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Author: julia-pfarr

docs/getting_started/folders_and_files/derivatives.md

@@ -175,62 +175,16 @@ Similarly, BIDS Raw datasets should be interpretable and distributable without
 all possible derivatives produced from them.
 
 This independence affords flexibility in the relative organization of datasets.
-The following examples show three ways to organize, relative to each other,
-a raw BIDS dataset, a preprocessed derivative dataset, and an analysis that uses both as inputs.
+The following examples show three ways to organize:
 
-A collection of derivative datasets may be stored in the `derivatives/` subdirectory
-of a BIDS (or BIDS Derivatives) dataset:
-
-```bash
-my_dataset/
-  derivatives/
-    preprocessed/
-    analysis/
-  sub-01/
-  ...
-  dataset_description.json
-```
-
-Disadvantage is that such organization would complicate distribution of the raw BIDS dataset
-by itself as it would require explicit exclusion of datasets within its `derivatives/` folder.
+#### 1. BIDS Raw with derivatives/
 
-A BIDS Derivative dataset may contain references to its input datasets
-(could be BIDS Raw, non-BIDS or even other BIDS Derivatives) in the `sourcedata/` subdirectory:
-
-```bash
-my_analysis/
-  sourcedata/
-    raw/
-      sub-01/
-      ...
-      dataset_description.json
-    preprocessed/
-  sub-01/
-  ...
+A collection of derivative datasets may be stored in the `derivatives/` subdirectory
+@@ -199,31 +201,46 @@
+analysis/
+sub-01/
+...
   dataset_description.json
 ```
 
-Note that the `sourcedata/` and `derivatives/` subdirectories constitute dataset boundaries.
-Any subfolders of these directories may be validated independently, if they are BIDS datasets
-which would be indicated by presence of `dataset_description.json` file(s) in them with a
-REQUIRED `"BIDSVersion"` key.
-It is important to note that their contents must not affect the interpretation of the nested
-or containing datasets.
-
-One potential disadvantage to nesting a BIDS Derivative dataset inside a BIDS Raw dataset, or vice versa,
-is that packaging them for independent sharing or publication can become more complicated.
-It is also possible to completely avoid nesting of BIDS Raw datasets into BIDS Derivative datasets (or vice versa),
-by simply placing them in separate folders, namely `sourcedata/` and `derivatives/` at root level:
-
-```bash
-my_study/
-  sourcedata/
-    raw/
-      sub-01/
-      ...
-  derivatives/
-    preprocessed/
-    analysis/
-```
-
 <!-- TODO derivatives JSON -->