nibabies
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RF: Move to fit/apply workflow
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
-
- surface reconstruction method
-
- 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 asspace-T2w
. Theaseg
andmask
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