Tedana BIDS App

[tsalo]

I was thinking it might be worth it to discuss creating a real BIDS App for tedana at this point.

Tedana writes out fairly BIDSish outputs already, but we're missing a few features.

1. A BIDS App interface:
   • User provides path to preprocessed BIDS dataset and output directory, and the BIDS App then finds appropriate input files from that information.
2. Fully BIDS-compliant outputs.
   • Instead of placing everything in a flat structure (the output folder), we would need a BIDS folder structure. Something like:

      tedana/
         dataset_description.json
         sub-<label>.html  # the tedana report for all runs for that subject
         logs/
             CITATION<.bib|.html|.md|.tex>
         sub-<label>/
             figures/
                 ...  # all of the figures for the report
             log/
                 <run-uuid>/
                     tedana.toml  # information about settings
                     crash-<..>.txt  # any crash logs
             ses-<label>/
                 func/
                     ...  # all of our outputs for that subject and session
     

3. The ability to provide a BIDS filter file, which would let users select the appropriate preprocessed files (rather than hardcoding in fMRIPrep's naming convention).
4. The ability to provide a dummy scan count, in order to skip certain volumes.
5. The ability to load confounds from the preprocessed derivatives, including motion!

I've been getting a lot of experience developing postprocessing BIDS Apps with XCP-D, so I think writing one for tedana wouldn't be too hard.

[tsalo]

I started working on this in fmripost-tedana. I'm happy to transfer ownership to the nipreps org if we (the ME-ICA team) don't want to maintain a BIDS App.