_<suffix>.<extension>
+        [<datatype>/]
+            tpl-<label>[_<entities>]_<suffix>.<extension>
 ```
 
 where [`suffix`](../glossary.md#suffix-common_principles) is any valid BIDS suffix
@@ -47,24 +46,11 @@ such as `T1w` or `PET`; and
 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`.
+substituting `tpl` for `sub`.
 
 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.
@@ -107,34 +93,32 @@ A guide for using macros can be found at
 
 ### 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).
+In the case that the template-generating pipeline derives several related templates,
+each template is assigned a unique label.
+In this example, a common prefix is used to indicate a family of related templates:
 
 <!-- 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": "",
-         },
+      "tpl-MNIPediatricAsym+1": {
+         "tpl-MNIPediatricAsym+1_T1w.nii.gz": "",
+         "tpl-MNIPediatricAsym+1_T2w.nii.gz": "",
+         "tpl-MNIPediatricAsym+1_PDw.nii.gz": "",
+         "tpl-MNIPediatricAsym+1_desc-brain_mask.nii.gz": "",
+         "tpl-MNIPediatricAsym+1_probseg.nii.gz": "",
+         "tpl-MNIPediatricAsym+1_probseg.json": "",
+      },
+      "...": "",
+      "tpl-MNIPediatricAsym+6": {
+         "tpl-MNIPediatricAsym+6_T1w.nii.gz": "",
+         "tpl-MNIPediatricAsym+6_T2w.nii.gz": "",
+         "tpl-MNIPediatricAsym+6_PDw.nii.gz": "",
+         "tpl-MNIPediatricAsym+6_desc-brain_mask.nii.gz": "",
+         "tpl-MNIPediatricAsym+6_probseg.nii.gz": "",
+         "tpl-MNIPediatricAsym+6_probseg.json": "",
       },
    }
 })
@@ -192,9 +176,8 @@ Template:
 <pipeline_name>/
     atlas-<label>_description.json
     tpl-<label>/
-        [cohort-<label>/]
-           [<datatype>/]
-               tpl-<label>[_cohort-<label>][_<entities>]_<suffix>.<extension>
+        [<datatype>/]
+            tpl-<label>[_<entities>]_<suffix>.<extension>
 ```
 
 ### Atlas identification and metadata

src/schema/meta/templates.yaml

@@ -163,4 +163,3 @@ atlas:
   base:
     entities:
       template: required
-      cohort: optional

src/schema/objects/entities.yaml

@@ -44,18 +44,6 @@ 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

src/schema/rules/directories.yaml

@@ -119,12 +119,6 @@ derivative:
     name: code
     level: optional
     opaque: true
-  cohort:
-    entity: cohort
-    level: optional
-    opaque: false
-    subdirs:
-      - datatype
   docs:
     name: docs
     level: optional
@@ -167,7 +161,6 @@ derivative:
     level: optional
     opaque: false
     subdirs:
-      - cohort
       - datatype
   datatype:
     value: datatype

src/schema/rules/entities.yaml

@@ -4,7 +4,6 @@
 - subject
 - template
 - session
-- cohort
 - sample
 - task
 - tracksys