Merge branch 'master' into minordoc

.pre-commit-config.yaml

@@ -33,7 +33,7 @@ repos:
         files: tools/schemacode
         args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]

DECISION-MAKING.md

@@ -30,6 +30,7 @@ Current and past members of the steering group can be found
 | Eric Earl ([@ericearl](https://github.com/ericearl))                      | 2h/week         |                                       | Dec 2021 |
 | Christine Rogers ([@christinerogers](https://github.com/christinerogers)) | 2h/mo           | Interoperability, EEG and multi-modal | Apr 2023 |
 | Nell Hardcastle ([@nellh](https://github.com/nellh))                      | 2h/week         |                                       | Jul 2023 |
+| Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay))                      | 1h/week         |                                       | Nov 2022 |
 
 In addition to the [BIDS Governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
 classification of a maintainer, maintainers may declare a limited scope of responsibility.

src/CHANGES.md

@@ -3,6 +3,7 @@
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
 -   \[FIX] Update links to BIDS examples [#1545](https://github.com/bids-standard/bids-specification/pull/1545) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] Clarify meaning of raw vs derivative datasets [#1537](https://github.com/bids-standard/bids-specification/pull/1537) ([CPernet](https://github.com/CPernet))
 -   \[FIX] match subject label in folder and filename in func example [#1536](https://github.com/bids-standard/bids-specification/pull/1536) ([Remi-Gau](https://github.com/Remi-Gau))
 -   FIX: Trail MEG directory formats with `/` [#1534](https://github.com/bids-standard/bids-specification/pull/1534) ([effigies](https://github.com/effigies))
 -   \[ENH] Permit CITATION.cff as structured alternative to some dataset_description fields [#1525](https://github.com/bids-standard/bids-specification/pull/1525) ([effigies](https://github.com/effigies))

src/derivatives/introduction.md

@@ -4,9 +4,30 @@ Derivatives are outputs of common processing pipelines, capturing data and
 meta-data sufficient for a researcher to understand and (critically) reuse those
 outputs in subsequent processing.
 Standardizing derivatives is motivated by use cases where formalized
-machine-readable access to processed data enables higher level processing.
+machine-readable access to processed data enables higher-level processing.
 
 The following sections cover additions to and divergences from "raw" BIDS.
+Raw data are data that have been curated into BIDS from a non-BIDS source.
+If a dataset is derived from at least one other valid BIDS dataset, then it is a derivative dataset.
+
+Examples:
+
+A defaced T1w image would typically be made during the curation process and is thus under raw
+
+```Text
+sourcedata/private/sub-01/anat/sub-01_T1w.nii.gz
+sub-01/anat/sub-01_T1w.nii.gz
+```
+
+A defaced T1w image could also, in theory, be derived from a BIDS dataset and would thus be under derivatives
+
+```Text
+sub-01/anat/sub-01_T1w.nii.gz
+derivatives/sub-01/anat/sub-01_desc-defaced_T1w.nii.gz
+```
+
+## Derivatives storage and directory structure
+
 Placement and naming conventions for derived datasets are addressed in
 [Storage of derived datasets][storage], and dataset-level metadata is included
 in [Derived dataset and pipeline description][derived-dataset-description].

src/modality-agnostic-files.md

@@ -5,7 +5,8 @@
 Templates:
 
 -   `dataset_description.json`
--   `README`
+-   `README[.md|.rst|.txt]`
+-   `CITATION.cff`
 -   `CHANGES`
 -   `LICENSE`