Question about full BIDS dataset generation workflow in XNAT

[Reda Fritet]

Hello XNAT community,

I am working with XNAT (tested on 1.8.9 and considering 1.9.3) and I would like to clarify the current limitations regarding BIDS dataset generation inside XNAT.

Here is my current pipeline and observations:

1) I successfully use the container:
   - xnat/dcm2bids-session

This works correctly and produces:
- NIFTI files
- BIDS-style JSON sidecars
at the scan/session level (stored under scan resources in XNAT).

2) I also configured a valid bidsmap.json at the project level via the REST API, and the mapping is applied correctly
(e.g. resting-state scans mapped to task-rest_bold).

3) After this step, I have valid scan-level BIDS outputs inside XNAT
(NIFTI + JSON), which is expected and works well.

However, my goal is to generate a FULL BIDS DATASET inside XNAT, meaning:
- a proper directory hierarchy:
  sub-*/ses-*/anat|func|dwi
- stored under a session or project-level BIDS resource
- directly usable by BIDS Apps (MRIQC, fMRIPrep, etc.)

I tried using:
- xnat/xnat2bids-setup

I was able to configure and run it through Container Service, but:
- it does not assemble a complete BIDS dataset
- it either exits silently or fails without producing a structured BIDS directory
- it seems to be a setup/initialization container rather than a dataset assembler

From my experiments, it appears that:
- dcm2bids-session handles conversion and scan-level BIDS annotation
- but XNAT does not provide a native container/command to assemble a full BIDS dataset internally

My questions are therefore:

1) Is there currently (XNAT 1.8.x / 1.9.x) an officially supported way to generate a full BIDS dataset *entirely within XNAT*?
2) Is xnat2bids-setup intended to be used directly for dataset assembly, or only as a preparation step?
3) Is the recommended approach still to export data and run xnat2bids or other BIDS assembly tools externally?

I want to confirm whether this is a known and expected limitation of XNAT, or if I am missing a specific container or workflow.

Thank you very much for your guidance.