RF: Move to fit/apply workflow

[mgxd]

The goal of this PR is mirror workflow changes in fMRIPrep, splitting the processing into "fit" and "apply" modes.

This is still a work-in-progress.

New features:

• --level {minimal, resampling, full} to specify levels of outputs:

  • minimal produces anatomical template, mask, anatomical -> template registrations, surface reconstruction. These can then be further processed and/or manually edited and reused as --derivatives inputs.
  • full produces all outputs, like previous versions of nibabies

• Increased control in the use of previously computed derivatives

  • Derivatives no longer need to be in native T1w/T2w space, as long as a T1w/T2w preprocessed template is include.

• Selective anatomical reference preference with --reference-anatomical flag

  • Previously, T1w was preferred as the output space.
  • If no option is specified, will select based on
    • 1. surface reconstruction method
    • 2. participant age

---

Example MCRIBS derivatives input and command

Generating surfaces with MCRIBS still requires precomputed segmentations - this is an example directory layout that can be used:

data/derivatives/anat
├── dataset_description.json
└── sub-01
    └── ses-1mo
        └── anat
            ├── sub-01_ses-1mo_desc-preproc_T1w.nii.gz
            ├── sub-01_ses-1mo_desc-preproc_T2w.nii.gz
            ├── sub-01_ses-1mo_space-T2w_desc-aseg_dseg.nii.gz
            └── sub-01_ses-1mo_space-T2w_desc-brain_mask.nii.gz

• Note that sub-01_ses-1mo_desc-preproc_T2w.nii.gz is a denoised and INU corrected image, and is used as space-T2w. The aseg and mask are in that image space.

nibabies /data /data/derivatives/nibabies participant \
-w /work --participant-label 01 \
--fs-subjects-dir /opt/freesurfer/subjects \
--derivatives anat=/data/derivatives/anat \
--anat-only --surface-recon-method mcribs --cifti-output -s 1mo

Closes #87, #218, #288, #294, #307

[mgxd]

Merging this in now as it's been delayed long enough - updates to the circle smoke test + documentation will be done in separate PRs