fix commits from code review

Author: julia-pfarr

docs/getting_started/folders_and_files/derivatives.md

@@ -177,14 +177,55 @@ all possible derivatives produced from them.
 This independence affords flexibility in the relative organization of datasets.
 The following examples show three ways to organize:
 
+The following examples show three ways to organize:
+
 #### 1. BIDS Raw with derivatives/
 
-A collection of derivative datasets may be stored in the `derivatives/` subdirectory
-@@ -199,31 +201,46 @@
-analysis/
+A collection of derivative datasets may be stored in the `derivatives/` subdirectory. 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.
+
+#### 2. BIDS Derivative with sourcedata/raw
+
+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/
 ...
   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.
+
+#### 3. BIDS Study with sourcedata/raw and derivatives/
+
+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 -->