Add --report-output-level parameter

[tsalo]

Summary

@mattcieslak and I discussed this today. The new parameter would be --report-output-level <root | subject | session> and would determine where HTML reports are written to.

If the user chooses session but the data are cross-sectional, QSIPrep will automatically change the level to subject with a warning.

This parameter can also be implemented in the preps, QSIRecon, and XCP-D.

[tsalo]

@mattcieslak do you think we need this for the HBCD release?

[mattcieslak]

the html reports are currently going into the subject level by default, which is different from where qsiprep puts them (in the session directory). Since they're not being written to the output root it's probably Ok loris/chrainwise to have them where they are. The qsirecon derivatives layout is so different from qsiprep that it might not even be that much extra confusing to have the reports at a different level. wdyt?

[tsalo]

AFAICT the HTML reports aren't going into the subject level in either package right now. Your session-wise QSIRecon PR will make it possible to write out the reports to the subject or session folder (though that won't be the default), but there's nothing like that for QSIPrep.

[mattcieslak]

ok, two admissions here. First, I was wrong about where the html reports are going in qsirecon. They're definitely going in the qsirecon-suffix/ directories. and second - I thought this issue was in qsirecon. I don't think we'll need to add anything like this for qsiprep.

[tsalo]

I think the HBCD folks will want reports in session folders in the long run, so I still think we should add this to QSIPrep.

[mattcieslak]

they reports will end up there as long as the anat level is set to session, so no flag needed for hbcd right?

[tsalo]

Discussed offline and we agreed to add the new parameter because it'll improve portability for cross-sectional datasets, but it's a low priority item and doesn't need to be done by the next release.