nipreps
Ensure non-cached templates are fetched on workflow start
What happened?
Running fmriprep with --derivatives anat=... on data processed with a template not already cached in the Docker image results in a few failures.
/scratch/fmriprep_0_0_wf/sub_01/ds_std_volumes_wf/_in_tuple_MNIPediatricAsymcohort-3.cohort3.resnative/gen_ref/scratch/fmriprep_0_0_wf/sub_01_wf/anat_fit_wf/anat_reports_wf/_in_tuple_MNIPediatricAsymcohort-- 3.cohort3.resnative/mask_std/scratch/fmriprep_0_0_wf/sub_01_wf/anat_fit_wf/anat_reports_wf/_in_tuple_MNIPediatricAsymcohort-3.cohort3.resnative/t1w_std/scratch/fmriprep_0_0_wf/sub_01_wf/bold_ses_1_task_emosent_run_01_wf/bold_std_wf/_in_tuple_MNIPediatricAsymcohort-3.cohort3.resnative/gen_ref
All of these are failing due to
nibabel.filebasedimages.ImageFileError: Empty file: '/home/fmriprep/.cache/templateflow/tpl-MNIPediatricAsym/cohort-3/tpl-MNIPediatricAsym_cohort-3_res-1_T1w.nii.gz'
And likely stem from not calling templateflow.get soon enough.
What command did you use?
nipreps/fmriprep:23.2.x /data /out participant --ignore slicetiming --mem_mb 15G --nthreads 4 -vv --notrack --skip-bids-validation --sloppy --fs-subjects-dir /opt/subjects --derivatives /deriv/anat -w /scratch --output-spaces MNIPediatricAsym:cohort-3
What version of fMRIPrep are you running?
Latest
How are you running fMRIPrep?
Docker
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
FreeSurfer, Anatomical derivatives, Work directory
Please copy and paste any relevant log output.
No response
Additional information / screenshots
No response
I think it's as simple as adding a templateflow.get() call for all template T1ws, which we can include in a bug fix
templateflow.get() is being called in the TemplateFlowSelect interface, which should be upstream of all these nodes. Are you able to see the template_iterator_wf/_in_tuple_MNIPediatricAsymcohort-3.cohort3.resnative/select_tpl node?