Question about derivatives chain flenaming

[Marie-Helene Bourget]

Hello BIDS community and Happy New Year!

I have a question regarding derivatives file naming, more specifically when naming files in a derivative "chain", and I'm looking for advice if anyone has encountered a similar situation.

As an example, let's say I have the following workflow:

Raw data: "anat" files for T1w and T2w

sub-01_T1w.nii.gz

sub-01_T2w.nii.gz

Derivative Pipeline 1: derivative of the Raw data of type "Preprocessed, coregistered and/or resampled volumes" where I would like to use the desc- entity as follows:

sub-01_desc-preproc_T1w.nii.gz

sub-01_desc-preproc_T2w.nii.gz

Ref: https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html#preprocessed-coregistered-andor-resampled-volumes 

Derivative Pipeline 2: derivative of the Pipeline 1 of type "Masks" where I would like to use the label- entity to identify the structure (e.g. GM for gray matter), as well as the desc- entity to identify the original suffix (T1w or T2w):

The template for this is:

<source_entities>[_space-<space>][_res-<label>][_den-<label>][_label-<label>][_desc-<label>]_mask.nii.gz

Here I'm not sure what <source_entities> refers to? Is it the source entities of the Raw data or the Pipeline 1 data?

Ref: https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html#masks

I see 3 possibilities:

1. sub-01_desc-preproc_label-GM_mask.nii.gz --> Not BIDS complaint because I kept desc-preproc from pipeline 1 and desc- is before label- (doesn't fit the template). In addition, I lost the reference to the original T1w or T2w.

2. sub-01_desc-preproc_label-GM_desc-T1w_mask.nii.gz --> Not BIDS complaint as desc- is repeated 2 times.

3. sub-01_label-GM_desc-T1w_mask.nii.gz --> The "link" to the pipeline 1 filename is lost (by removing desc-preproc from <sources_entities>), I'm not sure if it's compliant or not.

From this, I think the best option for naming files of pipeline 2 is the third one but I'm not sure I'm using it as intended.

Thank you for your help!

Marie-Helene