Open tsalo opened 2 months ago
If we want to support minimal derivatives, then we need to grab the slice_time_ref from the config file. However, I also think that limits the generalizability of the fMRIPost workflow. I think we want these fMRIPost workflows to theoretically work on any BIDS-compliant derivatives dataset with the right outputs, and the config file is a Nipreps-specific creation.
If you're doing minimal derivatives, you need to run the STC yourself, so you can give end-users the choice or make it for them.
We can either grab
StartTime
from the preprocessed BOLD file's sidecar or find the config.toml file from the fMRIPrep run and grab theconfig.workflow.slice_time_ref
value.Also, we might need to either patch in the selected reference as
config.workflow.slice_time_ref
or modifyfmriprep.workflows.bold.stc.init_bold_stc_wf
to accept the slice time reference as a parameter.