ENH: Large overhaul of the functional workflow w/focus on ME-EPI

oesteban commented 1 year ago

This PR refactors MRIQC to handle ME-EPI better. Incidentally, it also includes brain extraction (on the first echo, or single echo) with SynthStrip.

Specific changes:

[x] Head motion is estimated on the first echo
[x] Non-steady states are estimated on the second echo (the first has too much T1 contribution).
[x] Synthstrip is used in brain extraction (first echo or single echo).
[x] HMC is done with nitransforms, applying the estimation on first echo to all of them.
[x] Single report for all echos.

Resolves: #773. Resolves: #1152. Resolves: #1028.

oesteban commented 1 year ago

Seems to be performing as expected, both on circle (all of them se-epi) and locally (me-epi).

oesteban commented 1 year ago

Mainly checked the new SelectEcho interface and the synthstrip workflow.

Yes, those are the only things with reuse potential from fMRIPrep, and candidates for upsourcing into niworkflows.

nipreps / mriqc