Output of fmriprep not BIDS campatible?

[maalaria]

Dear all,

I am a new user of fmriprep and first want thank you for this amazing tool.
I have now completed the preprocessing of some subjects without errors but checking the /fmriprep/ folder with the BIDS validator gives some errors related to [Code 1] NOT_INCLUDED which is apparently because of the sub-[...].html files and some others. What is the best practice here, adding them to a .bidsignore file?
The second error is a bit weird: [Code 67] NO_VALID_DATA_FOUND_FOR_SUBJECT
It basically says for all included subjects that there is no BIDS compatible data:
e.g.

/sub-02                                           NaN KB |
Location:
/sub-02

Reason:

No BIDS compatible data found for subject 02

[emdupre]

Hi @maalaria --

fMRIPrep outputs BIDS Derivatives files, which are not yet considered part of the BIDS specification (see here for the distinction in BIDS between source, raw, and derived data).

There are a few PRs open on the specification to change this (see bids-standard/bids-specification#265 and bids-standard/bids-specification#207), but until they are merged the BIDS Validator won't process derivatives directories, such as those output by fMRIPrep.

If you are just trying to confirm that processing completed correctly, I would check the error log at the bottom of the HTML files !

[maalaria]

Thanks, @emdupre !