ICA-AROMA confusion/documentation

[l-espana]

Thanks so much for all your efforts on this project! I especially appreciate the quality check files with both individual subject and overall project info - this is incredibly helpful for our larger projects! 💯

Is your feature request related to a problem? Please describe.
It's not entirely clear to me how ICA-AROMA is used/handled. If it's excluded from confound removal, it still appears in the quality check (which I think is intended). From my understanding, the output from ICA-AROMA includes the "non-aggressive" denoised image, with more "aggressive" data saved for the user to handle later. Is this image used regardless of whether or not it's included in the confound removal? If it is included in the confound removal, does that mean that the more "aggressive" confounds are also removed or just that the "non-aggressive" image is used along with any additional confounds? It would appear ICA-AROMA runs no matter what, but it's not clear what outputs are used when.

Describe the solution you'd like
It'd be nice to have clearer documentation on what confounds are removed when and how ICA-AROMA data is used.

Describe alternatives you've considered
I've tried a couple of different runs of HALFpipe, with and without, ICA-AROMA and looked through the code, but can't quite tease this apart.

Additional context
Using HALFpipe v.1.2.2 ("1.2.2.post1.dev189+g5579a7f").