23.2.0 breaks anat-fast-track on dataset without T1w

[bpinsard]

What happened?

In the previous versions it was possible to have precomputed anat smriprep output from another dataset being used for a fMRI-only dataset with anat fast-track (with the same participants of course). This is a critical feature for the neuromod dataset.

The full refactor did break that feature, as it run BIDSDataGrabber without passing anat_derivatives

fmriprep/fmriprep/workflows/base.py

Lines 267 to 274 in de72651

	bidssrc = pe.Node(
	BIDSDataGrabber(
	subject_data=subject_data,
	anat_only=config.workflow.anat_only,
	subject_id=subject_id,
	),
	name='bidssrc',
	)

raising:
FileNotFoundError: No T1w images found for subject sub-01

As it seems that anatomical_cache can be filled from multiple source derivative folders.

fmriprep/fmriprep/workflows/base.py

Lines 250 to 263 in de72651

	anatomical_cache = {}
	if config.execution.derivatives:
	from smriprep.utils.bids import collect_derivatives as collect_anat_derivatives
	std_spaces = spaces.get_spaces(nonstandard=False, dim=(3,))
	std_spaces.append("fsnative")
	for deriv_dir in config.execution.derivatives:
	anatomical_cache.update(
	collect_anat_derivatives(
	derivatives_dir=deriv_dir,
	subject_id=subject_id,
	std_spaces=std_spaces,
	)
	)

it looks like it would be necessary to check that this cache is complete (likely using the smriprep io_spec.json) to be able to skip the need for T1w by setting bidssrc.inputs.anat_derivatives to anything but None.
Unless the anatomical_cache only needs to contain a minimally preprocessed T1w for the rest of the smriprep workflow to be able to run.

Before I try to fix that, @effigies am I missing anything in the whole fit/apply refactor that could cause it to break somewhere even after such minor changes?
Would that make sense to have an integration test that cover that use-case ( should be simple to implement, using existing test dataset, trying to run with anat fast-track after deleting the T1w from the source BIDS dataset)?

What command did you use?

datalad containers-run -m 'fMRIPrep_sub-01/ses-002' -n bids-fmriprep --input sourcedata/templateflow/tpl-MNI152NLin2009cAsym/ --input sourcedata/templateflow/tpl-OASIS30ANTs/ --input sourcedata/templateflow/tpl-fsLR/ --input sourcedata/templateflow/tpl-fsaverage/ --input sourcedata/templateflow/tpl-MNI152NLin6Asym/ --output . --input 'sourcedata/cneuromod.emotion-videos/sub-01/ses-002/fmap/' --input 'sourcedata/cneuromod.emotion-videos/sub-01/ses-002/func/' --input 'sourcedata/cneuromod.anat.smriprep.longitudinal/sub-01/anat/' --input sourcedata/cneuromod.anat.smriprep.longitudinal/sourcedata/cneuromod.anat.freesurfer_longitudinal/sub-01/ -- -w ./workdir --participant-label 01 --derivatives sourcedata/cneuromod.anat.smriprep.longitudinal --fs-subjects-dir sourcedata/cneuromod.anat.smriprep.longitudinal/sourcedata/cneuromod.anat.freesurfer_longitudinal --bids-filter-file code/fmriprep_study-cneuromod.emotion-videos_sub-01_ses-002_bids_filters.json --output-layout bids --ignore slicetiming --use-syn-sdc --output-spaces MNI152NLin2009cAsym T1w:res-iso2mm --cifti-output 91k --notrack --write-graph --skip_bids_validation --omp-nthreads 8 --nprocs 12 --mem_mb 49152 --fs-license-file code/freesurfer.license \--me-output-echos sourcedata/cneuromod.emotion-videos ./ participant

What version of fMRIPrep are you running?

23.2.0

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

FreeSurfer, Anatomical derivatives

Please copy and paste any relevant log output.

No response

Additional information / screenshots

No response