change output directory structure to be bids conform

[PeerHerholz]

Ahoi hoi folks,

mica-pipe currently takes a -bids and a -out argument and subsequently creates a new directory with the name of the participant specified via -sub within -out. While it's kinda "BIDS-y", it's not BIDS-conform. Following the BIDS derivatives, a new pipeline specific directory should be created under derivatives and within that a folder for each participant. Furthermore, a pipeline description and json sidecar files need to be generated. For example:

 bids_dataset
        derivatives
              mica-pipe
                    pipeline-description.json
                    sub-001
                            sub-001_T1w_desc-preproc.nii.gz
                            sub-001_T1w_desc-preproc.json
        dataset_description.json
        participants.tsv
        participants.json
        sub-001
        sub-002

• [x] place outputs under bids_dataset_root_folder/derivatives/micapipe
• [x] add pipeline_description.json
• [x] add json sidecar files
• [ ] maybe: remove -out as BIDS derivatives specify where things should go and thus only -bids is needed

Happy to provide further information for any of this.

Cheers, Peer

[rcruces]

Dear Peer,

On our latest push, we tried to amended all this issues, we created json files for the main outputs, and the pipeline_descrioption.json. We are looking forward to have a BIDS app conformed pipeline.

thank you for this and for further suggestions

[dkp]

I thought derivatives didn't need to be (and probably should not be) UNDER the main bids directory. Rather BIDS data should be a sibling to derivatives.

[PeerHerholz]

Hi @dkp,

thank you for bringing this up. BIDS actually allows both options as specified here: under a derivatives subdirectory in the root folder of the source BIDS dataset and as a standalone dataset independent of the source BIDS dataset. I think the preferred case depends on several factors surrounding the project at hand and thus we opted for the option that is used more commonly. However, you can of course move/detach the derivatives directory from your source BIDS dataset.

Cheers, Peer

[dkp]

Thanks for the reply...it isn't clear to me how you support the separate derivatives option. Do you mean I'm free to move derivatives AFTER running micapipe?

[PeerHerholz]

Hi @dkp,

it's not directly supported but as you outlined, you could simply move the derivatives directory (or only the micapipe parts) out of the source BIDS dataset.

Cheers, Peer