Merge pull request #334 from effigies/fix/relaxation

ENH: Clarify the position toward non-compliant derivative datasets and files

Author: effigies

src/02-common-principles.md

@@ -123,7 +123,8 @@ However, in the case that these data are to be included:
     `sourcedata/sub-01/ses-pre/func/sub-01_ses-pre_task-rest_bold.dicom.tgz` or
     `sourcedata/sub-01/ses-pre/func/MyEvent.sce`.
 
-1.  A README file SHOULD be found at the root of the `sourcedata` folder.
+1.  A README file SHOULD be found at the root of the `sourcedata` folder or the
+    `derivatives` folder, or both.
     This file should describe the nature of the raw data or the derived data.
     We RECOMMEND including the PDF print-out with  the actual sequence
     parameters generated by the scanner in the `sourcedata`  folder.
@@ -146,10 +147,14 @@ my_dataset/
     ...
 ```
 
-In this example **only the `rawdata` subfolder and all subfolders of `derivatives`
-need to be BIDS compliant** datasets. This specification does not prescribe 
-anything about the contents of `sourcedata` folders in the above example - nor 
-does it prescribe the `sourcedata`, `derivatives`, or `rawdata` folder names. 
+In this example, where `sourcedata` and `derivatives` are not nested inside
+`rawdata`, **only the `rawdata` subfolder** needs to be a BIDS-compliant
+dataset.
+The subfolders of `derivatives` MAY be BIDS-compliant derivatives datasets
+(see [Non-compliant datasets][non-compliant-datasets] for further discussion).
+This specification does not prescribe anything about the contents of `sourcedata`
+folders in the above example - nor does it prescribe the `sourcedata`,
+`derivatives`, or `rawdata` folder names.
 The above example is just a convention that can be useful for organizing raw, 
 source, and derived data while maintaining BIDS compliancy of the raw data 
 folder. When using this convention it is RECOMMENDED to set the `SourceDatasets`
@@ -450,3 +455,5 @@ special cases. They should be named using all lowercase with a name that
 reflects the nature of the scan (e.g., `calibration`). Naming of files within
 the directory should follow the same scheme as above (e.g.,
 `sub-control01_calibration_Xcalibration.nii.gz`)
+
+[non-compliant-datasets]: 05-derivatives/01-introduction.md#non-compliant-datasets

src/05-derivatives/01-introduction.md

@@ -222,3 +222,16 @@ sub-01/anat/sub-01_hemi-L_space-individual_thickness.json
     distinguish brain mask files derived from T1w and T2w images; or `_desc-sm4`
     and `_desc-sm8` to distinguish between outputs generated with two different
     levels of smoothing).
+
+-   When naming files that are not yet standardized, it is RECOMMENDED to use
+    names consistent with BIDS conventions where those conventions apply.
+    For example, if a summary statistic is derived from a given task, the file
+    name SHOULD contain `_task-<label>`.
+
+## Non-compliant datasets
+
+Nothing in this specification should be interpreted to disallow the
+storage/distribution non-compliant derivatives of BIDS datasets.
+In particular, if a BIDS dataset contains a `derivatives/` sub-directory,
+the contents of that directory may be a heterogeneous mix of BIDS Derivatives
+datasets and non-compliant derivatives.